1887

Abstract

Carbon metabolic pathways are important to the pathogenesis of , the causative agent of tuberculosis. However, extremely little is known about metabolic regulation in mycobacteria. There is growing evidence for lysine acetylation being a mechanism of regulating bacterial metabolism. Lysine acetylation is a post-translational modification in which an acetyl group is covalently attached to the side chain of a lysine residue. This modification is mediated by acetyltransferases, which add acetyl groups, and deacetylases, which remove the acetyl groups. Here we set out to test whether lysine acetylation and deacetylation impact acetate metabolism in the model mycobacteria , which possesses 25 candidate acetyltransferases and 3 putative lysine deacetylases. Using mutants lacking predicted acetyltransferases and deacetylases we showed that acetate metabolism in is regulated by reversible acetylation of acetyl-CoA synthetase (Ms-Acs) through the action of a single pair of enzymes: the acetyltransferase Ms-PatA and the sirtuin deacetylase Ms-SrtN. We also confirmed that the role of Ms-PatA in regulating Ms-Acs regulation depends on cAMP binding. We additionally demonstrated a role for Ms-Acs, Ms-PatA and Ms-SrtN in regulating the metabolism of propionate in . Finally, along with Ms-Acs, we identified a candidate propionyl-CoA synthetase, Ms5404, as acetylated in whole-cell lysates. This work lays the foundation for studying the regulatory circuit of acetylation and deacetylation in the cellular context of mycobacteria.

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2013-09-01
2024-12-02
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References

  1. Bai G., Knapp G. S., McDonough K. A. ( 2011). Cyclic AMP signalling in mycobacteria: redirecting the conversation with a common currency. Cell Microbiol 13:349–358 [View Article][PubMed]
    [Google Scholar]
  2. Bantscheff M., Lemeer S., Savitski M. M., Kuster B. ( 2012). Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 404:939–965 [View Article][PubMed]
    [Google Scholar]
  3. Barak R., Welch M., Yanovsky A., Oosawa K., Eisenbach M. ( 1992). Acetyladenylate or its derivative acetylates the chemotaxis protein CheY in vitro and increases its activity at the flagellar switch. Biochemistry 31:10099–10107 [View Article][PubMed]
    [Google Scholar]
  4. Barak R., Prasad K., Shainskaya A., Wolfe A. J., Eisenbach M. ( 2004). Acetylation of the chemotaxis response regulator CheY by acetyl-CoA synthetase purified from Escherichia coli. . J Mol Biol 342:383–401 [View Article][PubMed]
    [Google Scholar]
  5. Bondarenko P. V., Chelius D., Shaler T. A. ( 2002). Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 74:4741–4749 [View Article][PubMed]
    [Google Scholar]
  6. Castaño-Cerezo S., Bernal V., Blanco-Catalá J., Iborra J. L., Cánovas M. ( 2011). cAMP-CRP co-ordinates the expression of the protein acetylation pathway with central metabolism in Escherichia coli. . Mol Microbiol 82:1110–1128 [View Article][PubMed]
    [Google Scholar]
  7. Chelius D., Bondarenko P. V. ( 2002). Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 1:317–323 [View Article][PubMed]
    [Google Scholar]
  8. Collins M. O., Yu L., Choudhary J. S. ( 2008; ).. Analysis protein complexes by 1D-SDS-PAGE and tandem mass spectrometry. http://www.nature.com/protocolexchange/protocols/455
  9. Cox J., Mann M. ( 2011). Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem 80:273–299 [View Article][PubMed]
    [Google Scholar]
  10. Cox J., Neuhauser N., Michalski A., Scheltema R. A., Olsen J. V., Mann M. ( 2011). Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10:1794–1805 [View Article][PubMed]
    [Google Scholar]
