Mycobacterial proteomics: analysis of expressed proteomes and post-translational modifications to identify candidate virulence factors

References

• Phillips L. TB’s revenge. Nature 2013;493:14-16
   PubMed Web of Science ®Google Scholar
• De Souza GA, Wiker HG. A proteomic view of mycobacteria. Proteomics 2011;11:3118-27
   PubMedGoogle Scholar
• Wallis RS, Pai M, Menzies D, et al. Biomarkers and diagnostics for tuberculosis: progress, needs, and translation into practice. Lancet 2010;375:1920-37
   PubMed Web of Science ®Google Scholar
• Gordon SV, Bottai D, Simeone R, et al. Pathogenicity in the tubercle bacillus: molecular and evolutionary determinants. Bioessays 2009;31:378-88
   PubMedGoogle Scholar
• Karakousis PC, Bishai WR, Dorman SE. Mycobacterium tuberculosis cell envelope lipids and the host immune response. Cell Microbiol 2004;6:105-16
   PubMedGoogle Scholar
• McDonough K, Kress Y, Bloom B. Pathogenesis of tuberculosis: interaction of Mycobacterium tuberculosis with macrophages. Infect Immun 1993;61:2763-73
   PubMed Web of Science ®Google Scholar
• Cosma CL, Sherman DR, Ramakrishnan L. The secret lives of the pathogenic mycobacteria. Annu Rev Microbiol 2003;57:641-76
   PubMed Web of Science ®Google Scholar
• Casadevall A, Pirofski L. The damage-response framework of microbial pathogenesis. Nat Rev Microbiol 2003;1:17-24
   PubMed Web of Science ®Google Scholar
• Wu H-J, Wang AH, Jennings MP. Discovery of virulence factors of pathogenic bacteria. Curr Opin Chem Biol 2008;12:93-101
   PubMed Web of Science ®Google Scholar
• Pérez E, Samper S, Bordas Y, et al. An essential role for phoP in Mycobacterium tuberculosis virulence. Mol Microbiol 2001;41:179-87
   PubMed Web of Science ®Google Scholar
• Raghavan S, Manzanillo P, Chan K, et al. Secreted transcription factor controls Mycobacterium tuberculosis virulence. Nature 2008;454:717-21
   PubMed Web of Science ®Google Scholar
• Cole ST, Brosch R, Parkhill J, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998;393:537-44
   PubMed Web of Science ®Google Scholar
• Rickman L, Saldanha JW, Hunt DM, et al. A two-component signal transduction system with a PAS domain-containing sensor is required for virulence of Mycobacterium tuberculosis in mice. Biochem Biophys Res Commun 2004;314:259-67
   Google Scholar
• Manabe YC, Dannenberg AM, Tyagi SK, et al. Different strains of Mycobacterium tuberculosis cause various spectrums of disease in the rabbit model of tuberculosis. Infect Immun 2003;71:6004-11
   PubMed Web of Science ®Google Scholar
• Fleischmann R, Alland D, Eisen J, et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 2002;184:5479-90
   PubMed Web of Science ®Google Scholar
• Brosch R, Pym AS, Gordon SV, Cole ST. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol 2001;9:452-8
   PubMed Web of Science ®Google Scholar
• Sassetti CM, Rubin EJ. Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci USA 2003;100:12989-94
   PubMed Web of Science ®Google Scholar
• Smith I. Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence. Clin Microbiol Rev 2003;16:463-96
   PubMed Web of Science ®Google Scholar
• Bell C, Smith GT, Sweredoski MJ, Hess S. Characterization of the Mycobacterium tuberculosis proteome by liquid chromatography mass spectrometry-based proteomics techniques: a comprehensive resource for tuberculosis research. J Proteome Res 2011;11:119-30
   PubMedGoogle Scholar
• Coiras M, Camafeita E, López-Huertas MR, et al. Application of proteomics technology for analyzing the interactions between host cells and intracellular infectious agents. Proteomics 2008;8:852-73
