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Response of Escherichia coli Processes
for the Production of Heterologous
Inclusion Bodies by
Oscillating Cultivation Conditions in a
Scale-Down Bioreactor
Ping Lu, Berlin 2016
Response of Escherichia coli Processes for the Production of
Heterologous Inclusion Bodies by Oscillating Cultivation
Conditions in a Scale-Down Bioreactor
vorgelegt von
M. Sc. Ping Lu
aus Henan (China)
von der Fakultät III – Prozesswissenschaften
der Technischen Universität Berlin
zur Erlangung des akademischen Grades
Doktor der Naturwissenschaften
- Dr. rer. nat. -
genehmigte Dissertation
Promotionsausschuss:
Vorsitzender: Prof. Dr. Roland Lauster
Gutachter: Prof. Dr. Peter Neubauer
Gutachter: Prof. Dr. Thomas Schweder
Tag der wissenschaftlichen Aussprache: 15.03.2016
Berlin 2016
D83
The present work was performed from October 2012 – March 2016 in the research
group of Prof. Dr. Peter Neubauer (Chair of Bioprocess Engineering) at the
Department of Biotechnology, Technische Universität Berlin.
I
Abstract
In the pharmaceutical, chemical and food industries, microorganisms are widely
cultivated under controlled conditions to produce recombinant proteins and organic
molecules. However, inhomogeneities unavoidably exist in large-scale cultivations.
The high concentration of feeding solution in industrial cultivations, combined with
limitation of mixing power, results in excess substrate and oxygen limitation at the
feeding zone. On the contrary, at other regions which are far away from the feeding
zone, cells are exposed to starvation where there is almost no substrate available. In
order to study the cellular responses to oscillations of substrate and oxygen
availability in Escherichia coli industrial large-scale fed-batch bioprocesses at the
laboratory scale, not only a two-compartment scale-down bioreactor (2CR) that
simulates the feeding zone characterized by a high substrate and low oxygen
availability, but also a three-compartment scale-down bioreactor (3CR) that mimics
additionally a zone of low substrate availability was used in this study. With the help
of the scale-down bioreactors, E. coli K-12 W3110 wild-type strain and two
recombinant strains expressing leucine-rich proteins were cultivated to investigate
the influence of heterogeneous condition on production and integration of the
non-canonical amino acids norvaline, norleucine and β-methylnorleucine into
recombinant proteins.
The results showed a diminished productivity of recombinant strains in the first few
hours after induction under oscillating conditions. The accumulation and
misincorporation of non-canonical amino acids, especially norleucine, into
recombinant proteins is affected by oscillating conditions. Though there are much
less methionine residues in both recombinant proteins, norleucine was observed
misincorporated into proteins with higher rate than norvaline and
β-methylnorleucine. The main carbon source for α-ketobutyrate, which is the
precursor of the considered non-canonical amino acids and isoleucine derived from
threonine under normal conditions, while it is directly derived from pyruvate under
oscillation conditions.
This study provides a solid basis for future cell engineering approaches to overcome
the challenges in view of the production quality.
Keywords scale-down, large-scale, non-canonical amino acids, norvaline, norleucine,
II
β-methylnorleucine, recombinant proteins, misincorporation, E. coli
III
Zusammenfassung
Die Kultivierung von Mikroorganismen unter kontrollierten Bedingungen zur
Produktion von rekombinanten Proteinen und anderen organischen Molekülen ist
weit verbreitet sowohl in der pharmazeutischen und chemischen als auch in der
Lebensmittelindustrie. Obwohl kontrolliert lassen sich Inhomogenitäten in
Kultivierungen unter Industriemaßstab nicht vermeiden. Die hohe Konzentration der
eingesetzten Feeding-Lösung in Verbindung mit limitierter Mischleistung führt zu
Substrat-Ü berschuss und Sauerstoff-Limitation im Bereich der Zufütterung.
Gleichzeitig erfahren Zellen in Bereichen entfernt der Zufütterungsstelle
Hungerbedingungen ohne verfügbares Substrat. Um die zellulären Reaktionen auf
diese Oszillationen hinsichtlich Substrat- und Sauerstoffverfügbarkeit in industriellen
Großmaßstabs-Bioprozessen mit Escherichia coli im Labormaßstab untersuchen zu
können, wurden ein Zwei-Kompartiment scale-down Bioreaktor (2CR), der einen
Fütterungsbereich mit hoher Substrat- und niedriger Sauerstoffverfügbarkeit
simuliert, sowie ein Drei-Kompartiment scale-down Bioreaktor (3CR), der zusätzlich
eine Zone mit geringer Substratverfügbarkeit darstellt, eingesetzt. In diesen
Scale-down-Systemen wurde der Einfluss von inhomogenen
Kultivierungsbedingungen auf die Produktion der nicht-kanonischen Aminosäuren
Norvalin, Norleucin und β-methylnorleucin in einem E. coli W3110 Wildtyp sowie
zwei rekombinanten Derivaten untersucht. Gleichzeitig wurde überprüft, ob und in
welcher Menge Fehleinbau dieser nicht-kanonischen Aminosäuren in die
produzierten Leucin-reichen rekombianten Proteine erfolgte.
Die Studien zeigten eine reduzierte Produktivität der rekombinanten Stämme
innerhalb einigen Stunden nach der Induktion unter oszillierenden Bedingungen.
Auch die Akkumulation und der Fehleinbau von nicht-kanonischen Aminosäuren in
die rekombinanten Proteine, speziell Norleucin, ist durch oszillierende
Kultivierungsbedingungen beeinflusst. Obwohl Methionin als Tauschpartner am
geringsten in beiden rekombinanten Proteinen vorkommt, zeigte Norleucine im
Vergleich zu Norvalin und β-methylnorleucin die höchste Fehleinbaurate. Als Quelle
für α-ketobutyrat, das Ausgangsmolekül für die genannten nicht-kanonischen
Aminosäuren und Isoleucin, dient Threonin unter normalen
Kultivierungsbedingungen, während es unter oszillerenden Bedingungen aus Pyruvat
abgeleitet wird.
IV
Diese Arbeit bildet eine gute Basis für zukünftige Stammverbesserungen, um
Probleme und Herausforderungen in Bezug auf Produktqualität zu überwinden.
Schlagworte: Scale-down, Industriemaßstab, nicht-kanonische Aminosäuren,
Norvalin, Norleucin, β-methylnorleucin, rekombinante Proteine, Fehleinbau, E. coli
V
Acknowledgements
Many people have made invaluable contributions, both directly and indirectly to the
successful completion of this work. I would like to take this opportunity to express
my gratitude to all of these people.
My deepest gratitude goes first and foremost to my supervisor Professor Peter
Neubauer for giving me the opportunity to work in his group. His inspired ideas and
enthusiastic attitude towards academic research deeply impressed and impacted me.
During last three and half years, he offered me generous encouragement, patient
guidance and instructive advice in the academic studies. I was deeply moved by his
kindness, gentleness during this period and full support for the application of
scholarships.
I would also like to express my great gratitude to Dr. Stefan Junne for his constructive
suggestions and inspiring advice during each discussion.
Especially, I feel grateful to Eva Brand for working together with me in the first year,
leading me to overall understand of this project, training me on the bioreactor
cultivation techniques and evaluating the data. Working with her and talking about
the things in life are really happy memories for me and I will never forget it. I would
also like to thank Christian Reitz for excellent teamwork on the second recombinant
strain cultivations. We performed so many bioreactor cultivations together. No
matter start very early in the morning or finish very late in the night, we gave each
other support and encourage and shared the exciting moment when succeeded in
each cultivation. Furthermore, I would like to extend my thank to Christoph Klaue for
his contributions in the interleuckin-2 cultivations, Sergej Trippel for teaching me
how GC-MS analysis really work and properly evaluating the BioScope data, Anika
Bockisch, Julia Glazyrina and Anna Maria for their kind help and discussion about
Flow Cytometry analysis.
I would like to acknowledge the funding of German Research Foundation (DFG) to
support this work through the project NE1360/2-1 “Metabolic responses to
bioreactor inhomogeneities: Understanding the flux to modified branched chain
VI
amino acids”. I would also like to express my graditude to Sanofi Chimie to support
part of the thesis by the collaboration project “Scale-up / scale-down of
bioprocesses”.
I would also like to gratefully acknowledge the China Scholarship Council (CSC) for
the main scholarship of initial three years and the Technische Universität Berlin for
the Promotions-Abschluss-Stipendium. In addition, I would like to thank the Berlin
International Graduate School of Natural Sciences and Engineering (BIG-NSE) of the
Cluster of Excellence “Unifying Concepts in Catalysis” (UniCat) for their support,
especially, many thanks to Dr. Jean-Philippe Lonjaret for his great effort on
organizations of all BIG-NSE activities. And I also would like to thank all the PhD
students from the BIG-NSE for the nice moments being together.
I would like to express my gratitude to all the colleagues at the Bioprocess
Engineering Laboratory. Irmgard Maue-Mohn, Brigitte Burckhardt and Thomas Högl
for their technical support, Sabine Lühr-Müller for help with bureaucracy, Dr. Xinrui
Zhou and Dr. Jian Li for being good friends and their endless encouragement and
useful advice in my difficult times, Emmanuel Anane for proof reading of the
dissertation by his perfect English, Dr. Mirja Krause for encouraging me and gave me
a “lucky pig” when she left our institute, Ongey Elvis Legala for nice talk about life
and study, Dr. Nicolas Cruz-Bournazou, Dr. Andreas Knepper, Florian Glauche, Andri
Hutari, Anja Lemoine, Erich Kielhorn, Basant El Kady, Heba Yehia, Funda Cansu Erterm,
Qin Fan and all other colleagues for creating a pleasant working environment.
I also would like to thank my Master’s supervisor Professor Shoutao Zhang for his
kind concern and support, all my lovely good friends for their love, care and
encouragement.
Most importantly, I greatly appreciate to my beloved family members, my parents
and husband for their love, continuous support and understanding. My heart swells
with gratitude to all the people who helped me.
VII
Contributions
Besides the author (Ping Lu), this dissertation work also involved contributions from
Eva Brand, Christian Reitz, Christoph Klaue and Sergej Trippel with detailed
description as below. And all the cultivations were supervised by Dr. Stefan Junne.
For E. coli W3110 wild-type stain cultivations, EB participated in the bioreactor
cultivations experiments, samples analysis and data evaluations.
For E. coli W3110_pCTUT7_His_IL2 cultivations, EB and CK participated in the
bioreactor cultivation experiments. CK performed samples analysis (except BioScope
samples) and participated in the relative data evaluations. And these data was also
used for the diploma thesis of CK. ST participated in the carbon labeling experiments.
For E. coli W3110M_pSW3 cultivations, CR participated in the bioreactor cultivations
experiments, performed the SDS-PAGE gel analysis, and carried out the samples
analysis laboratory work for carboxylic acids and relative data evaluation.
VIII
IX
Table of Contents
Abstract ................................................................................................................. I
Zusammenfassung ............................................................................................... III
Acknowledgements............................................................................................... V
Contributions ...................................................................................................... VII
Table of Contents ................................................................................................. IX
Abbreviations .................................................................................................... XIII
1. Introduction .................................................................................................. 1
1.1. Basic metabolism in E. coli cultivations ........................................................ 1
1.1.1. Glucose metabolism of E. coli ............................................................ 2
1.1.2. Overflow metabolism ......................................................................... 3
1.1.3. Mixed-acid fermentation and pyruvate metabolism in E. coli ........... 4
1.1.4. Biosynthesis of proteinogenic amino acids ........................................ 6
1.2. Overview of non-canonical amino acid synthesis and incorporation into
recombinant production in E. coli .......................................................................... 9
1.2.1. Biosynthesis of non-canonical amino acids ..................................... 10
1.2.2. Misincorporation mechanism of non-canonical amino acids into
heterogonous proteins ................................................................................. 14
1.2.3. Strategies to reduce misincorporation of non-canonical amino acids
into recombinant proteins ........................................................................... 16
1.3. E. coli fermentation processes ................................................................... 18
1.3.1. Cultivation medium .......................................................................... 18
1.3.2. Cultivation modes ............................................................................ 19
1.3.3. Inclusion body (IB) productions ....................................................... 20
1.4. Bioprocess Scale-up and Scale-down ......................................................... 21
1.4.1. Gradients in large-scale bioprocesses .............................................. 21
X
1.4.2. Simulating large-scale cultivations in Scale-down devices .............. 24
1.5. Metabolic flux analysis of biosynthesis pathway of non-canonical amino
acids in E. coli ....................................................................................................... 26
1.5.1. Basic idea of metabolic flux analysis ................................................ 26
1.5.2. Rapid sampling devices .................................................................... 27
1.6. Research motivation and objectives .......................................................... 30
2. Materials and Methods ................................................................................ 32
2.1. Bacterial strains .......................................................................................... 32
2.2. Cultivation media ....................................................................................... 32
2.2.1. LB medium ....................................................................................... 32
2.2.2. Mineral salts medium and EnBase Flo medium............................... 32
2.3. Bioreactor cultivation ................................................................................. 33
2.3.1. Preculture ......................................................................................... 35
2.3.2. On-line measurements .................................................................... 35
2.4. Sampling ..................................................................................................... 36
2.4.1. Cell growth determination ............................................................... 36
2.4.2. Supernatant sampling ...................................................................... 37
2.4.3. Methanol quenched sampling ......................................................... 37
2.4.4. Perchloric acid quenching ................................................................ 38
2.4.5. Protein sampling .............................................................................. 38
2.4.6. BioScope sampling ........................................................................... 38
2.5. Analysis of metabolites............................................................................... 39
2.5.1. Quantitative analysis of carboxylic acids by high performance liquid
chromatography (HPLC) ............................................................................... 39
2.5.2. Quantitative analysis of amino acids by high performance liquid
chromatography (HPLC) ............................................................................... 40
2.5.3. Quantitative analysis of amino acids by Gas Chromatography-Mass
Spectrometry (GC-MS) ................................................................................. 42
XI
2.5.4. Quantitative analysis of carboxylic acids by Gas
Chromatography-Mass Spectrometry (GC-MS) ........................................... 47
2.5.5. Quality of protein analysis ............................................................... 48
2.6. Flow cytometry analysis ............................................................................. 50
3. Results ......................................................................................................... 53
3.1. Behavior of E. coli W3110 in STR and 2CR cultivations .............................. 53
3.1.1. Cultivation characteristics ................................................................ 53
3.1.2. Carboxylic Acids ............................................................................... 57
3.1.3. Amino Acids ..................................................................................... 62
3.2. Behavior of the interleukin-2 producing strain E. coli
W3110_pCTUT7_His_IL2 in STR and 2CR cultivations ......................................... 65
3.2.1. Cultivation characteristics ................................................................ 66
3.2.2. Protein quantification ...................................................................... 69
3.2.3. Carboxylic Acids ............................................................................... 71
3.2.4. Amino acids ...................................................................................... 73
3.2.5. Carbon Labeling Experiments .......................................................... 80
3.3. Behavior of the insulin producing strain E. coli W3110M_pSW3 in STR, 2CR
and 3CR cultivations ............................................................................................. 84
3.3.1. Cultivation characteristics ................................................................ 84
3.3.2. Protein quantification ...................................................................... 88
3.3.3. Carboxylic Acids ............................................................................... 89
3.3.4. Amino acids ...................................................................................... 94
3.3.5. Flow cytometry analysis ................................................................. 101
4. Discussion .................................................................................................. 104
4.1. Accumulation of non-canonical amino acids during cultivations ............ 104
4.1.1. Effect of oscillations ....................................................................... 104
4.1.2. Effect of expression of leucine-rich proteins ................................. 105
4.1.3. Effect of addition of trace elements .............................................. 108
XII
4.2. The favored synthesis pathway of non-canonical amino acids under
different cultivations .......................................................................................... 109
4.3. Misincorporation of non-canonical amino acids into proteins ................ 110
4.4. Cell physiology .......................................................................................... 111
5. Conclusions and Outlook ............................................................................ 113
6. Theses ........................................................................................................ 114
7. References ................................................................................................. 115
8. Appendix .................................................................................................... 125
8.1. Behavior of E. coli W3110 in STR and 2CR cultivations ............................ 125
8.2. Behavior of E. coli W3110_pCTUT7_His_IL2 in STR and 2CR cultivations 132
8.3. Behavior of E. coli W3110M_pSW3 in STR, 2CR and 3CR cultivations ..... 141
Curriculum Vitae ................................................................................................ 146
XIII
Abbreviations
2CR Two-compartment reactor
3CR Three-compartment reactor
Acetyl-CoA Acetyl Coenzyme A
ACKA Acetate kinase
AHAS Acetohydroxy acid synthase
ATP Adenosine triphosphate
DCW Dry cell weight
DO Dissolved oxygen
DOT Dissolved oxygen tension
E4P Erythrose 4-phosphate
FADH2 Flavin adenine dinucleotide
FHL Formate hydrogen lyase
GTP Guanosine triphosphate
HCD High cell density
HPLC High performance liquid chromatography
IB Inclusion body
IMPS Isopropylmalate synthase
IPMD Isopropylmalate dehydrogenase
IPMI Isopropylmalate isomerase
IPTG Isopropylthiogalactoside
LB Luria Bertani
LDH Lactate dehydrogenase
MSM Mineral salts medium
NAD+ Nicotinamide adenine dinucleotide
NADPH Nicotinamide adenine dinucleotide phosphate
OD Optical density
XIV
PEP Phosphoenolpyruvate
PFL Pyruvate formate-lyase
PFR Plug flow reactor
pO2 Dissolved oxygen concentration
POXB Pyruvate oxidase
PTA Phosphotransacetylase
R5PP Ribose 5-phosphate
RID Refractive index detector
SDS-PAGE Sodium dodecyl sulfate-polyacrylamide gel
STR Stirrer tank reactor
TCA Tricarboxylic acid cycle
tRNA Transfer RNA
1. Introduction
1
1. Introduction
1.1. Basic metabolism in E. coli cultivations
Escherichia coli is a robust cell factory and very popular with scientists and industries
for recombinant protein productions (Zerbs et al. 2009), largely because of its simple
cultivation, well-understood primary metabolism, rapid growth rate, easiness to
handle and inexpensive investment, though E. coli as a heterologous host also has
significant drawbacks, such as lack of compatible post-translational enzymes,
incorrect folding of heterologous proteins, but many of the limitations can be
overcome by engineering technology and optimization.
The cellular metabolism of E. coli, like all the other organisms, is very complex,
containing reaction networks and regulatory mechanisms of response to conditions.
Therefore, this section will focus on the critical metabolism for cell growth and
expression of recombinant production in cultivation process. Understanding this is
all-important for efficient optimization of cultivation process. A reduced metabolic
network used in this thesis is shown in Figure 1.1.
1. Introduction
2
Figure 1.1: Schematic representation of simplified metabolism in E. coli.
1.1.1. Glucose metabolism of E. coli
As a facultative anaerobe E. coli can grow and generate energy not only under
aerobic conditions through respiration, but also via fermentation when oxygen is not
available. E. coli is capable of utilizing various organic compounds as carbon sources.
However, glucose is the preferred carbon source when available in the growth
medium (Deutscher 2008). Adaption to the preferred carbon source such as glucose
is regulated by carbon catabolite repression (CCR) where the synthesis of the
enzymes necessary for the transport and metabolism of less favorable carbon
sources are repressed (Görke and Stülke 2008) by the dominating carbon source. The
rapid utilization of glucose depends on the phosphoenolpyruvate (PEP):
carbohydrate phosphotransferase system (PTS), which catalyzes the uptake and
concomitant phosphorylation of several carbohydrates and plays a major role in
Gllucose-6-P
Glucose
Pyruvate
Acetyl-CoA
Formate pfl
Acetate
fhlH2 + CO2
Pentose-5-PHistedine
poxB
pdh
TCA
Lactate ldh
α -ketoisovalerate
Valine
Leucine
α -ketobutyrate Isoleucine
α -ketovalerate β-Methylnorleucine
Norvaline
Norleucine
3-P-Glycerate
PEP
Erythrose-4-P
ChorismateTyrsine
Phenylalanine
Tryptophan
Acka, pta
acs
Malic acid
Fumaric acid
Oxaloacetic acid
α-ketoglutarate
Succinic acid
Glycine
Serine
Cysteine
Alanine
Asparagine
Aspartate
Lysine
Threonine
Homoserine
Methionine
proline
Glutamate
Argnine
Glutamine
1. Introduction
3
bacterial CCR (Deutscher 2008; Deutscher et al. 2006). Glucose is a good substrate
and after uptake by cells it is catabolised mainly though glycolysis
(Embden–Meyerhof–Parnas pathway). Glycolysis decomposes each mole of glucose
into two moles of pyruvate, coupled with generation of two moles of adenosine
triphosphate (ATP) via substrate-level phosphorylation and two moles of NADH
(Madigan et al. 2014).
Pyruvate plays a key role in the main metabolite processes including the tricarboxylic
acid cycle (TCA), aerobic overflow metabolism into acetate in E. coli, mixed-acids
fermentation when oxygen is unavailable and amino acids syntheses. One molecule
of pyruvate in aerobic conditions via the TCA is oxidized into three molecules carbon
dioxide (CO2), along with formation of one molecule guanosine triphosphate (GTP),
four molecules of NADH+H+ and one molecule of flavin adenine dinucleotide (FADH2).
In electron transport chain, NADH+H+ and FADH2 with energy-rich electrons support
electrons to electron acceptor (O2). Finally, H2O and great yield of energy formed. In
addition, intermediates, such as oxaloacetate and α-ketoglutarate serve as
precursors of some amino acids (Madigan et al. 2014).
1.1.2. Overflow metabolism
The formation and accumulation of the undesired product acetate in aerobic
conditions using glucose as carbon source is a problem in high cell density
cultivations of E. coli. This has several disadvantages. Firstly, under substrate excess,
cells consume glucose with a higher rate and by the imbalance of the glycolysis and
TCA, they excrete acetate, and thus lose a significant portion of carbon source
(Farmer and Liao 1997; Kleman and Strohl 1994). Secondly, numerous reports have
shown that acetate inhibits cell growth in E. coli cultivations (Korz et al. 1995; Luli
and Strohl 1990; Yee and Blanch 1993). Thirdly, accumulation of acetate above ca. 1 g
L-1 also reduces the yield of the target recombinant protein synthesis (Contiero et al.
1. Introduction
4
2000; Jensen and Carlsen 1990; Sakamoto et al. 1994) and has a negative effect on
the stability of intracellular proteins (Stephanopoulos 1998), possibly by its influence
on the intracellular pH.
It is considered that overflow metabolites are produced under aerobic condition
when the carbon flux exceeds the capacity of TCA cycle and respiration. There are
two pathways to biosynthesis of acetate as by-product in E. coli under aerobic
conditions, either from Acetyl-Coenzyme A (Acetyl-CoA) via phosphotransacetylase
(pta)/acetate kinase (ackA) proceeding through the unstable intermediate acetyl
phosphate (acetyl-P), or directly from pyruvate by pyruvate oxidase (poxB) activity
(Figure 1.4) (Dittrich et al. 2005; Valgepea et al. 2010). The first pathway is active in
both anaerobic and aerobic conditions; cells metabolite Acetyl-CoA into acetate
using pta-ackA pathway and generating ATP (Kumari et al. 2000). The pta and ackA
genes which are encoded within one operon (Kakuda et al. 1994) are vital to the
balanced carbon flux during the exponential phase of cell growth (Chang et al. 1999).
While it was found that poxB is also crucial to aerobic growth efficiency in E. coli
(Abdel-Hamid et al. 2001) and more active during the late exponential and stationary
phase (Dittrich et al. 2005). Under aerobic fermentations the level of acetate
produced is complex, depending on the culture medium, actual glucose
concentration, the E. coli strains, and growth conditions (Wolfe 2005). So in high cell
density fed-batch E. coli cultivations the question of how to reduce the accumulation
of acetate on the bioprocess level and the genetic level has been widely studied over
the years (De Mey et al. 2007).
1.1.3. Mixed-acid fermentation and pyruvate metabolism in E. coli
Generally, E. coli is capable of making use of glucose in the culture medium under
both aerobic and anaerobic conditions. In the absence of oxygen as electron acceptor,
E. coli adapts to mixed-acid fermentation, which produces partly oxidised
1. Introduction
5
fermentation products acetate, lactate, formate, ethanol, succinate and format with
H2 and CO2 as the end products (Figure 1.2) (Clark 1989). All the mixed-acids
fermentation products except succinate come from pyruvate which is derived from
glucose oxidation though glycolysis pathway, whereas succinate is from
phosphoenolpyruvate (PEP) via oxaloacetate (Xu et al. 1999a).
Figure 1.2: Schematic representation of overflow metabolite (Manfredini et al.) and mixed-acids
fermentation (green) metabolism in E. coli.
In the absence of oxygen, lactate is produced by lactate dehydrogenase (LDH) from
pyruvate. At the same time, under anaerobic conditions, pyruvate is also cleaved
with the help of pyruvate formate-lyase (PFL) into acetyl-CoA which can be further
transformed into acetate though the PTA-ACKA pathway accompanying ATP
generation or ethanol with nicotinamide adenine dinucleotide (NAD+), and formate
which is further split into H2 and CO2 via formate hydrogen lyase (FHL) (Sawers and
Clark 2004; Xu et al. 1999a). It was found that a fully functional FHL complex needs
ADP
ATP
PEP
Glucose
Pyruvate
CoA, NAD
CO2, NADH2
Acetyl-CoA
Acetyl-CoA
Formate
PFL
PTA
CoASH PiAcetyl-P
ATP ADP
ACKAAcetate
PTA
CoASH PiAcetyl-P
ATP ADP
ACKAAcetate
ADH
NAD+,CoASH
NADHAcetaldehyde
NAD+ NADH
ADHEthanol
FHL complexH2 + CO2
OxaloacetateSuccinate
POXB
FADH
FAD+ PDH
TCA
Lactate NAD+
NADHLDH
1. Introduction
6
trace amounts of molybdenum, selenium, and nickel in the culture medium, due to
the three formate dehydrogenase (FDH) components of the FHL complex are
molybdo-seleno enzymes, and HycE component is NiFe hydrogenases in E. coli
(Pinsent 1954; Sawers 2005). Therefore, in anaerobic E. coli cultivations, these trace
elements are particularly added into cultivation medium (Yoshida et al. 2005). Result
on addition of trace elements proved that it can significantly reduce formate
accumulation (Soini et al. 2008b) and production of non-canonical amino acids
(Biermann et al. 2013).
1.1.4. Biosynthesis of proteinogenic amino acids
In living organisms, proteins play important roles and perform a vast majority of
functions, such as structural support, transport molecules, catalyzing biochemical
reactions. The monomers of proteins are amino acids. 20 of more than 300 AAs in
nature are directly encoded by the genetic code and serve as building blocks of
proteins. These amino acids which are known as proteinogenic AAs represent the
most essential components of living cells. E. coli is able to synthesise them using other
substrates in the cultivation medium, such as glycolysis and TCA cycle intermediates and
inorganic nitrogen source, to satisfy the demand for cell growth or produce recombinant
proteins (Madigan et al. 2014). On account of precursor molecules from which carbon
skeletons of amino acids are derived, they are divided into alanine family, serine family,
aromatic family, glutamate family, aspartate family and histidine (Figure 1.3).