  11. Crosby H. A., Heiniger E. K., Harwood C. S., Escalante-Semerena J. C. ( 2010). Reversible N epsilon-lysine acetylation regulates the activity of acyl-CoA synthetases involved in anaerobic benzoate catabolism in Rhodopseudomonas palustris. . Mol Microbiol 76:874–888 [View Article][PubMed]
    [Google Scholar]
  12. Datta P., Shi L., Bibi N., Balázsi G., Gennaro M. L. ( 2011). Regulation of central metabolism genes of Mycobacterium tuberculosis by parallel feed-forward loops controlled by sigma factor E (σE). J Bacteriol 193:1154–1160 [View Article][PubMed]
    [Google Scholar]
  13. Eisenreich W., Dandekar T., Heesemann J., Goebel W. ( 2010). Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nat Rev Microbiol 8:401–412 [View Article][PubMed]
    [Google Scholar]
  14. Gardner J. G., Escalante-Semerena J. C. ( 2009). In Bacillus subtilis, the sirtuin protein deacetylase, encoded by the srtN gene (formerly yhdZ), and functions encoded by the acuABC genes control the activity of acetyl coenzyme A synthetase. J Bacteriol 191:1749–1755 [View Article][PubMed]
    [Google Scholar]
  15. Gardner J. G., Grundy F. J., Henkin T. M., Escalante-Semerena J. C. ( 2006). Control of acetyl-coenzyme A synthetase (AcsA) activity by acetylation/deacetylation without NAD(+) involvement in Bacillus subtilis. . J Bacteriol 188:5460–5468 [View Article][PubMed]
    [Google Scholar]
  16. Garrity J., Gardner J. G., Hawse W., Wolberger C., Escalante-Semerena J. C. ( 2007). N-lysine propionylation controls the activity of propionyl-CoA synthetase. J Biol Chem 282:30239–30245 [View Article][PubMed]
    [Google Scholar]
  17. Gillespie J. J., Wattam A. R., Cammer S. A., Gabbard J. L., Shukla M. P., Dalay O., Driscoll T., Hix D., Mane S. P. & other authors ( 2011). PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 79:4286–4298 [View Article][PubMed]
    [Google Scholar]
  18. Glickman M. S., Cox J. S., Jacobs W. R. Jr ( 2000). A novel mycolic acid cyclopropane synthetase is required for cording, persistence, and virulence of Mycobacterium tuberculosis. . Mol Cell 5:717–727 [View Article][PubMed]
    [Google Scholar]
  19. Gu J., Deng J. Y., Li R., Wei H., Zhang Z., Zhou Y., Zhang Y., Zhang X. E. ( 2009). Cloning and characterization of NAD-dependent protein deacetylase (Rv1151c) from Mycobacterium tuberculosis. . Biochemistry (Mosc) 74:743–748 [View Article][PubMed]
    [Google Scholar]
  20. Gunawardena H. P., Huang Y., Kenjale R., Wang H., Xie L., Chen X. ( 2011). Unambiguous characterization of site-specific phosphorylation of leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) in Toll-like receptor 4 (TLR4)-mediated signaling. J Biol Chem 286:10897–10910 [View Article][PubMed]
    [Google Scholar]
  21. Horswill A. R., Escalante-Semerena J. C. ( 1999). The prpE gene of Salmonella typhimurium LT2 encodes propionyl-CoA synthetase. Microbiology 145:1381–1388 [View Article][PubMed]
    [Google Scholar]
  22. Kim D., Yu B. J., Kim J. A., Lee Y. J., Choi S. G., Kang S., Pan J. G. ( 2013). The acetylproteome of Gram-positive model bacterium Bacillus subtilis . Proteomics 13:1726–1736 [View Article][PubMed]
    [Google Scholar]
  23. Kumari S., Tishel R., Eisenbach M., Wolfe A. J. ( 1995). Cloning, characterization, and functional expression of acs, the gene which encodes acetyl coenzyme A synthetase in Escherichia coli. . J Bacteriol 177:2878–2886[PubMed]
    [Google Scholar]
  24. Lee H. J., Lang P. T., Fortune S. M., Sassetti C. M., Alber T. ( 2012). Cyclic AMP regulation of protein lysine acetylation in Mycobacterium tuberculosis. . Nat Struct Mol Biol 19:811–818 [View Article][PubMed]
    [Google Scholar]