   PubMed Web of Science ®Google Scholar
• Gunawardena HP, Feltcher ME, Wrobel JA, et al. Comparison of the membrane proteome of virulent Mycobacterium tuberculosis and the attenuated Mycobacterium bovis BCG vaccine strain by label-free quantitative proteomics. J Proteome Res 2013;12:5463-74
   PubMed Web of Science ®Google Scholar
• Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014;14:547-65
   PubMed Web of Science ®Google Scholar
• Cordwell SJ, Nouwens AS, Walsh BJ. Comparative proteomics of bacterial pathogens. Proteomics 2001;1:461-72
   PubMed Web of Science ®Google Scholar
• Görg A, Postel W, Günther S. Two-dimensional electrophoresis. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 1988;9:531-46
   PubMed Web of Science ®Google Scholar
• Görg A, Weiss W, Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004;4:3665-85
   PubMed Web of Science ®Google Scholar
• Singhal N, Sharma P, Kumar M, et al. Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates. Proteome Sci 2012;10:14
   PubMed Web of Science ®Google Scholar
• Tan T, Lee WL, Alexander DC, et al. The ESAT-6/CFP-10 secretion system of Mycobacterium marinum modulates phagosome maturation. Cell Microbiol 2006;8:1417-29
   PubMed Web of Science ®Google Scholar
• He X-Y, Zhuang Y-H, Zhang X-G, Li G-L. Comparative proteome analysis of culture supernatant proteins of Mycobacterium tuberculosis H37Rv and H37Ra. Microbes Infect 2003;5:851-6
   PubMed Web of Science ®Google Scholar
• Sonnenberg MG, Belisle JT. Definition of Mycobacterium tuberculosis culture filtrate proteins by two-dimensional polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and electrospray mass spectrometry. Infect Immun 1997;65:4515-24
   PubMed Web of Science ®Google Scholar
• Rosenkrands I, Weldingh K, Jacobsen S, et al. Mapping and identification of Mycobacterium tuberculosis proteins by two-dimensional gel electrophoresis, microsequencing and immunodetection. Electrophoresis 2000;21:935-48
   PubMed Web of Science ®Google Scholar
• Urquhart BL, Cordwell SJ, Humphery-Smith I. Comparison of predicted and observed properties of proteins encoded in the genome of Mycobacterium tuberculosis H37Rv. Biochem Biophys Res Commun 1998;253:70-9
   PubMedGoogle Scholar
• Jungblut P, Schaible U, Mollenkopf H-J, et al. Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. Mol Microbiol 1999;33:1103-17
   PubMed Web of Science ®Google Scholar
• Betts JC, Dodson P, Quan S, et al. Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology 2000;146:3205-16
   PubMedGoogle Scholar
• Monteoliva L, Albar JP. Differential proteomics: an overview of gel and non-gel based approaches. Brief Funct Genomic Proteomic 2004;3:220-39
   PubMedGoogle Scholar
• Pietrogrande MC, Marchetti N, Dondi F, Righetti PG. Spot overlapping in two-dimensional polyacrylamide gel electrophoresis maps: relevance to proteomics. Electrophoresis 2003;24:217-24
   PubMedGoogle Scholar
• Gu S, Chen J, Dobos KM, et al. Comprehensive proteomic profiling of the membrane constituents of a Mycobacterium tuberculosis strain. Mol Cell Proteomics 2003;2:1284-96
   PubMedGoogle Scholar
• Chapman JD, Goodlett DR, Masselon CD. Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev 2014;33:452-70
   PubMed Web of Science ®Google Scholar
• Thakur SS, Geiger T, Chatterjee B, et al. Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol Cell Proteomics 2011;10(8): M110.003699
   PubMed Web of Science ®Google Scholar
• Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009;6:359
   PubMed Web of Science ®Google Scholar
• Treumann A, Thiede B. Isobaric protein and peptide quantification: perspectives and issues. Expert Rev Proteomics 2010;7:647-53
