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SYNOPSIS OF THE THESIS
. Tuberculosis (TB), caused by Mycobacterium tuberculosis, has long been the
scourge of humanity, claiming millions of lives. It is the most devastating infectious
disease of the world in terms of mortality as well as morbidity (WHO, 2009). The
lack of a uniformly effective vaccine against TB, the development of resistance in
the Mycobacterium tuberculosis against the present antitubercular drugs and its
synergy with AIDS has made the situation very alarming. This therefore necessitates
a search for new antitubercular drugs as well as the identification of new and
unexplored drug targets (Broun et aI., 1992). Coenzyme A is an essential cofactor
for all organisms and is synthesized in organisms from pantothenate by a universally
conserved pathway (Spry et al., 2008; Sassetti and Rubin, 2003). The first enzyme of
the pathway, pantothenate kinase catalyzes the most important step of the
biosynthetic process, being the first committed step of CoA biosynthesis and the one
at which all the regulation takes place (Gerdes et aI., 2002)
This thesis describes the successful cloning of PanK from Mycobacterium
tuberculosis, its expression in E. coli, single step affinity purification, and complete
biochemical and biophysical characterization. In this work, pantothenol, a widely
believed inhibitor of pantothenate kinase, has been shown to act as a substrate for
the mycobacterial pantothenate kinase. Further it was shown that the product, 4'-
phosphopantothenol, thus formed, inhibited the next step of the CoA biosynthesis
pathway in vitro. The study was extended to find outthe fate of pantothenol inside
the cell and it was demonstrated that the CoA biosynthetic enzymes metabolized the
latter into the pantothenol derivative of CoA which then gets incorporated into acyl
carrier protein. Lastly, it was decisively shown that pantothenate kinase is not only
regulated by feedback inhibition by CoA but, also regulated through feed forward
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stimulation by Fructose 1, 6 biphosphate (FBP), a glycolytic intermediate. The
binding site of FBP was determined by docking and mutational studies of MtPanK.
Chapter 1 presents a brief survey of the literature related to Coenzyme A
biosynthesis pathway and describes the objective of the thesis. It also presents a
history of TB and briefly reviews literature describing TB as well as the life cycle,
biology, survival strategy, mode of infection and the metabolic pathways operational
in the TB parasite, Mycobacterium tuberculosis. The chapter details the enzymes
involved in CoA biosynthesis pathway from various organims.
Chapter 2 In this chapter, cloning of the ORF (Rv1092c), annotated as
pantothenate kinase in the Tuberculist database
(http://genolist.pasteur.frfTubercuList), its expression in E. coli and purification
using affinity chromatography has been described. Protein identity was confirmed
by MALDI-TOF and by its ability to complement the pantothenate kinase
temperature sensitive mutant, DV70. This chapter also illustrates the oligomeric
status of MtPanK in solution and describes the biochemical characterization of
MtPanK by means of two different methods, spectrophotometrically by a coupled
assay and calorimetrically by using Isothermal Titration Calorimetry. Feedback
inhibition of MtPanK by CoA is also discussed in this chapter.
Chapter 3 describes the biophysical characterization of MtPanK. It,
discusses the enthalpy (~H) and free energy change (~G) accompanying the binding
of a non-hydrolysable analogue of ATP; CoA; acetyl CoA and malonyl-CoA to
MtPanK. The chapter details the energetics observed upon ATP binding to
pantothenate-saturated MtPanK further elucidating the order of the reaction. This
chapter also describes the various strategies which were designed and tested to
remove CoA from the enzyme as the latter is always purified from the cell in
conjunction with CoA. Validation of these strategies for complete CoA removal (by
studying the n value from ITC studies) is further described.
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Chapter 4 discusses the interaction of the well-studied inhibitor of
pantothenate kinases from other sources (e.g. the malarial parasite), pantothenol,
with the mycobacterial enzyme. In order to investigate the interaction of this
. compound with MtPanK, its effect on the kinetic reaction carried out by the enzymewas studied by several methods. Surprisingly, a new band corresponding to 4'-
phosphopantothenol appeared when the reaction mix of MtPanK with pantothenol
and ATP was separated on TLC. The identity of the new spot was confirmed by
mass spectrometry analyses of the MtPanK reaction mixture.. These findings
established the fact that pantothenol is a substrate of pantothenate kinase. To delve
deeper into the mechanism of interaction of this compound with the enzymes of the
coenzyme A biosynthesis pathway, the ability of pantothenol to serve as a substrate
for the next step of the pathway, MtCoaBC was studied. Using various approaches it
was established that pantothenol is actually a substrate for the MtPanK and the
inhibition observed earlier (Saliba et aI., 2005) is actually due to the inability of
CoaBC to utilize 4' -phosphopantothenol as substrate.