1. Introduction
7
Figure 1.3: Overview of proteinogenic amino acid biosynthesis. The carbon skeletons of amino
acids are derived from glycolysis (green), citric acid cycle (TCA) (blue) and pentose phosphate
pathway (pink).
AA families derived from TCA cycle intermediates are the glutamate and aspartate
family. α-ketoglutarate is the precursor molecule for the biosynthesis of glutamate.
Further, ammonium salt in the mineral medium provides the nitrogen source for
glutamate and glutamine formation. Almost all the nitrogen assimilated from
ammonia enters the metabolism as glutamine amine group and glutamate amino
group which is then further distributed to the biosynthesis of other amino acids. The
glutamate and glutamine pathway play an important role in ammonia assimilation of
organisms (Nelson and Cox 2008; Reitzer and Magasanik 1996; Umbarger 1978).
Serine is derived from 3 –Phosphoglycerate which is an intermediate of glycolysis.
Glycine is synthesized from serine via serine hydroxymethyltransferase by removing a
carbon atom. Bacteria produce sulfide from environmental sulfate, then react with
the carbon skeleton from serine to form cysteine. Aspartate synthesis from TCA
1. Introduction
8
intermediate oxaloacetate via a glutamate-aspartate transaminase includes a
transamination of the amino group from glutamate, accompanied by α-ketoglutarate
as byproduct. Asparagine is produced via transamination reaction from aspartate.
Methionine, threonine and isoleucine are synthesized from aspartate via homoserine,
with lysine branching from this route (Greene 1996; Patte 1996; Umbarger 1978).
Alanine is directly derived from pyruvate via transamination. Alanine and aspartate
family combine together with branched-chain amino acids and synthesize valine,
leucine and isoleucine from pyruvate and α-ketobutyrate.
The biosynthesis of branched chain amino acids plays an important role in E. coli,
because it is closely connected with the overflow metabolism and the formation of
non-canonical amino acids. Pyruvate, which is directly linked to glycolysis, serves as
the common precursor for the synthesis pathway of branched chain amino acids. The
beginning of valine and leucine pathway is that pyruvate is catabolised into
α-acetolactate and α-ketobutyrate. Then α-acetolactate is metabolised to
α-ketoisovalerate, which is the precursor for either leucine synthesis via
α-isopropylmalate or valine (Umbarger 1996). Isoleucine biosynthesis pathway
occurs in parallel with valine pathway. α-ketobutyrate generated besides from
pyruvate, and also from threonine serves as precursor for isoleucine formation. The
first enzyme of isoleucine-valine synthetic pathway is acetohydroxy acid synthetase
(AHAS), which is encoded by the largest group of ilv family, containing AHAS I
(encoded by ilvBN) AHAS II (encoded by ilvGM) and AHAS III (encoded by ilvIH). The
function of AHAS is regulated by end-product feedback inhibition by one or more of
the branched chain amino acids. AHAS I and AHAS III can be inhibited by high
concentration of valine, while AHAS II is insensitive to valine inhibition (Andersen et
al. 2001). Since the E. coli K-12 strain has a frameshift mutation in the ilvG gene, that
is to say, AHAS II (encoded by ilvG) has no function in E. coli K-12 strain (Lawther et al.
1981). As a result, when excess valine accumulates in the cellular environment, it
1. Introduction
9
leads to the valine toxicity phenomenon, which is known as the inhibition of leucine
and isoleucine synthesis especially in E. coli K-12 strains, even in the case of leucine /
isoleucine starvation (Andersen et al. 2001).
1.2. Overview of non-canonical amino acid synthesis and incorporation
into recombinant production in E. coli
Apart from the 20 proteinogenic amino acids, there are also non-canonical amino
acids existing in E. coli or other gram-negative organisms, e.g. norvaline, norleucine
and β-methylnorleucine, which are formed as byproducts of the branched chain
amino acids pathway. As early as 1953, the first report about non-canonical amino
acids showed that norvaline was as part of antifungal peptide produced by Bacillus
subtilis (Nandi and Sen 1953). Later Kisumi and colleagues reported that norleucine
was synthesized as side product of isoleucine in mutants of Serratia marcescens
(Kisumi et al. 1976a; Kisumi et al. 1976b; Kisumi et al. 1977b). Besides, norleucine
(Kisumi et al. 1976a) and β-methylnorleucine formation (Sugiura et al. 1981a; Sugiura
et al. 1981b) was also found corresponding to norvaline pathway in Serratia
marcescens .
The formation of non-canonical amino acids is beginning to draw increasing attention
as it has been found that in various researches they can substitute proteinogenic
amino acids at different positions within recombinant proteins. Norvaline is able to
substitute leucine in proteins of E. coli (Apostol et al. 1997; Tang and Tirrell 2002),
Norleucine was shown to substitute methionine (Bogosian et al. 1989; Cirino et al.
2003; Kiick et al. 2001), and β-methylnorleucine can substitute isoleucine in bacterial
proteins (Muramatsu et al. 2003; Muramatsu et al. 2002). Lots of studies found that,
especially in leucine-rich recombinant proteins, non-canonical amino acids can be
misincorporated, e.g. norvaline into recombinant hemoglobin which includes 72
1. Introduction
10
leucine residues in 575 total amino acids residues (Apostol et al. 1997) norleucine
into interleukin2 containing 152 amino acid residues, of which 26 are leucine
residues (Lu et al. 1988; Tsai et al. 1988). Since pharmaceutically used proteins must
be of high product quality and purity, such incorporations are highly unwanted.
1.2.1. Biosynthesis of non-canonical amino acids
The exact synthesis pathway of non-canonical amino acids is not finally determined
yet. Figure 1.4 shows the biosynthetic pathway of branched chain amino acids and
proposed pathway of norvaline, norleucine and β-methylnorleucine based on former
literature surveys (Muramatsu et al. 2003; Sycheva et al. 2007; Umbarger 1996).
1. Introduction
11
Figure 1.4: Biosynthetic pathway of branched chain amino acids (blue) and proposed pathway of
non-canonical amino acids (red), adapted from (Muramatsu et al. 2003; Sycheva et al. 2007;
Umbarger 1996). AHAS: acetohydroxy acid synthesis; ilvA: threonine deaminase (TD); ilvC:
1. Introduction
12
ketoacid isomeroreductase; ilvD: dihydroxyacid dehydratase; ilvE: transaminase B; avtA:
transaminase C; tyrA: aromatic transaminase; tyrB: aromatic transaminase; leuA: isopropylmalate
synthase (IPMS); leuCD: isopropylmalate isomerase (IPMI); leuB: isopropylmalate dehydrogenase
(IPMD).
Kisumi and colleagues hypothesized that the synthesis of norvline is from
α-ketobutyrate and norleucine is from α-ketovalerate in Serratia marcescens, using
the leucine biosynthetic enzymes which are encoded by leuABCD operon, including
isopropylmalate synthase (IMPS, coded by leuA), isopropylmalate isomerase (IPMI,
coded by leuCD), and isopropylmalate dehydrogenase (IPMD, coded by leuB ), due to
their broad substrate specificity (Kisumi et al. 1976a). Furthermore, this was
confirmed by Sycheva and colleagues in E. coli (Sycheva et al. 2007). α-ketobutyrate
is catalised by chain elongation to α-ketovalerate, which is either directly catalysed to
norvaline or converted to α-ketocaproate serving as the precursor for the formation
of norleucine. Also it was proposed that β-methylnorleucine is synthesized also from
α-ketovalerate via α-keto-β-methylcaproate, via the isoleucine-valine biosynthetic
pathway enzymes that also have broad substrate specificity as well as leucine
biosynthetic enzymes (Muramatsu et al. 2003; Sugiura et al. 1981b).
It is well known that α-ketobutyrate serving as precursor of the branched chain
amino acids, is derived from the oxaloacetate precursor with aspartate and
homoserine as intermediates, and then threonine involved in deamination.
Additionally, it has been observed that blocking the synthetic pathway of
α-ketobutyrate from threonine by knocking out of the ilvA gene in E. coli was not
able to prevent the synthesis of norvaline and norleucine (Sycheva et al. 2007). Thus,
this indicated that there is an alternative way to form α-ketobutyrate, probably
directly from pyruvate.
1. Introduction
13
The conditions resulting in the biosynthesis of non-canonical amino acids are not
totally clear, but various studies discussed several factors. One factor is glucose
overflow in the cultivation process, which leads to pyruvate accumulation during
glucose overflow. Soini and colleagues showed that a combined high glucose
availability and oxygen limitation results in the accumulation of pyruvate and
consequently in an overflow towards α-ketobutyrate, and finally in an overflow to
norvaline synthesis. The high level of pyruvate was obtained by a high sudden
glucose influx after a shift from aerobic to anaerobic conditions. It was proposed that
a high pyruvate level is the prerequisite for the direct shunt to α-ketobutyrate, and a
high α-ketobutyrate level is a prerequisite for non-canonical amino acids formation
(Soini et al. 2008a). Because the enzyme IPMS has lower Km value for any other
substrates than α-ketoisovalerate (Kohlhaw et al. 1969; Umbarger 1996). But when
excess α-ketobutyrate presents, IPMS utilizes it instead of α-ketoisovalerate (Sycheva
et al. 2007). Additionally, Sycheva et al. deleted the ilvA gene in mutant E. coli, which
is responsible for the synthesis of α-ketobutyrate from threonine, but norvaline and
norleucine were still synthesised. This demonstrated that an alternative pathway for
the biosynthesis of α-ketobutyrate was functional, maybe directly from pyruvate,
rather than from threonine (Sycheva et al. 2007). Non-canonical amino acids are a
function and result of pyruvate overflow metabolism.
The other highly probable factor that leads to the formation of non-canonical amino
acids is the high expression of the leuABCD operon, which encodes the first enzyme
of isoleucine and non-canonical amino acid biosynthesis pathway and regulated by
the pool of free leucine in the cells. As shown in Figure 1.4 and explained above,
enzymes involved in branched chain amino acids and non-canonical amino acids
biosynthetic pathway are mainly encoded by the leuABCD operon and ilv operons.
Sycheva and coworkers showed that an increased expression of leuABCD operon
results in an elevated level of non-canonical amino acids (Sycheva et al. 2007).
1. Introduction
14
Moreover, it was found that leucine level regulates the expression of leuABCD operon
(Burns et al. 1966). Bogosian and co-workers postulated that high level expression of
leucine-rich proteins may promote the formation of norleucine in E. coli. This was
supported by Apostol and his colleagues that induction of leucine-rich protein
hemoglobin expression leading to leucine pool rapidly decrease and parallel with
pyruvate accumulation, resulting in an immediate norvaline accumulation, and with
a delay also in the accumulation of norleucine (Apostol et al. 1997). The synthesis of
leucine-rich heterologous proteins in E. coli demands for a large amount of leucine
during production, leading to an increased expression of the leuABCD operon by cell
adaptation to this higher demand of leucine. As a result, when leucine biosynthesis
enzymes are present at a sufficient high level, combined with high level of
α-ketobutyrate, the formation of non-canonical amino acids occurs.
Another factor that probably leads to the formation of non-canonical amino acids is
the activity of AHAS. Valine toxicity phenomenon exists in the E. coli K-12 W3110
strain, which has been described above. It was also proposed that AHAS II has the
highest efficiency in conversion of α-ketobutyrate (Barak et al. 1987). As a result,
except valine toxicity, inactivation of AHAS II and the low flux into the isoleucine
pathway can elevate the concentration of α-ketobutyrate, which in turn serves as the
precursor for non-canonical amino acids.
1.2.2. Misincorporation mechanism of non-canonical amino acids into
heterogonous proteins
Generally, under usual circumstances, non-canonical amino acids do not get
misincorporated into proteins, due to the well documented well-functioning of
protein synthesis in E. coli. The recognized mechanism of protein synthesis relies on
the acylation of transfer RNA (tRNA), binding aminoacyl transfer RNAs (aa-tRNAs) to
ribosome by the elongation factor Tu (EF-Tu) in bacteria, and the recognition
1. Introduction
15
verification process of messenger RNA (mRNA) codons with tRNA anticodons
(Cvetesic et al. 2013; Ling et al. 2009; Zaher and Green 2009).
The acylation of tRNA is a two-step reaction, catalyzed by aminoacyl tRNA
synthetases (aaRSs) including the conversion of single cognate amino acids with ATP
to aminoacyl adenylate (aa-AMP) and followed by transferring the appropriate amino
acid to the 3’-end of the cognate tRNA (Ibba and Soll 2000; Ling et al. 2009). Only
within the synthesis reaction, many aaRSs are not able to discriminate cognate
against non-cognate amino acids with great accuracy. Meanwhile, aaRSs also play an
important inherent role in editing and proof-reading activity which could hydrolyze
either misactivated non-cognate aa-AMP in pre-transfer editing activity or
misacylated aa-tRNA in post-transfer editing activity (Ling et al. 2009). So aaRSs most
stringently controls the protein synthesis (Ibba and Soll 2000).
Lots of reports showed that many aaRSs have lowered substrate specificity, because
some amino acids are so similar that aaRSs can hardly discriminate between them
with high specificity. For example, it was shown that leucyl-tRNA synthetase (LeuRS)
in E. coli is able to accept several leucine analogues, including norvaline (Martinis and
Fox 1997; Tang and Tirrell 2002). Moreover, Cvetesic and colleagues demonstrated
EF-Tu has similar affinities in binding Nva-tRNALeu and Leu-tRNALeu, leading leuRS has
incapability of hydrolytic editing against norvaline (Cvetesic et al. 2013). As a result,
norvaline is misincorporated into proteins instead of leucine (Apostol et al. 1997). A
similar principle was found as well for methionyl-tRNA synthetase (MetRS) (Bogosian
et al. 1989; Kiick et al. 2001) and isoleucyl-tRNA synthetase (IleRS) (Muramatsu et al.
2003). The premise of misincorporation is a high ratio of the substitute to natural
substrate. It was studied that the ratio of free norvaline to leucine pool plays a critical
role in misincorporation of norvaline for leucine, and results showed that the
percentage of substitutions in the recombinant protein is directly proportional to the
1. Introduction
16
ratio of norvaline to leucine available in the culture broth (Apostol et al. 1997). If
under certain growth conditions, which favor non-canonical amino acid syntheses
and accumulation, it will definitely cause misincorporation into recombinant proteins.
Soini and co-workers found that under oxygen limited cultivation conditions with
pyruvate accumulation, the amount of norvaline reaches millimolar concentrations,
which is already far above the level leading to a great threat to biosynthesis of
proteins in E. coli (Soini et al. 2008a).
1.2.3. Strategies to reduce misincorporation of non-canonical amino acids into
recombinant proteins
Along with the knowledge of misincorporation mechanism of non-canonical amino
acids into heterologous proteins, numerous scientists have tried to deal with such
situations with different methods and strategies to reduce the occurrence of
misincorpoation.
One strategy to reduce the misincorporation could be the optimization of the culture
medium. A common and reliably effective method is to interfere with the
incorporation of non-canonical amino acids into protein by supplying the culture
media with competitive canonical compounds of non-canonical amino acids. This
was supported by Bogosian and his colleagues using media supplementations with
exogenous methionine or 2-hydroxy-4-methylthiobutanoic acid that can convert into
methionine in E. coli to guarantee excess intracellular pool of methionine in the cells
to effectively compete with norleucine in charging of the methionyl tRNA, and as a
result, reduction in norleucine incorporation was observed (Bogosian et al. 1989). As
it is well known that the level of leucine is able to regulate the first enzyme of the
leucine biosynthesis pathway (Umbarger 1996), another medium supplementation
experiment with leucine performed by Tsai and his colleagues demonstrated an
exciting reduction of the norleucine incorporation in IL-2 from 19 to 2% in a minimal
1. Introduction
17
medium cultivation (Tsai et al. 1988). Most recently, another method was
demonstrated successfully with supplementation of trace elements molybdenum,
nickel and selenium, presenting significant justifications to prove that these trace
elements can effectively suppress norvaline and norleucine biosynthesis under
conditions of limited oxygen and excess glucose (Biermann et al. 2013). This is
because these trace elements play important roles in the fully functionality and
catalysis of formate hydrogen lyase (FHL) complex that is the most dedicated enzyme
in the pyruvate metabolism in E. coli under anaerobic conditions, which was
previously described in Section 1.1.3. So molybdenum, nickel and selenium lead to a
higher activity of the formate hydrogen lyase (FHL) complex to catalyse pyruvate and
release dihydrogen and carbon dioxide. Therefore pyruvate is not accumulated so
much after a downshift of oxygen under high glucose concentration and thus the
direct chain elongation from pyruvate to α-ketobutyrate, which is the precursor of
non-canonical amino acids, would be less.
The other strategy is using genetic tools to engineer E. coli strains to prevent the
misincorporation of non-canonical amino acids. One method is inactivating the genes
involved in their biosynthesis pathway. It was shown that deleting one or more genes
of the leu operon (namely leuA, leuB, leuC and leuD) or ilvA gene in E. coli, which
encodes the leucine biosynthetic enzymes, successfully eliminated the biosynthesis
of norleucine (Bogosian et al. 1989; Tsai et al. 1988). However, this approach has the
disadvantage of requiring the supplementation of leucine or other branched chain
amino acids in the culture medium, due to the bacterial strains inability to produce
its own. Another method is mutating genes involved in methionine biosynthesis and
regulation (metA, metK, and metJ) to obtain overexpression of methionine as an
alternative to continuous methionine feeding during cultivations to prevent
norleucine misincorporation and improve product purity and quality (Veeravalli et al.
2015).
1. Introduction
18
Another strategy to reduce or eliminate the misincorporation is using the cells and
DNA constructs to co-express or to enhance the expression of a protein like the
glutamate dehydrogenase, which is capable of degrading non-canonical amino acids
(Bogosian et al. 2013).
The strategy also could be choosing proper host expression strains of recombinant
proteins to reduce the misincorporation of non-canonical amino acids. Experimental
data gained by Ni and his colleagues showed that, a lower biosynthesis of norvaline
and norleucine, and misincorporation into vaccine candidate protein were measured
in the E. coli BL21(DE3) strain than E. coli K-12 strain, without a significant loss in
expression level (Ni et al. 2015).
1.3. E. coli fermentation processes
Whether in laboratory research or large-scale industrial processes, maximizing the
yield of productions is a major objective in cultivations. For this reason, attaining high
cell density is required to achieve high productivity (Fass et al. 1991; Riesenberg and
Guthke 1999; Seo and Chung 2011). In order to reach high cell density, various
strategies including medium compounds optimization, cultivation techniques
improvement, substrate feeding strategies together with molecular strain
development have been carried out (Choi et al. 2006; Shiloach and Fass 2005).
1.3.1. Cultivation medium
One of the vital factors to achieve high cell density and cultivation success is the
choice and optimization of medium used in cultivation process, which should contain
carbon source, nitrogen source, essential salts, minerals and certain growth factors
for the growth of E. coli (Shiloach and Fass 2005). Basically, media can be classified as
1. Introduction
19
chemically defined or undefined. An undefined or complex medium such as Luria
Bertani (LB) broth contains undefined compositions including yeast extract or protein
hydrolysates. Though complex medium has the advantages of lower price and more
robust cell growth, cultivation process may lead to unexpected productivity and
batch to batch variation with protein expression and quality because of the variations
of undefined materials (Zhang and Greasham 1999). In contrast, a defined medium,
such as mineral medium widely used in both laboratory and industrial scale, has
completely and precisely known constituents and can be easily controlled during
cultivation, showing the merit of improvement of upstream and downstream
processing, process control and scale-up (Lee 1996; Zhang and Greasham 1999).
1.3.2. Cultivation modes
A batch bioprocess is the simplest mode to cultivate microorganisms. Right at the
beginning of cultivation, it already has all the carbon and energy sources and other
nutrients, minerals and trace elements, which are needed for all the growth of the
cells. Though batch cultivation in shake flask is mainly popular in small scale
experiments (Panula-Perälä et al. 2008), there obviously exist disadvantages, for
instance, high substrate concentrations in the cultivation medium limit cell growth
and undesired inhibitory metabolites could be produced (Enfors et al. 2001; Xu et al.
1999a). Besides, when one of the substrate is depleted or one of the products
inhibits the growth, the culture comes to stationary phase (Jones and Kelly 1983).
Therefore, these constitute major challenges in bringing cells to a high density as
required in large-scale cultivations.
In order to obtain high cell density and increase recombinant protein volumetric
productivity, fed-batch is one of the successful approaches in bioreactor cultivations
and it has been applied widely for decades ago, e.g. see reviews by (Choi et al. 2006;
Gélinas 2014; Riesenberg and Guthke 1999; Shiloach and Fass 2005). The fed-batch
1. Introduction
20
strategy has many benefits: by-product inhibition can be avoided under glucose or
substrate limited fed-batch processes (Enfors et al. 2001; Xu et al. 1999a) and cell
growth rate could be also controlled by a controlled supply of the nutrient(s)
(Shiloach and Fass 2005). Usually, a glucose-limited fed-batch by supplying high
concentration of glucose is simple and most commonly used in cultivations. The
largest benefit in using this mode is the possibility to control the oxygen
consumption of E. coli which can keep cells in aerobic cultivation all the time
independent on the cell density, and the possibility to avoid overflow metabolism
(Shiloach and Fass 2005). This is why fed-batch is favored by both laboratory and
industry scale cultivations. Nowadays, lots of commercial production processes, such
as the production of baker’s yeast [for a recent review see (Gélinas 2014)], amino
acids (Konstantinov et al. 1991) and therapeutic proteins (Seo and Chung 2011) are
obtained through high cell density fed-batch processes in E. coli.
1.3.3. Inclusion body (IB) productions
The expression of recombinant proteins in bacterial hosts such as E. coli is a useful,
normal and essential tool to obtain productions for basic research containing of
structural proteomics, therapeutic applications and biotechnology industry. However,
numerous of products usually accumulate in insoluble aggregates which are
commonly called inclusion bodies (IBs) (Fahnert et al. 2004; Mayer and Buchner
2004). Most of them are caused by overexpression of heterogonous proteins.
Generally, the recombinant protein aggregates in IBs in an inactive form. Research on
HCD fed-batch fermentations at scale-down model with various IPTG inductions at
different time shows harmful effect on individual cell physiology, which causes the
final biomass yield significantly reduce (Hewitt et al. 2007). Until now, investigators
have put lots of efforts on methods optimization aiming to get soluble, active and
correctly folded form of proteins e.g. development on cultivation strategy,
production of new strains and vectors. However, the optimization process usually is
1. Introduction
21
unpredictable and time-lasting, mostly still resulting in low product yield (Fahnert et
al. 2004; Neubauer et al. 2006). Despite IB-based expression has above-mentioned
limitations, the most attractive advantage is high concentration of target proteins
and easy purification (Neubauer et al. 2006; Ventura and Villaverde 2006). Moreover,
it is an efficient and simple strategy of IB-based cultivation process, and many
current processes for recombinant proteins in E. coli are IB-based processes, see a
review (Neubauer et al. 2006).
1.4. Bioprocess Scale-up and Scale-down
1.4.1. Gradients in large-scale bioprocesses
In the pharmaceutical, chemical and food industries, microorganisms are widely
cultivated under controlled conditions to produce recombinant proteins and organic
molecules. However, inhomogeneities unavoidably exist in large-scale cultivations.
Industrial-scale bioreactors may have volumes from 10 to more than 500 m3.
Technical limitations in large-scale bioprocesses, such as power input or volumetric
oxygen transfer rate, cause the formation of gradients in substrate, dissolved oxygen
concentration (pO2), pH and other parameters (Enfors et al. 2001; Lara et al. 2006a).
Many studies have measured or predicted gradients in large-scale bioprocesses. Cells
move through different zones in a large-scale bioreactor and, consequently, are
exposed to the changing conditions. As a result, they show a different physiology
compared with cells grown in homogeneous cultures.
The most important parameter concerning gradients in large-scale bioreactors is the
pO2, This is because pO2 plays an important role in aerobic processes. For instance,
Manfredini and co-workers studied the axial oxygen distribution in a 112 m3
industrial stirred tank reactor with Streptomyces aureofacies cultivations using a
flexible vertically mounted dissolved oxygen and temperature probe, and measured
1. Introduction
22
that the dissolved oxygen concentration was up to 65% (with respect to air saturation)
near the sparger throughout the cultivation, while it was only 30% at the top part of
reactor (Manfredini et al. 1983). Similar phenomena were observed by Steel and
Maxon (Steel and Maxon 1966) and Oosterhuis (Oosterhuis 1984). Besides, there are
also many groups that studied and predicted the existence of dissolved oxygen
gradients in reactors through computational fluid dynamics (CFD) tools (Ochieng et al.
2009; Schmalzriedt et al. 2003).
With the popularity of fed-batch culture to gain high cell density in industrial
processes (Choi et al. 2006), gradients of substrate are observed with addition of
concentrated substrate into the reactor especially in larger bioreactor scales. For
instance, Lasson et al. investigated the gradients of glucose in time and space in a 30
m3 cultivation of Saccharomyces cerevisiae and showed the concentration of
substrate was at all times different at three sampling parts (bottom/middle/top) of
the reactor. In cultivations, the inhomogeneities of substrate are usually associated
with oxygen gradients as substrate (mostly glucose) consumption and respiration are
closely related with each other. Because in industry cultivations, the concentration of
the feeding solution is always very high (normally well above 500 g L-1), at the limited
mixing power in large-scale bioreactors, mostly substrate excess is coupled with
oxygen limitation at the feeding zone. This leads to alteration of intracellular
metabolic fluxes and synthesis of unexpected byproducts (Neubauer et al. 1995b; Xu
et al. 1999a). On the contrary, at other regions, which are far away from the feeding
zone where there is almost no substrate available, cells are exposed to starvation.
Thus, cells continuously move quickly between excess substrate and starvation zones,
whereby the time constants depend on the circulation and mixing time of the
distinctive process. With the mixing in the bioreactor, cells are hereby exposed to
substrate and oxygen oscillations (Enfors et al. 2001; Junne et al. 2011). Studies
focusing on substrate and pO2 gradients showed a reduced biomass yield and
1. Introduction
23
increased by-product formation of volatile fatty acids (Bylund et al. 1998).
Another important parameter is pH-value and its variable is often measured and
controlled throughout cultivations. In large-scale bioprocess, pH control is usually
based on the point measurements of local pH which usually at well-mixed part of the
bioreactor. By contract, the controlling agent (e.g. concentrated base or acid)
normally is added at poorly mixed top surface of the liquid (Singh et al. 1986). As a
result, the local pH values near the addition point may be different from the bulk pH,
leading to overfeeding of the pH controlling agent and pH gradients in the reactor.
One example is that Langheinrich and Nienow showed the pH gradients of high pH
value in the alkali addition zone in large-scale free suspension animal cell culture
(Langheinrich and Nienow 1999). Since microbial activity is affected by the medium
pH, small fluctuations in pH may therefore potentially cause oscillations of large
amplitudes in cell metabolism. One of the studies performed on oscillations of
ammonia to control the pH showed lower biomass yield and negative effect on cell
viability when cells were exposed to high pH (pH > 7.0) with a mean residence time
of more than 100 seconds (Onyeaka et al. 2003). Another study simulating the pH
fluctuations of B. subtilis cultivations in a scale-down bioreactor clearly showed that
spatial pH gradients led to the change of cellular metabolism and accumulation of
by-products (Amanullah et al. 2001).
