MASS SPECTROMETRY-BASED APPROACHES TO CHARACTERIZE MYCOBACTERIUM TUBERCULOSIS

Main Article Content

Authors

S. Atavliyeva

National Center for Biotechnology, 13/5, Korgalzhyn road, Astana, 010000, Kazakhstan

P. Tarlykov

National Center for Biotechnology, 13/5, Korgalzhyn road, Astana, 010000, Kazakhstan

E. Zholdybayeva

National Center for Biotechnology, 13/5, Korgalzhyn road, Astana, 010000, Kazakhstan

Ye. Ramankulov

National Center for Biotechnology, 13/5, Korgalzhyn road, Astana, 010000, Kazakhstan

Abstract

Mass spectrometry has greatly contributed to the study and understanding of the pathogenesis of human tuberculosis. Current methods of mass spectrometry have been rapidly evolving over the past two decades in response to the limitations of early proteomic studies. Modern proteomic research includes protein secretion, activation, degradation, and modifications, since post-translational modifications are an additional step in the evolution of pathogenic mycobacteria that gain virulence. The other application of mass spectrometry is in epidemiological studies of mycobacteria, in particular, determining the genetic spoligotype based on matrix-assisted laser desorption/ionization. This review explores M. tuberculosis studies carried out by mass spectrometry, including proteomic profiling with the shotgun-based approach and targeted proteomics. In addition, the most important post-translational modifications studied by mass spectrometry are described.

Keywords

mass spectrometry, Mycobacterium tuberculosis, proteome, spoligotyping

Article Details

References

Otto A., Becher D., Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics, 2014, vol. 14, no. 4-5, pp. 547-565. doi:10.1002/pmic.201300403

World Health Organization. Global tuberculosis report 2017. Available at: URL (accessed at 9 September 2018).

Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C. et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 1998, vol. 393, pp. 537–544. doi: 10.1038/31159

Sassetti C., Rubin E.J. Genetic requirements for mycobacterial survival during infection. Proc. Natl. Acad. Sci. USA, 2004, vol. 100, pp. 12989–12994.

Calder B., Soares N.C., de Kock E., Blackburn J.M. Mycobacterial proteomics: analysis of expressed proteomes and post-translational modifications to identify candidate virulence factors. Expert Rev Proteomics, 2015, vol. 12, no. 1, pp. 21-35. doi:10.1586/14789450.2015.1007046

Banaei-Esfahani A., Nicod C., Aebersold R., Collins B.C. Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis. Curr Opin Microbiol., 2017, vol. 39, pp. 64-72. doi:10.1016/j.mib.2017.09.013

Aebersold R., Mann M. Mass-spectrometric exploration of proteome structure and function. Nature, 2016; vol. 537, pp. 347-355. doi:10.1038/nature19949

Kaufmann S.H.E., Aebersold R., Schubert O.T., Mouritsen J., Gengenbacher M. Mycobacterium tuberculosis in the Proteomics Era. Microbiol Spectr, 2014, vol. 2, pp. 1-19. doi:10.1128/microbiolspec.MGM2-0020-2013

Schmidt F., Donahoe S., Hagens K., Mattow J., Schaible U. E., Kaufmann S. H., Aebersold R., Jungblut P. R. Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol. Cell. Proteomics, 2004, vol. 3, no. 1, pp. 24–42.

Bell C., Smith G.T., Sweredoski M.J., 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., 2012, vol. 11, no. 1, pp. 119-130. doi:10.1021/pr2007939

Malen H., De Souza G., Pathak S, Softeland T., Wiker H.G. Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains. BMC Microbiol., 2011, vol. 11, no. 18, pp. 1-10.

Verma R., Pinto S.M., Patil A.H., et al. Quantitative Proteomic and Phosphoproteomic Analysis of H37Ra and H37Rv Strains of Mycobacterium tuberculosis. J Proteome Res., 2017, vol. 16, no. 4, pp. 1632-1645. doi:10.1021/acs.jproteome.6b00983

Mattow J., Schaible U.E., Schmidt F. et al. Comparative proteome analysis of culture supernatant proteins from virulent Mycobacterium tuberculosis H37Rv and attenuated M. bovis BCG Copenhagen. Electrophoresis, 2003, vol. 24, no. 19-20, pp. 3405-3420. doi:10.1002/elps.200305601

Tan T., Lee W.L., Alexander D.C., Grinstein S., Liu J. Cell Microbiol., 2006, vol. 8, no. 9, pp. 1417–1429.

Gunawardena H. P., Feltcher M. E., Wrobel J. A., Gu Sh., Braunstein M., Chen X. 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, vol. 12, no.12, pp. 5463–5474. doi:10.1021/pr400334k.