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Gerber SA, et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999;17:994-9
   PubMed Web of Science ®Google Scholar
• Cho SH, Goodlett D, Franzblau S. ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis. Tuberculosis (Edinb) 2006;86:445-60
   PubMed Web of Science ®Google Scholar
• Ong S-E, Blagoev B, Kratchmarova I, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002;1:376-86
   PubMed Web of Science ®Google Scholar
• Wang H, Dong D, Tang S, et al. PPE38 of Mycobacterium marinum triggers the cross-talk of multiple pathways involved in the host response, as revealed by subcellular quantitative proteomics. J Proteome Res 2013;12:2055-66
   PubMed Web of Science ®Google Scholar
• Harding CV, Boom WH. Regulation of antigen presentation by Mycobacterium tuberculosis: a role for Toll-like receptors. Nat Rev Microbiol 2010;8:296-307
   PubMed Web of Science ®Google Scholar
• Chang ST, Linderman JJ, Kirschner DE. Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages. Proc Natl Acad Sci USA 2005;102:4530-5
   PubMed Web of Science ®Google Scholar
• Shui W, Gilmore SA, Sheu L, et al. Quantitative proteomic profiling of host- pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J Proteome Res 2008;8:282-9
   Google Scholar
• Geiger T, Cox J, Ostasiewicz P, et al. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 2010;7:383-5
   PubMed Web of Science ®Google Scholar
• Ong S-E, Mann M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc 2007;1:2650-60
   Web of Science ®Google Scholar
• Wiese S, Reidegeld KA, Meyer HE, Warscheid B. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 2007;7:340-50
   PubMed Web of Science ®Google Scholar
• Christoforou AL, Lilley KS. Isobaric tagging approaches in quantitative proteomics: the ups and downs. Anal Bioanal Chem 2012;404:1029-37
   PubMed Web of Science ®Google Scholar
• Werner T, Sweetman G, Savitski MF, et al. Ion coalescence of neutron encoded TMT 10-plex reporter ions. Anal Chem 2014;86:3594-601
   PubMed Web of Science ®Google Scholar
• Unwin RD, Griffiths JR, Whetton AD. Simultaneous analysis of relative protein expression levels across multiple samples using iTRAQ isobaric tags with 2D nano LC-MS/MS. Nat Protoc 2010;5:1574-82
   PubMed Web of Science ®Google Scholar
• Roe MR, Griffin TJ. Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes. Proteomics 2006;6:4678-87
   PubMed Web of Science ®Google Scholar
• Mehaffy C, Hess A, Prenni JE, et al. Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis. Proteomics 2010;10:1966-84
   PubMed Web of Science ®Google Scholar
• Evans C, Noirel J, Ow SY, et al. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012;404:1011-27
   PubMed Web of Science ®Google Scholar
• Altelaar A, Frese CK, Preisinger C, et al. Benchmarking stable isotope labeling based quantitative proteomics. J Proteomics 2013;88:14-26
   PubMed Web of Science ®Google Scholar
• Zhu W, Smith JW, Huang C-M. Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol 2010:1-6
   Google Scholar
• Kovanich D, Cappadona S, Raijmakers R, et al. Applications of stable isotope dimethyl labeling in quantitative proteomics. Anal Bioanal Chem 2012;404:991-1009
   PubMedGoogle Scholar
• Hsu J-L, Huang S-Y, Chow N-H, Chen S-H. Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 2003;75:6843-52
   PubMed Web of Science ®Google Scholar
• Van Oudenhove L, Devreese B. A review on recent developments in mass spectrometry instrumentation and quantitative tools advancing bacterial proteomics. Appl Microbiol Biotechnol 2013;97:4749-62