Besides the gradients of parameters mentioned above, there are also other
inhomogeneities likely to appear in large-scale cultivations, such as temperature
gradients (Gorenflo et al. 2007). All above studies clearly prove that cells respond to
inhomogeneities that exist in large-scale bioprocesses. So an increasing number
researchers focus on finding ways to simulate large-scale bioprocess in laboratory
scale cultivations to study cellular responses to inhomogeneities with the aim to
better understand the metabolism of cells in large-scale industrial systems.
1. Introduction
24
1.4.2. Simulating large-scale cultivations in Scale-down devices
Scale-down approaches aim to provide a smaller scale experiment to simulate the
same inhomogeneites in the environment that exists at the larger industrial scale and
provide a cheaper and more efficient laboratorial tool to study the impact of
inhomogeneities in large-scale industrial cultivations. There are several approaches
to mimic large-scale conditions in scale-down models. Such simulators could be one-,
two- or more-compartment systems consisting of Stirrer tank reactors (STR),
modified STRs, or tubular reactors.
Examples for one-compartment scale-down system are single STRs that simulate the
fluctuations of dissolved oxygen with switching the air supply into the reactor on and
off (Namdev et al. 1993) or manipulating the compositions of inflowing gases
(nitrogen and oxygen) (Cortés et al. 2005). Simulations of substrate gradients can be
designed in one STR also with intermittent feeding of the glucose solution (Lin and
Neubauer 2000; Neubauer et al. 1995a) or coupled with a rapid sampling unit.
Considering where the disturbance taken place, the rapid perturbation technique can
be classified into substrate pulse into the bioreactor and external disturbance. For
instance, Schaefer et al. performed fast injection of a glucose solution into the
bioreactor and using an automated sampling device to investigate the dynamics of
intracellular metabolites in E. coli (Schaefer et al. 1999). External disturbance can be
achieved by mixing the culture from bioreactor with glucose solutions outside of the
bioreactor and connected with a rapid sampling unit to study cells response to
glucose gradients in large-scale bioreactors (De Mey et al. 2010; Lara et al. 2009).
Two comportment models, either with two coupled STRs (STR-STR) or one STR plus a
plug flow reactor (STR-PFR) are employed most commonly and many articles have
certified them as useful scale-down modules. Dissolved oxygen tension (DOT)
1. Introduction
25
oscillations were studied by Sandoval-Basurto et al. (Sandoval-Basurto et al. 2005)
and Lara et al. (Lara et al. 2006b) with two interconnected stirrer tank bioreactors
which each had different levels for the DOT. The STR-PFR device was originally set up
with an aerobic STR and a single PFR without static mixers inside. But recently lots of
researchers set up the PFR module containing static mixers in the by-pass with
efficient mixing especially the gas-liquid formulation. It was firstly used to study
substrate oscillation conditions in Saccharomyces cerevisiae (George et al. 1993) and
E. coli (Neubauer et al. 1995b). Remarkable research work has been carried out using
such STR-PFR device including simultaneous assessment of the heterogeneities of
glucose, dissolved oxygen, and pH concentrations (Onyeaka et al. 2003). Recently,
besides the sampling ports, the PFR module was updated by equipping it with five
dissolved oxygen and pH sensors as the most advanced scale-down model until now.
This advanced version consists of a normal STR and 4 meters high PFR equipped with
static mixers. Cells continuously go through the STR and PFR to be exposed to
oscillating conditions (Figure 1.5A) (Junne et al. 2011). This scale-down bioreactor
has been used to study substrate and dissolved oxygen concentration oscillations on
Bacillus subtilis in fed-batch cultivations. As a result, the authors found a reduced
glucose uptake, ethanol formation and changes in the amino acid biosynthesis (Junne
et al. 2011). Furthermore, Lemoine et al. investigated the response of
Corynebacterium glutamicum on substrate and oxygen supply oscillations not only in
such two-compartment reactor (2CR), but also on this basis newly developed a novel
three-compartment reactor (3CR) by adding an additional non-aerated PFR module
(Lemoine et al. 2015). In their set up the PFR1 simulated the feeding zone in
large-scale cultivations, and the PFR2 mimicked the starvation zone which is far away
from the feeding substrate, presenting substrate depletion (Figure 1.5B).
1. Introduction
26
Figure 1.5: Scheme of the advanced version of scale-down two-compartment reactor and the
novel three-compartment reactor.
1.5. Metabolic flux analysis of biosynthesis pathway of non-canonical
amino acids in E. coli
1.5.1. Basic idea of metabolic flux analysis
Metabolite flux analysis (MFA) has become one of the pivotal and valuable tools to
describe the insight of complex metabolic control mechanism in living cell, based on
metabolic fluxes’ detailed quantification in the central metabolism of a
microorganism, which is very useful in metabolic engineering (Zhao and Shimizu
2003). Fluxes are able to describe the rate of metabolite interconversion in the whole
cell. Metabolic fluxes are crucial to observe and to understand metabolic regulation
and to define targets for improving biotechnological processes (Schwender 2008).
Initially, MFA started with stoichiometric knowledge of metabolic fluxes in the early
1990s. One important assumption was that the regarded biological system is in a
stationary or quasi-stationary state with respect to no change of intracellular pool
size (Wiechert 2001). However, there exits apparently shortcomings and limits of
stoichiometric MFA. For example, it cannot be applied in parallel fluxes, certain
1. Introduction
27
metabolic cycles, bidirectional fluxes, and complex fluxes with energy resources
generated or re-assimilated (Wiechert 2001).
In consideration of above-mentioned drawbacks of stoichiometric MFA, 13C MFA
method emerged and can overcome these problems, hence it is becoming a much
more powerful tool for accurately quantifying the metabolic network. 13C MFA is
based on carbon labeling experiments (CLE) with cells exposed to 13C-labeled
substrate like glucose, following isotopomers of labeling patterns in certain
intracellular metabolites measured by either nuclear magnetic resonance (NMR) or
mass spectrometry (MS) (Shimizu 2013; Wiechert 2001; Wiechert et al. 2001).
Though Szyperski has shown NMR spectra as a useful approach in studying the
regulation of metabolite in E. coli (Szyperski 1995), it also has a shortcoming of
requirement for large amount samples, while gas chromatography mass
spectrometry (GC-MS) is more popular with less sample volume (Sauer 2006;
Wittmann 2007).
1.5.2. Rapid sampling devices
Kinetic modeling of the metabolism in in vivo conditions requires information of
enzyme levels, metabolic fluxes and concentrations of metabolites under different
conditions. These can be gained from perturbations of controlled steady-state
cultures.
Considering where the disturbance took place, the rapid perturbation technique can
be classified into substrate pulse into the bioreactor and external disturbance. For
example, this technique was initially applied inside the bioreactor to study the kinetic
metabolite responses of Saccharomyces cerevisiae in in vivo conditions, performed
by a fast sampling technique allowing sampling with a frequency of 5 s from a bench
scale bioreactor (Theobald et al. 1993). Another technique was also developed to
1. Introduction
28
connect a helical sampling tube device to the reactor to enable continuous sampling,
inactivation and extraction of the intracellular metabolites, studying the response to
a glucose pulse (Weuster-Botz 1997). Further, sampling methods were developed to
be taken from a continuous stirred tank reactor, by using an automated sampling
device with a sampling rate of 4.5 s-1 to investigate the dynamics of intracellular
metabolites in E. coli (Schaefer et al. 1999). These devices mentioned above have an
obvious shortcoming. When carrying out a perturbation experiment, the steady-state
condition in the reactor is disturbed and the culture can only be used again until
reaching a new steady-state condition. In order to avoid this drawback, there are also
some devices with disturbance outside the bioreactor without interference with the
steady-state condition. For instance, Buziol and colleagues introduced a sampling and
perturbation device based on stop-flow technique, performing with mixing the
continuous culture from bioreactor with glucose solutions outside of bioreactor by a
mixing chamber (Weuster-Botz 1997). Further it was improved with the name of
“BioScope” by equipping it with oxygen permeable silicon tubing, and allowing
longer perturbation times with residence times from 4 to 69 s (Visser et al. 2002).
This first generation of BioScope was further improved by Mashego et al. in yeast
cultivation and overcomes the drawbacks of first version, coupled with a silicon
membrane separating the gas and culture hemispherical channels and allowing O2
and CO2 diffusion (Mashego et al. 2006). Because the metabolites response of E. coli
is much faster, De Mey et al. redesigned the second generation of BioScope with
significantly decreased sampling intervals especially for E. coli (De Mey et al. 2010).
The BioScope device can be considered as a mini plug-flow reactor and is able to be
coupled with a bioreactor, allowing sampling intervals of sub-seconds to seconds and
studying cellular reaction within seconds to minutes (De Mey et al. 2010;
Taymaz-Nikerel et al. 2013).
1. Introduction
29
Figure 1.6: Schematic representation of the BioScope device. a - 2D figure of BioScope with
serpentine channels and valves; b – cross-section of the channel (De Mey et al. 2010).
The adapted BioScope system (Figure 1.6) is operated by feeding labeled substrate
(e.g. 13C glucose) into the broth, which is pumped out of the bioreactor, to realize
pulse experiments, with no perturbation of the steady-state condition inside the
bioreactor. Meanwhile, it is coupled with fast sampling from the several sampling
spots along the plug flow reactor part controlled by valves. There are two pumps
required in such equipment. One is used to regulate the speed of broth entering the
BioScope, and the other is applied to control the feeding velocity of labeled substrate
into the channel. Due to the serpentine-shaped hemispherical gas and liquid
channels separated by a thin silicon membrane allowing O2 permeability into the
broth and CO2 removal from the culture, it is possible to realize aerobic conditions
during pulse experiments by flushing air or O2 into the hemispherical gas channel of
the BioScope. Hence, the flow through is saturated with oxygen during all the time of
sampling (De Mey et al. 2010).
1. Introduction
30
1.6. Research motivation and objectives
The industrial microbial production strain E. coli K-12 W3110 is able to accumulate
non-canonical amino acids in the presence of excess glucose and anaerobiosis in the
broth during cultivations, which are always likely to occur in the feeding zone in
industrial large-scale bioprocess. Consequently the accumulated non-canonical
amino acids can be misincorporated into proteins, which is highly unfavorable for
proteins for pharmaceutical use. In addition, the level of the branched chain amino
acids leucine, isoleucine and valine, which changes with the expression rate of
leucine-rich recombinant protein, also affects the synthesis and misincorporation of
non-canonical amino acids, and this effect is not yet fully clear.
Therefore, this doctoral dissertation study performed with E. coli W3110 wild-type
and two different recombinant strains expressing leucine-rich proteins, aims to
investigate the cellular responses to the oscillations of substrate and oxygen
availability caused by insufficient mixing during industrial large-scale cultivations. The
oscillations were simulated in a 2CR and recently developed 3CR scale-down
bioreactors (described in 1.2.2), and especially focuses on the analysis of the
non-canonical amino acids norvaline, norleucine and β-methylnorleucine. Thus, the
principal objectives of this project were:
1) To better understand the synthesis pathway and conditions that favour the
formation of non-canonical amino acids norvaline, norleucine and
β-methylnorleucine.
2) To study the influence on incorporation of non-canonical amino acids into
recombinant proteins, since a strong expression of leucine-rich protein seems to
provoke accumulation and misincorporation of non-canonical amino acids into
the target protein.
3) To study the effect of recombinant, leucine-rich proteins expressions and cell
1. Introduction
31
physiology at oscillating large-scale conditions.
2. Materials and Methods
32
2. Materials and Methods
2.1. Bacterial strains
Bacterial strains used in this dissertation work were: E. coli W3110 wild-type stain
obtained from E. coli Genetic stock center, E. coli W3110_pCTUT7_His_IL2 and E. coli
W3110M_pSW3 obtained from laboratory strain collection.
E. coli strains were stored as cryo stocks, which was prepared as follows: Cells were
cultivated overnight at 37 °C on an LB agar plate. If necessary, appropriate antibiotics
were added to the medium depending on different strains. The next day, a colony
was isolated from this plate, and inoculated into 25 mL LB medium with the
appropriate antibiotics in 125 mL Ultra Yield FlasksTM (Thomson Instrument Company,
California, USA), and cultured overnight at 37 °C. Then 1 mL of the overnight
culture was added to 200 μL sterile 100% glycerol (Carl Roth GmbH + Co.KG,
Karlsruhe, Germany) and distributed into 60 μL to 1.5 mL Eppendorf tubes, then
frozen in liquid nitrogen and immediately stored at -80 °C.
2.2. Cultivation media
2.2.1. LB medium
LB medium contained 10 g L-1 tryptone, 5 g L-1 yeast extract (Carl Roth GmbH) and 10
g L-1 NaCl (VWR International GmbH, Darmstadt, Germany), followed by adjustment
to a pH of 7, then sterilized at 121 °C for 20 min, and stored at room temperature.
2.2.2. Mineral salts medium and EnBase Flo medium
The composition of the medium used for cultivations is described below. The macro
elements, trace elements, magnesium sulfate were autoclaved separately at 121°C
for 20 min. Before sterilization, the macro element solution was supposed to have a
2. Materials and Methods
33
pH=7.0. If not, it was adjusted to pH=7 with 2 M sodium hydroxide solution.
Thiamine hydrochloride and antibiotics were sterile-filtered through a 2 μm sterile
filter (Carl Roth GmbH), MgSO4 was not added to the media until just before the
inoculation into the reactor.
For E. coli W3110 wild-type cultivations, EnBase Flo medium (BioSilta, Oulu, Finland)
as described in previous reports (Krause et al. 2010) without complex additives was
used. Additionally, 0.1 ml L-1 Antifoam Sigma 204 (Sigma Aldrich) was added to the
medium to prevent foaming. 200 μl of polymer degrading catalyst (BioSilta, Oulu,
Finland) was added into the medium shortly before inoculation to catalyze releasing
glucose.
For E. coli W3110_pCTUT7_His_IL2 cultivations, the same EnBase Flo medium
described above with additional 2 g L-1 glucose and 34 μg L-1 Chloramphenicol was
used.
For E. coli W3110M_pSW3 cultivations, MSM medium was used, containing macro
elements [2 g L-1 Na2SO4, 2.468 g L-1 (NH4)2SO4, 0.5 g L-1 NH4Cl, 14.6 g L-1 K2HPO4, 3.6
g L-1 NaH2PO4, 1 g L-1 (NH4)2-H-citrate], 0.1 mL L-1 Antifoam Sigma 204), trace
elements [1 mg L-1 CaCl2 • 2H2O, 0.36 mg L-1 ZnSO4 • 7H2O, 0.2 mg L-1 MnSO4 • H2O,
40.2 mg L-1 Na2-EDTA, 33.4 mg L-1 FeCl3•6H2O, 0.32 mg L-1 CuSO4•5H2O, 0.36 mg L-1
CoCl2•6H2O], 2 mM MgSO4, 0.1 g L-1 Thiamine, 5 g L-1 glucose and 0.1 g L-1 Ampicillin.
2.3. Bioreactor cultivation
To investigate cell responses to the substrate oscillation conditions in industrial
large-scale cultivations, a scale-down two-compartment reactor (2CR, Figure 1.5A)
was used. It consists of a normal 15 L BioStat E stirred tank reactor (STR, Satorius
2. Materials and Methods
34
stedim Biotech GmbH, Göttingen, Germany) and a plug flow reactor (PFR) with a 1.2
L working volume. The PFR was equipped with four static mixer modules (Kenics
series KM, distributed by Lewa GmbH). In order to maintain the temperature in the
PFR module, it was insulated with a polymer foam jacket. Between each static mixer
module, spacers, equipped with three sample ports, are mounted. Each spacer
contains one manual sampling port and equipped with pH and DO sensors. Thus, five
sampling points along the PFR allows analysis of the kinetics of the cell responses,
coupled with online pH and DO monitoring. A pump (Lewa GmbH, Leonberg,
Germany) was connected between the STR and PFR, and the culture circulated
through the STR and PFR with a pump rate of 1.73 L min-1, corresponding to a
residence time of 68 s in the whole PFR module. The feed solution was added at the
entrance of the PFR and no extra air was introduced there. As a result, cells
repeatedly circulated between substrate excess / oxygen limitation zones for 68 s and
the aerated glucose-limited STR module. In order to avoid backflow at the feed pump,
a back-pressure valve was integrated between the feeding tube and PFR module.
Moreover, the three-compartment reactor (3CR, Figure 1.5B) was also used in this
study. It included one STR and two identical PFR modules, containing not only
feeding-loop, but also a starvation loop, which was connected no feed solution and
without aeration. The STR was sterilized at 121 °C for 20 min, and PFR was sterilized
with steam for 40 min.
The feed solution contained 400 g/L glucose, macro elements, trace elements and
thiamine of which the concentrations are the same as in the bioreactor. There is no
addition of IPTG in the feed solution. For stable growth of the cells, MgSO4 were
added into a bioreactor frequently after increasing of OD600 by 20.
This dissertation work was based on seven bioreactor cultivations, using three
different kinds of strains. All the cultivations were performed in a fed-batch mode.
2. Materials and Methods
35
For each strain, one homogeneous STR cultivation and one scale-down 2CR
cultivation with feeding-loop were done. In addition, for strain
W3110_pCTUT7_His_IL2, both of the STR and 2CR cultivation were connected with
Bioscope with an anaerobic sampling. At the entrance of the Bioscope, the culture
from the STR module was fed with 13C glucose and representing the substrate excess
conditions in the PFR. For W3110M_pSW3, a third scale-down 3CR bioreactor
cultivation was applied. Each of STR cultivation serves as a reference for respective
the scale-down cultivation in order to compare the impact of long-term oscillations
on the response to a sudden glucose pulse.
2.3.1. Preculture
Firstly, the cryo culture (50 μL) taken from a frozen stock stored at -80 °C, was
inoculated into LB medium in a sterile 125 mL Ultra Yield Flask, and incubated at
37 °C, 250 rpm. This was named as start-culture. The aim of this step was to grow
cells until exponential phase avoiding long lag phase or cell death. Because cells in
cryo culture had adapted to LB medium when frozen, if they would be directly
changed from a complex medium (LB) to a minimal medium (mineral salt medium),
cells maybe lack the ability to deal with this shock and adapt for a long time. When
the cells reached OD600 of appr. 1, they were used to inoculate mineral salt medium
in a sterile 2.5 L Ultra Yield Flask, which was called preculture. When the preculture is
ready, it was used to inoculate into the bioreactor. If necessary, the medium
mentioned above was added with appropriate antibiotics depending on different
strains.
2.3.2. On-line measurements
In the STR, a pt-100 temperature sensor, a DO sensor (Mettler-Toledo Deutschland
GmbH, Gießen, Germany) and a pH sensor (65/90 VT, Mettler-Toledo Deutschland
GmbH, Gießen, Germany) are installed to monitor the temperature, DO and pH,
2. Materials and Methods
36
respectively. At each spacer of the PFR, an optical DO sensor (Visiferm DO ARC 120;
Hamilton Inc., Bonaduz, Switzerland) and a pH sensor (Polilyte Plus ARC 120;
Hamilton Inc., Bonaduz, Switzerland) are used to measure the corresponding
parameters along the height of the PFR.
The oxygen sensors were calibrated to 0% with nitrogen-sparged water and to 100%
with air-sparged water, using the software (ARC sensor configurator) to set the
calibration values, while the pH sensors were calibrated with pH 7.0 and pH 4.0
standard buffers.
2.4. Sampling
Samples were collected in different ways for the analysis of optical density (OD), dry
cell weight (DCW), carboxylic acids, amino acids and protein. Generally, the
suspension sampling was taken from STR every one hour. The supernatant, methanol
and perchloric acid quenched sampling were taken from the STR every one hour, and
every two hours from the 5 sampling ports in the PFR.
2.4.1. Cell growth determination
To monitor cell growth in the bioreactors, about 10 mL of suspension sample was
taken from the STR sampling port, using a syringe. Firstly, 1 mL sample after a certain
dilution was used to measure OD600 values with a 1 cm path length cuvette at
different time points during the cultivation using a UV/Visible spectrophotometer
(Ultrospec 2100 pro, Amersham Biosciences, Germany). Secondly, for dry cell weight
measurement, 2 mL sample was centrifuged in a previously weighted and dry
Eppendorf tube at 4 °C, 15000 rpm for 10 min with a centrifuge CT15RE (VWR, by
Hitachi Koli Co., Ltd, Japan). The supernatant was discarded and the pellet was
washed with 1 mL 0.9% NaCl solution. After centrifugation under the same
2. Materials and Methods
37
conditions the pellet was collected and dried in an oven (WTC binder, Tuttlingen,
Germany) at 70 °C for 1 day, then transferred to a desiccator at room temperature for
1 day to cool down. Lastly, those Eppendorf tubes with dried samples were
reweighed and the difference with the empty tube represents the biomass in 2 mL
reactor volume. Both the OD and DCW were measured in triplicates at each sampling
point and an average of the three values was taken as the final OD or DCW. The
Offline pH measurement was done using a pH meter CG 842 series (Schott Geräte
GmbH, Hofheim, Germany).
2.4.2. Supernatant sampling
For analysis of the extracellular pool of amino acids, carboxylic acids and sugars, the
supernatant sample was pulled out by a 20 mL syringe through a 0.22 μm PVDF filter
directly from the STR bioreactor sampling port. The sample was quickly transferred
into a 1.5 mL Eppendorf tube and immediately frozen at -80°C.
2.4.3. Methanol quenched sampling
In order to immediately stop the cellular activity, quenching was applied by preparing
cooled -80 °C liquids in which the suspension was quenched. Methanol quenched
was selected for the amino acids analysis, because methanol does not destroy the
cell walls during the quenched procedure, which not only can keep the extra and
intra cellular amino acids separated, but also does not destroy any amino acids.
Therefore each 5 mL syringe was filled with 2 mL methanol (Carl Roth GmbH), and
closed with a Sarstedt adapter, then pre-cooled in -80 °C freezer at least for one day
before use. For sampling during cultivations, 3 mL suspension were pulled into each
of these syringes from the sampling port of STR or PFR, followed by immediate
mixing and freezing in -80 °C. These samples were stored until further analysis.
2. Materials and Methods
38
2.4.4. Perchloric acid quenching
Perchloric acid quenching was used for the analysis of carbonic acids, for HClO4 is
able to destroy the cells immediately and makes a later cell disruption unnecessary.
So 1-Butanol (Sigma-Aldrich Chemie GmbH) was added into HClO4 (Carl Roth GmbH)
to a final concentration of 0.5 g L-1. 1 mL of the mixture was pulled into each 5 mL
syringe and closed with a Sarstedt adapter, then pre-cooled in -80 °C freezer at least
for one day before use. For sampling during cultivations, 4 mL suspension was pulled
into each of these syringes from the sampling port of STR or PFR. After mixing, the
samples were immediately stored on ice on a horizontal shaker for 7.5 min and then
in the reverse direction for 7.5 min to ensure efficient cell lysis. Then sample was
transferred to a 50 mL falcon-tube, and 845 μL 5 M K2CO3 (Carl Roth GmbH) was
gently added, followed by centrifugation at 5200 rpm, -2 °C for 10 min with a
centrifuge Avanti J-26 XP (Beckman Coulter GmbH, Germany). Lastly, 2 mL
supernatant was pipetted to a new 2 mL Eppendorf tube and immediately stored at
-80 °C freezer for further analysis.
2.4.5. Protein sampling
For protein sampling, every hour 1 ml of suspension from STR sampling port was
pipetted into 1.5 ml Eppendorf tube from start of induction, then centrifuge at 4 °C,
15000 rpm for 10 min. The supernatant was discarded and the cell pellet was
immediately stored at -80 °C until protein analysis.
2.4.6. BioScope sampling
BioScope samples were also taken by methanol quenched method. Eppendorf tubes
were balanced before and after filling with 800 µL methanol. The tubes were put into
a vessel that was filled with ethanol (Carl Roth GmbH), and pre-cooled in -80 °C
freezer at least for 12 hours prior to the start of sampling. Each sampling port and
2. Materials and Methods
39
tube of BioScope should be washed with VE-water before sampling. Then connected
the N2-bottle and keep gas flow rate at 600 mL min-1 and connected the BioScope to
the bioreactor through a needle. The BioScope-Pump was started with 0.6 mL min-1
and the last sampling spot in the BioScope was opened until first drop came out.
Feed-Pump (Pharmacia, Pharmacia LKB Pump P-1) was started with 0.06 mL min-1
until equilibrium between the medium and the labeled substrate was reached, which
took for about three minutes. Then begin to do sampling as given in Table 2.1. When
the samples were done, the BioScope-Pump was changed to 1.73 ml min-1, and
sampling from spot #7 was done. When all the samples were finished, the vessel
with the samples in the Eppendorf tubes was stored at -80 °C until analysis.
Table 2.1 Sampling schedule and the residence time correspondingly in BioScope.
Eppi Nr. 1 2 3 4 5 6 7 8 9 10
Residence time 0 4.96 6.03 7.39 12.46 14.45 18.81 30.53 40.09 56.95
Port in BioScope Zero 1 3 5 7 5 6 7 8 9
1,73 ml/min +10% Feed x x x x x
0,6 ml/min +10% Feed x x x x x
2.5. Analysis of metabolites
2.5.1. Quantitative analysis of carboxylic acids by high performance liquid
chromatography (HPLC)
The analysis of carboxylic acids was done from supernatant samples (extracellular;
see 2.4.2) and from perchloric acid-quenched samples [total amount (cells plus
medium); see 2.4.4]. After the samples from -80 °C freezer thawed on ice, they were
centrifuged at 15000 x g; +4 °C for 10 min. 200 µL of centrifuged supernatant was
transferred into vial (FisherbrandTM) with 200 μL micro-inlets (FisherbrandTM) and
screwed with caps (Thermo Fisher Scientific GmbH, Schwerte, Germany) containing 8
mm silicone septum (VWR GmbH) inside. Here the gas phase above the liquid has to
be as small as possible to avoid evaporation of volatile compounds. Lastly, the
2. Materials and Methods
40
prepared vials with samples were directly placed into the sample port of the Agilent
1200 Series HPLC System (Agilent Technologies, Waldbronn, Germany) and analyzed.
The intracellular concentration of carboxylic acids was calculated from the total
amount of carboxylic acids (cells plus medium) minus extracellular concentration of
carboxylic acids.
Standard curves were obtained from analyzing D(+) glucose anhydrous (Carl Roth
GmbH), Formic acid Rotipuran®pur. > 99.8% (Carl Roth GmbH), Acetic acid (Merck
KgaA), Ethanol pur. > 99.8% (Carl Roth GmbH), Pyruvic acid > 98% (Carl Roth GmbH),
Lactic acid (Merck KgaA). Prepared samples were analyzed by refractive index
detector (HPLC-RID) using a HyperRez XP Carbohydrate H+ column, 300 × 7.7 mm,
particle size 8 μm (Thermo Fisher Scientific, GmbH, Schwerte, Germany). The eluents
used were HPLC grade water, purified using an RF ultrapure water system (Wilhelm
Werner GmbH, Leverkusen, Germany), and 5 mM H2SO4 (Carl Roth GmbH). The
isocratic pump rate was kept at 0.5 ml min-1 at 15 °C. The pressure limit was adjusted
to a maximum of 60 bars. The injection volume was set to 20 μL. The draw speed and
injection speed were both set to 200 μL min-1.