Schubert O.T., 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, vol. 13, no. 5, pp. 602-612. doi:10.1016/j.chom.2013.04.008

SRM Atlas. Available at: URL (accessed at 20 September 2018).

Picotti P., Bodenmiller B., Mueller L.N. et al. Full dynamic range proteome analysis of s. cerevisiae by targeted proteomics. Cell, 2009,vol. 138, pp. 795-806.

de Souza G.A., Wiker H.G. A proteomic view of mycobacteria. Proteomics, 2011, vol. 1, no. 15, pp. 3118-3127. doi:10.1002/pmic.201100043

Calder B., Albeldas C., Blackburn J.M., Soares N.C. Mass spectrometry offers insight into the role of ser/thr/tyr phosphorylation in the mycobacteria. Front Microbiol., 2016, vol. 7, no. 141, pp.1-8. doi:10.3389/fmicb.2016.00141

Nakedi K. C., Nel A. J., Garnett S., Blackburn J. M., Soares, N. C. Comparative Ser/Thr/Tyr phosphoproteomics between two mycobacterial species: the fast growing Mycobacterium smegmatis and the slow growing Mycobacterium bovis BCG. Front. Microbiol., 2015, vol. 6, no. 237, pp.1-12 doi: 10.3389/fmicb.2015.00237

Prisic S., Dankwa S., Schwartz D. et al. Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc Natl Acad Sci., 2010, ;vol. 07, no. 16, pp. 7521-7526. doi:10.1073/pnas.0913482107

Kusebauch U., Ortega C., Ollodart A., Rogers R. S., Sherman D. R., Moritz R. L. et al. Mycobacterium tuberculosis supports protein tyro- sine phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 2014, vol. 111, pp. 9265–9270. doi: 10.1073/pnas.1323894111

Ren J., Sang Y., Lu J., Yao Y.F. Protein Acetylation and Its Role in Bacterial Virulence. Trends Microbiol., 2017, vol. 25, no. 9, pp. 768-779. doi:10.1016/j.tim.2017.04.001

Okkels L.M., Müller E.C., Schmid M. et al. CFP10 discriminates between nonacetylated and acelylated ESAT-6 of Mycobacterium tuberculosis by differential interaction. Proteomics. 2004;4(10):2954-2960. doi:10.1002/pmic.200400906

Liu F., Yang M., Wang X. et al. Acetylome Analysis Reveals Diverse Functions of Lysine Acetylation in Mycobacterium tuberculosis. Mol Cell Proteomics, 2014, vol. 13, no. 12, pp. 3352-3366. doi:10.1074/mcp.M114.041962

Bi J., Wang Y., Yu H. et al. Modulation of Central Carbon Metabolism by Acetylation of Isocitrate Lyase in Mycobacterium tuberculosis. Sci Rep., 2017, vol. 7, pp. 1-11. doi:10.1038/srep44826

Yang H., Sha W., Liu Z. et al. Lysine acetylation of DosR regulates the hypoxia response of Mycobacterium tuberculosis article. Emerg Microbes Infect., 2018, vol. 7, no. 34, pp. 1-14. doi:10.1038/s41426-018-0032-2

Geoffrey T., Michael J., Sweredoski. O-linked glycosylation sites profiling in Mycobacterium tuberculosis culture filtrate proteins. J. Proteomics, 2014, vol. 97, pp. 296–306. doi:10.1016/j.jprot.2013.05.011.

González-Zamorano M., Hernández G.M., Xolalpa W. et al. Mycobacterium tuberculosis glycoproteomics based on ConA-lectin affinity capture of mannosylated proteins. J Proteome Res., 2009, vol. 8, no. 2, pp. 721-733. doi:10.1021/pr800756a

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., 2013, vol. 110, pp. 6560-6565.

Brudey K., Driscoll J. R., Rigouts L., Prodinger W. M., Gori A., Al-Hajoj S. A., Allix C. L.et al. Mycobacterium tuberculosis complex genetic diversity: mining the Fourth International Spoligotyping Database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 2006, vol. 6, no. 23, pp. 1-17.

Honisch C., Mosko M., Arnold C., Gharbia S.E., Diel R., Niemann S. Replacing reverse line blot hybridization spoligotyping of the Mycobacterium tuberculosis complex. J Clin Microbiol., 2010, vol.48, no. 5, pp.1520-1526. doi:10.1128/JCM.02299-09

Shitikov E., Ilina E., Chernousova L. et al. Mass spectrometry based methods for the discrimination and typing of mycobacteria. Infect. Genet. Evol., 2012, vol. 12, no. 4, pp. 838-845. doi:10.1016/j.meegid.2011.12.013