   PubMed Web of Science ®Google Scholar
• Chopra T, Hamelin R, Armand F, et al. Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis. Mol Cell Proteomics 2014;3:3014-28
   Google Scholar
• Meissner F, Mann M. Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology. Nat Immunol 2014;15:112-17
   PubMed Web of Science ®Google Scholar
• Mueller LN, Brusniak M-Y, Mani D, Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 2008;7:51-61
   PubMed Web of Science ®Google Scholar
• Albrethsen J, Agner J, Piersma SR, et al. Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems. Mol Cell Proteomics 2013;12:1180-91
   PubMed Web of Science ®Google Scholar
• Sala A, Bordes P, Genevaux P. Multiple toxin-antitoxin systems in Mycobacterium tuberculosis. Toxins (Basel) 2014;6:1002-20
   PubMedGoogle Scholar
• De Souza GA, Fortuin S, Aguilar D, et al. Using a label-free proteomics method to identify differentially abundant proteins in closely related hypo-and hypervirulent clinical Mycobacterium tuberculosis Beijing isolates. Mol Cell Proteomics 2010;9:2414-23
   PubMed Web of Science ®Google Scholar
• Målen H, De Souza GA, Pathak S, et al. Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains. BMC Microbiol 2011;11:18
   PubMed Web of Science ®Google Scholar
• Kelkar DS, Kumar D, Kumar P, et al. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics 2011;10(12): M111.011627
   PubMed Web of Science ®Google Scholar
• Schubert OT, Mouritsen J, Ludwig C, et al. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host Microbe 2013;13:602-12
   PubMed Web of Science ®Google Scholar
• Kendall SL, Withers M, Soffair CN, et al. A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Mol Microbiol 2007;65:684-99
   PubMed Web of Science ®Google Scholar
• Lee W, VanderVen BC, Fahey RJ, Russell DG. Intracellular Mycobacterium tuberculosis exploits host-derived fatty acids to limit metabolic stress. J Biol Chem 2013;288:6788-800
   PubMed Web of Science ®Google Scholar
• McKinney JD, zu Bentrup KH, Muñoz-Elías EJ, et al. Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 2000;406:735-8
   PubMed Web of Science ®Google Scholar
• Stahl-Zeng J, Lange V, Ossola R, et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 2007;6:1809-17
   PubMed Web of Science ®Google Scholar
• Domon B, Aebersold R. Challenges and opportunities in proteomics data analysis. Mol Cell Proteomics 2006;5:1921-6
   PubMed Web of Science ®Google Scholar
• Ernoult E, Bourreau A, Gamelin E, Guette C. A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation. J Biomed Biotechnol 2010:1-9
   Google Scholar
• Makarov A, Denisov E, Lange O, Horning S. Dynamic range of mass accuracy in LTQ Orbitrap hybrid mass spectrometer. J Am Soc Mass Spectrom 2006;17:977-82
   PubMed Web of Science ®Google Scholar
• De Godoy LM, Olsen JV, de Souza GA, et al. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol 2006;7:R50
   PubMed Web of Science ®Google Scholar
• Doerks T, Van Noort V, Minguez P, Bork P. Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. PLoS One 2012;7:e34302
   Google Scholar
• Lange V, Malmström JA, Didion J, et al. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics 2008;7:1489-500
   PubMed Web of Science ®Google Scholar
• Mehaffy MC, Kruh-Garcia NA, Dobos KM. Prospective on Mycobacterium tuberculosis proteomics. J Proteome Res 2011;11:17-25
   PubMedGoogle Scholar
• Picotti P, Bodenmiller B, Mueller LN, et al. Full dynamic range proteome analysis of s. cerevisiae by targeted proteomics. Cell 2009;138:795-806
   PubMed Web of Science ®Google Scholar