2.5.2. Quantitative analysis of amino acids by high performance liquid
chromatography (HPLC)
The analysis of extracellular free amino acids by HPLC was carried out from
supernatant samples (see 2.4.2). After samples from -80 °C thawed on ice, they were
centrifuged at 15000 x g at 4 °C for 10 min. 100µL of supernatant was pipetted into
HPLC vial with inlet, added with 100µL of internal standard (225 µM α-aminobutyric
acid). Then the samples were placed into the sample ports of the Agilent 1290
Infinity HPLC System (Agilent Technologies, Waldbronn, Germany). Here the internal
standard was firstly prepared as 18 mM α-aminobutyric acid (Sigma Aldrich)
2. Materials and Methods
41
dissolved in 40 mM sodium dihydrogenphosphate-dihydrate (Buffer A). When
needed, it was diluted 1:80 to 225 µM with 1:10 Buffer A (40 mM NaH2PO4).
The methanol-quenched samples were used to analyze the concentration of total
free amino acids (cells plus medium). Because this analysis requires cell disruption,
samples were diluted with Buffer A (40 mM NaH2PO4) to final OD600 of 1 for
sonications. The final volume of diluted samples was 0.5 ml in 1.5 ml Eppendorf
tubes. The diluted samples were lysed under sonication by the ultrasonic processor
UP200S series (Hielscher Ultrasound Technology, Teltow, Germany). The amplitude of
the ultrasonic processor was set to 30%, and cells were then vortexed shortly and
sonication was performed in a mixture of water and ice for 5 cycles. One cycle lasted
for 30 seconds of sonication and 30 second of break to protect samples from
overheating. The lysed cells were then centrifuged at 15000 × g, 4 °C for 10 min. 250
µL of supernatant cell-free top phase was mixed with 250 µL internal standard in
HPLC vials. Prepared samples were placed into the sample ports of the Agilent 1290
Infinity HPLC System.
Prepared samples were analyzed by HPLC with a fluorescence detector (HPLC-FLD),
using a GEMINI® column (5 µ, 100 Å, 150 x 4.6 mm) with a Security Guard (Gemini
C18) pre-column (Phenomenex, Aschaffenburg, Germany). The applied method is
described in Table 2.2 below. The solvent compositions were Buffer A (40 mM
NaH2PO4), Buffer B (45% ACN: 45% methanol: 10% H2O). The column was heated at
40 °C. Injection volume was 10 μL, and injection speed was 600 μL min-1. Draw speed
was set to 200 μL min-1.
The concentration of intracellular free amino acid was calculated from the
concentration of total free amino acids (cells plus medium) minus extracellular free
amino acids.
2. Materials and Methods
42
Table 2.2 HPLC gradient operation for analysis of amino acids.
Time (min) Buffer A (%) Buffer B (%) Flow (mL min-1
)
0 100.0 0.0 1.000
40.5 59.5 40.5 1.000
41 39.0 61.0 1.000
43 39.0 61.0 1.000
44 18.0 82.0 1.000
44.5 0.0 100.0 1.000
59.5 0.0 100.0 1.000
61 100.0 0.0 1.000
64 100.0 0.0 1.000
2.5.3. Quantitative analysis of amino acids by Gas Chromatography-Mass
Spectrometry (GC-MS)
The free amino acids were analyzed by GC-MS from supernatant samples
(extracellular free amino acids; see 2.4.2) and methanol-quenched samples [total
free amino acids (cells plus medium); see 2.4.3]. The methanol-quenched samples
were firstly diluted to an OD600 of 5 for disruption with phosphoric buffer (4 mM
NaH2PO4) in 1.5 mL Eppendorf tubes to a final volume of 0.5 mL per tube. The
diluted samples underwent sonication as described before. After sonication, samples
were centrifuged at 15 000 x g, 4°C for 10 min. For supernatant samples, 150 µL
cell-free supernatant was transferred into a 1.5 mL Eppendorf tube after thawing on
ice, and centrifuged at 15 000 x g, 4°C for 10 min. 125 μL supernatant from each of
the centrifuged cell-free extracts as well as the sonication samples were added into
1.5 mL brown glass Fisherbrand™ vials with 9 mm neck (Thermo Fisher Scientific)
containing 125 μL of internal standard (225 µM α-aminobutyric acid) and 750 µL of
0.1 M HCl (VWR International GmbH). All opened vials containing samples were
stored in a speed vacuum pump (Bachofer GmbH, Reutlingen, Germany) for drying by
centrifugation at 30 °C for 3 hours.
2. Materials and Methods
43
The total amino acids of supernatant samples were analysed by acidic hydrolysis
followed by GC-MS measurement (extracellular total amino acids; see 2.4.2) as well
as methanol-quenched samples (total amino acids; see 2.4.3). The
methanol-quenched samples were firstly diluted to an OD600 of 1 for disruption with
phosphoric buffer (4 mM NaH2PO4) to a final volume of 0.5 mL per tube. The diluted
samples were dealt with sonication as described above and centrifuged at 15 000 x g,
4°C for 10 min. For supernatant samples, 150 µL was transferred into an 1.5 mL
Eppendorf tube, and centrifuged at 15 000 x g, 4°C for 10 min. 125 μL supernatant
from each of the centrifuged supernatant samples as well as the sonication samples
was added in 1.5 mL brown glass vials ø 9mm containing 125 μL of internal standard
(225 µM α-aminobutyric acid) and 750 µL of 6 M HCl. All vials containing samples
were put into a Block heater H250 (Carl Roth GmbH) and heated at 80 °C for 24 hours.
Then the vials were stored into a speed vacuum pump for drying by centrifugation at
30 °C for 3 hours.
After complete evaporation of liquid, 50 μL of acetonitrile (VWR International GmbH)
was added to each vial, followed by 50 μL
N-(tert-butyldimethylsilyl)-N-methyl-trifluoroacetamide (MTBSTFA) (Sigma-Aldrich
Chemie GmbH, Germany) and 5 μL 1-butanol (Fluka Chemie AG). Here, because
MTBSTFA is sensitive to oxygen, the opened MTBSTFA-vial was continuously flushed
with nitrogen via a pipe connection from nitrogen bottle to the headspace of the
MTBSTFA-vial, using a gas flow meter (Bailey-Fischer & Porter GmbH, Göttingen,
Germany) for adjustment of the gas flow rate at 2 L min-1. 1-butanol was previously
dewatered with molecular sieve 5 Å (Carl Roth GmbH). Then all the vials were closed
and transferred into a heating block for derivatization at 60 °C for 60 min. After
derivatization the liquid was transferred using pasteurized pipettes (Carl Roth GmbH)
into a 1.5 mL brown vial (ø 8mm), which contained a spring and a 50 μL micro inlet
(All from Thermo Fisher Scientific). Vials were then closed with black caps (ø 8mm)
2. Materials and Methods
44
with septum and placed at the injection platform of the GC-MS system (Agilent
Technologies Deutschland GmbH & Co. KG, Waldbronn, Germany) using
DB-5MS-column (5% Phenyl – 95% Methylpolysiloxan, 30m x 250µm x 0,25µm) in the
GC. The applied method for analysis of quantitative amino acids is summarized in
Table 2.3 and Table 2.4. The quadrupole settings for the quantitative analysis of
amino acids are shown in Table 2.5.
Table 2.3 General settings of the GC-MS for amino acids analysis.
Parameter Value
Heater 290 °C
Pressure 18.842 kPa
Total Flow 18 mL min-1
Septum Purge Flow 15 mL min-1
Split Ratio 2:1
Split Flow 2 mL min-1
Aux 2 150 °C for 0 min
MS Source 230 °C
Table 2.4 The settings used for column of the GC for amino acids analysis.
Parameter Value
Initial 150 °C
Pressure 91.924 kPa
Flow 1 mL min-1
Average Velocity 38.051 cm sec-1
Holdup time 1.314 min
Table 2.5 The Quadrupole settings for the quantitative analysis of amino acids. The bold labeled
fragments are basis-ion fragments.
Nr. Group name Fragments [m/z] Approx. retention time [min]
1 Ala
Gly
317 302 260 232 158
303 288 246 218 144
3.00 (Solvent Delay)
2 ABA 331 316 274 246 172 6.00
3 Val
Norval
345 330 288 260 186
345 330 288 260 186
6.80
2. Materials and Methods
45
4 Leu Ile Norl
Pro
359 344 302 274 200
343 328 286 258 184
7.90
5 Beta-Methylnorl 214 215 288 289 316
317 359 374
10.00
6 Met 377 362 320 292 218 14.69
7 Ser 447 432 390 362 288 15.20
8 Thr 461 446 404 376 303
302
16.15
9 Phe
Homoserin
393 378 336 308 234
461 446 404 376 302
17.90
10 Asp 475 460 418 390 316 19.88
11 Cystein 463 448 406 378 304 21.10
12 Glu
Asn
489 474 432 404 330
474 459 417 389 315
22.90
13 Lys Gln 488 473 431 403 329 25.40
14 Arg 499 484 442 414 340 27.40
15 His
Tyr
497 482 440 412 338
523 508 466 438 364
29.00
16 Tryptophan 273 347 375 417 432 30.93
The concentration of intracellular free amino acid was calculated from the
concentration of total free amino acids (cells plus medium) minus extracellular free
amino acids.
Samples for the analysis of isotope distribution in amino acids were obtained from
the BioScope experiments (see 2.4.6). They were based on the same preparation
procedure of analysis of free amino acids from methanol-quenched samples (see
above part of 2.5.3). The settings of the applied GC-MS method were also the same
with methods for the amino acids-analysis (see Table 2.3 and Table 2.4). The only
difference is the quadrupole settings which are shown in Table 2.6.
Table 2.6 The Quadrupole settings for the isotope distribution analysis of amino acids.
Nr. Group name Fragments [m/z] Approx.
retention
time [min]
2. Materials and Methods
46
1 Ala
Gly
144 145 158 159 160 218 219 232 233 234 246 247 248 260
261 262 263 288 289 290 302 303 304 305 317 318 319 320
3.00
2 ABA 172 246 274 316 331 6.00
3 Val
Norval
186 187 188 189 190 260 261 262 263 264 288 289 290 291
292 293 330 331 332 333 334 335 345 346 347 348 349 350
6.80
4 Leu Ile Norl
Pro
184 185 186 187 188 200 201 202 203 204 205 258 259 260
261 262 274 275 276 277 278 279 286 287 288 289 290 291
302 303 304 305 306 307 308 328 329 330 331 332 333 343
344 345 346 347 348 349 350 359 360 361 362 363 364 365
7.90
5 Beta-Methylnorl 214 215 216 217 218 219 220 288 289 290 291 292 293 294
316 317 318 319 320 321 322 323 324 359 360 361 362 363
364 365 366 374 375 376 377 378 379 380 381
10.00
6 Met 218 219 220 221 222 292 293 294 295 296 320 321 322 323
364 365 366 367 377 378 324 325 362 363 379 380 381 382
14.69
7 Ser 288 289 290 362 363 364 390 391 392 393 432 433 434 435
447 448 449 450
15.2
8 Thr 302 303 304 305 376 377 378 379 404 405 406 407 408 446
447 448 449 450 461 462 463 464 465
16.15
9 Phe
Homoserin
234 235 236 237 238 239 240 241 242 302 303 304 305 308
336 337 338 339 340 341 342 343 344 345 376 377 378 379
380 381 382 383 384 385 386 387 393 394 395 396 397 398
399 400 401 402 404 405 406 407 408 446 447 448 449 450
461 462 463 464
17.90
10 Asp 316 317 318 319 390 391 392 393 418 419 420 421 422 460
461 462 463 464 475 476 477 478 479
19.88
11 Cystein 304 305 306 378 379 380 406 407 408 409 448 449 450 451
463 464 465 466
21.10
12 Glu
Asn
315 316 317 318 330 331 332 333 334 389 390 391 392 404
405 406 407 408 417 418 419 420 421 432 433 434 435 436
437 459 460 461 462 463 474 475 476 477 478 479 489 490
491 492 493 494
22.90
13 Lys Gln 329 330 331 332 333 334 403 404 405 406 407 408 431 432
433 434 435 436 437 473 474 475 476 477 478 479 488 489
490 491 492 493 494
25.40
14 Arg 340 341 342 343 344 345 414 415 416 417 418 419 442 443
444 445 446 447 448 484 485 486 487 488489 490 499 500
501 502 503 504 505
27.40
15 His 338 339 340 341 342 343 412 413 414 415 416 417 440 441
442 443 444 445 446 482 483 484 485 486 487 488 497 498
499 500 501 502 503
29.00
16 Tyr 364 365 366 367 368 369 370 371 372 438 439 440 441 442 30.30
2. Materials and Methods
47
443 444 445 446 466 467 468 469 470 471 472 473 474 475
508 509 510 511 512 513 514 515 516 517 523 524 525 526
527 528 529 530 531 532
17 Tryptophan 273 274 275 276 277 278 279 280 281 282 283 347 348 349
350 351 352 353 354 355 356 357 375 376 377 378 379 380
381 382 383 384 385 386 417 419 420 421 422 423 424 425
426 427 428 432 433 434 435 436 437 438 439 440 441 442
443
30.93
2.5.4. Quantitative analysis of carboxylic acids by Gas Chromatography-Mass
Spectrometry (GC-MS)
Due to a sufficient separation of carboxylic acids with HPLC, only the distribution of
isotopes was investigated with GC-MS. Samples were obtained from BioScope
sampling (see 2.4.6), and firstly diluted to OD600=5 with 4 mM NaH2PO4 (pH=7.8) to a
final volume of 0.5 mL. Thereafter the diluted samples underwent sonication by the
same method mentioned above (see 2.5.3) and subsequent centrifugation at 15 000
x g, 4 °C for 10 min. 125 μL of the supernatant was carefully pipetted into a 1.5 mL
brown vial (ø 9mm) containing 125 μL of internal standard (225 µM α-aminobutyric
acid), 740 µL of 0.1 M HCl and 10 μL 56 mg mL-1 O-Ethylhydroxylamine hydrochloride
(Sigma Aldrich). The vials were closed with blue screw caps (ø 9mm) with septum
and heated at 40 °C for 90 min in the heating block. After oximation, the vials were
unscrewed and centrifuged in the vacuum centrifuge at 30 °C for 3 h. When the
samples were completely dry, 30 μL pyridine (Sigma Aldrich) was added to each vial,
as well as 70 μL N-(tert-butyldimethylsilyl)-N-methyl-trifluoroacetamide (MSTFA;
Fluka Chemie AG) and 5 μL 1-butanol. Here the MSTFA was flushed with nitrogen and
1-butanol was previously dewatered with molecular sieve. Then all the vials were
closed and transferred to a heating block for derivatization at 40 °C for 50 min. After
the derivatisation, the liquid was carefully transferred into a 1.5 mL brown vial (ø
8mm) containing a spring and a micro inlet inside. Then vials were closed and sent to
GC-MS (EI-quadrupole) for analysis. The applied method for the isotope distribution
2. Materials and Methods
48
analysis of carboxylic acids is summarized in Table 2.7 and Table 2.8.
Table 2.7 General settings of the GC-MS for the isotope distribution analysis of carboxylic acids
Parameter Value
Heater 290 °C
Pressure 60.732 kPa
Total Flow 26 mL min-1
Septum Purge Flow 15 mL min-1
Split Ratio 10:1
Split Flow 10 mL min-1
Aux 2 150 °C for 0 min
MS Source 230 °C
Table 2.8 The settings used for column of the GC for the isotope distribution analysis of carboxylic
acids.
Parameter Value
Initial 70 °C
Pressure 60.732 kPa
Flow 1 mL min-1
Average Velocity 36.796 cm sec-1
Holdup time 13.588 min
2.5.5. Quality of protein analysis
Protein extraction and purification was done using BugBuster Protein Extraction
reagent (Merck KGaA, Darmstadt, Germany). In order to compare bands directly in a
sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), 1 ml of
harvested frozen cell pellets were normalized to the same optical density with OD600
= 15. The samples were re-suspended in the corresponding volume of BugBuster
solution with 1 μL Benzonase nuclease (25 U) and 1 μL lysozyme (50 mg mL-1) in 1 mL
BugBuster solution. The amount of Bugbuster added per pellet was calculated
according to the following equation:
2. Materials and Methods
49
mount Bugbuster µL 600 culture volume µL
600
After the pellet was fully re-suspended by gently pipetting up and down, it was
incubated on a shaking platform for 15 min with a slow setting at room temperature,
followed by centrifugation at 16 000 x g, 4 °C for 20 min. Then 50 μL supernatant was
transferred into a fresh 1.5 mL Eppendorf tube as soluble protein fraction for
SDS-PAGE analysis. The pellet after discarding the rest of the supernatant was
re-suspended with the same amount of BugBuster solution as in the first step,
followed by washing with 1:10 diluted BugBuster solution three times with
centrifugation at 5 000 x g, 4 °C for 15 min. Lastly, the pellet was re-suspended in the
same amount of 1:10 diluted BugBuster solution like the beginning as the insoluble
fraction (inclusion bodies fractions). The soluble and insoluble proteins were
analyzed by SDS-PAGE, and amino acid content of proteins was analyzed by GC-MS
with inclusion bodies fractions.
a) SDS-PAGE analysis
In order to analyze the expression levels of recombinant proteins under different
cultivation conditions, 15% SDS-PAGE gels were used, which were prepared as
described in Table 2.9. Both soluble and insoluble fractions were prepared by 1:1
addition of with 2x SDS loading buffer (100 mM Tris-HCl pH 6.8, 20 % glycerol, 200
mM DTT, 4 % SDS, 0.2 % bromophenol blue). The samples were then incubated at
95 °C for 7 min for denature the proteins. After cooling to room temperature, 15 μL
of each sample and a protein molecular weight marker named Spectra Multicolor
Broad Range Protein Ladder (Thermo Scientific, Waltham, USA) were loaded on to 15%
SDS-PAGE gels for analysis. Electrophoresis was performed in running buffer (25 mM
Tris-HCl pH 8.3, 192 mM glycine, 500 mM urea, 0.1 % SDS, 1 mM EDTA) with
electrophoresis power supply – EPS 300 (Amersham Pharmacia Biotech Inc.) at 90 V
2. Materials and Methods
50
firstly until dye front passed the boundary of stacking gel, and then changed to 140V
until dye front reached the bottom of the gel. When finished, gels were washed
three times with ddH2O on a shaker for 5 min after heating in a 600W microwave for
30 s. Afterwards, the water was discarded, and the gels were stained in Coomassie
staining solution (80 mg L-1 Brilliant Blue G-250, 35 mM HCl) for 1 h on the shaker.
After staining, the gels were destained with ddH2O on the shaker until the protein
lines appear clearly. Here ddH2O was changed several times and paper towel was put
in the corner for fast and sufficiently distaining. Finally, gels were scanned and the gel
pictures were stored.
Table 2.9 The composition of the resolving and stacking gels for SDS-PAGE.
Component (per gel) 15﹪ Resolving gel (5 ml) [ml] 5﹪ Stacking gel (1 ml) [ml]
H2O 1.1 0.68
30﹪acrylamide 2.5 0.17
1.5M Tris-HCl (pH8.8) 1.3 /
1M Tris-HCl (pH6.8) / 0.13
10﹪SDS 0.05 0.01
10﹪APS 0.05 0.01
TEMED 0.002 0.002
b) Analysis of amino acids in proteins
The analysis of amino acid content, especially non-canonical amino acids, of proteins
was done though the analysis of inclusion bodies by GC-MS. 125 μL diluted inclusion
body samples were hydrolyzed in 1.5 mL brown glass vials ø 9mm containing 125 μL
of internal standard (225 µM α-aminobutyric acid) and 750 µL of 6 M HCl at 80 °C for
24 hours, then vials were prepared and analyzed with GC-MS as described in 2.5.3.
2.6. Flow cytometry analysis
Flow cytometry analysis was done using a MACSQuant® analyser (Miltenyi Biotec
GmbH, Bergisch Gladbach, Germany) and the method from the study of Marba et al.
2. Materials and Methods
51
(Marba et al. 2016). Calibration was performed automatically with MACSQuant®
Calibration Beads. Samples preparation was done as follows: 2 mL suspension taken
from the culture in the bioreactor was filtered by the vacuum filter with a vacuum
pump KNF L B (Neuberger, Freiburg, Germany) using a filter pore size of 0.2 μm
(Satorius Stedim, Göttingen, Germany), and washed with 2 mL of 0.9 % NaCl solution.
The cells stuck on the filter were re-suspended with 10 mL phosphate buffered saline
(PBS, pH=7.2) in a 15 mL falcon tube. Then the re-suspension was diluted and
adjusted the concentration to 106 particles mL-1 with PBS. The PBS used here was
filtered through a MCE filter with a pore size of 0.2 μm (Carl Roth GmbH) to avoid
undesired particles and background noises during the flow cytometry analysis. The
stock of PI (Sigma-Aldrich, Munich, Germany) was prepared as 1 mg mL-1, and BOX
(Sigma-Aldrich, Munich, Germany) as 5 mg mL-1. Syto13 was purchased as a
concentration of 1 mg mL-1. All the stock solutions were stored at -20 °C. The working
solutions of dyes were prepared freshly when needed with a concentration of 40 µg
mL-1 for PI, 25 µg mL-1 for BOX added with 4 mM ethylenediaminetetraacetic acid
(EDTA), and 8 µg mL-1 for Syto13.
Once the sample had the concentration of ca. 106 particles mL-1, the samples were
prepared for measurement in 1.5 mL Eppendorf tubes according to Table 2.10 with a
final volume of 200 µL and stained in the dark which was achieved either in the
closed drawer or cupboard. Meanwhile, both negative and positive controls were
also applied. The negative control for all dyes was considered to be the unstained
sample. This sample is used to set up the threshold and detector sensitivity settings.
The positive control was obtained by heating the cell suspension in a heating block
(Thermomixer comfort, Eppendorf, Hamburg, Germany) for 1 h, which resulted in
loss of the cell viability, following staining with the same methods as described above
of this section.
2. Materials and Methods
52
For measurements, the filters used were: a 488/10 bandpass filter for FSC/SSC,
525/50 bandpass filter for SYTO13 and BOX stained samples, and a 655-730 longpass
filter for PI stained samples. Every analysis was carried out in triplicate. Data
collection was performed using M CSQuantify™ software (Miltenyi Biotec GmbH,
Bergisch Gladbach, GER), and data analysis was done with FlowJo™ sofrware
(TreeStar Inc., Ashland, USA).
Table 2.10: Overview of the applied samples stained conditions for flow cytometric
measurements.
Dyes Final Concentration (µg mL-1
) Staining time (min) Temperature (°C)
PI 1 2 4
BOX 0.5 4 Room temperature
Syto13 0.6 2 4
3. Results
53
3. Results
3.1. Behavior of E. coli W3110 in STR and 2CR cultivations
In order to mimic the different zones in industrial scale, and to investigate the cellular
responses of E. coli to gradients of glucose and dissolved oxygen, E. coli W3110
wild-type strain was cultivated in a scale-down two-compartment reactor (2CR, see
Figure 1.5A) in lab scale. This 2CR system consisted of a normal stirred tank reactor
(STR, 15 L Bioreactor and working volume is 10 L) and a plug flow reactor (PFR,
working volume is 1.2 L), and feeding was performed at the inlet of PFR, so cells
continuously moved through the STR and PFR module, and were exposed to the
oscillating cultivation conditions with high concentration of glucose and oxygen
limitation for a short time (68 seconds) in the PFR. The cultivation in the STR without
PFR was also performed as the reference to the scale down 2CR cultivation, and the
feed solution was added to the top gas phase of the bioreactor (detail see 2.3).
3.1.1. Cultivation characteristics
The cultivation process is performed in two parts. Firstly, cells were cultivated
overnight in the EnBase Flo medium as starter culture for high cell density
cultivations, which would confer cells with consistent intracellular physiological
conditions, avoiding overflow metabolism in the initial cultivation phase (Glazyrina et
al. 2012). Enbase simulates a glucose-limited fed-batch cultivation with leaner
glucose feed rate by continuously releasing glucose from soluble starch-derived
polymer with the addition of a specified concentration of a polymer degrading
biocatalyst (Grimm et al. 2012; Panula-Perälä et al. 2008). During overnight
cultivation the cells grew until the glucose release rate became growth-limiting and
grew for about four hours of glucose limiting fed-batch. Secondly, the exponential
glucose feeding was applied with a targeted specific growth rate (μset) of 0.2 h-1.
During the whole cultivations, cells were maintained at 37 °C with the pH was
3. Results
54
controlled by the addition of 25 % ammonium hydroxide to control the pH at a set
point of pH 7. The DO was maintained above 30 % (Figure 3.1B).
At the end of the cultivations, the biomass of the 2CR cultivation reached 26 g L-1 at
6.75 h after feed start, while it was around 27 g L-1 at 7.42 h after feed start in the
reference STR cultivation (Figure 3.1A), which showed a similar profile. The feed
solution contained 400 g L-1 glucose, and was pumped into the inlet of PFR in 2CR
cultivation, while it was directly pumped into the bioreactor in the reference
cultivation. So in the results, in the PFR module of 2CR, cells were under oxygen
limitation from the first port of the PFR, which could be seen from Figure 3.1C.
3. Results
55
Figure 3.1: Shows the E. coli W3110 wild-type strain cultivation data of the STR cultivation
(reference) and the 2CR scale-down cultivation. Feed start point starts from 0 h. (A) Dry cell
weight. (B) Profile of online DO and pH data in the STR module. (C) Profile of online DO data in
the PFR module of 2CR scale-down cultivation.
In Figure 3.2A and B there is a sharp increase of qO2 and qCO2 values at about 2.83 h
after feed start in the reference cultivation, that is due to the removal of sharp bend
in exhaust gas pipe at this moment, which also led to the sharp DOT decrease at the
0 2 4 6 8
DO
[%
]
0
20
40
60
80
100
120
pH
[-]
0
2
4
6
8
10
12STR DO
2CR DO
STR pH
2CR pH
0 2 4 6 8
DO
[%
]
0
1
2
3
4
5
6Port 1
Port 2
Port 3
Port 4
Feed time [h]
-2 0 2 4 6 8
DC
W [
g L
-1]
0
5
10
15
20
25
30
STR DCW
2CR DCW
STR DCW fitted
2CR DCW fitted
Feed time [h]
A
B
C
3. Results
56
same time (Figure 3.1B). Under oscillating cultivation the specific oxygen
consumption rate (qO2) is continually higher than the control after feed start until the
end of cultivations, while the specific carbon dioxide formation rate (qCO2) of both
cultivations is similar. As a result, the relationship between these parameters, the
respiration quotient (RQ) was lower in 2CR scale-down cultivation than in the
reference cultivation. This demonstrates an increased oxygen demand of E. coli cells
under oscillating conditions, and indicates that cells have an increased respiratory
activity and a higher metabolite production in such cultivation.
