Advertisement

Metabolomics

, Volume 8, Issue 6, pp 1194–1203 | Cite as

A metabolomics investigation of a hyper- and hypo-virulent phenotype of Beijing lineage M. tuberculosis

  • Reinart J. Meissner-Roloff
  • Gerhard Koekemoer
  • Robert M. Warren
  • Du Toit LootsEmail author
Original Article

Abstract

Despite a number investigations using rapid sequencing and comparative genomic techniques, attempting to characterise the phenomenon of varying degrees of virulence within the Mycobacterium tuberculosis species, the underlying causes for this still remain largely unexplained. The Beijing lineage of M. tuberculosis has received much attention due to a reported increased pathogenicity and global dissemination. In order to better understand these varying states of virulence, a GCxGC-TOFMS metabolomics research approach was used to compare the varying metabolomes of a hyper- and hypo-virulent Beijing strain of M. tuberculosis, and subsequently identify those metabolite markers differing between these strains. Multi- and univariate statistical analysis of the analysed metabolome data was used to identify those metabolites contributing most to the differences seen between the two sample groups. A general decrease in various carbohydrates, amino acids and lipids associated with cell wall structure and function, were detected in the hyper-virulent Beijing strain, comparatively. Additionally, components of mycothiol metabolism, virulence protein formation and energy production in mycobacteria, were also seen to differ when comparing the two groups. This metabolomics investigation is the first to identify the metabolite markers associated with an increased state of virulence, indicating increased metabolic activity, increased growth/replication rates, increased cell wall synthesis and an altered antioxidant mechanism, all of which would contribute to this organisms increased pathogenicity and survival ability.

Keywords

Beijing M. tuberculosis Metabolomics Hyper- and hypo-virulence 

Supplementary material

11306_2012_424_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOC 15 kb)
11306_2012_424_MOESM2_ESM.csv (60 kb)
Supplementary material 2 (CSV 61 kb)
11306_2012_424_MOESM3_ESM.csv (169 kb)
Supplementary material 3 (CSV 170 kb)