  25. Li R., Gu J., Chen P., Zhang Z., Deng J., Zhang X. ( 2011a). Purification and characterization of the acetyl-CoA synthetase from Mycobacterium tuberculosis. . Acta Biochim Biophys Sin (Shanghai) 43:891–899 [View Article][PubMed]
    [Google Scholar]
  26. Li Z., Wen J., Lin Y., Wang S., Xue P., Zhang Z., Zhou Y., Wang X., Sui L. & other authors ( 2011b). A Sir2-like protein participates in mycobacterial NHEJ. PLoS ONE 6:e20045 [View Article][PubMed]
    [Google Scholar]
  27. Lima B. P., Antelmann H., Gronau K., Chi B. K., Becher D., Brinsmade S. R., Wolfe A. J. ( 2011). Involvement of protein acetylation in glucose-induced transcription of a stress-responsive promoter. Mol Microbiol 81:1190–1204 [View Article][PubMed]
    [Google Scholar]
  28. Lima B. P., Thanh Huyen T. T., Bäsell K., Becher D., Antelmann H., Wolfe A. J. ( 2012). Inhibition of acetyl phosphate-dependent transcription by an acetylatable lysine on RNA polymerase. J Biol Chem 287:32147–32160 [View Article][PubMed]
    [Google Scholar]
  29. Marrero J., Rhee K. Y., Schnappinger D., Pethe K., Ehrt S. ( 2010). Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection. Proc Natl Acad Sci U S A 107:9819–9824 [View Article][PubMed]
    [Google Scholar]
  30. McKinney J. D., Höner zu Bentrup K., Muñoz-Elías E. J., Miczak A., Chen B., Chan W. T., Swenson D., Sacchettini J. C., Jacobs W. R. Jr, Russell D. G. ( 2000). Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 406:735–738 [View Article][PubMed]
    [Google Scholar]
  31. McNerney R., Kiepiela P., Bishop K. S., Nye P. M., Stoker N. G. ( 2000). Rapid screening of Mycobacterium tuberculosis for susceptibility to rifampicin and streptomycin. Int J Tuberc Lung Dis 4:69–75[PubMed]
    [Google Scholar]
  32. Muñoz-Elías E. J., McKinney J. D. ( 2005). Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence. Nat Med 11:638–644 [View Article][PubMed]
    [Google Scholar]
  33. Muñoz-Elías E. J., McKinney J. D. ( 2006). Carbon metabolism of intracellular bacteria. Cell Microbiol 8:10–22 [View Article][PubMed]
    [Google Scholar]
  34. Nambi S., Basu N., Visweswariah S. S. ( 2010). cAMP-regulated protein lysine acetylases in mycobacteria. J Biol Chem 285:24313–24323 [View Article][PubMed]
    [Google Scholar]
  35. Nambi S., Gupta K., Bhattacharyya M., Ramakrishnan P., Ravikumar V., Siddiqui N., Thomas A. T., Visweswariah S. S. ( 2013). Cyclic AMP-dependent protein lysine acylation in mycobacteria regulates fatty acid and propionate metabolism. J Biol Chem 288:14114–14124 [View Article][PubMed]
    [Google Scholar]
  36. Ramakrishnan R., Schuster M., Bourret R. B. ( 1998). Acetylation at Lys-92 enhances signaling by the chemotaxis response regulator protein CheY. Proc Natl Acad Sci U S A 95:4918–4923 [View Article][PubMed]
    [Google Scholar]
  37. Rhee K. Y., de Carvalho L. P. S., Bryk R., Ehrt S., Marrero J., Park S. W., Schnappinger D., Venugopal A., Nathan C. ( 2011). Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier. Trends Microbiol 19:307–314 [View Article][PubMed]
    [Google Scholar]
  38. Schnappinger D., Ehrt S., Voskuil M. I., Liu Y., Mangan J. A., Monahan I. M., Dolganov G., Efron B., Butcher P. D. & other authors ( 2003). Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J Exp Med 198:693–704 [View Article][PubMed]
    [Google Scholar]
  39. Singh A., Mai D., Kumar A., Steyn A. J. ( 2006). Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc Natl Acad Sci U S A 103:11346–11351 [View Article][PubMed]
    [Google Scholar]
  40. Snapper S. B., Melton R. E., Mustafa S., Kieser T., Jacobs W. R. Jr ( 1990). Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. . Mol Microbiol 4:1911–1919 [View Article][PubMed]
    [Google Scholar]