Figure 3.2: (A) Specific oxygen uptake rate, (B) Specific carbon dioxide production rate, and (C)
Feed time [h]
0 2 4 6 8
RQ
[-]
0.0
0.5
1.0
1.5
2.0
STR
2CR
0 2 4 6 8
qC
O2 [
mm
ol g
DC
W
-1 h
-1]
0
2
4
6
STR
2CR
0 2 4 6 8
qO
2 [
mm
ol g
DC
W
-1 h
-1]
0
2
4
6
STR
2CR
A
B
C
3. Results
57
Respiratory quotient in the STR module of the reference (black) and 2CR scale-down (red) E. coli
W3110 wild-type strain cultivations.
3.1.2. Carboxylic Acids
The properties of a culture and the behavior of microbes during a cultivation process
are reflected by their metabolic components at various time points, transcriptional
factors and physiological influences. In this study, the metabolic components of
carboxylic acids were studied. Therefore, samples taken from STR module from
cultivations were analyzed for TCA cycle and glycolytic intermediates at different time
points during cultivations. The carboxylic acids of interest here were analyzed by
HPLC chromatogram using the refractive index detector (RID) as describe in 2.5.1.
From the extracellular concentration of compounds of main carbon metabolism in
STR module of E. coli W3110 wild-type strain cultivations (Figure 3.3), which means
concentration and composition of carbonic metabolism in the supernatant, it could
be seen that during the 2CR scale-down cultivation, the concentration profile of
glucose polymer and glucose are almost the same as in the reference cultivation, and
both cultivations were glucose limited with a concentration of glucose lower than 0.3
g L-1. Pyruvate, as the starting point for most of the measured metabolites and of
special interest, was only slightly increased to 0.45 mM at 1.92 h after feed start
point in non-oscillation cultivation, then turned back below the limit for analysis in
two hours and kept depletion until the end. While it dramatically increased to 2.2
mM at 1.75 h after start of feeding in 2CR cultivation, then it decreased steeply to 0.1
mM in three hours and then remained quite constant until the end of cultivation.
Pyruvate decreased steeply from 1.75 h after feed start, because a great portion of
the main carbon flux was directed to carboxylic acids, like acetate, formate, malate
and fumarate. Among the intermediates of the tricarboxylic acid (TCA) cycle, the
concentrations of malate and fumarate were most affected by oscillating conditions.
3. Results
58
Compared to the non-oscillating control cultivation, both components showed an
increased level in the 2CR scale-down cultivation. No remarkable differences were
detected in the extracellular concentration of lactate, succinate and oxaloacetate
between the two cultivation types.
Figure 3.3: Extracellular concentration of compounds of the main carbon metabolism in STR
Glc
-2 0 2 4 6 80.0
0.3
0.6
0.9Glc polymer
-2 0 2 4 6 80
5
10
15
20
Feed time [h]
Concentr
ation [g L
-1]
Pyr
0
1
2
3
Oxa
-2 0 2 4 6 80.0
0.1
0.2
Mal
0.0
0.2
0.4
0.6
For
0
1
2
3Suc
0.0
0.1
0.2
0.3
Lac
-2 0 2 4 6 80.0
0.2
0.4
0.6
Concentr
ation [
mM
]
Ace
0.0
0.2
0.4 Fum
0.0
0.1
0.2
0.3
Feed time [h]
3. Results
59
module of E. coli W3110 wild-type strain cultivations, analyzed by HPLC. Data are shown from
around feed start (0h). White circles – STR reference cultivation; black triangles up – 2CR
scale-down cultivation.
Feeding solution with high concentration of glucose (400 g L-1) was fed at entrance of
PFR module in the 2CR scale-down system without the addition of extra oxygen. As a
result, in the PFR, cells with high local volumetric rates for consumption of glucose
and oxygen could easily cause oxygen limitation, or even oxygen depletion, which
was witnessed from Figure 3.1C. So in the plug flow loop (PFR), it is possible to study
the dynamics of metabolic and stress responses to a short period (68 s) of substrate
excess / oxygen limitation condition.
Figure 3.4 shows the extracellular concentration of compounds of the main carbon
metabolism along the PFR at different process times after feed start. With the
consumption of glucose over the residence time in the PFR, acetate and lactate
accumulated quickly under substrate excess and oxygen limitation conditions.
Especially at 3.75 h and 5.75 h after start of feeding the formation rate of both
components was even higher. Meanwhile, for formate and succinate, there was also
a slight increasing trend along the PFR. Acetate can be produced not only via glucose
overflow metabolism, but also via mixed acid fermentation, and is thus not an
exclusive product from oxygen starvation, but also from glucose excess (Xu et al.
1999a; Xu et al. 1999b). However, these two pathways use different enzymes for
acetate formation. Pyruvate is catalyzed by the aerobic pyruvate dehydrogenase to
produce acetyl-CoA, which is the precursor of acetate in aerobic glucose overflow
metabolism. Acetate is the main by-product. When E. coli is exposed to oxygen
limitation or anaerobic conditions, E. coli adapts to mixed-acid fermentation. So in
mixed-acid fermentation pyruvate is catalyzed by the anaerobic pyruvate
formate-lyase to produce formate. As a result, besides acetate, formate, succinate
3. Results
60
and lactate are formed. The rapid accumulation of lactate and acetate in the PFR also
obviously witnessed that enzymes inhibited by oxygen during aerobic growth
(formate-lyase and lactate dehydrogenase) were present in sufficient concentrations
to produce compounds of mixed acid fermentation within 1 minute when exposed to
oxygen limitation conditions inside the PFR (Enfors et al. 2001; Xu et al. 1999a).
Interestingly, though there was a significant accumulation of acetate and lactate
along the PFR (Figure 3.4), there was no higher accumulation of lactate and only a
little higher accumulation of acetate in the STR module of 2CR cultivation than the
reference cultivation (Figure 3.3). This shows re-assimilation when cells were
returned to the STR module, under aerobic and glucose limitation conditions. As it
was described in literature, the re-assimilation of mixed acid fermentation products
is usually observed at cultivations with gradients of substrate and dissolved oxygen
(Enfors et al. 2001; Käß et al. 2014). As a result, due to different re-assimilation rates
of the fatty acids, their accumulations during the process were affected.
For the last two intermediates of the TCA cycle, namely malate and fumarate, under
oscillating conditions, the extracellular concentration of malate fluctuated with an
increasing trend, resulting in a higher concentration than the control. The amount of
fumarate concentration in the extracellular environment continuously increased up
to 0.17 mM at the end of 2CR scale-down cultivation, while in the STR control the
value was around 0.05 mM (Figure 3.3).
For succinate no difference was seen in the supernatant samples of STR module in
two cultivations (Figure 3.3).
3. Results
61
Figure 3.4: Extracellular concentration of compounds of the main carbon metabolism in PFR
module (PFR with feed addition) of E. coli W3110 wild-type strain 2CR scale-down cultivation,
analyzed by HPLC. Data shown are the samples from time points 0.75 h (white triangles up), 1.75
h (gray triangles down), 3.75 h (dark gray squares) and 5.75 h (black diamonds) after feed start
over the residence time in the PFR.
Glc
Residence time [s]
0 30 40 50 60 70
Concentr
ation [
g L
-1]
0.0
0.2
0.4
0.6
0.8
STR
Pyr
0
2
4
Oxa
0 30 40 50 60 700.00
0.05
0.10
0.15
Mal
0.0
0.3
0.6
For
0
2
4 Suc
0.0
0.2
0.4
Lac
0 30 40 50 60 700
1
2
3
Concentr
ation [
mM
]
Residence time [s]
Ace
0.0
0.3
0.6
0.9 Fum
0.0
0.1
0.2
STRSTR
3. Results
62
3.1.3. Amino Acids
In order to provide reasonable information for cellular responses to oscillating
conditions of substrate and dissolved oxygen concentrations, the concentrations of
total free canonical amino acid plus three common non-canonical amino acids
(norvaline, norleucine and β-methylnorleucine) in the STR module were analyzed by
HPLC (Figure 3.5). With regards to leucine, valine and alanine which all belong to the
alanine family and use pyruvate as precursor molecule in their biosynthetic pathways,
in the STR module of 2CR sale-down cultivation, only alanine showed an increasing
trend up to 24.3 μmol gDCW-1 at 2.75 h after feed start, following with a drastic
decrease in one hour and then has a relatively constant course (Figure 3.5). No clear
difference could be seen between the two cultivations for the leucine and valine
concentration. For the decrease of alanine after 2.75 h, one possible explanation is
that the carbon flux flows to other directions. Soini et al. showed that the amino
acids of the alanine family accumulate during oxygen limitation which was performed
mainly with a downshift of oxygen supply during the cultivation, exposing cells to
oxygen depletion over the whole process (Soini et al. 2008a). In the PFR module of
the 2CR scale-down cultivation with feed addition at its inlet, cells were exposed to
substrate excess and oxygen-limited conditions. It was observed that alanine
accumulated rapidly within 68 s in the crude extract at 0.75 h, 1.75 h, 3.75 h and 5.75
h after feed start over the residence time in the PFR (Figure 3.6).
Isoleucine, which belongs to the aspartate family, substantially increased over the
time in scale-down cultivation, while it had a stable level in the control cultivation.
Thus, a huge difference between these two cultivations was observed with
significantly higher amounts under scale-down conditions. At the end of the
cultivation the concentration of isoleucine was about three times higher compared
to the control (Figure 3.5). Along the PFR, the formation of isoleucine marginally
increased at 3.75 h and 5.75 h after feed start (Figure 3.6).
3. Results
63
Regarding the non-canonical amino acids, it was observed that norvaline was
produced by the cells under heterogeneous and homogenous conditions, with the
amount substantially increasing over the time in both cultivations. However, under
oscillation conditions the formation rate of norvaline is higher than the control,
consequently the concentration of total free norvaline is about twice of that in the
reference approach, with the data 0.53 μmol gDCW-1 at 6.92 h after feed start in
control cultivation and 0.95 μmol gDCW-1 at 6.75 h after feed start under
heterogeneous conditions (Figure 3.5). This shows that the oscillations of substrate
and dissolved oxygen have a strong impact on the formation of norvaline. Soini et al.
reported norvaline accumulation under anaerobic conditions (Soini et al. 2008a). In
this study, the mount of norvaline per cell of crude extract data at 5.75 h after feed
start in PFR showed that norvaline was even able to massively synthesis within 68 s
under glucose excess and oxygen limited conditions (Figure 3.6).
β-methylnorleucine is not very well reported as a product of heterogeneities in
bioprocesses. In this work, β-methylnorleucine was also produced in both
cultivations with higher measured values for the scale-down cultivation over the time
after feed start. Figure 3.5 showed that under oscillating conditions, the amount of
β-methylnorleucine per cell was significantly elevated within two hours after feed
start, and fluctuated for the rest of the cultivation time.
In the scale-down approach, the accumulation of isoleucine and non-canonical
amino acids in the STR module and their fast formation within 68 s under oxygen
limitation conditions in the PFR could be an indication for an increased flux of carbon
over the enzymes of the leuABCD operon to α-ketobutyrate, which is the precursor of
isoleucine and non-canonical amino acids. Here the elongation of pyruvate takes
place as a side activity of the enzymes rather than the canonical pathway over
3. Results
64
threonine. Besides, the data also demonstrated that non-canonical amino acids are
synthesized as side product of isoleucine.
Figure 3.5: Concentration of total free alanine, leucine, valine, isoleucine, norvaline,
β-methylnorleucine in suspension samples (cells plus medium) over the time in STR module of E.
coli W3110 wild-type strain cultivations, analyzed by HPLC. The time point zero represents feed
start. White circles – STR reference cultivation; black triangles – 2CR scale-down cultivation. The
total concentrations reflect the intracellular concentrations, as the extracellular level was
neglectable for all shown amino acids.
Figure 3.6: Concentrations of total free alanine, isoleucine, norvaline from reactor suspension
samples (cells plus medium) in PFR module (PFR with feed addition) of E. coli W3110 wild-type
Ala
-2 0 2 4 6 80
10
20
30
Val
-2 0 2 4 6 80
50
100
150
200Nva
-2 0 2 4 6 80.0
0.5
1.0
1.5
Leu
-2 0 2 4 6 80
5
10
15
20Ile
-2 0 2 4 6 80
5
10
15
20
β - Mnl
-2 0 2 4 6 80
1
2
3
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
Ala
0 30 40 50 60 700
20
40
60Nva
0 30 40 50 60 700
1
2
3
4
5Ile
0 30 40 50 60 700
20
40
60
80
STRSTRSTR
Co
ncentr
atio
n [μmolg
DC
W-1
]
Residence time [s]
3. Results
65
strain 2CR scale-down cultivation, analyzed by HPLC. Data shown are the samples from time
points 0.75 h (white triangles up), 1.75 h (gray triangles down), 3.75 h (dark gray squares) and
5.75 h (black diamonds) after feed start over the residence time in the PFR.
3.2. Behavior of the interleukin-2 producing strain E. coli
W3110_pCTUT7_His_IL2 in STR and 2CR cultivations
It has been found that in the scale-down cultivation E. coli W3110 wild-type strain is
able to accumulate non-canonical amino acids (norvaline and β-methylnorleucine)
under oscillation of glucose and oxygen concentrations conditions which is simulating
the gradients of substrate and dissolved oxygen in large-scale (see 3.1). It could be
proposed that in industrial large-scale cultivation non-canonical amino acids could be
synthesized if high substrate zones occur in these reactors. It is well known that when
non-canonical amino acids accumulated in the cell, they are falsely incorporated into
some recombinant proteins, e.g. norvaline was incorporated into human hemoglobin
(Apostol et al. 1997) and it was found that β-methylnorleucine was misincorporated
into recombinant hirudin (Muramatsu et al. 2003). Lots of studies found that,
especially in leucine-rich recombinant proteins, non-canonical amino acids can be
misincorporated, e.g. norvaline into recombinant haemoglobin which includes 72
leucine residues in 575 total amino acids residues (Apostol et al. 1997) norleucine
into interleukin2 containing 152 amino acid residues, of which 26 are leucine
residues (Lu et al. 1988; Tsai et al. 1988). But the effect of expression rate of
leucine-rich recombinant protein on the synthesis and misincorporation of
non-canonical amino acids into recombinant proteins is not yet fully clear. Such
misincorporations are highly unwanted and unfavored especially for pharmaceutical
proteins. Therefore in this work, a scale-down research was performed on cellular
responses to oscillation conditions using E. coli W3110_pCTUT7_His_IL2 strain which
expresses interleukin-2, a leucine-rich recombinant protein in inclusion bodies.
3. Results
66
3.2.1. Cultivation characteristics
The gradients of glucose and oxygen availability in industrial large scale were also
simulated in the same two-compartment reactor adding feed solution without
aeration at the inlet of PFR as described in Section 3.1. The cultivation process is also
performed with two parts. Firstly, cells were cultivated overnight only in STR module
in fed-batch-like EnBase Flo medium with 2 g L-1 glucose and 34 mg L-1
chloramphenicol as starter culture for high cell density cultivations until the glucose
release rate became limiting. For this phase the aeration of the culture was set to 0.5
vvm and the DOT was controlled above 30 % by regulating the stirrer speed. Secondly,
after overnight cultivation, the PFR module was connected and the mechanical
glucose feeding was applied in the inlet of PFR with a targeted specific growth rate
(μset) of 0.2 h-1. At 1 h after feed start, IPTG was injected into the STR module though
a 0.22 μm sterile filter to the final concentration of 1 mM for induction. During the
whole cultivations, in the STR module cells were kept at 37 °C and the pH was
controlled by addition of 25 % ammonium hydroxide to pH 7. The DO was
maintained above 30 % by manually changing the stirrer speed and the aeration rate.
Besides, the control cultivation was performed only in the STR without the PFR part,
and the feed solution was added to the top gas phase of the bioreactor.
Figure 3.7A shows that the biomass values from 2CR scale-down cultivation have no
distinct difference from the control until 3 hours after induction it became a bit lower.
At the same time of 3 h after induction the maximum of biomass concentration in
the 2CR scale-down cultivation was only 12 g L-1, while in control cultivation, it
reaches to about 13 g L-1, and at the end, the maximum biomass concentration in the
control was about 14 g L-1. This is because cells grow slower under oxygen limitation
conditions (Soini et al. 2008a). It is already well known that cells are in a stressful
environment when they are exposed to repeated oscillations of the substrate
3. Results
67
concentration and dissolved oxygen. The cells need to repeatedly try to adapt to such
stressful condition, which causes a loss of biomass (Enfors and Häggström 2000). The
oxygen limitation condition could be seen from Figure 3.7C, which shows that in the
PFR module of 2CR scale-down cultivation cells are under oxygen limitation from the
first port of the PFR immediately after feed start where with all the DOT values are
not more than 0.5 % throughout the whole cultivation.
Figure 3.7: Shows the E. coli W3110_pCTUT7_His_IL2 cultivations data of the STR cultivation
0 1 2 3 4 5 6
DO
[%
]
0
20
40
60
80
100
120
pH
[-]
0
2
4
6
8
10
12STR DO
2CR DO
STR pH
2CR pH
0 1 2 3 4 5
DO
[%
]
0
1
2
3
4Port 1
Port 2
Port 4
Port 5
Feed time [h]
-1 0 1 2 3 4 5 6
DC
W [
g L
-1]
4
6
8
10
12
14
16
STR DCW
2CR DCW
STR DCW fitted
2CR DCW fitted
Feed time [h]
A
B
C
3. Results
68
(reference) and the 2CR scale-down cultivation. Feed start point starts from 0 h. Dashed line –
induction time, 1h after feed start point. (A) Dry cell weight. (B) Profile of online DO and pH data
in the STR module. (C) Profile of online DO data in the PFR module of 2CR scale-down cultivation.
For the exhaust gas analysis, Figure 3.8C shows that the profile of the respiratory
quotient (RQ) in 2CR scale-down cultivation is almost the same as in the STR
cultivation. RQ was observed to be increasing after the mechanical glucose feeding in
both cultivations up to a value of about 1. After induction the level of RQ slightly
decreased, followed by relatively constant value until the end of both cultivations.
After the start of feed the specific gas consumption rates (qO2 and qCO2) increased to
a certain level, and increasing again after the induction time, and then staying
constant until the end of cultivations (Figure 3.8). It needs to be remarked, that there
were jumps of qO2 and qCO2 at 1 h and 2.3 h after feed start in control cultivation,
which are probably caused by the system. After induction, in both cultivations qO2
and qCO2 increased with a slightly decreased RQ, indicating an imbalance between
respiration and carbon dioxide production directly after induction. The increase of
qO2 and qCO2 after induction may be caused by the stress of induction of
interleukin-2.
3. Results
69
Figure 3.8: (A) Specific oxygen uptake rate, (B) Specific carbon dioxide production rate, and (C)
Respiratory quotient in the STR module of the reference (black) and 2CR scale-down (red) E. coli
W3110_pCTUT7_His_IL2 cultivations. Feed start point starts from 0 h. Dashed line – induction
time, 1h after feed start point.
3.2.2. Protein quantification
In order to quantify the recombinant protein when cells were exposed to different
conditions, the recombinant protein production was analyzed by SDS-PAGE with a 15 %
Feed time [h]
0 2 4 6
RQ
[-]
0.0
0.5
1.0
1.5
2.0
STR
2CR
0 2 4 6
qC
O2 [
mm
ol g
DC
W
-1 h
-1]
0
4
8
12
STR
2CR
0 2 4 6
qO
2 [
mm
ol g
DC
W
-1 h
-1]
0
4
8
12
STR
2CR
A
B
C
3. Results
70
SDS-gel. The first sample (0h) was taken just before the induction, following with
samples taken at 0.25 h, 0.5 h, 1 h, 2 h, 3 h, 4 h and 5.3 h after induction time. In
order to compare all the protein production among different samples at the same
level, the samples were normalized to the certain same OD as described previously
(Section 2.5.5). And protein samples were separated into soluble and insoluble
fraction using BugBuster Kit.
Figure 3.9: SDS-PAGE of the soluble and inclusion body protein fractions prepared by BugBuster
Kit for the reference and the 2CR scale-down cultivations of E. coli W3110_pCTUT7_His_IL2 from 0
h to 5.3 h after induction. The arrow indicates the expected position of interleukin-2. M= protein
molecular weight marker.
Figure 3.9 shows that the interleukin-2 was successfully expressed as inclusion
bodies with no interleukin-2 expressed at induction time. The concentration of
induced target protein is increasing over the cultivation time of both cultivations. But
it illustrated that the bands of interleukin-2 are a bit thinner in the first three hours
of 2CR scale-down cultivation than at the same time point of the control cultivation,
indicating less interleukin-2 expression and reduced productivity of strain E. coli
W3110_pCTUT7_His_IL2 under oscillating conditions of substrate and dissolved
oxygen compared with homogenous cultivation. However, the final amount of
interleukin-2 seems not to be significantly different between control and scale-down
cultivations.
Soluble inclusion body inclusion body solubleSTR 2CR
3. Results
71
3.2.3. Carboxylic Acids
Figure 3.10 shows a fast accumulation of lactate and acetate in 2CR scale-down
cultivation in comparison to the control. The concentration of lactate is always higher
in oscillating cultivation than the reference cultivation, even at the feed start point. In
the reference cultivation, the lactate concentration continuously increased to 0.35
mM at 5 h after feed start, while in 2CR scale-down approach, it significantly
increased to 0.72 mM at 4 h after feed start. For acetate, during the control
cultivation, it almost was not detected during the first 2 h after feed start, but from 3
h on, its concentration increased to reach a peak of 4.81 mM at 5 h after feed start.
While in 2CR scale-down cultivation, the concentration of acetate significantly
increased to 8.0 mM at 3 h after feed start (Figure 3.10). No remarkable differences
were detected in the extracellular concentration of malate, succinate and fumarate
between the two cultivation types (Figure 3.10). At 1 h after feed start in the PFR
module of 2CR scale-down cultivation, under oxygen limited condition with the
pyruvate accumulation, lactate and formate accumulated quickly over the residence
time along the PFR (Figure 3.11). It is apparent that the mixed-acid fermentation
enzyme system which is inhibited by oxygen under aerobic condition were present,
and could produce detectable mixed-acid fermentation products within 1 min even in
seconds when exposed to oxygen limitation in the PFR (Enfors et al. 2001). There was
no more accumulation of formate at 3 h after glucose feed start in the PFR module.
One possible explanation could be adaption of cells to the oscillating conditions of
substrate and dissolved oxygen. The mixed-acids products produced in the oxygen
limited zone (PFR module), and re-assimilated when exposed to oxygen sufficient /
substrate limited zone (STR module) could also be one reason which led to reduction
in growth rate (Figure 3.7) and the productivity of interleukin-2 decreased (Figure
3.9).
3. Results
72
Figure 3.10: Extracellular concentration of compounds of the main carbon metabolism in STR
module of E. coli W3110_pCTUT7_His_IL2 cultivations, analyzed by HPLC. Data are shown after
feed start (0h). Dashed line – induction time, 1 h after feed start point; white circles – STR
reference cultivation; black triangles up – 2CR scale-down cultivation.
Glc
Feed time [h]
-1 0 1 2 3 4 5 6
Conce
ntr
atio
n [
g L
-1]
0.0
0.3
0.6
0.9 Pyr
Feed time [h]
-1 0 1 2 3 4 5 60.00
0.15
0.30
Conce
ntr
atio
n [
mM
]
Feed time [h]
For
0.0
1.5
3.0
4.5
Lac
-1 0 1 2 3 4 5 60.0
0.4
0.8
1.2
Ace
0
4
8
12 Mal
0.0
0.4
0.8
1.2
Suc
-1 0 1 2 3 4 5 60.0
0.4
0.8
1.2
Feed time [h]
Fum
0.0
1.5
3.0
4.5C
once
ntr
atio
n [
mM
]C
once
ntr
atio
n [
mM
]
3. Results
73
Figure 3.11: Extracellular concentration of compounds of the main carbon metabolism in PFR
module (PFR with feed addition) of E. coli W3110_pCTUT7_His_IL2 2CR scale-down cultivation,
analyzed by HPLC. White triangles up – 1 h and grey triangles down – 3 h after glucose feed start.
3.2.4. Amino acids
The main objective of analyzing the amino acid concentration over the cultivation
time after glucose feed start is to focus on the response of substrate oscillation on
biosynthesis of leucine-rich protein interleukin-2, especially non-canonical amino
acids accumulation and their false incorporation into recombinant protein.
Co
nce
ntr
atio
n [
mM
]
Pyr
Residence time [s]
0 30 40 50 60 700.00
0.03
0.06
Residence time [s]
Mal
0.0
0.2
0.4
0.6
Suc
0 30 40 50 60 700.0
0.1
0.2
0.3
0.4
Fum
0.0
1.5
3.0
4.5C
once
ntr
atio
n [
mM
]C
once
ntr
atio
n [
mM
]
Glc
Residence time [s]
0 30 40 50 60 70
Co
nce
ntr
atio
n [
g L
-1]
0.0
0.4
0.8
1.2
Residence time [s]
For
0
1
2
3
4
Lac
0 30 40 50 60 700.0
0.4
0.8
1.2
Ace
0
4
8
12
STR STR
STRSTR
3. Results
74
With regards to canonical amino acids, the extracellular concentration of serine and
glycine increased during the 2CR scale-down cultivation compared with the control
(Figure 3.13). Alanine showed the most profound enhancement under oscillating
conditions, resulting in as much as 67.1 μM at 4 h after feed start, which is nearly
five-fold higher than control of 14.3 μM (Figure 3.13). Moreover, the total free amino
acid concentrations in the STR module of 2CR scale-down cultivation continuously
increased as well (Figure 3.12). These results show a strong redirection of carbon
fluxes to serine and alanine, while no clear difference between the two cultivations
for the leucine concentration could be seen (Figure 3.12). Isoleucine, which belongs
to the aspartate family, substantially increased over the time in the scale-down
cultivation, while it had an approximately constant level in the control cultivation.
Therefore a huge difference between these two cultivations is visible with
significantly higher amounts of isoleucine under scale-down conditions (Figure 3.12).
However, the concentrations of glutamine and aspartate involved in TCA cycle, were
lower under oscillating conditions compared to the reference STR cultivation (Figure
3.12). This may be caused by the insufficient supply of the carbon flux to the
precursors of these compounds though TCA cycle for their formation.
Along the PFR, leucine, valine and isoleucine show a slight increase in their
concentrations within 68 seconds in the crude extract in the 1 h and 3 h samples
after feed start over the residence time in the PFR (Figure 3.14).
The non-canonical amino acids concentrations were analyzed by HPLC, however this
method is not able to detect norleucine, so no data of total and extracellular free
norleucine concentrations are available (Figure 3.12, Figure 3.13). At the same time,
another analysis method with GC-MS is used to evaluate the misincorporation of
norleucine, norvaline and β-methylnorleucine into recombinant proteins (Figure
3.15). Figure 3.12 and Figure 3.13 show that, there are accumulation of norvaline
3. Results
75
and β-methylnorleucine in both cultivations, even in the control STR cultivation. But
the amount of norvaline per cell is not significantly increasing over the time in both
cultivations (Figure 3.12). Whereas norvaline accumulation occurred earlier in the
2CR scale-down cultivation with the cells exposed to oxygen limitations in the loop of
the PFR (Figure 3.13). Norvaline accumulation in the broth seems to occur during the
residence of the cells in oxygen limitation, due to Figure 3.14 showed that the mount
of free norvaline per cell of crude extract data at 1 h and 3 h after feed start has an
increasing trend under glucose excess and oxygen limited conditions. The
concentrations of total and extracellular free β-methylnorleucine all showed no
significant difference between the two cultivations, while except the data of total
free β-methylnorleucine at 4 h after feed start maybe an outlier (Figure 3.12 and
Figure 3.13). Even in the PFR module, the concentration of β-methylnorleucine is not
increasing, but has slightly decreasing trend over the residence in the PFR (Figure
3.14). One could assume that the non-canonical amino acid is bound by an aminoacyl
tRNA synthetase (aaRS) onto the tRNA and is therefore not measured anymore.
