Lecture 4: Bacterial Fueling and Assimilation

Lecture 2Text: pages 343-352 DNA replicationText: pages 362-368, 441 RNA transcriptionText: pages 369-376 Translation

Reading assignments in Text: Lengeler et al. 1999Text: pages 116-122 AssimilationText: pages 177-182 Assimilation reactionsText: pages 155-157 Storage compounds

Lecture 3Text: pages 114-116, 123-128 Central metabolismText: pages 52-58 Substrate level phosphorylationText: pages 62-67 Electrontransport-coupled phosphorylationText: pages 296-307 FermentationText: pages 263-266 Oxygen and metabolismText: pages 524 Energy generation

Fermentation products

Yeast: Bread, beer, wine...

Bacteria: Rye breads

Butter milk (Lactobacilli)

Sourdough bread

Yogurt

Olives Sausages “Thousand year” eggs

Coffee (husk removal)

SauerkrautVegetables / mushrooms (Lactobacillus plantarum)

Vinegar (acetic acid)

Organic acids, ketones, alcohols, ...

Hydrogen gas

AssemblyFuelling Biosyn. Polymer.

Lecture 1

Pili

Flagella

Lecture 2Lectures 3,4

DNA, RNAProtein

CM Central Metabolism

PM Peripheral Met.

Foods: glucose,

ribose, acetate, ...

Strangefoods:oils,

benzene, pesticides, ...

12 MP’s Met. Precursors ( 2C - 6C units)

“substrate-level”

ATP

[1-C units]

NADH

= Glycolysis (EMP Pw)

Pentose phosphate cycle (PPC)

Citric acid [Kreb’s] cycle (TCA)

Reducing Power NADPH eTS (electron-

Transp. Sys.)

PMF(Proton Motive Force)

F0F1

ATPase

“oxidative phosphorylation”

Overview of Metabolism

FermentationN, SP

1-C unit metabolism, Tetra Hydofolate (THF) and sulfa antibiotics

Serine (AA)|

CH2OH

+ THF Glycine (AA)|

H

+ THF||

CH2

“mobile 1-C carrier”

Many Biosyn.

Rxns

Methionine (AA)Purines (A, G)Thiamine (Vit. B1)Thymine (dUMP > dTMP)

Coenzyme A, etc...

THF = (1 + 2 +3)1

Pteridine ring+2

p-amino-benzoic acid

+3Glutamate (AA)

NNH

O||

C--O_NH

COO-

COO-CH2

Competitive inhibitorDHF

NH2 SO2 NH2

Sulfanilamide 1st antibiotics

Folic acid (Food, Vitamin)

2nd path way

people bacteria Benefits ?

Problems ?Non-competitive inhibitor

Trimethoprin

COO-

H-C-OH

HO-C-H

3-CP

Entner-Doudoroff Pathway and glycolysis

Glycolysis (EMP Pw)

Glucose

Glucose-6-P (6C)

Fructose-6-P

Triose 3-P (2x 3C)

Fructose 1,6-P

3-Phosphoglycerate

2-Phosphoglycerate

Phosphoenolpyruvate

Pyruvate

1, 3-Diphosphoglycerate

-2 ATP

+4 ATP

+6 ATP

Net: +8 ATP plus 2x

NAD(P)H6-P Gluconate

COO-

C=O

H-C-H

3-CP

2-Keto, 3-deoxy-6-P Gluconate

-H2O-1 ATP

+3 ATP

NADH

+3 ATP

+2 ATP

Net: +7 ATP plus 2x Pyruvate TCA

Aerobic glucose utilization

NADH2x

Dumping excess electrons (NAD+ from NADH)

S P

ATP NADH

NAD+

PH2

Bug?

eTS

Dissimulatory reduction

e.g. nitrate > nitrite >> ammonium > nitrogen gas

Assimilatory reduction

Fermentation

H2

CO2

= anaerobic respiration

Geobacter sulfurreducens

Oxidize Organics CO2

Fumarate, Malate, Sulfur, Fe(III), Mn(IV)(terminal electron acceptors, “dissimulatory reduction”)

Dominate many subsurface environmentsAttach to, and reduce insoluble Sulfur, Fe(III) and Mn(IV) oxides

Sulfu

r

N Assimilation

NH3 Ketoglutarate (MP)

NADPH

Glutamate(AA)

GDH

GDH = Glutamate Dehydrogenase

Glutamine(AA)

GS

GS = Glutamine SynthetaseBiosyn. Biosyn.

(big pool)

All N-compounds

Direct organic sources: R-NH2 (amino acids) R=N-R’(purines, etc...)

ATP

NH3

? No preferred N-sources: Assimilatory reductases

Nitrate Nitrite Nitrous oxide NH3

Dissimulatory reductases (anaerobic respiration)

:N N: gas

FixationLithotrophic oxidation

Nitrogen cycle

~80% atmosphere

~20 Mega-year turnover

Nitrogen fixation, conflict with oxygen

NH3 :N N: gas

Nitrogenase Proteins (FeS) (Mo)

poison

Air = ~80 nitrogen (food)

~20% oxygen

Four fixation strategies:

Cyanobacteria sps.

Rhizobia sps.

Clostridium pasteurianum (pages 8, 304)

Strict anaerobe

Azotobacter vinlandii (pages 8, 44)

Obligate aerobe

soil

N2 O2 air

N2

O2

Size, rapid respirationprotect Nitrogenase

PS II makes oxygen

Cell differentiation into “Heterocyst”

Cell differentiation into “Bacteroid”

Symbiosis with plants, form nodule organ

S Assimilation

NH2 COO-

CH2

Cysteine (AA)

SH

O-Acetyl serine

NH2 COO-

CH2

O-Acetyl SH2

MethionineLipoic acidCoenzyme A

Thiamine, FeS clusters, etc...

Anaerobic respiration

“Dissimulatory reduction”e.g. Geobacter sp.

Geological / volcanic

? Sources:

+ O2

SO42-

“Assimilatory reduction”

3 ATP4 NADPH

[S-P-5’Adenosine 3’P]

Adenosine phosphosulfate carrier

P Assimilation

PO43- free R-O-PO3

2- esters

IM

PS

OM (-) porins

Alkaline Phosphatase5’ Nucleosidases, etc...PO4

3- R-OH

PO43-

H+

+ ADP ATPF0F1

EMP Rxn, etc...

Poly-Phosphate

n = 1 to 1,000

Storage

Inclusion bodies “volutin”

Pre-biotic

Molecular cloning

Many roles:O - P - (O -P- O)n - P - O

O O O

O O O

Stress tolerance, virulence, etc...

Lecture Overview

Metabolism (Inside and Out)

Growth

Survival strategies

Diversity and environmental niches

Cell differentiation

Sporulation

Symbiosis

Adaptation mechanisms

Rapid responses through altered enzyme activities

Altering genetic expression