Chapter 5 takes the story from Chapter 4 further detailing the effects of
pantothenol on cultures of E. coli and M. smegmatis. I observed that pantothenol
does not inhibit the culture of E. coli or M. smegmatis. So, further studies were
carried out to know the fate of pantothenol once it is converted into 4'-
phosphopantothenoi. Since, the next enzyme of the pathway does not utilize 4'-
phosphopantothenol, I checked the further downstream enzyme of the pathway,
CoaD, and found that it converts 4' -phosphopantothenol to thepantothenol
derivative of dephospho-CoA. The next enzyme of the pathway, CoaE, took up this
pantothenol derivative of dephospho-CoA as a substrate and converted it to the
pantothenol derivative of CoA which was then transferred to apo-ACP by holo-ACP
synthase. The holo-ACP thus synthesized enters into the dedicated pathway of fatty
acid synthesis.
Extensive investigations have been carried out on the regulation of
pantothenate kinases, by the product of the pathway, Coenzyme A and its thioesters,
xx
establishing the latter as the feedback regulators of these enzymes. In order to
determine if the cell employs mechanisms to sense available carbon sources and
consequently modulate its coenzyme A levels by regulating activity of the enzymes
involved in CoA biosynthesis, glycolytic intermediates were tested against MtPanK
for their possible role in the regulation of MtPanK activity. Chapter 6 details my
identification of a novel regulator of MtPanK activity, fructose-I, 6-bisphosphate
(FBP), a glycolytic intermediate, which enhances the MtPanK catalyzed
phosphorylation of pantothenate by three fold. Further, the possible mechanisms
through which FBP mediates MtPanK activation are also discussed. This chapter
also describes the experiments carried out to identify the binding site of FBP on
MtPariK.Interestingly, docking of FBP on MtPanK revealed that FBP binds close to
the ATP binding site on the enzyme with one of its phosphates overlapping with the
3'~phosphateof CoA thereby validating its competitive binding relative to CoA on
MtPanK. Based on these observations I propose that the binding of FBP to MtPanK
lowers the activation energy of pantothenate phosphorylation by PanK.
Chapter 7 presents a summary of the findings of this work. Coenzyme A
biosynthesis pathway harbors immense potential in the development of drug against
many communicable diseases, thanks to its essentiality for the pathogens and the
differences between the pathogen and host CoA biosynthetic enzymes. The work
done in this thesis extensively characterizes the first committed enzyme of the CoA
biosynthetic pathway, pantothenate kinase, from Mycobacterium tuberculosis
(MtPanK). The thesis also deals with the fate of a known inhibitor of PanK and
proves it as a substrate for MtPanK. Finally this thesis describes a new link between
glycolysis and CoA biosynthesis.
Biotin, like coenzyme A, is another essential cofactor required by several
enzymes in critical metabolic pathways. De novo synthesis of this critical metabolite
has been reported only in plants and microorganisms. Therefore targeting the
synthesis of biotin in the tubercular pathogen is another effective means of
handicapping the tubercle pathogen. During the course of my studies, I also
XXI
7. Spry, c., Kirk, K., and Saliba, K. J. (2008) FEMS Microbiol Rev 32,56-106
investigated the mycobacterial biotin biosynthesis pathway, studying the first
enzyme of the pathway, 7-keto-8-aminopelargonic acid (KAPA) synthase (bioF) in
extensive detail. Appendix 1 elucidates the kinetic properties of 7-keto-8-
aminopelargonic acid synthase (bioF) from Mycobacterium tuberculosis and proves
beyond doubt that D-alanine which has previously been reported to act as a
competitive inhibitor for the B. sphaericus enzyme (Ploux et al., 1999), is actually a
substrate for the mycobacterial bioF.
References:
1. WHO. (2009) Global tuberculosis control - epidemilogy, strategy and
financing http://www.afro.who.int/tb/reportsI2007tb surveillance report.pdf
2. Braun, M. M., Kilburn, J. 0., Smithwick, R. W., Coulibaly, I. M., Coulibaly,
D., Silcox, V. A., Gnaore, E., Adjorlolo, G., and De Cock, K. M. (1992) AIDS 6,
1327-1330
3. Gerdes, S. Y., Scholle, M. D., D'Souza, M., Bernal, A., Baev, M. V., Farrell,
M., Kurnasov, O. V., Daugherty, M. D., Mseeh, F., Polanuyer, B. M., Campbell, J.
W., Anantha, S., Shatalin, K. Y.,Chowdhury, S. A., Fonstein, M. Y., and Osterman,.
4.
A. L. (2002) J Bacterioll84, 4555-4572
Ploux, 0., Breyne, 0., Carillon, S., and Marquet, A. (1999) Eur. J. Biochem.
5.
259, 63-70
Saliba, K. J., Ferm, I., and Kirk, K. (2005) Antimicrob Agents Chemother 49,
6.
632-637
Sassetti, C. M., and Rubin, E. J. (2003) Proc Natl Acad Sci USA 100,
12989-12994
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