3. Results
76
Figure 3.12: Total free amino acid concentration of suspension samples (cells plus medium) in
the STR module of E. coli W3110_pCTUT7_His_IL2 cultivations from the glucose feed start (0 h),
analyzed by HPLC. Dashed line – induction time, 1 h after feed start point; white circles – STR
reference cultivation; black triangles up – 2CR scale-down cultivation.
Ser
-1 0 1 2 3 4 5 60
5
10
15
20
25Gly
-1 0 1 2 3 4 5 60
10
20
30
40
50
60
70Ala
-1 0 1 2 3 4 5 60
10
20
30
40
50
60
70
Glu
-1 0 1 2 3 4 5 60
200
400
600
800
1000
1200
1400Gln
-1 0 1 2 3 4 5 60
2
4
6
8
10Asp
-1 0 1 2 3 4 5 60
20
40
60
80
100
120
140
160
Thr
-1 0 1 2 3 4 5 60
1
2
3
4
5
6
Val
-1 0 1 2 3 4 5 60
20
40
60
80
100
120
140
160
180
Leu
-1 0 1 2 3 4 5 60
2
4
6
8
10
12
14
16
18Ile
-1 0 1 2 3 4 5 60
5
10
15
20
25
30
Nva
-1 0 1 2 3 4 5 60
1
2
3
4
5 β - Mnl
-1 0 1 2 3 4 5 60
10
20
30
40
50
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
3. Results
77
Figure 3.13: Extracellular free serine, glycine, alanine, norvaline and β-methylnorleucine
concentration of supernatant samples in STR module of E. coli W3110_pCTUT7_His_IL2
cultivations from the glucose feed start (0 h), analyzed by HPLC. Dashed line – induction time, 1 h
after feed start point; white circles – STR reference cultivation; black triangles up – 2CR
scale-down cultivation.
Figure 3.14: Total free branched chain amino acid concentration in the suspension (cells and
medium) samples over the residence time of the PFR module (PFR with feed addition) in E. coli
Ser
0
10
20
30
40Gly
0 1 2 3 4 5 60
20
40
60
80Ala
0 1 2 3 4 5 60
20
40
60
80
Nva
0 1 2 3 4 5 60
10
20
30
40 β - Mnl
0 1 2 3 4 5 60
10
20
30
40
Co
ncentr
atio
n [μM
]
Feed time [h]
Nva
0 30 40 50 60 700
2
4
6
8
Leu
0
5
10
15Ile
0
5
10
15
β -Mnl
0 30 40 50 60 700
2
4
6
8
Val
0 30 40 50 60 700
20
40
60
80
STR STR
STR
Co
ncentr
atio
n [μmolg
DC
W-1
]
Residence time [s]
3. Results
78
W3110_pCTUT7_His_IL2 2CR scale-down cultivation, analyzed by HPLC. White triangles up – 1 h
and grey triangles down – 3 h after glucose feed start.
Figure 3.15 shows the concentration of non-canonical amino acids and the natural
counterparts which they replace from the induction time (1 h after feed start) in
inclusion bodies of E. coli W3110_pCTUT7_His_IL2 cultivations over the cultivation
time. Regarding the composition of canonical amino acids in the inclusion bodies, a
continuously increasing trend of leucine, isoleucine and methionine over the time
period of protein expression was observed, indicating the increasing production of
interleukin-2. This was already clearly shown by the SDS-PAGE gel (Figure 3.9).
Looking at the non-canonical amino acids in control STR and 2CR scale-down
cultivation, a maximum amount of 0.13 μmol gDCW-1 and 0.24 μmol gDCW
-1 norvaline
were falsely incorporated into interleukin-2 proteins at 3 h after feed start,
respectively (Figure 3.15). For norleucine, the misincorporation reached a maximum
of 0.64 μmol gDCW-1 at 5 h after feed start in control and 1.2 μmol gDCW
-1 in the 2CR
scale-down cultivation at 4 h after feed start, while β-methylnorleucine was maximal
around 0.5 μmol gDCW-1 at the end of both cultivations (Figure 3.15). Though there
are much less methionine residues in IL2, norleucine was observed misincorporated
into proteins with higher rate than norvaline and β-methylnorleucine. The ratio of
non-canonical amino acid / natural substrate (for example norvaline / leucine) is an
important factor in non-canonical amino acid misincorporation into heterologous
protein (Apostol et al. 1997), because of lowered substrate specificity of the
aminoacyl-tRNA synthetase (aaRS) (Cvetesic et al. 2014; Kiick et al. 2001; Tang and
Tirrell 2002). In own results, the ratio of norvalin / leucine and β-methylnorleucine /
isoleucine in Figure 3.16 seemed to have a high correlation with the misincorporation
rate of non-canonical amino acids into proteins in Figure 3.15. A slight increased ratio
of norvalin / leucine led to slightly higher norvaline incorporation into proteins in 2CR
scale-down cultivation than the control cultivation.
3. Results
79
Though there are accumulation and incorporation into proteins of non-canonical
amino acids in both cultivations, it could be seen that in the 2CR scale-down
cultivation more non-canonical amino acid were synthesized and got
misincorporated into the target protein (Figure 3.15). Especially, norleucine has a
higher incorporation rate than norvaline and β-methylnorleucine, though there is
much less methionine residues in IL2. This may be explained by the oscillations of
substrate and dissolved oxygen in the 2CR scale-down cultivation, which was caused
by cells rapidly and repeatedly move between PFR (oxygen limitation and substrate
excess situation) and STR module (sufficient oxygen). Soini et al. showed that a
combination of oxygen limitation and pyruvate overflow result in norvaline
accumulation (Soini et al. 2008a).
Figure 3.15: A: The amino acid sequence of interleukin-2 protein and the possible incorporation
position by non-canonical amino acids. B: Shows the concentration of non-canonical amino acids
Nva
-1 0 1 2 3 4 5 60.0
0.5
1.0
1.5
Nle
-1 0 1 2 3 4 5 60.0
0.5
1.0
1.5
β - Mnl
-1 0 1 2 3 4 5 60.0
0.5
1.0
1.5
Leu
-1 0 1 2 3 4 5 60
300
600
900
1200
Met
-1 0 1 2 3 4 5 60
100
200
300
400
Ile
-1 0 1 2 3 4 5 60
100
200
300
400
IL2: 147 aa
Leucine residue 22 15.0 %
Methionine residue 5 3.4 %
Isoleucine residue 9 6.1 %
A B
1
21
41
61
81
101
121
MHHHHHHGGG GSASAPTSSS
GINNYKNPKL TRMLTFKFYM
SNINVIVLEL KGSETTFMCE
141 SIISTLT
YADETATIVE FLNRWITFCQ
PKKATELKHL QCLEEELKPL
EEVLNLAQSK NFHLRPRDLI
TKKTQLQLEH LLLDLQMILN
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
3. Results
80
and the natural counterparts which they replace in inclusion bodies of E. coli
W3110_pCTUT7_His_IL2 cultivations from the induction time (1h), analyzed by GC-MS. Dashed
line – induction time, 1 h after feed start point ; White circles – STR reference cultivation; black
triangles up – 2CR scale-down cultivation.
Figure 3.16: The ratio of total free concentration of non-canonical amino acids / the natural
counterparts which they replace in the homogenized suspension (cells plus medium) samples
collected from the STR in cultivations with E. coli W3110_pCTUT7_His_IL2 from the glucose feed
start (0 h). Dashed line – induction time, 1 h after feed start point; white circles – STR reference
cultivation; black triangles up – 2CR scale-down cultivation.
3.2.5. Carbon Labeling Experiments
In order to study the changes in metabolic fluxes of E. coli w3110_pCTUT7_His_IL2
immediately exposed to substrate excess and combined oxygen limitation during
different cultivation conditions, carbon labeling experiments have been done for
Metabolic Flux analysis C13-labeled glucose using the rapid sampling unit Bioscope,
which was connected with the STR module of both 2CR scale-down and reference
cultivations at 2 h after feed start that also means 1 h after induction time.
Suspension samples from the STR were supplied with the C13-labeled glucose at the
entry point of the Bioscope and then pumped through its tube structure. Meanwhile,
the hemispherical gas channel of BioScope was flushed with nitrogen, representing
no aeration in the PFR of 2CR scale-down cultivation. Samples were taken by
Nva / Leu
-1 0 1 2 3 4 5 60.0
0.5
1.0
1.5
2.0
β - Mnl / Ile
-1 0 1 2 3 4 5 60.0
0.5
1.0
1.5
2.0
Ra
tio
[-]
Feed time [h]
3. Results
81
methanol quenched method (as described in 2.4.6) within 1 min representing the
residence time in the PFR.
The results are shown in Table 3.1 and Table 3.2, with numbers in cells of tables
giving information about values of the pool of fragments with 13C-isotopes and the
color intensity demonstrating the pool of labeled compounds by sight.
Table 3.1 shows the labeling of compounds in STR control cultivation with rapid
anaerobic sampling, indicating a steady increase of labeling in pyruvate, lactate and
malate. Alanine, aspartate and leucine labeling reached their maximal degree at the
end of the sampling time. The labeling profile of threonine shows fluctuations with
maximal at 5.0 s and 14.5 s. Glutamate reached a first peak at 5.0 s and maximal at
the end of sampling. Isoleucine shows highest labeling at 7.4 s. Norvaline, norleucine
and β-methylnorleucine have maximal labeling ratios at 6.0 s, 14.5 s and 12.5 s,
respectively. From the result, it could be seen that threonine reaches its maximal
portion of incorporation of labeled carbon before norvaline, norleucine,
β-methylnorleucine and isoleucine, so the main carbon source for α-ketobutyrate,
which is the precursor of non-canonical amino acids, derives from threonine through
TCA cycle under normal conditions. The labeling peak of aspartate can be explained
by the fork flux from aspartate to asparagine and homoserine, however these
compounds could not be detected in labeled fractions.
The labeling of compounds in 2CR scale-down cultivation with rapid anaerobic
sampling is shown in Table 3.2, which indicates a different behavior. The pyruvate
profile shows a small peak at 12.5 s and then fluctuations to the maximal at the end.
The maximal labeling value for lactate is shifted to an earlier time at 40.1 s. Under
the oscillating cultivation condition, fumarate and malate seems to have no
difference compared with STR cultivation. The maximal degree of labeling of
3. Results
82
glutamate and aspartate was detected at the end of sampling. Another amino acid
derived from the TCA cycle, threonine, shows fluctuations with its maximum at 18.8 s
and 40.1 s. The earlier labeling of non-canonical amino acids and isoleucine under
oscillation conditions is remarkable, with norleucine, β-methylnorleucineare and
isoleucine all labeled at 5.0 s, and norvaline labeled at 7.4 s. Obviously, the fast
13C-labeling in isoleucine and non-canonical amino acids, compared to a tardy
13C-labeling of the intermediates from TCA-cycle including threonine, reveals changes
in metabolic flux distribution within the branched chain amino acids biosynthesis
pathway. Therefore, the main carbon source for α-ketobutyrate, which is the
precursor of non-canonical amino acids and isoleucine, cannot be derived from
threonine, but are directly synthesized by chain elongation from pyruvate through
the much shorter direct pathway under oscillation conditions with the LeuABCD
complex. The highest labeling of valine and leucine also came earlier than in the STR
control experiment. The probable reason is the enhanced substrate availability under
oscillation conditions, which might change the distribution of the carbon flux from
pyruvate to valine and leucine.
3. Results
83
Table 3.1: Labeling of compounds in STR control cultivation of W3110_pCTUT7_His_IL2 with
anaerobic rapid samples taking, analyzed by GC-MS. Samples were taken at 2 h after glucose feed
start and 1 h after induction. Numbers in cells of tables gives information about values of the pool
of fragments with 13C-isotopes and the color intensity demonstrates the pool of labeled
compounds by sight.
Name Fragment Mass Isotope 0.0 5.0 6.0 7.4 12.5 14.5 18.8 30.5 40.1 56.9
Pyruvic acid 160 m3 0.0 1.9 2.2 2.6 3.5 4.1 5.2 6.9 13.0 16.0
Lactic acid 191 m2 0.3 1.9 2.2 2.1 1.9 2.2 2.2 3.0 3.7 4.1
Malate 233 m2 3.6 6.8 7.9 8.1 8.5 7.6 9.5 9.5 9.8 9.9
Alanine 158 m2 8.8 8.6 9.1 9.3 9.5 9.7 10.8 13.1 15.0 18.5
Glutamate 432 m3 3.9 4.3 4.1 4.1 4.1 4.2 4.2 4.2 4.2 4.4
Aspartate 418 m3 3.8 3.8 4.1 3.9 3.9 4.0 4.0 4.3 4.4 5.0
Threonine 404 m1 7.3 8.6 7.7 8.5 7.9 8.6 8.3 8.4 8.2 8.2
Isoleucine 200 m4 0.0 1.7 2.4 4.1 1.2 1.3 0.7 1.9 1.1 2.2
Norleucine 200 m1 16.1 14.5 15.5 15.2 15.9 17.4 15.1 15.8 17.0 14.9
Norvaline 288 m2 5.8 5.7 6.7 5.8 6.0 6.0 5.3 6.3 5.6 5.7
β-Methylnorleucine 214 m3 11.5 14.1 11.5 10.9 25.9 19.5 9.9 11.6 15.9 8.2
Valine 288 m1 10.6 9.2 9.9 9.2 9.3 9.2 9.6 9.2 8.4 8.9
Leucine 200 m1 15.0 15.4 15.4 15.0 15.2 15.4 16.1 15.9 17.1 17.6
Table 3.2: Labeling of compounds in 2CR scale-down cultivation of W3110_pCTUT7_His_IL2 with
anaerobic rapid samples taking, analyzed by GC-MS. Samples were taken at 2 h after glucose feed
start and 1 h after induction. Numbers in cells of tables gives information about values of the pool
of fragments with 13C-isotopes and the color intensity demonstrates the pool of labeled
compounds by sight.
Name Fragment Mass Isotope 0.0 5.0 6.0 7.4 12.5 14.5 18.8 30.5 40.1 56.9
Pyruvic acid 160 m3 3.9 2.7 0.9 1.2 4.0 1.8 3.6 3.6 6.2 7.9
Lactic acid 191 m2 1.7 1.8 2.1 1.9 1.8 1.9 2.1 2.0 2.6 2.5
Malate 233 m2 0.0 5.8 6.4 7.8 8.1 7.5 7.8 7.6 9.1 9.2
Alanine 158 m2 8.3 8.4 8.2 8.5 8.5 8.5 9.2 9.6 11.1 12.3
Glutamate 432 m3 4.0 4.1 4.1 4.1 4.2 3.9 4.1 4.1 4.2 4.2
Aspartate 418 m3 3.9 3.8 3.8 3.8 3.9 4.2 3.9 4.0 4.2 4.6
Threonine 404 m2 4.2 4.4 4.3 4.5 4.2 4.1 4.7 4.4 4.8 4.5
Isoleucine 200 m4 1.1 3.0 1.5 1.8 1.3 0.3 1.2 1.0 0.6 0.4
Norleucine 200 m1 15.4 25.8 17.8 15.1 13.3 14.9 16.2 15.5 15.9 16.0
Norvaline 260 m1 9.1 9.4 8.7 10.3 9.3 8.2 9.2 9.2 9.9 9.9
β-Methylnorleucine 214 m3 6.7 34.6 13.2 7.5 6.9 10.1 1.9 5.4 1.8 15.5
Valine 288 m3 0.7 0.6 0.3 0.6 0.6 0.9 0.6 0.6 0.6 0.7
Leucine 200 m3 1.1 1.7 2.0 1.4 1.5 1.6 1.3 1.8 1.4 1.4
3. Results
84
3.3. Behavior of the insulin producing strain E. coli W3110M_pSW3 in
STR, 2CR and 3CR cultivations
The 2CR scale-down cultivations with PFR with feed addition mimicking the feed
zone in industrial large-scale cultivations were performed with E. coli W3110
wild-type strain and E. coli W3110_pCTUT7_His_IL2 recombinant strain, indicated
that besides short fatty acids formation, non-canonical amino acids also accumulate
and are false incorporated into the recombinant target protein. Therefore it was
interesting to apply another recombinant strain with expression of a leucine-rich
protein and simultaneously simulating other zones in industrial large-scale
cultivations besides the feed zone. Due to the high affinity of E. coli to glucose,
corresponding to a low Ks value, one can assume glucose starvation zones exist in
large-scale bioreactors. Such zones could be either connected to high or low DOT.
Considering these, in this work, another recombinant leucine-rich protein was
expressed in E. coli. In the case of this insulin producing strain we also applied a
three-compartment system aside from the two-compartment reactor. This 3CR,
which was earlier described by Lemoine et al. consists of one normal STR and two
similar PFR modules with addition of feed solution and no aeration at the entrance of
PFR1 and no-feeding and no-aeration to the PFR2 (Lemoine et al. 2015). PFR1
simulates the feed zone while PFR2 mimics a starvation zone in large-scale
cultivations. In our system the residence time in both PFRs was 68 s. Here we applied
a higher feed rate of μset = 0.3 h-1 was applied, as this strain had a higher max and
such a higher feed rate would generate a higher flux of carbon to pyruvate and the
branched-chain amino acid pathway, also suggesting a higher production of the
non-canonical amino acids.
3.3.1. Cultivation characteristics
The scale-down cultivations were both performed in three phases. Firstly, cells were
3. Results
85
cultivated as a batch cultivation overnight only in STR module in MSM medium with
5 g L-1 glucose and 100 mg L-1 ampicillin until glucose depletion. For this phase the
aeration of the culture was set to 0.5 vvm and the stirrer speed was set at 400 rpm.
After overnight cultivation at around 14 hours, the PFR modules were connected and
the exponential glucose feeding by an external pump was applied to the inlet of PFR1
with a targeted specific growth rate (μset) of 0.3 h-1; meanwhile, the speed of the
stirrer was increased to 1100 rpm. 3 h after feed start, the inducer IPTG was added
into the STR module though a 0.22 μm sterile filter to a final concentration of 1 mM
(calculated for a volume of 10 mL 1 M IPTG into 10 L culture) for induction. And the
feeding strategy was changed into constant feeding. During the whole cultivations, in
the STR module cells were grown at 35 °C at a pH of 7.0, which was controlled by
addition of 25 % ammonium hydroxide. The control cultivation was performed only
in the STR without the PFR parts, and the feed solution was added to the top phase
of the bioreactor.
From Figure 3.17A, it can be seen that there are no differences in the biomass yield
between the three cultivations before induction. But after induction, the biomass
concentration of the 2CR scale-down cultivation was higher compared to the control
cultivation until the end, while the cell density was a bit lower in the 3CR scale-down
cultivation. As the cell density in 3CR scale-down cultivation decreased, the
cultivation was stopped at 2h after induction (Figure 3.17). Because of the steadily
increasing biomass, the concentration of dissolved oxygen decreased over the whole
cultivation time in PFR1 of the 2CR and 3CR scale-down cultivations (Figure 3.17B
and C). The DO at port 1 in PFR1 showed oxygen depletion at round 1.7 h after feed
start at a biomass concentration of 5.4 g L-1 in the 2CR scale-down cultivation (Figure
3.17B), while it was seen earlier in the 3CR scale-down cultivation (1.2 h after feed
start) at a biomass concentration of 4 g L-1 (Figure 3.17C). The reason was that the
additional PFR2 module led to overall lower liquid level in the STR module of 3CR
3. Results
86
scale-down cultivation, causing a lower oxygen transfer and a lower DO level with the
same stirrer set-up. Figure 3.17D shows the DOT profile measured in the PFR2
module of the 3CR scale-down cultivation. Here oxygen depletion occurred at around
2.8 h after feed start, and after this, the cells were exposed to a more stressful
environment in 3CR scale-down cultivation.
Figure 3.17: Shows the E. coli W3110M_pSW3 cultivations data of the STR cultivation (reference)
0 2 4 6 8
DO
[%
]
0
20
40
60
80
100Port 1
Port 2
Port 4
Port 5
Feed time [h]
0 2 4 6 8
DC
W [g L
-1]
0
5
10
15
20STR DCW
2CR DCW
3CR DCW
0 1 2 3 4
DO
[%
]
0
20
40
60
80
100PFR2_Port 1
PFR2_Port 5
0 1 2 3 4
DO
[%
]
0
20
40
60
80
100PFR1_Port 1
PFR1_Port 5
A
B
C
D
3. Results
87
and scale-down cultivations. Feed start point starts from 0 h. Dashed line – induction time, 3 h
after feed start. (A) Dry cell weight measured in the STR module of three cultivations (B) Profile
of online dissolved oxygen concentration data in the PFR1 module of 2CR scale-down cultivation.
(C) Profile of dissolved oxygen concentration measured in the PFR1 module of 3CR scale-down
cultivation. (D) Profile of dissolved oxygen concentration measured in the PFR2 module of 3CR
scale-down cultivation. As the cell density in 3CR scale-down cultivation decreased, the
cultivation was stopped at 2h after induction.
For the exhaust gas analysis, in the control STR cultivation, the rates for qO2 and qCO2
increased slightly within the first two hours after the exponential feed start but
afterwards showed a slight decrease (Figure 3.18) which most likely triggered by the
switch of the cultivation mode to constant feed at the time of induction.
In the 2CR scale-cultivation qO2 was higher than in the control cultivation after feed
start until the end of cultivations, while qCO2 was similar before induction, but
afterwards showed a slight continuous increase. This indicates an increased oxygen
demand and carbon dioxide formation of the cells under oscillating conditions.
Interestingly, this is even stronger in the 3CR cultivation. The increase of qO2 and
qCO2 in both scale-down cultivations was the same in relative terms, which is
obvious from the same and constant RQ in both cultivations (Figure 3.18). RQ in
these scale-down cultivations was lower than the reference. This demonstrated an
increased oxygen demand of cells under inhomogenous conditions, and indicating
that the cells have an increased respiration activity and a higher carbon dioxide
production in such cultivations.
3. Results
88
Figure 3.18: (A) Specific oxygen uptake rate, (B) Specific carbon dioxide production rate, and (C)
Respiratory quotient in the STR module of the reference and scale-down E. coli W3110M_pSW3
cultivations.
3.3.2. Protein quantification
The production of recombinant insulin in the different cultivation scenarios were
analyzed by SDS-PAGE in whole cell samples.
Feed time [h]
0 2 4 6 8
RQ
[-]
0
1
2
3
4STR
2CR
3CR
0 2 4 6 8
qC
O2 [
mm
ol g
DC
W
-1 h
-1]
0
5
10
15STR
2CR
3CR
0 2 4 6 8
qO
2 [
mm
ol g
DC
W
-1 h
-1]
0
5
10
15STR
2CR
3CR
A
B
C
3. Results
89
Figure 3.19: SDS-PAGE of the whole cells of the reference and scale-down cultivations from 0 h to
7 h after feed start. The arrow indicates the expected position of recombinant insulin. M= protein
molecular weight marker.
Figure 3.19 shows that the recombinant insulin can be not detected before induction
(0 and 3 h samples) and its concentration increases over the cultivation time in the
reference culture as well as in the 2CR scale-down cultivation. The product
accumulates mainly in the first two hours after induction in both cultivations.
However the accumulation of insulin is slightly lower in the 2CR cultivation, although
the final amount seems not to be significantly different. This indicates that in the
applied construct insulin expression is not significantly influenced by the oscillations.
Unfortunately the 3CR culture had to be stopped one hour after induction due to cell
lysis. However, the one hour sample still shows the same insulin concentration as the
other cultivations.
3.3.3. Carboxylic Acids
Though Figure 3.17A showed that the inhomogenous conditions have no impact on
the biomass yield before induction time for the three different cultivations, but it was
seen accumulation of glucose between the feed start and the induction event
increased to over 1 g L-1, indicating a slightly lower specific glucose uptake rate. So
the cultures were less limited for glucose under oscillating conditions. Because of the
STR 2CR
M 0 3 4 5 6 7 0 3 4 5 6 7 3 4
3CR
KDa26014010070
50
40
35
25
15
10
3. Results
90
increasing biomass yield, the volumetric glucose uptake rate increased, combined
with the change from exponential to constant feed at 3 h after feed start (induction
time), which caused the glucose concentration to decline and to be non-detectable
at 3 h after induction. It can be assumed that the 3CR shows a similar trend, although
the cultivation had to be stopped earlier.
Under oscillating conditions, extracellular accumulation of acetate and lactate, which
are typical for overflow metabolism and anaerobic conditions, were detected in the
STR module (Figure 3.20B). In the 2CR scale-down cultivation, the concentration of
acetate continuously increased to 0.6 mM at the end, achieving a 6 fold higher level
compared to the cultivation under homogeneous conditions with the value of 0.1
mM. The level of acetate had a further increased trend in the 3CR scale-down
cultivation. While no lactate was detected under non-oscillating conditions, a larger
amount of lactate was synthesized in the scale-down set-up s, with a profile
increasing until 0.5 mM at 5 h after feed start in 2CR scale-down cultivation and then
declining. Also here a stronger increase was detected in the 3CR scale-down
cultivation with a level of 1 mM at 4 h after feed start. No significant change was
detected for the extracellular concentrations of formate, fumarate and malate in the
STR module, indicating that oscillating conditions have no effect on the carbon fluxes
to these metabolites.
3. Results
91
Figure 3.20: Extracellular concentration of compounds of the main carbon metabolism in STR
module of E. coli W3110M_pSW3 cultivations, analyzed by HPLC. Data are shown after feed start
(0h). Dashed line – induction time, 3 h after feed start; white circles – STR; grey triangles up –
2CR scale-down cultivation; black squares – 3CR scale-down cultivation.
For the extracellular concentration of compounds of the main carbon metabolism
within the PFR module of scale-down cultivations, only the concentration of lactate
was slightly increased at 3 h, 5 h and 7 h after feed start over the residence time of
Mal
0.0
0.1
0.2
0.3
For
0.0
0.1
0.2
0.3
Lac
0 2 4 6 80.0
0.5
1.0
1.5
Conce
ntr
ation [
mM
]
Ace
0.0
0.5
1.0
1.5
Fum
0 2 4 6 80.0
0.1
0.2
0.3
Feed time [h]
A
B
Glc
0 2 4 6 80
1
2
3
4
Feed time [h]
Concentr
ation [
g L
-1]
3. Results
92
PFR1 in the 2CR scale-down cultivation (Figure 3.21), while in the PFR1 of the 3CR
scale-down cultivation acetate, lactate, formate and malate all accumulated along
the PFR module at 3 h after feed start (Figure 3.22) under the oxygen limitation in the
PFR (cf. Figure 3.17B, Figure 3.17C). However, due to the short cultivation time of 3CR
scale-down cultivation, the PFR2 was not really starvation yet at 3 h after feed start.