• Sinha S, Kosalai K, Arora S, et al. Immunogenic membrane-associated proteins of Mycobacterium tuberculosis revealed by proteomics. Microbiology 2005;151:2411-19
   PubMed Web of Science ®Google Scholar
• Sampson SL. Mycobacterial PE/PPE proteins at the host-pathogen interface. Clin Dev Immunol 2011;2011:497203
   PubMedGoogle Scholar
• Kruh NA, Troudt J, Izzo A, et al. Portrait of a pathogen: the Mycobacterium tuberculosis proteome in vivo. PLoS One 2010;5:e13938
   PubMed Web of Science ®Google Scholar
• Cash P. Investigating pathogen biology at the level of the proteome. Proteomics 2011;11:3190-202
   PubMed Web of Science ®Google Scholar
• Becker D, Selbach M, Rollenhagen C, et al. Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 2006;440:303-7
   PubMed Web of Science ®Google Scholar
• Mann M, Jensen ON. Proteomic analysis of post-translational modifications. Nat Biotechnol 2003;21:255-61
   PubMed Web of Science ®Google Scholar
• Olsen JV, Mann M. Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics 2013;12:3444-52
   PubMed Web of Science ®Google Scholar
• Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. Mass Spectrom Rev 2014. [Epub ahead of print]
   PubMedGoogle Scholar
• Nørregaard Jensen O. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol 2004;8:33-41
   PubMedGoogle Scholar
• Soufi B, Soares NC, Ravikumar V, Macek B. Proteomics reveals evidence of cross-talk between protein modifications in bacteria: focus on acetylation and phosphorylation. Curr Opin Microbiol 2012;15:357-63
   PubMed Web of Science ®Google Scholar
• Cain JA, Solis N, Cordwell SJ. Beyond gene expression: the impact of protein post-translational modifications in bacteria. J Proteomics 2014;97:265-86
   PubMed Web of Science ®Google Scholar
• Whitmore SE, Lamont RJ. Tyrosine phosphorylation and bacterial virulence. Int J Oral Sci 2012;4:1-6
   PubMedGoogle Scholar
• Graham RL, Hess S. Mass spectrometry in the elucidation of the glycoproteome of bacterial pathogens. Curr Proteomics 2010;7:57-81
   Web of Science ®Google Scholar
• Liu C-F, Tonini L, Malaga W, et al. Bacterial protein-O-mannosylating enzyme is crucial for virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2013;110:6560-5
   PubMed Web of Science ®Google Scholar
• Smith GT, Sweredoski MJ, Hess S. O-linked glycosylation sites profiling in Mycobacterium tuberculosis culture filtrate proteins. J Proteomics 2014;97:296-306
   PubMed Web of Science ®Google Scholar
• González-Zamorano M, Mendoza-Hernández G, Xolalpa W, et al. Mycobacterium tuberculosis glycoproteomics based on ConA-lectin affinity capture of mannosylated proteins. J Proteome Res 2009;8:721-33
   Google Scholar
• Prisic S, Dankwa S, Schwartz D, et al. Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc Natl Acad Sci USA 2010;107:7521-6
   PubMed Web of Science ®Google Scholar
• Macek B, Mann M, Olsen JV. Global and site-specific quantitative phosphoproteomics: principles and applications. Annu Rev Pharmacol Toxicol 2009;49:199-221
   PubMed Web of Science ®Google Scholar
• Jers C, Soufi B, Grangeasse C, et al. Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks. Expert Rev Proteomics 2008;5:619-27
   PubMed Web of Science ®Google Scholar
• Voisin S, Watson DC, Tessier L, et al. The cytoplasmic phosphoproteome of the Gram-negative bacterium Campylobacter jejuni: evidence for modification by unidentified protein kinases. Proteomics 2007;7:4338-48
   PubMedGoogle Scholar
• Kobir A, Shi L, Boskovic A, et al. Protein phosphorylation in bacterial signal transduction. Biochim Biophys Acta 2011;1810:989-94
   PubMed Web of Science ®Google Scholar