  41. Starai V. J., Escalante-Semerena J. C. ( 2004). Identification of the protein acetyltransferase (Pat) enzyme that acetylates acetyl-CoA synthetase in Salmonella enterica. . J Mol Biol 340:1005–1012 [View Article][PubMed]
    [Google Scholar]
  42. Starai V. J., Celic I., Cole R. N., Boeke J. D., Escalante-Semerena J. C. ( 2002). Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science 298:2390–2392 [View Article][PubMed]
    [Google Scholar]
  43. Starai V. J., Takahashi H., Boeke J. D., Escalante-Semerena J. C. ( 2003). Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae. . Genetics 163:545–555[PubMed]
    [Google Scholar]
  44. Stover C. K., de la Cruz V. F., Fuerst T. R., Burlein J. E., Benson L. A., Bennett L. T., Bansal G. P., Young J. F., Lee M. H. & other authors ( 1991). New use of BCG for recombinant vaccines. Nature 351:456–460 [View Article][PubMed]
    [Google Scholar]
  45. Thao S., Chen C. S., Zhu H., Escalante-Semerena J. C. ( 2010). Nϵ-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. PLoS ONE 5:e15123 [View Article][PubMed]
    [Google Scholar]
  46. Timm J., Post F. A., Bekker L. G., Walther G. B., Wainwright H. C., Manganelli R., Chan W. T., Tsenova L., Gold B. & other authors ( 2003). Differential expression of iron-, carbon-, and oxygen-responsive mycobacterial genes in the lungs of chronically infected mice and tuberculosis patients. Proc Natl Acad Sci U S A 100:14321–14326 [View Article][PubMed]
    [Google Scholar]
  47. UniProt Consortium ( 2012). Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40:Database issueD71–D75 [View Article][PubMed]
    [Google Scholar]
  48. Upton A. M., McKinney J. D. ( 2007). Role of the methylcitrate cycle in propionate metabolism and detoxification in Mycobacterium smegmatis. . Microbiology 153:3973–3982 [View Article][PubMed]
    [Google Scholar]
  49. van Kessel J. C., Hatfull G. F. ( 2008). Mycobacterial recombineering. Methods Mol Biol 435:203–215 [View Article][PubMed]
    [Google Scholar]
  50. van Kessel J. C., Marinelli L. J., Hatfull G. F. ( 2008). Recombineering mycobacteria and their phages. Nat Rev Microbiol 6:851–857 [View Article][PubMed]
    [Google Scholar]
  51. Wang Q., Zhang Y., Yang C., Xiong H., Lin Y., Yao J., Li H., Xie L., Zhao W. & other authors ( 2010). Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327:1004–1007 [View Article][PubMed]
    [Google Scholar]
  52. WHO( 2013). Tuberculosis; fact sheet no. 104. http://www.who.int/mediacentre/factsheets/fs104/en#global Geneva: World Health Organization;
    [Google Scholar]
  53. Wu X., Vellaichamy A., Wang D., Zamdborg L., Kelleher N. L., Huber S. C., Zhao Y. ( 2013). Differential lysine acetylation profiles of Erwinia amylovora strains revealed by proteomics. J Proteomics 79:60–71 [View Article][PubMed]
    [Google Scholar]
  54. Xu H., Hegde S. S., Blanchard J. S. ( 2011). Reversible acetylation and inactivation of Mycobacterium tuberculosis acetyl-CoA synthetase is dependent on cAMP. Biochemistry 50:5883–5892 [View Article][PubMed]
    [Google Scholar]
  55. Yan J., Barak R., Liarzi O., Shainskaya A., Eisenbach M. ( 2008). In vivo acetylation of CheY, a response regulator in chemotaxis of Escherichia coli. . J Mol Biol 376:1260–1271 [View Article][PubMed]
    [Google Scholar]
  56. Yu B. J., Kim J. A., Moon J. H., Ryu S. E., Pan J. G. ( 2008). The diversity of lysine-acetylated proteins in Escherichia coli. . J Microbiol Biotechnol 18:1529–1536[PubMed]
    [Google Scholar]
  57. Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C. F., Grishin N. V., Zhao Y. ( 2009). Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. . Mol Cell Proteomics 8:215–225[PubMed] [CrossRef]
    [Google Scholar]
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