Therefore lactate showed a slight increasing trend over the residence time of PFR2
with over 1 g L-1 extracellular glucose (Figure 3.23). Interestingly, in the 2CR
scale-down cultivation, despite fast accumulation of lactate was detected at 5 h and
7 h after feed start along the PFR1 module (Figure 3.21), a continuously declining
concentration of lactate have been measured in the STR module after the swich to
constant feed (from 0.5 mM at 5 h to 0.2 mM at 7 h, Figure 3.20). This shows that
lactate is re-assimilated when cells are exposed to sufficient oxygen combined with
glucose limitation conditions in the STR module, as published before (Xu et al.
1999a).
Figure 3.21: Extracellular concentration of lactate in PFR1 module (PFR with feed addition) of E.
coli W3110M_pSW3 in 2CR scale-down cultivation, analyzed by HPLC. Data shown are the
samples from time points 0 h (white triangles up), 3 h (gray triangles down), 5 h (dark gray
squares) and 7 h (black diamonds) after feed start over the residence time in the PFR.
Lac
0 30 40 50 60 700.0
0.2
0.4
0.6
0.8
Concentr
ation [
mM
]
Residence time [s]
STR
3. Results
93
Figure 3.22: Extracellular concentration of compounds of the main carbon metabolism in PFR1
module (PFR with feed addition) of E. coli W3110M_pSW3 in 3CR scale-down cultivation,
analyzed by HPLC. Data shown are the samples from time points 1 h (white triangles up), 3 h
(gray triangles down) after feed start over the residence time in the PFR.
Mal
0.00
0.05
0.10
0.15
For
0.00
0.05
0.10
0.15
Lac
0 30 40 50 60 700.0
0.2
0.4
0.6
0.8
Conce
ntr
ation [
mM
]
Residence time [s]
Ace
0.0
0.2
0.4
0.6
0.8
Fum
0 30 40 50 60 700.00
0.05
0.10
0.15
Glc
Residence time [s]
0 30 40 50 60 70
Co
nce
ntr
atio
n [
g L
-1]
0.0
0.5
1.0
1.5
2.0
2.5
A
B
STR
STR
STR
3. Results
94
Figure 3.23: Extracellular concentration of compounds of the main carbon metabolism in the
PFR2 module (starvation loop) of E. coli W3110M_pSW3 in the 3CR scale-down cultivation,
analyzed by HPLC. Data shown are the samples from time points 1 h (white triangles up), 3 h
(gray triangles down) after feed start over the residence time in the PFR.
3.3.4. Amino acids
The amino acid analysis in this chapter was performed by GC-MS (see Materials and
methods section 2.5.3).
Mal
0.00
0.05
0.10
0.15
For
0.00
0.05
0.10
0.15
Lac
0 30 40 50 60 700.0
0.2
0.4
0.6
0.8
Conce
ntr
ation [
mM
]
Residence time [s]
Ace
0.0
0.2
0.4
0.6
0.8
Fum
0 30 40 50 60 700.00
0.05
0.10
0.15
Glc
Residence time [s]
0 30 40 50 60 70
Co
nce
ntr
atio
n [
g L
-1]
0
1
2
A
B
STR
STR
STR
3. Results
95
Figure 3.24 shows the concentration of total free amino acids in the suspension (cells
plus medium) from samples collected from the STR module in reference and
scale-down cultivations. For canonical amino acids, concentrations of leucine, valine
and isoleucine were all lower compared to the reference cultivation after induction,
but there was no significant difference between 2CR and 3CR scale-down cultivations
(considering that the last sample from the 3CR reactor was collected 1 hour after
induction). No clear difference for the concentration of other free canonical amino
acids in the suspension could be observed among these three cultivations.
The amount of free non-canonical amino acids norvaline, norleucine and
β-methylnorleucine in the total broth remained low in the control cultivation before
induction. No significant increase for each of them was observed within the three
hours of feeding. However after induction all three increased, while the
accumulation was highest for β-methylnorleucine with the value as high as 1 μmol
gDCW-1, and lowest for norvaline with 0.3 μmol gDCW
-1 at 6 h after feed start (Figure
3.24). This picture changed in the 2CR cultivation. While β-methylnorleucine and
norvaline still remained low before induction, norleucine was already strongly
increased. After induction also the concentration of norleucine remained always
significantly higher compared to the control cultivation, but also the
β-methylnorleucine and norvaline were little bit higher compared to the control
fermentation (Figure 3.24). This indicates that the accumulation of
β-methylnorleucine is only minor influenced by oscillating conditions, while it can be
seen that norleucine is the most affected by such inhomogeneous conditions. The
total accumulation of all three non-canonical amino acids was highest in the 3CR
cultivation, which however unfortunately could not be continued until the end
(Figure 3.24). The results from the analysis of the cultivation broth (cells plus
medium) are also confirmed by the analysis of the extracellular free amino acid
3. Results
96
concentrations, which show the same trend (Figure 3.25).
These results allow the following conclusion, which however has to be still verified by
repetitions of the experiments. In our cultivation set-up the accumulation of the
non-canonical amino acids is mainly favored by the induction of the recombinant
product, which is a leucine-rich protein. However interestingly, we could not observe
a decrease of the leucine pool after induction in the well-mixed STR cultivation, but
even an increase. However, in the 2CR system the leucine pool was reduced by 50%
but this in turn did not result in a higher synthesis of either one of the non-canonical
amino acids. Therefore it seems that the changed metabolic fluxes after induction
cause the formation of these non-canonical amino acids and not the derepression of
the leu or ilv operons. On top to these metabolic changes oscillations as they occur in
the 2CR system seem to further increase this effect.
3. Results
97
Figure 3.24: Total free amino acid concentration in the suspension (cells plus medium) samples
collected from the STR module in cultivations with E. coli W3110M_pSW3 from the glucose feed
start (0 h), analyzed by GC-MS. Dashed line – induction time, 3 h after feed start point; white
circles – STR reference cultivation; grey triangles up – 2CR scale-down cultivation; black squares
– 3CR scale-down cultivation.
Ile
0 2 4 6 80
1
2
3Leu
0 2 4 6 80
1
2
3
Nva
0 2 4 6 80
1
2
3 β - Mnl
0 2 4 6 80
1
2
3Nle
0 2 4 6 80
1
2
3
Met
0 2 4 6 80
1
2
3
Ala
0 2 4 6 80
5
10
15Gly
0 2 4 6 80
1
2Val
0 2 4 6 80
1
2
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
3. Results
98
Figure 3.25: Extracellular free amino acid concentration in the supernatant samples of STR
module of E. coli W3110M_pSW3 cultivations from the glucose feed start (0 h), analyzed by GC-MS.
Dashed line – induction time, 3 h after feed start; white circles – STR reference cultivation; grey
triangles up – 2CR scale-down cultivation; black squares – 3CR scale-down cultivation.
As described above, non-canonical amino acids can be falsely incorporated into the
recombinant (and cellular) proteins, where norvaline can substitute leucine,
β-methylnorleucine is able to substitute isoleucine and norleucine can replace
methionine. In order to analyse the quantity of recombinant protein, non-canonical
Ala
0 2 4 6 80
50
100
150
200Gly
0 2 4 6 80
10
20
30
40
Val
0 2 4 6 80
100
200
300Ile
0 2 4 6 80
50
100
150Leu
0 2 4 6 80
50
100
150
Nva
0 2 4 6 80
10
20
30 β - Mnl
0 2 4 6 80
10
20
30
Thr
0 2 4 6 80
20
40
60
Ser
0 2 4 6 80
5
10
15
20
Nle
0 2 4 6 80
10
20
30
Asp
0 2 4 6 80
20
40
60Glu
0 2 4 6 80
500
1000
1500
2000
Co
ncentr
atio
n [μM
]
Feed time [h]
3. Results
99
amino acids and the natural counterparts which they replace, we performed a
quantitative amino acid analysis by GC-MS of the inclusion body fractions from 3 h
after feed start (start of induction) onwards. While the concentration profiles of
leucine, isoleucine and methionine in inclusion bodies were similar over the time in
three cultivations, maximal to 0.39 μmol gDCW-1 norleucine at 6 h after feed start was
falsely incorporated into recombinant proteins in 2CR scale-down cultivation, which
is about double as high as the amount in the well mixed STR control cultivation at the
same time, and further increased was detected in 3CR sale-down cultivation (Figure
3.26). For β-methylnorleucine, its concentration in inclusion bodies has similar
increasing trend in the 2CR scale-down cultivation as in the control, both with the
maximal amount of about 0.08 μmol gDCW-1 at 6 h after feed start, and only a slight
increased further in 3CR scale-down cultivation (Figure 3.26). In comparison to
β-methylnorleucine and norleucine, which were already misincorporated in the
control cultivation, no misincorporation of norvaline was found during the reference
cultivation. Surprisingly, even under scale-down cultivations norvaline was triggered
to incorporate into recombinant protein under the value of 0.02 μmol gDCW-1 (Figure
3.26), though leucine-rich recombinant protein contains much more leucine residues
than methionine and isoleucine. The misincorporation rate of these non-canonical
amino acids into proteins in Figure 3.26 seems parallel with the ratio of norvalin /
leucine, β-methylnorleucine / isoleucine and norleucine / methionine in Figure 3.27.
The ratio of norleucine / methionine was observed higher than norvalin / leucine and
β-methylnorleucine / isoleucine. Even in the STR control cultivation, the ratio of
norleucine / methionine was as high as 7. Moreover, this ratio was doubled in 2CR
scale-down cultivation, and further increased in 3CR cultivation (Figure 3.27). This led
to a similar increasing trend for the incorporation of norleucine into proteins (Figure
3.26). Obviously, all these data show that the misincorporation of norleucine was
largest affected by the substrate and dissolved oxygen oscillating conditions among
these three non-canonical amino acids, though there is only small amount of
3. Results
100
methionine residues in the recombinant protein.
Figure 3.26: Shows the concentration of non-canonical amino acids and the natural counterparts
which they replace in inclusion bodies of E. coli W3110M_pSW3 cultivations from the induction
time (3 h), analyzed by GC-MS. Dashed line – induction time, 3 h after feed start point ; white
circles – STR reference cultivation; grey triangles up – 2CR scale-down cultivation; black squares
– 3CR scale-down cultivation. Please remark that the last sample (2h after induction) of the
inclusion bodies in the 3CR scale-down cultivation was taken during the time when the culture
was lysing (see Figure 3.17).
Ile
0 2 4 6 80
20
40
60
80
100
Leu
0 2 4 6 80
50
100
150
200Nva
0 2 4 6 80.0
0.1
0.2
0.3
0.4
0.5
β - Mnl
0 2 4 6 80.0
0.1
0.2
0.3
0.4
0.5
Nle
0 2 4 6 80.0
0.1
0.2
0.3
0.4
0.5Met
0 2 4 6 80
20
40
60
80
100
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
3. Results
101
Figure 3.27: The ratio of concentration of total free non-canonical amino acids / the natural
counterparts which they replace in the homogenized suspension (cells plus medium) samples
collected from the STR in cultivations with E. coli W3110M_pSW3 from the glucose feed start (0 h).
Dashed line – induction time, 3 h after feed start point; white circles – STR reference cultivation;
grey triangles up – 2CR scale-down cultivation; black squares – 3CR scale-down cultivation.
3.3.5. Flow cytometry analysis
In order to investigate the impact of oscillating conditions on cell physiology in
scale-down cultivations, flow cytometry studies were performed. In the three
cultivations, PI, BOX and Syto13 were applied to stain with cell samples. PI and BOX
staining was used to analyze the cellular viability. When cells lost their membrane
integrity (permeability), PI can enter the cells and has the ability to stain nucleic acids.
BOX cannot pass through a polarized membrane because of its anionic charge.
However when cells lose or partially lose their membrane potential, BOX can
passively diffuse through the membrane of structurally intact and stain with
positively charged proteins or unspecifically to the hydrophobic regions. It is
apparent from Figure 3.28 that the concentration of PI-staining cells is under 1 % and
BOX-staining cells is under 10 % over the whole cultivation time in all three
cultivations, and the profile of PI- and BOX-staining in the three cultivations are quite
similar, showing that the oscillating conditions have no influence on the cell viability.
Syto13 was applied for the purpose of staining the overall cell population or the
Nva / Leu
0 2 4 6 80.0
0.5
1.0
1.5
2.0
β - Mnl / Ile
0 2 4 6 80.0
0.5
1.0
1.5
2.0
Nle / Met
0 2 4 6 80
5
10
15
20
Ratio
[-]
Feed time [h]
3. Results
102
viable cells. Syto13 is a cell permeable dye, which is able to passively diffuse through
the membranes of E. coli cells and stain the nucleic acids DNA, and RNA as well with
lower affinity. Though Figure 3.28C indicates that there is no difference with the
Syto13 staining profile between the three cultivations, a different evolution of the
Syto13 stained cells can be seen from Figure 3.29. Over the feed time in the STR
reference cultivation, the culture was homogeneous except the value at 7 h after
feed start. In difference, two populations were clearly observed at 5 h after feed start
in the 2CR scale-down cultivation, and even earlier in the 3CR scale-down cultivation
at 3 h after feed start. This could be a suggestion of the weak cells which were going
to die, but this was not seen with PI- and BOX-stained cells. This could also be
doublets or some adaption of the cells under stress conditions. These are only initial
results, which have to be confirmed in the further.
Figure 3.28: Flow cytometric analysis (PI-, BOX- and Syto13 staining) of E. coli W3110M_pSW3
cultivations.
A B C
0
1
2
3
4
5
-3 -1.5 0 1.5 3 4.5 6 7.5
PI (
+)
%
Feed time [h]
PI
0
20
40
60
80
100
-3 -1.5 0 1.5 3 4.5 6 7.5
BO
X (
+) %
Feed time [h]
BOX
0
20
40
60
80
100
-3 -1.5 0 1.5 3 4.5 6 7.5
Syto
13
(+
) %
Feed time [h]
Syto13
STR
2CR
3CR
3. Results
103
Figure 3.29: Evolution of the Syto13 stained cells. Samples from the STR module of E. coli
W3110M_pSW3 STR reference, 2CR and 3CR scale-down cultivations. Time means after feed start.
The cross lines are the setting of gate using the negative control.
Figure 3.30: Density plots of the negative (A) and positive (B) control for Syto13 staining. Cells
obtained from the growth phase (1 h before feed start) from the STR, negative control: unstained
cells, positive control: cells heated at 80 for 1 h and stained with Syto13.
0 h 3.1 h 5 h 7 h
SSC
0 h 3 h 5 h 7 h
0 h 3 h
SSC
SSC
STR
2CR
3CR
Syto Syto Syto Syto
Syto Syto Syto Syto
Syto Syto
4. Discussion
104
4. Discussion
4.1. Accumulation of non-canonical amino acids during cultivations
4.1.1. Effect of oscillations
In large-scale fed-batch processes, the feeding with high concentrated glucose leads
to an immediate high glucose uptake and consumption by E. coli. Additionally, due to
insufficient mixing, oxygen limitation arises at the feed zone because of enhanced
respiration of the bacteria. As a result, this leads to gradients of substrate and
dissolved oxygen in large scale (Neubauer and Junne 2010). This problem has been
known for a long time. It is noticeable that, Junne et al. successfully used an
advanced STR-PFR scale-down bioreactor to study the response of Bacillus subtilis on
substrate and dissolved oxygen concentration oscillations in fed-batch cultivations
(Junne et al. 2011). Moreover, Lemoine et al. investigated the response of
Corynebacterium glutamicum on substrate and oxygen supply oscillations not only in
such two-compartment reactor (2CR), but also on this basis newly developed a novel
three-compartment reactor (3CR) by adding an additional non-aerated PFR module
(Lemoine et al. 2015). So, these 2CR and 3CR scale-down bioreactors were also used
in this study.
A study performed with the Bioscope indicated a fast response of E. coli to the high
glucose concentration is a high glycolytic flux, and as a result, pyruvate increased
immediately (De Mey et al. 2010). Under oscillating substrate and oxygen availability
conditions, Xu et al. indicated that the accumulation of pyruvate always occurred (Xu
et al. 1999a). In addition, it was suggested that pyruvate is the starting metabolite for
the formation of non-canonical amino acids norvaline and norleucine (Soini et al.
2008a; Sycheva et al. 2007). In the experiments, a wild-type E. coli K-12 strain was
cultivated aerobically without oxygen down-shift and showed no accumulation of
norvaline. After an oxygen down-shift, norvaline accumulation was detected. It is
4. Discussion
105
assumed, that due to the oxygen limitation the pyruvate concentration reaches a
limit and results in overflow to the formation of non-canonical amino acids (Soini et
al. 2008a). Our results also witnessed this. For E. coli W3110 wild-type strain, it was
observed that about maximal to 0.95 μmol gDcw-1 total free norvaline was
biosynthesized in 2CR scale-down cultivation, which is two-fold as in the well-mixed
control cultivation. The result about the accumulation of norvaline under
inhomogeneities was consistent with previous research. Additionally, under such
oscillating conditions, an elevated amount of β-methylnorleucine was also observed,
which is very interesting since seldom of earlier investigations reported.
4.1.2. Effect of expression of leucine-rich proteins
Two recombinant proteins were involved in this study. Interleukin-2 contains 22
leucine residues (15.0 %) and valine residues (2.7 %) out of 147 total amino acids.
Insulin contains similar leucine amount of residues to interleukin-2. In contrast,
typical E. coli proteins contain on average 8.4 % of leucine and 7.9 % valine
(Neidhardt and Umbarger 1996). This distinction classifies interleukin-2 and insulin as
leucine-rich proteins.
Researching the response of E. coli processes for the expression of leucine-rich
proteins to oscillating conditions in scale-down approaches is quite interesting. Since
as far as we know, this is the first time such investigation has been performed using
recombinant strains producing a target protein. Most attention of earlier researches
have been focused on different species of bacteria like the S. marcescens (Kisumi et
al. 1977a; Kisumi et al. 1977b), genetic knock-out studies in E. coli (Sycheva et al.
2007), expression of recombinant protein in E. coli in homogeneous conditions
(Apostol et al. 1997) and the use of wild-type E. coli strains to study oscillating
condition (Soini et al. 2008a; Soini et al. 2011).
4. Discussion
106
Bogosian et al. hypothesized that inducing a high level synthesis of a leucine-rich
protein was able to lead depression of the enzymes of the leucine biosynthetic
pathway, resulting in accumulation of non-canonical amino acids (Bogosian et al.
1989). Moreover, Sycheval et al. showed that leucine synthesis pathway enzymes
play a very important role in formation of non-canonical amino acids (Sycheva et al.
2007). LeuABCD operon, which encodes the first enzyme of isoleucine pathway, is
regulated by leucine (Burns et al. 1966). A depletion of leucine leads to an increased
expression of leuABCD. And an increased expression of leuABCD operon could cause
to an increased non-canonical amino acids level (Sycheva et al. 2007). However
interestingly, though in our cultivation set-up the accumulation of the non-canonical
amino acids is mainly favored by the induction of a leucine-rich protein, we could not
observe a decrease of the leucine pool after induction in the suspension of three
cultivations of W3110M_pSW3. It even increased in the W3110M_pSW3 well-mixed
STR cultivation and W3110_pCTUT7_His_IL2 2CR system. Furthermore, though in the
W3110_pCTUT7_His_IL2 STR control cultivation the leucine pool was reduced by 30%,
but this in turn did not result in a higher synthesis of either one of the non-canonical
amino acids. Our results are conflict with the observation by Apostol et al. In their
experiment, a leucine-rich protein human hemoglobin was expressed in E. coli, and it
was observed that, with the expression of hemoglobin, leucine concentration
decreased to a steady level, alongside pyruvate pool increased simultaneously,
followed by norvaline accumulation (Apostol et al. 1997). However our results have
to be still verified by further repetitions of the experiments.
Another important factor that has intimate relationship with the formation of
non-canonical amino acids is the activity of AHAS, which is encoded by the largest
group of ilv family. As it can be seen from the compositions of proteins, in typical E.
coli nearly the same amount of leucine and valine is required for cell biosynthesis,
which equals the close biosynthesis pathway. In contrary, the amount of leucine in
4. Discussion
107
interleukin-2 and insulin composition is much higher than the valine content. It
assumed that when expression such leucine-rich protein in E. coli K12 W3110, a
higher leuABCD operon expression initiates a stronger α-ketobutyrate synthesis. This
could lead to valine accumulation, due to a lower valine / leucine ratio in the
interleukin-2 and insulin than in the composition of host cell proteins. Since E. coli
K-12 W3110 strain has a frameshift mutation in ilvG gene, that is to say no function
of AHAS II (Lawther et al. 1981). As a result, when excess valine accumulates in the
cellular environment, it leads to the valine toxicity phenomenon, which is known as
inhibition of leucine and isoleucine product especially in E. coli K-12 strains, even in
the case of leucine / isoleucine starvation (Andersen et al. 2001). However
interestingly, we did not observe the accumulation of valine after induction in the
suspension of W3110_pCTUT7_His_IL2 well-mixed control cultivation and
W3110M_pSW3 scale-down cultivations, and it even decreased in the
W3110_pCTUT7_His_IL2 control cultivation. Meanwhile, though it was observed the
increasing valine pool in W3110_pCTUT7_His_IL2 2CR scale-down cultivation and
W3110M_pSW3 well-mixed reference cultivation, the leucine pool in both not
declined, even increased.
Therefore it seems that the changed metabolic fluxes after induction cause the
formation of these non-canonical amino acids and not the derepression of the leu or
ilv operons. On top to these metabolic changes oscillations as they occur in the
scale-down systems seem to further increase this effect. Moreover in this study, we
want to highlight the fact that the oscillating conditions have more effect on the
accumulation of norleucine than norvaline and β-methylnorleucine. There were
already high and noticeable amount of β-methylnorleucine even in the STR control
cultivation.
4. Discussion
108
4.1.3. Effect of addition of trace elements
In this study, E. coli W3110 and W3110_pCTUT7_His_IL2 strain were cultivated in
EnBase Flo medium with addition of molybdenum, nickel and selenium trace
elements. While the cultivations of W3110M_pSW3 were performed in MSM
medium without these three trace elements.
There were profound increased accumulations of non-canonical amino acids in
W3110M_pSW3 cultivations under oscillating conditions compared to the control
cultivation. In difference, for the scale-down cultivations of W3110_pCTUT7_His_IL2,
the concentrations of total free norvaline and β-methylnorleucine showed no
significant difference to the control cultivation. It could be thought, the addition of
molybdenum, nickel and selenium in the growth medium suppressed non-canonical
amino acids biosynthesis under conditions of limited oxygen and excess glucose, as
reported by Biermann et al. (Biermann et al. 2013). This is because these trace
elements play important roles in the fully functionality and catalysis of formate
hydrogen lyase (FHL) complex that is the most dedicated enzyme in the pyruvate
metabolism in E. coli under anaerobic conditions. Soini and his colleagues showed
that the supplementation of culture medium with these trace elements was able to
prevent formate accumulation in high cell density cultivations (Soini et al. 2008b). So
molybdenum, nickel and selenium lead to a higher activity of the formate hydrogen
lyase (FHL) complex to catalyse pyruvate and release dihydrogen and carbon dioxide.
As seen in the results, the extracellular concentration of formate in the 2CR
cultivation was not higher than the control cultivation. Moreover, there was
increased accumulation of free serine and alanine pool in the 2CR scale-down
cultivation compared to the reference cultivation, showing a strong redirection of
carbon fluxes to serine and alanine. Therefore pyruvate is not accumulated too more
under oscillating conditions than the control, and thus the direct chain elongation
from pyruvate to α-ketobutyrate, which is the precursor of non-canonical amino
4. Discussion
109
acids, would not too more than the control cultivation.
4.2. The favored synthesis pathway of non-canonical amino acids
under different cultivations
From the results of free amino acid concentration in the suspension of
W3110_pCTUT7_His_IL2 strain, it was observed that the amino acids from TCA cycle,
glutamate, glutamine, aspartate and threonine were lower in scale-down cultivations
than in the control, indicating redirection of carbon flux. However the concentrations
of isoleucine and misincorporation of non-caononical amino acids increased.
Generally α-ketobutyrate, as the precursor of isoleucine and non-cannonical amino
acids pathway, was considered originating from threonine pathway (Umbarger 1996).
This concept was contradicted with the accumulation of isoleucine and
non-canonical amino acids. Several earlier studies have presented alternative
isoleucine pathway from pyruvate for other organisms (Risso et al. 2008; Xu et al.
2004) or through knock-out strategies in E. coli (Sycheva et al. 2007). So this makes
sense it is therefore apparent that α-ketobutyrate was derived from accumulation of
pyruvate under oscillating conditions, and non-canonical amino acids were
synthesized as side product of the isoleucine pathway.
Moreover, the data of carbon labeling experiments using the rapid sampling unit –
Bioscope further proved this theory. Under normal conditions, threonine reaches its
maximal portion of incorporation of labeled carbon before norvlaline, norleucine,
β-methylnorleucine and isoleucine. The main carbon source for α-ketobutyrate,
which is the precursor of non-canonical amino acids, is derived from threonine
through the TCA cycle under normal conditions. While under oscillating conditions,
the fast 13C-labeling in isoleucine and non-canonical amino acids, compared to a
tardy 13C-labeling of the intermediates from TCA-cycle including threonine, reveals
4. Discussion
110
changes in metabolic flux distribution within the branched chain amino acids
biosynthesis pathway. Therefore, the main carbon source for α-ketobutyrate cannot
be derived from threonine, but is directly derived from pyruvate though a much
shorter pathway.
4.3. Misincorporation of non-canonical amino acids into proteins
Due to the lower demand of prokaryotic host cells, more and more different types of
recombinant proteins are produced in living E. coli cells in industrial productions. As a
result, additional stress is induced into cells when expressing heterogonous proteins.
In this study, a lower productivity of heterogeneous protein was observed in the first
few hours after induction in both recombinant stains expressing leucine-rich proteins
under oscillating conditions. This was caused by the redirection of carbon flow to
mixed-acid fermentation. An earlier research also showed that the production of
recombinant pre-proinsulin was reduced in recombinant E. coli cultivation under the
oscillating dissolved oxygen tension in a STR-STR two-compartment scale-down
system (Sandoval-Basurto et al. 2005). However, the impacts of oscillating conditions
on the foreign proteins productivity are different, depending on the strain and target
recombinant protein. For example, Bylund et al. reported that 10% increased amount
of the target recombinant protein was found under oscillating of high substrates and
low oxygen concentration conditions (Bylund et al. 2000).
Moreover, besides the quantity, the quality of the proteins was analyzed. The results
showed that the oscillating conditions in scale-down cultivations increased
misincorporation of non-canonical amino acids into recombinant proteins. The
misincorporation of norvaline into interleukin-2 and β-methylnorleucine into insulin
was slightly increased under oscillating conditions. Furthermore, the
misincorporation of norleucine into both proteins was significantly enhanced in
4. Discussion
111
scale-down cultivations. The misincorporation of non-canonical amino acids occurs
over mis-aminoacylation of tRNAs, due to a lowered substrate specificity of the
aminoacyl-tRNA synthetase. Several articles have been published and reported that
this misincorporation of non-canonical amino acids was triggered by the ratio of
accumulation non-canonical amino acids to the corresponding canonical amino acid
(Apostol et al. 1997; Barker and Bruton 1979; Muramatsu et al. 2003). This is verified
in our results. The misincorporation of non-canonical amino acids into proteins
appeared to be paralleled closely by its ratio to corresponding canonical amino acid.
The higher of this ratio, the more non-canonical amino acids incorporate into
proteins. The most remarkable is the misincorporation of norleucine into insulin was
mostly affected by the oscillating conditions, though there are much lower
methionine residues than leucine in insulin. This can also be explained by the ratio of
norleucine / methionine. Because the accumulation of norleucine which is the most
elevated by the heterogeneous conditions, combined with lower amount of free
methionine in the cells with reducing carbon flux to TCA cycle, lead to higher ratio of
norleucine / methionine in scale-down cultivations. Eventually, this caused higher
misincorporation of norleucine into the recombinant proteins. Compared with the
reference cultivation, the misincorporation raised in 2CR cultivation with the ratio of
norleucine / methionine = 15, and further enhanced in 3CR scale-down cultivation
with further elevated norleucine / methionine ratio.
4.4. Cell physiology
In the W3110M_pSW3 cultivations, flow cytometry analysis was applied to
investigate the impact of oscillating conditions on cell physiology in scale-down
cultivations. Though lower quality of insulin with higher misincorporation rate of
non-canonical amino acids into proteins were observed under environmental
oscillating conditions, the W3110M_pSW3 strain showed robust under gradients of
4. Discussion
112
substrate and dissolved oxygen availability. Results of flow cytometry analysis
showed that the oscillating conditions have no significant influence on the cell
viability and cytoplasmic membrane polarity. This is quite surprising and interesting.
It might be expected that PI- and BOX-stained cells should be higher under stress
environment. But this phenomenon is not unique. Our results agreed with earlier
studies. Onyeaka et al. showed lower BOX- and PI-stained E. coli cells under
oscillatory conditions than small-scale well-mixed cultivation, indicating cell viability
not reduced by such oscillations (Onyeaka et al. 2003). Similar result also was
reported by Hewitt et al. (Hewitt et al. 2000). Another flow cytometry analysis
studies on cellular response to inhomogeneities also demonstrated that oscillatory
conditions had no impact on viability of C. glutamicum, even elevated cell
polarisability in 3CR scale-down cultivation (Lemoine et al. 2015). The reason is
thought to be one of a number of interlinked regulatory stress response pathways
was induced when E. coli exposed to unfavorable growth conditions. This is reflected
as the response that the amount of certain intracellular signaling molecules (ppGpp
and cAMP) and the induction of alternative sigma factors increase quickly in E. coli
(Andersson et al. 1996; Teich et al. 1999). As a result, the cell physiological activity
decreased, what is called dormant cells to survive under stressful conditions.
5. Conclusions and Outlook
113
5. Conclusions and Outlook
A higher degree of accumulation and misincorporation of non-canonical amino acids
into recombinant proteins was observed under the oscillating scale-down bioreactors
compared to the homogeneous control cultivation. This suggests that the oscillating
conditions as they typically occur in large-scale bioreactors may be critical for the
production quality. This study provides a solid basis for cell engineering approaches
to overcome such misincorporation challenges of product quality in the future and
allows to estimate, which degree of heterogeneity becomes critical for the process.
Furthermore it is necessary to more closely investigate the mechanisms, which
trigger the formation of these non-canonical amino acids, regarding their formation
even under homogenous conditions in the wild-type strain.
The scale-down models used in this study are able to simulate the feed zone, bulk
zone and starvation zones in industrial large-scale cultivation. Moreover, there exists
several and complex inhomogeneous conditions, the setup of simulators in lab scale
can be optimized in future in order to mimic even closer conditions of the industrial
scale process.
6. Theses
114
6. Theses
1. Oscillating conditions not always lead to a reduction in growth of E. coli.
2. Inhomogeneous cultivation conditions lead to a diminished productivity of
recombinant strain in the first few hours after induction, but the final expression
amount seems not significantly different.
3. It seems that the changed metabolic fluxes after induction cause the formation of
the non-canonical amino acids and not the derepression of the leu or ilv operons.
On top to these metabolic changes oscillations as they occur in the scale-down
systems seem to further increase this effect.
4. The accumulation and misincorporation of non-canonical amino acids, especially
norleucine, into recombinant proteins is affected by oscillating conditions.
5. The addition of molybdenum, nickel and selenium in the growth medium
suppressed non-canonical amino acids biosynthesis under conditions of limited
oxygen and excess glucose.
6. Norleucine was observed misincorporated into proteins with higher rate than
norvaline and β-methylnorleucine.
7. The misincorporation of non-canonical amino acids into proteins appeared to
have high correlation with its ratio to corresponding canonical amino acid.
8. The main carbon source for α-ketobutyrate, which is the precursor of the
considered non-canonical amino acids and isoleucine derived from threonine
under normal conditions, while it is directly derived from pyruvate under
oscillation conditions.
9. Oscillating conditions have no significant influence on the cell viability and
cytoplasmic membrane polarity.
7. References
115
7. References
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Zhang J, Greasham R. 1999. Chemically defined media for commercial fermentations.
Applied Microbiology and Biotechnology 51(4):407-421.
Zhao J, Shimizu K. 2003. Metabolic flux analysis of Escherichia coli K12 grown on
13C-labeled acetate and glucose using GC-MS and powerful flux calculation
method. J Biotechnol 101(2):101-17.
8. Appendix
125
8. Appendix
8.1. Behavior of E. coli W3110 in STR and 2CR cultivations
Figure 8.1: Total concentration of compounds of the main carbon metabolism in the suspension
(cell plus medium) samples from the STR module of E. coli W3110 wild-type strain cultivations,
analyzed by HPLC. Data are shown from around feed start (0h). White circles – STR reference
cultivation; black triangles up – 2CR scale-down cultivation.
Pyr
0.000
0.005
0.010
0.015
Oxa
-2 0 2 4 6 80.00
0.01
0.02
Mal
0.00
0.02
0.04
For
0.0
0.1
0.2
0.3Suc
0.00
0.01
0.02
0.03
Lac
-2 0 2 4 6 80.00
0.05
0.10
0.15
Concentr
ation [
mm
ol g
DC
W
-1]
Ace
0.00
0.01
0.02
0.03Fum
0.00
0.03
0.06
0.09
Feed time [h]
8. Appendix
126
Figure 8.2: Intracellular concentration of compounds of the main carbon metabolism in STR
module of E. coli W3110 wild-type strain cultivations, calculated from the total concentration
(cells plus medium) minus extracellular concentration of each compound. Data are shown from
around feed start (0h). White circles – STR reference cultivation; black triangles up – 2CR
scale-down cultivation.
Pyr
0.000
0.005
0.010
0.015
Oxa
-2 0 2 4 6 80.000
0.005
0.010
0.015
Mal
0.000
0.003
0.006
For
0.00
0.05
0.10
0.15 Suc
0.000
0.005
0.010
Lac
-2 0 2 4 6 80.00
0.03
0.06
0.09
Con
cen
tration
[m
mol g
DC
W
-1]
Ace
0.00
0.02
0.04 Fum
0.00
0.03
0.06
0.09
Feed time [h]
8. Appendix
127
Figure 8.3: Total concentration of compounds of the main carbon metabolism in the suspension
(cell plus medium) samples from the PFR module (PFR with feed addition) of E. coli W3110
wild-type strain 2CR scale-down cultivation, analyzed by HPLC. Data shown are the samples from
time points 0.75 h (white triangles up), 1.75 h (gray triangles down), 3.75 h (dark gray squares)
and 5.75 h (black diamonds) after feed start over the residence time in the PFR.
Pyr
0.00
0.05
0.10
0.15
Oxa
0 30 40 50 60 700.00
0.01
0.02
0.03
Mal
0.00
0.02
0.04
For
0.0
0.1
0.2
0.3Suc
0.00
0.01
0.02
0.03
0.04
Lac
0 30 40 50 60 700.00
0.05
0.10
0.15
Concentr
ation [
mm
ol gD
CW
-1]
Residence time [s]
Ace
0.00
0.03
0.06 Fum
0.00
0.03
0.06
0.09
STRSTR
8. Appendix
128
Figure 8.4: Intracellular concentration of compounds of the main carbon metabolism in PFR
module (PFR with feed addition) of E. coli W3110 wild-type strain 2CR scale-down cultivation,
calculated from the total concentration (cells plus medium) minus extracellular concentration of
each compound. Data shown are the samples from time points 0.75 h (white triangles up), 1.75 h
(gray triangles down), 3.75 h (dark gray squares) and 5.75 h (black diamonds) after feed start
over the residence time in the PFR.
Pyr
0.00
0.03
0.06
0.09
Oxa
0 30 40 50 60 700.00
0.01
0.02
Mal
0.000
0.002
0.004
0.006
For
0.0
0.1
0.2 Suc
0.000
0.005
0.010
0.015
Lac
0 30 40 50 60 700.00
0.02
0.04
Concentr
ation [
mm
ol gD
CW
-1]
Residence time [s]
Ace
0.000
0.005
0.010 Fum
0.00
0.03
0.06
0.09
STRSTR
8. Appendix
129
Figure 8.5: Total free amino acid concentration of the suspension samples (cells plus medium)
over the time in STR module of E. coli W3110 wild-type strain cultivations, analyzed by HPLC. The
time point zero represents feed start. White circles – STR reference cultivation; black triangles –
2CR scale-down cultivation.
Asp
-2 0 2 4 6 80
10
20
30Glu
-2 0 2 4 6 80
100
200
300
400Gln
-2 0 2 4 6 80
5
10
15
Ser
-2 0 2 4 6 80
10
20
30Gly
-2 0 2 4 6 80
100
200
300Ala
-2 0 2 4 6 80
10
20
30
Thr
-2 0 2 4 6 80
20
40
60
Val
-2 0 2 4 6 80
50
100
150
200Nva
-2 0 2 4 6 80.0
0.5
1.0
1.5
Leu
-2 0 2 4 6 80
5
10
15
20Ile
-2 0 2 4 6 80
5
10
15
20
β - Mnl
-2 0 2 4 6 80
1
2
3
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
8. Appendix
130
Figure 8.6: Concentration of intracellular free amino acids over the time in STR module of E. coli
W3110 wild-type strain cultivations, calculated from the concentration of total free amino acids
(cells plus medium) minus extracellular free amino acids. The time point zero represents feed
start. White circles – STR reference cultivation; black triangles – 2CR scale-down cultivation.
Asp
-2 -1 0 1 2 3 4 5 6 7 80
10
20
30Glu
-2 0 2 4 6 80
100
200
300Gln
-2 0 2 4 6 80
5
10
Ser
-2 0 2 4 6 80
10
20
30Gly
-2 0 2 4 6 80
100
200
300Ala
-2 0 2 4 6 80
20
40
Thr
-2 0 2 4 6 80
20
40
60
Nva
-2 0 2 4 6 80.0
0.5
1.0
1.5
Leu
-2 0 2 4 6 80
5
10
15Ile
-2 0 2 4 6 80
10
20
β - Mnl
-2 0 2 4 6 80
1
2
3
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
8. Appendix
131
Figure 8.7: Concentration of extracellular free amino acids over the time in STR module of E. coli
W3110 wild-type strain cultivations, analyzed by HPLC. The time point zero represents feed start.
White circles – STR reference cultivation; black triangles – 2CR scale-down cultivation.
Asp
-2 -1 0 1 2 3 4 5 6 7 80
10
20
30Glu
-2 0 2 4 6 80
50
100
150
200Gln
-2 0 2 4 6 80
20
40
60
Ser
-2 0 2 4 6 80
2
4
6Gly
-2 0 2 4 6 80
10
20
30
40Ala
-2 0 2 4 6 80
5
10
15
20
Thr
-2 0 2 4 6 80.0
0.1
0.2
0.3
0.4Leu
-2 0 2 4 6 80
50
100Ile
-2 0 2 4 6 80
20
40
60
β - Mnl
-2 0 2 4 6 80.0
0.5
1.0
1.5
Co
ncentr
atio
n [μM
]
Feed time [h]
8. Appendix
132
Figure 8.8: Total free amino acids concentration from the suspension samples (cells plus medium)
in PFR module (PFR with feed addition) of E. coli W3110 wild-type strain 2CR scale-down
cultivation, analyzed by HPLC. Data shown are the samples from time points 0.75 h (white
triangles up), 1.75 h (gray triangles down), 3.75 h (dark gray squares) and 5.75 h (black
diamonds) after feed start over the residence time in the PFR.
8.2. Behavior of E. coli W3110_pCTUT7_His_IL2 in STR and 2CR
cultivations
Asp
0
20
40
60
80Glu
0
200
400
600Gln
0
5
10
15
Ser
0
20
40
60Gly
0
200
400
600
Val
0 30 40 50 60 700
50
100
150
Ala
0
20
40
60
Thr
0
50
100
150
Nva
0 30 40 50 60 700
1
2
3
4
5
Leu
0
20
40
60Ile
0
20
40
60
80
β -Mnl
0 30 40 50 60 700
3
6
9
STRSTRSTR
Co
ncentr
atio
n [μmolg
DC
W-1
]
Residence time [s]
8. Appendix
133
Figure 8.9: Intracellular concentration of compounds of the main carbon metabolism in STR
module of E. coli W3110_pCTUT7_His_IL2 cultivations, calculated from the total concentration
(cells plus medium) minus extracellular concentration of each compound. Data are shown after
feed start (0h). Dashed line – induction time, 1 h after feed start point; white circles – STR
reference cultivation; black triangles up – 2CR scale-down cultivation.
Pyr
0.0000
0.0025
0.0050
0.0075 Mal
0.000
0.004
0.008
0.012
For
Concentr
ation [
mm
ol gD
CW
-1]
0.000
0.025
0.050
0.075 Suc
-1 0 1 2 3 4 5 60.000
0.001
0.002
0.003
Lac
-1 0 1 2 3 4 5 60.00
0.02
0.04
0.06 Feed time [h]
Ace
0.0
0.2
0.4
0.6Fum
0.0
0.1
0.2
0.3
Feed time [h]
8. Appendix
134
Figure 8.10: Total concentration of compounds of the main carbon metabolism in the suspension
samples (cells plus medium) from STR module of E. coli W3110_pCTUT7_His_IL2 cultivations,
analyzed by HPLC. Data are shown after feed start (0h). Dashed line – induction time, 1 h after
feed start point; white circles – STR reference cultivation; black triangles up – 2CR scale-down
cultivation.
Pyr
0.000
0.005
0.010Mal
0.00
0.03
0.06
For
0.0
0.1
0.2
0.3Suc
-1 0 1 2 3 4 5 60.00
0.03
0.06
Lac
-1 0 1 2 3 4 5 60.00
0.05
0.10
Concentr
ation [m
mol g
DC
W
-1]
Feed time [h]
Ace
0.0
0.4
0.8
1.2Fum
0.0
0.2
0.4
Feed time [h]
8. Appendix
135
Figure 8.11: Intracellular concentration of compounds of the main carbon metabolism in PFR
module (PFR with feed addition) of E. coli W3110_pCTUT7_His_IL2 2CR scale-down cultivation,
calculated from the total concentration (cells plus medium) minus extracellular concentration of
each compound. White triangles up – 1 h and grey triangles down – 3 h after glucose feed start.
Pyr
0.000
0.004
0.008
For
0.00
0.02
0.04
Lac
0 30 40 50 60 700.00
0.03
0.06
Conce
ntr
ation [
mm
ol gD
CW
-1]
Residence time [s]
Ace
0.0
0.1
0.2
0.3
Mal
0.000
0.003
0.006
Suc
0 30 40 50 60 700.00
0.01
0.02
0.03
Fum
0.00
0.02
0.04
Residence time [s]
STR
STR
8. Appendix
136
Figure 8.12: Total concentration of compounds of the main carbon metabolism in the suspension
samples (cells plus medium) from the PFR module (PFR with feed addition) of E. coli
W3110_pCTUT7_His_IL2 2CR scale-down cultivation, analyzed by HPLC. White triangles up – 1 h
and grey triangles down – 3 h after glucose feed start.
Pyr
0.000
0.005
0.010
For
0.00
0.07
0.14
0.21
Lac
0 30 40 50 60 700.00
0.06
0.12
0.18
Conce
ntr
atio
n [
mm
ol gD
CW
-1]
Residence time [s]
Ace
0.0
0.3
0.6
0.9
1.2
Mal
0.00
0.02
0.04
Suc
0 30 40 50 60 700.000
0.015
0.030
0.045
Fum
0.0
0.1
0.2
0.3
Residence time [s]
STR
STR
8. Appendix
137
Figure 8.13: Intracellular concentration of free amino acid in STR module of E. coli
W3110_pCTUT7_His_IL2 cultivations from the glucose feed start (0 h), calculated from the
concentration of total free amino acids (cells plus medium) minus extracellular free amino acids.
Dashed line – induction time, 1 h after feed start point; white circles – STR reference cultivation;
black triangles up – 2CR scale-down cultivation.
Asp
-1 0 1 2 3 4 5 60
50
100
150
Glu
-1 0 1 2 3 4 5 60
500
1000
1500
2000Gln
-1 0 1 2 3 4 5 60
2
4
6
8
Ser
-1 0 1 2 3 4 5 60
5
10
15
20
25
30Gly
-1 0 1 2 3 4 5 60
10
20
30
40
50
60Ala
-1 0 1 2 3 4 5 60
20
40
60
80
Thr
-1 0 1 2 3 4 5 60
1
2
3
4
5
6
Nva
-1 0 1 2 3 4 5 60
2
4
6
Leu
-1 0 1 2 3 4 5 60
2
4
6
8
10
12Ile
-1 0 1 2 3 4 5 60
10
20
30
β - Mnl
-1 0 1 2 3 4 5 60
20
40
60
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
8. Appendix
138
Figure 8.14: Extracellular free amino acid concentration over the time in the STR module of E. coli
W3110_pCTUT7_His_IL2 cultivations from the glucose feed start (0 h), analyzed by HPLC. Dashed
line – induction time, 1 h after feed start point; white circles – STR reference cultivation; black
triangles up – 2CR scale-down cultivation.
Asp
0
1000
2000
3000
4000Glu
0
1500
3000
4500 Gln
0 1 2 3 4 5 60
10
20
30
40
50
Ser
0
15
30
Gly
0 1 2 3 4 5 60
10
20
30
40
50
60
70Ala
0 1 2 3 4 5 60
20
40
60
80
Thr
0 1 2 3 4 5 60.0
0.5
1.0
1.5
2.0
2.5
3.0
Nva
0 1 2 3 4 5 60
5
10
15
20
25
30
35
Leu
0 1 2 3 4 5 60
20
40
60
80
100Ile
0 1 2 3 4 5 60
10
20
30
40
50
60
β - Mnl
0 1 2 3 4 5 60
2
4
6
8
10
12
14
16
Co
ncentr
atio
n [μM
]
Feed time [h]
8. Appendix
139
Figure 8.15: Additional total free amino acid concentration in the suspension samples (cells plus
medium) over the residence time of the PFR module (PFR with feed addition) in E. coli
W3110_pCTUT7_His_IL2 2CR scale-down cultivation, analyzed by HPLC. White triangles up – 1 h
and grey triangles down – 3 h after glucose feed start.
Asp
0 30 40 50 60 700
20
40
60
80Glu
0
100
200
300
400
500
Ser
0
5
10
15
20
Gln
0 30 40 50 60 700
1
2
3
4
5
6
7
Gly
0
5
10
15
20
25
30
35Ala
0
10
20
30
40
50
Thr
0 30 40 50 60 700
1
2
3
4
5
STR
STR STR
Co
ncentr
atio
n [μmolg
DC
W-1
]
Residence time [s]
8. Appendix
140
Figure 8.16: Intracellular free amino acid concentration over the residence time of the PFR
module (PFR with feed addition) in E. coli W3110_pCTUT7_His_IL2 2CR scale-down cultivation,
calculated from the concentration of total free amino acids (cells plus medium) minus
extracellular free amino acids. White triangles up – 1 h and grey triangles down – 3 h after
glucose feed start.
Asp
0
20
40
60
80Glu
0
100
200
300
400
500Gln
0
1
2
3
4
5
6
Ser
0
5
10
15
20
25Gly
0
5
10
15
20
25
30
35
Val
0 30 40 50 60 700
10
20
30
40
50
60
70
Ala
0
20
40
60
Thr
0
1
2
3
4
5
Nva
0 30 40 50 60 700
2
4
6
Leu
0
2
4
6
8
10
12
14 Ile
0
2
4
6
8
β -Mnl
0 30 40 50 60 700.0
0.5
1.0
1.5
2.0
STRSTRSTR
Co
ncentr
atio
n [μmolg
DC
W-1
]
Residence time [s]
8. Appendix
141
Figure 8.17: Extracellular free amino acid concentration over the residence time of the PFR
module (PFR with feed addition) in E. coli W3110_pCTUT7_His_IL2 2CR scale-down cultivation,
analyzed by HPLC. White triangles up – 1 h and grey triangles down – 3 h after glucose feed start.
8.3. Behavior of E. coli W3110M_pSW3 in STR, 2CR and 3CR
cultivations
Asp
0
100
200
300
400
500Glu
0
500
1000
1500
2000
2500Gln
0
10
20
30
Ser
0
5
10
15
20
25
30Gly
0
20
40
60
80
Val
0 30 40 50 60 700
100
200
300
400
Ala
0
20
40
60
80
100
Thr
0
1
2
3
4
Nva
0 30 40 50 60 700
10
20
30
40
Leu
0
20
40
60
80Ile
0
20
40
60
80
β -Mnl
0 30 40 50 60 700
10
20
30
40
STRSTRSTR
Co
ncentr
atio
n [μM
]
Residence time [s]
8. Appendix
142
Figure 8.18: Extracellular concentration of compounds of the main carbon metabolism in PFR1
module (PFR with feed addition) of E. coli W3110M_pSW3 in 2CR scale-down cultivation,
analyzed by HPLC. Data shown are the samples from time points 0 h (white triangles up), 3 h
(gray triangles down), 5 h (dark gray squares) and 7 h (black diamonds) after feed start over the
residence time in the PFR.
Mal
0.00
0.05
0.10
0.15
For
0.00
0.05
0.10
0.15
Lac
0 30 40 50 60 700.0
0.2
0.4
0.6
0.8
Conce
ntr
ation [
mM
]
Residence time [s]
Ace
0.0
0.2
0.4
0.6
0.8
Fum
0 30 40 50 60 700.00
0.05
0.10
0.15
Glc
Residence time [s]
0 30 40 50 60 70
Concentr
ation [
g L
-1]
0.0
0.5
1.0
1.5
2.0
2.5
A
B
STR
STR
STR
8. Appendix
143
Figure 8.19: Complete concentration of amino acids pool after hydrolysis in the suspension (cells
plus medium) samples of STR module of E. coli W3110M_pSW3 cultivations from the glucose feed
start (0 h), analyzed by GC-MS. Dashed line – induction time, 3 h after feed start point; white
circles – STR reference cultivation; grey triangles up – 2CR scale-down cultivation; black squares
– 3CR scale-down cultivation.
Ala
0 2 4 6 80
200
400
600Gly
0 2 4 6 80
100
200
300
Val
0 2 4 6 80
100
200Ile
0 2 4 6 80
100
200Leu
0 2 4 6 80
200
400
600
800
Nva
0 2 4 6 80.0
0.5
1.0
1.5 β - Mnl
0 2 4 6 80
2
4
Thr
0 2 4 6 80
50
100
Ser
0 2 4 6 80
20
40
60
80
Nle
0 2 4 6 80
2
4
Asp
0 2 4 6 80
100
200
300Glu
0 2 4 6 80
200
400
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
8. Appendix
144
Figure 8.20: Total free amino acid concentration in the suspension samples (cells plus medium)
of STR module of E. coli W3110M_pSW3 cultivations from the glucose feed start (0 h), analyzed by
GC-MS. Dashed line – induction time, 3 h after feed start point; white circles – STR reference
cultivation; grey triangles up – 2CR scale-down cultivation; black squares – 3CR scale-down
Ala
0 2 4 6 80
5
10
15Gly
0 2 4 6 80
1
2
Val
0 2 4 6 80
1
2
Thr
0 2 4 6 80
1
2
3
4
Ser
0 2 4 6 80.0
0.5
1.0
Asp
0 2 4 6 80
5
10
15
Glu
0 2 4 6 80
50
100
150Gln
0 2 4 6 80.0
0.5
1.0
1.5
Lys
0 2 4 6 80.0
0.1
0.2
0.3
0.4
0.5
Ile
0 2 4 6 80
1
2
3Leu
0 2 4 6 80
1
2
3
Nva
0 2 4 6 80
1
2
3 β - Mnl
0 2 4 6 80
1
2
3Nle
0 2 4 6 80
1
2
3
Met
0 2 4 6 80
1
2
3
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
Co
ncentr
atio
n [μmolg
DC
W-1
]
Feed time [h]
8. Appendix
145
cultivation.
Figure 8.21: Total free amino acid concentration of the suspension samples (cells plus medium)
in PFR1 module (PFR with feed addition) of E. coli W3110M_pSW3 in 2CR scale-down cultivation,
analyzed by GC-MS. Data shown are the samples from time points 0 h (white triangles up), 3 h
(grey triangles down), 5 h (dark gray squares) and 7 h (black diamonds) after feed start over the
residence time in the PFR.
Ala
0
10
20
30Gly
0.0
0.5
1.0
1.5
2.0
Val
0
2
4
6Ile
0
2
4
6Leu
0
1
2
3
Nva
0 30 40 50 60 700
1
2Nle
0 30 40 50 60 700
1
2 β - Mnl
0 30 40 50 60 700
1
2
Thr
0
1
2
3
Ser
0.0
0.2
0.4
0.6
0.8
1.0
Asp
0
2
4
6Glu
0
50
100
150
STRSTRSTR
Co
ncentr
atio
n [μmolg
DC
W-1
]
Residence time [s]
Curriculum Vitae
146
Curriculum Vitae
Ping Lu (Female)
Place of Birth: Henan, China
Education:
10/2012 – 03/2016 Technische Universität Berlin (Berlin, Germany)
Ph.D student, research in Bioprocess Engineering
09/2009 - 07/ 2012 Zhengzhou University (Henan, China)
Master of science in Biochemistry and Molecular Biology
09/2005 - 06/2009 Zhengzhou University (Henan, China)
Bachelor of science in Biotechnology
Publications (10/2012 – 03/2016):
Li J, Jaitzig J, Lu P, Sussmuth R, Neubauer P. 2015. Scale-up bioprocess development
for production of the antibiotic valinomycin in Escherichia coli based on consistent
fed-batch cultivations. Microbial Cell Factories 14(1):83.
Poster presentation (10/2012 – 03/2016):
Ping Lu, Eva Brand, Christoph Klaue, Sergej Trippel, Christian Reitz, Stefan Junne,
Peter Neubauer. “Cellular responses in large-scale fed-batch bioprocess: Effects of
substrate oscillation on the synthesis of interleukin2 in Escherichia coli”.
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