References

  1. Acharya, P. V., & Goldman, D. S. (1970). Chemical composition of the cell wall of the H37Ra strain of Mycobacterium tuberculosis. Journal of Bacteriology, 102(3), 733–739.PubMedGoogle Scholar
  2. Aguilar, D., Hanekom, M., Mata, D., Gey van Pittius, N. C., van Helden, P. D., Warren, R., et al. (2009). Mycobacterium tuberculosis strains with the Beijing genotype demonstrate variability in virulence associated with transmission. Tuberculosis, 90(5), 319–325.CrossRefGoogle Scholar
  3. Bifani, P. J., Mathema, B., Kurepina, N. E., & Kreiswirth, B. N. (2002). Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends in Microbiology, 10, 45–52.PubMedCrossRefGoogle Scholar
  4. Brennan, P. J. (2003). Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis. Tuberculosis, 83, 91–97.PubMedCrossRefGoogle Scholar
  5. Brennan, P. J., & Nikaido, H. (1995). The envelope of mycobacteria. Annual Review of Biochemistry, 64, 29–63.PubMedCrossRefGoogle Scholar
  6. Bryk, R., Lima, C. D., Erdjument-Bromage, H., Tempst, P., & Nathan, C. (2002). Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein. Science, 295, 1073–1077.PubMedCrossRefGoogle Scholar
  7. Buchrieser, C., & Cole, S. T. (2009). From functional genomics to systems (micro)biology. Current Opinions in Microbiology, 12(5), 528–530.CrossRefGoogle Scholar
  8. Chatterjee, D. (1997). The mycobacterial cell wall: Structure, biosynthesis and sites of drug action. Current Opinion in Chemical Biology, 1(4), 579–588.PubMedCrossRefGoogle Scholar
  9. Chatterjee, D., & Khoo, K. H. (1998). Mycobacterial lipoarabinomannan: An extraordinary lipoheteroglycan with profound physiological effects. Glycobiology, 8(2), 113–120.PubMedCrossRefGoogle Scholar
  10. Chen, I. W., & Charalampous, C. F. (1966). Biochemical studies on inositol. IX. D-Inositol 1-phosphate as intermediate in the biosynthesis of inositol from glucose 6-phosphate, and characteristics of two reactions in this biosynthesis. Journal of Biological Chemistry, 241(10), 2194–2199.PubMedGoogle Scholar
  11. Coates, A., Hu, Y., Bax, R., & Page, C. (2002). The future challenges facing the development of new antimicrobial drugs. Nature Reviews Drug Discovery, 1(11), 895–910.PubMedCrossRefGoogle Scholar
  12. Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Chucher, C., Harris, D., et al. (1998). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Natutre, 393, 537–544.CrossRefGoogle Scholar
  13. De Carvalho, L. P. S., Fischer, S. M., Marrero, J., Nathan, C., Ehrt, S., & Rhee, K. Y. (2010). Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates. Cell, 17, 1122–1131.Google Scholar
  14. de Souza, G. A., Fortuin, S., Aguilar, D., Pando, R. H., McEvoy, C. R., van Helden, P. D., et al. (2010). Using a label-free proteomics method to identify differentially abundant proteins in closely related hypo- and hypervirulent clinical Mycobacterium tuberculosis Beijing isolates. Molecular and Cellular Proteomics, 9(11), 2414–2423.PubMedCrossRefGoogle Scholar
  15. Deb, C., Daniel, J., Sirakova, T. D., Abomoelak, B., Dubey, V. S., & Kolattukudy, P. E. (2007). A novel lipase belonging to the hormone-sensitive lipase family induced under starvation to utilize stored triacylglycerol in Mycobacterium tuberculosis. Journal of Biological Chemistry, 281(7), 3866–3875.CrossRefGoogle Scholar
  16. Dormans, J., Burger, M., Aguilar, D., Hernandez-Pando, R., Kremer, K., Roholl, P., et al. (2004). Correlation of virulence, lung pathology, bacterial load and delayed type hypersensitivity responses after infection with different Mycobacterium tuberculosis genotypes in a BALB/c mouse model. Clinical and Experimental Immunology, 137, 460–468.PubMedCrossRefGoogle Scholar
  17. Fiehn, O., Kopka, J., Trethewey, R. N., & Willmitzer, L. (2000). Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Analytical Chemistry, 72, 3573–3580.PubMedCrossRefGoogle Scholar
  18. Field, A. (2005). Non parametric tests. In A. Field (Ed.), Discovering statistics using SPSS (pp. 532–533). London: SAGE publications.Google Scholar
  19. Filliol, I., Driscoll, J. R., van Soolingen, D., Kreiswirth, B. N., Kremer, K., Valetudie, G., et al. (2003). Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. Journal of Clinical Microbiology, 41, 1963–1970.PubMedCrossRefGoogle Scholar
  20. Glynn, J. R., Whiteley, J., Bifani, P. J., Kremer, K., & van Soolingen, D. (2002). Worldwide occurrence of Beijing/W strains of Mycobacterium tuberculosis: A systematic review. Emerging Infectious Diseases, 8(8), 843–849.PubMedCrossRefGoogle Scholar
  21. Gordon, S. V., Brosch, R., Billault, A., Garnier, T., Eiglmeier, K., & Cole, S. T. (1999). Identification of variable regions in the genome of tubercle bacilli using bacterial artificial chromosome arrays. Molecular Microbiology, 32(3), 643–655.PubMedCrossRefGoogle Scholar
  22. Kamio, Y., Itoh, Y., Terawaki, Y., & Kusano, T. (1981). Cadaverine is covalently linked to peptidoglycan in Selenomonas ruminantium. Journal of Bacteriology, 145(1), 122–128.PubMedGoogle Scholar
  23. Kanani, H., Chrysanthopoulos, P. K., & Klapa, M. I. (2008). Standardizing GC-MS metabolomics. Journal of Chromatography, 871, 191–201.PubMedCrossRefGoogle Scholar
  24. Karboul, A., Mazza, A., Gey Van Pittius, N. C., Ho, J. L., Brousseau, R., & Mardassi, H. (2008). Frequent homologous recombination events in Mycobacterium tuberculosis PE/PPE multigene families: Potential role in antigenic variability. Journal of Bacteriology, 190(23), 7838–7846.PubMedCrossRefGoogle Scholar
  25. Kendall, S. L., Withers, M., Soffair, C. N., Moreland, N. J., Gurcha, S., Sidders, B., et al. (2007). A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Molecular Microbiology, 65(3), 684–699.PubMedCrossRefGoogle Scholar
  26. Kremer, K., van-der-Werf, M. J., Au, B. K., Anh, D. D., Kam, K. M., van-Doorn, H. R., et al. (2009). Vaccine-induced immunity circumvented by typical Mycobacterium tuberculosis Beijing strains. Emerging Infectious Diseases, 15(2), 335–339.PubMedCrossRefGoogle Scholar
  27. Lopez, B., Aguilar, D., Orozco, H., Burger, M., Espitia, C., Ritacco, V., et al. (2003). A marked difference in pathogenesis and immune response induced by different Mycobacterium tuberculosis genotypes. Clinical and Experimental Immunology, 133, 30–37.PubMedCrossRefGoogle Scholar
  28. Målen, H., De Souza, G. A., Pathak, S., Søfteland, T., & Wiker, H. G. (2011). Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains. BMC Microbiology, 24(11), 18.CrossRefGoogle Scholar
  29. Manca, C., Tsenova, L., Bergtold, A., Freeman, S., Tovey, M., Musser, J. M., et al. (2001). Virulence of a Mycobacterium tuberculosis clinical isolate in mice is determined by failure to induce Th1 type immunity and is associated with induction of IFN-alpha/beta. Procedings of the National Academy of Sciences USA, 98, 5752–5757.CrossRefGoogle Scholar
  30. Neely, M. N., & Olson, E. R. (1996). Kinetics of expression of the Escherichia coli cad operon as a function of pH and lysine. Journal of Bacteriology, 178(18), 5522–5528.PubMedGoogle Scholar
  31. Newton, G. L., Av-Gay, Y., & Fahey, R. C. (2000). A novel mycothiol-dependent detoxification pathway in mycobacteria involving mycothiol S-conjugate amidase. Biochemistry, 39(35), 10739–10746.PubMedCrossRefGoogle Scholar
  32. O’Barr, T. P., & Everett, K. A. (1970). Effect of l-homoserine of growth of Mycobacterium tuberculosis. Infection and Immunity, 3(2), 328–332.Google Scholar
  33. Paley, S. M., & Karp, P. D. (2006). The pathway tools cellular overview diagram and omics viewer. Nucleic Acids Research, 34(13), 3771–3778.PubMedCrossRefGoogle Scholar
  34. Parish, T., Liu, J., Nikaido, H., & Stoker, N. G. (1997). A Mycobacterium smegmatis mutant with a defective inositol monophosphate phosphatase gene homolog has altered cell envelope permeability. Journal of Bacteriology, 179(24), 7827–7833.PubMedGoogle Scholar
  35. Parish, T., Smith, D. A., Kendall, S., