Abstract
The recent discovery of fatty acyl-AMP ligases (FAALs) in Mycobacterium tuberculosis (Mtb) provided a new perspective of fatty acid activation. These proteins convert fatty acids to the corresponding adenylates, which are intermediates of acyl-CoA–synthesizing fatty acyl-CoA ligases (FACLs). Presently, it is not evident how obligate pathogens such as Mtb have evolved such new themes of functional versatility and whether the activation of fatty acids to acyladenylates could indeed be a general mechanism. Here, based on elucidation of the first structure of an FAAL protein and by generating loss-of-function and gain-of-function mutants that interconvert FAAL and FACL activities, we demonstrate that an insertion motif dictates formation of acyladenylate. Because FAALs in Mtb are crucial nodes in the biosynthetic network of virulent lipids, inhibitors directed against these proteins provide a unique multipronged approach to simultaneously disrupting several pathways.
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References
Trivedi, O.A. et al. Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria. Nature 428, 441–445 (2004).
Weber, T. & Marahiel, M.A. Exploring the domain structure of modular nonribosomal peptide synthetases. Structure 9, R3–R9 (2001).
Fischbach, M.A. & Walsh, C.T. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem. Rev. 106, 3468–3496 (2006).
Stachelhaus, T., Mootz, H.D. & Marahiel, M.A. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem. Biol. 6, 493–505 (1999).
Gomez, J.E. & McKinney, J.D.M. tuberculosis persistence, latency, and drug tolerance. Tuberculosis (Edinb.) 84, 29–44 (2004).
World Health Organization. Global tuberculosis control: surveillance, planning, financing (WHO/HTM/TB/2008.393) (World Health Organization Geneva, 2008).
Barry, C.E., Crick, D.C. & McNeil, M.R. Targeting the formation of the cell wall core of M. tuberculosis. Infect. Disord. Drug Targets 7, 182–202 (2007).
Brennan, P.J. & Crick, D.C. The cell-wall core of Mycobacterium tuberculosis in the context of drug discovery. Curr. Top. Med. Chem. 7, 475–488 (2007).
Gokhale, R.S., Sankaranarayanan, R. & Mohanty, D. Versatility of polyketide synthases in generating metabolic diversity. Curr. Opin. Struct. Biol. 17, 736–743 (2007).
Gokhale, R.S., Saxena, P., Chopra, T. & Mohanty, D. Versatile polyketide enzymatic machinery for the biosynthesis of complex mycobacterial lipids. Nat. Prod. Rep. 24, 267–277 (2007).
Jackson, M., Stadthagen, G. & Gicquel, B. Long-chain multiple methyl-branched fatty acid-containing lipids of Mycobacterium tuberculosis: biosynthesis, transport, regulation and biological activities. Tuberculosis (Edinb.) 87, 78–86 (2007).
Kolattukudy, P.E., Fernandes, N.D., Azad, A.K., Fitzmaurice, A.M. & Sirakova, T.D. Biochemistry and molecular genetics of cell-wall lipid biosynthesis in mycobacteria. Mol. Microbiol. 24, 263–270 (1997).
Krithika, R. et al. A genetic locus required for iron acquisition in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103, 2069–2074 (2006).
Trivedi, O.A. et al. Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Mol. Cell 17, 631–643 (2005).
Portevin, D. et al. The acyl-AMP ligase FadD32 and AccD4-containing acyl-CoA carboxylase are required for the synthesis of mycolic acids and essential for mycobacterial growth: identification of the carboxylation product and determination of the acyl-CoA carboxylase components. J. Biol. Chem. 280, 8862–8874 (2005).
Cole, S.T. et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544 (1998).
Fontan, P., Aris, V., Ghanny, S., Soteropoulos, P. & Smith, I. Global transcriptional profile of Mycobacterium tuberculosis during THP-1 human macrophage infection. Infect. Immun. 76, 717–725 (2008).
Van der Geize, R. et al. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc. Natl. Acad. Sci. USA 104, 1947–1952 (2007).
Conti, E., Franks, N.P. & Brick, P. Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure 4, 287–298 (1996).
Gulick, A.M., Starai, V.J., Horswill, A.R., Homick, K.M. & Escalante-Semerena, J.C. The 1.75 A crystal structure of acetyl-CoA synthetase bound to adenosine-5′-propylphosphate and coenzyme A. Biochemistry 42, 2866–2873 (2003).
May, J.J., Kessler, N., Marahiel, M.A. & Stubbs, M.T. Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases. Proc. Natl. Acad. Sci. USA 99, 12120–12125 (2002).
Hisanaga, Y. et al. Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. J. Biol. Chem. 279, 31717–31726 (2004).
Goyal, A. et al. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of FadD28, a fatty-acyl AMP ligase from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62, 350–352 (2006).
Conti, E., Stachelhaus, T., Marahiel, M.A. & Brick, P. Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J. 16, 4174–4183 (1997).
Linne, U., Schafer, A., Stubbs, M.T. & Marahiel, M.A. Aminoacyl-coenzyme A synthesis catalyzed by adenylation domains. FEBS Lett. 581, 905–910 (2007).
Nakama, T., Nureki, O. & Yokoyama, S. Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase. J. Biol. Chem. 276, 47387–47393 (2001).
Ferreras, J.A., Ryu, J.S., Di Lello, F., Tan, D.S. & Quadri, L.E. Small-molecule inhibition of siderophore biosynthesis in Mycobacterium tuberculosis and Yersinia pestis. Nat. Chem. Biol. 1, 29–32 (2005).
Somu, R.V. et al. Rationally designed nucleoside antibiotics that inhibit siderophore biosynthesis of Mycobacterium tuberculosis. J. Med. Chem. 49, 31–34 (2006).
Copeland, R.A. Tight binding inhibitors. in Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis##305–317 (Wiley-VCH, New York, 2000).
Hansen, D.B., Bumpus, S.B., Aron, Z.D., Kelleher, N.L. & Walsh, C.T. The loading module of mycosubtilin: an adenylation domain with fatty acid selectivity. J. Am. Chem. Soc. 129, 6366–6367 (2007).
Black, P.N. & DiRusso, C.C. Yeast acyl-CoA synthetases at the crossroads of fatty acid metabolism and regulation. Biochim. Biophys. Acta 1771, 286–298 (2007).
Wang, F., Langley, R., Gulten, G., Wang, L. & Sacchettini, J.C. Identification of a type III thioesterase reveals the function of an operon crucial for Mtb virulence. Chem. Biol. 14, 543–551 (2007).
Arora, P., Vats, A., Saxena, P., Mohanty, D. & Gokhale, R.S. Promiscuous fatty acyl CoA ligases produce acyl-CoA and acyl-SNAC precursors for polyketide biosynthesis. J. Am. Chem. Soc. 127, 9388–9389 (2005).
Lu, Y.J. et al. Acyl-phosphates initiate membrane phospholipid synthesis in Gram-positive pathogens. Mol. Cell 23, 765–772 (2006).
Jiang, Y., Chan, C.H. & Cronan, J.E. The soluble acyl-acyl carrier protein synthetase of Vibrio harveyi B392 is a member of the medium chain acyl-CoA synthetase family. Biochemistry 45, 10008–10019 (2006).
Kholodenko, B.N. Cell-signalling dynamics in time and space. Nat. Rev. Mol. Cell Biol. 7, 165–176 (2006).
Strogatz, S.H. Exploring complex networks. Nature 410, 268–276 (2001).
Morphy, R. & Rankovic, Z. Designed multiple ligands. An emerging drug discovery paradigm. J. Med. Chem. 48, 6523–6543 (2005).
Bloch, H. & Segal, W. Biochemical differentiation of Mycobacterium tuberculosis grown in vivo and in vitro. J. Bacteriol. 72, 132–141 (1956).
Jain, M. et al. Lipidomics reveals control of Mycobacterium tuberculosis virulence lipids via metabolic coupling. Proc. Natl. Acad. Sci. USA 104, 5133–5138 (2007).
Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).
Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).
Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).
Evans, S.V. SETOR: hardware-lighted three-dimensional solid model representations of macromolecules. J. Mol. Graph. 11, 134–138 (1993).
Barton, G.J. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 6, 37–40 (1993).
Castro-Pichel, J. et al. Synthesis and antiviral activity of 5′-O-(substituted) sulfamoyl pyrimidine nucleosides. Arch. Pharm. (Weinheim) 322, 11–15 (1989).
Morrison, J.F. & Walsh, C.T. The behavior and significance of slow-binding enzyme inhibitors. Adv. Enzymol. 61, 201–301 (1988).
Phetsuksiri, B. et al. Antimycobacterial activities of isoxyl and new derivatives through the inhibition of mycolic acid synthesis. Antimicrob. Agents Chemother. 43, 1042–1051 (1999).
Camacho, L.R. et al. Analysis of the phthiocerol dimycocerosate locus of Mycobacterium tuberculosis. Evidence that this lipid is involved in the cell wall permeability barrier. J. Biol. Chem. 276, 19845–19854 (2001).
Cox, J.S., Chen, B., McNeil, M. & Jacobs, W.R. Jr. Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice. Nature 402, 79–83 (1999).
Acknowledgements
We thank L. Eltis (University of British Columbia) for Rhodococcus sp. RHA1 strain and S. Cole (Pasteur Research Institute, France) for the M. tuberculosis BAC genomic DNA library. P.A., A.G. and E.R. are Senior Research Fellows of the Council of Scientific and Industrial Research, India. R.S. is supported by a Wellcome Trust International Senior Research Fellowship in India. R.S.G. is supported by a Howard Hughes Medical Institute International Fellowship. This work is also partially supported by a Swarnajayanti Fellowship from the Department of Science and Technology of India and by a Centre of Excellence Grant from the Department of Biotechnology of India.
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P.A., A.G., V.T.N., R.S. and R.S.G. designed the experiments, analyzed the data and wrote the manuscript. E.R. and M.Y. participated in structural studies. P.V., R.G. and O.A.T. participated in biochemical and mechanistic studies. D.M. and A.T. provided valuable advice.
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Arora, P., Goyal, A., Natarajan, V. et al. Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat Chem Biol 5, 166–173 (2009). https://doi.org/10.1038/nchembio.143
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DOI: https://doi.org/10.1038/nchembio.143
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