• Cozzone AJ. Role of protein phosphorylation on serine/threonine and tyrosine in the virulence of bacterial pathogens. J Mol Microbiol Biotechnol 2006;9:198-213
   Google Scholar
• Wehenkel A, Bellinzoni M, Graña M, et al. Mycobacterial Ser/Thr protein kinases and phosphatases: physiological roles and therapeutic potential. Biochim Biophys Acta 2008;1784:193-202
   PubMed Web of Science ®Google Scholar
• Sassetti CM, Boyd DH, Rubin EJ. Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 2003;48:77-84
   PubMed Web of Science ®Google Scholar
• Walburger A, Koul A, Ferrari G, et al. Protein kinase G from pathogenic mycobacteria promotes survival within macrophages. Science 2004;304:1800-4
   PubMed Web of Science ®Google Scholar
• Parandhaman DK, Sharma P, Bisht D, Narayanan S. Proteome and phosphoproteome analysis of the serine/threonine protein kinase E mutant of Mycobacterium tuberculosis. Life Sci 2014;109:116-26
   PubMedGoogle Scholar
• Chao JD, Papavinasasundaram KG, Zheng X, et al. Convergence of Ser/Thr and two-component signaling to coordinate expression of the dormancy regulon in Mycobacterium tuberculosis. J Biol Chem 2010;285:29239-46
   PubMedGoogle Scholar
• Ortega C, Liao R, Anderson LN, et al. Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch. PLoS Biol 2014;12:e1001746
   PubMed Web of Science ®Google Scholar
• Chao J, Wong D, Zheng X, et al. Protein kinase and phosphatase signaling in Mycobacterium tuberculosis physiology and pathogenesis. Biochim Biophys Act 2010;1804:620-7
   PubMedGoogle Scholar
• Macek B, Mijakovic I, Olsen JV, et al. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics 2007;6:697-707
   PubMed Web of Science ®Google Scholar
• Macek B, Gnad F, Soufi B, et al. Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol Cell Proteomics 2008;7:299-307
   PubMed Web of Science ®Google Scholar
• Kusebauch U, Ortega C, Ollodart A, et al. Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proc Natl Acad Sci USA 2014;111:9265-70
   PubMed Web of Science ®Google Scholar
• Hayden JD, Brown LR, Gunawardena HP, et al. Reversible acetylation regulates acetate and propionate metabolism in Mycobacterium smegmatis. Microbiology 2013;159:1986-99
   PubMed Web of Science ®Google Scholar
• Eisenreich W, Dandekar T, Heesemann J, Goebel W. Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nat Rev Microbiol 2010;8:401-12
   PubMed Web of Science ®Google Scholar
• Liu F, Yang M, Wang X, et al. Acetylome analysis reveals diverse functions of lysine acetylation in Mycobacterium tuberculosis. Mol Cell Proteomics 2014;13(12):3352-66
   PubMedGoogle Scholar
• Armengaud J. A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr Opin Microbiol 2009;12:292-300
   PubMed Web of Science ®Google Scholar
• Swanepoel CC, Loots DT. The use of functional genomics in conjunction with metabolomics for Mycobacterium tuberculosis research. Dis Markers 2014;2014:124218
   PubMedGoogle Scholar
• Meissner-Roloff RJ, Koekemoer G, Warren RM, et al. A metabolomics investigation of a hyper-and hypo-virulent phenotype of Beijing lineage M. tuberculosis. Metabolomics 2012;8:1194-203
   Web of Science ®Google Scholar
• Sun X, Ge F, Xiao C-L, et al. Phosphoproteomic analysis reveals the multiple roles of phosphorylation in pathogenic bacterium Streptococcus pneumoniae. J Proteome Res 2009;9:275-82
   Web of Science ®Google Scholar
• Misra SK, Milohanic E, Aké F, et al. Analysis of the serine/threonine/tyrosine phosphoproteome of the pathogenic bacterium Listeria monocytogenes reveals phosphorylated proteins related to virulence. Proteomics 2011;11:4155-65
   PubMed Web of Science ®Google Scholar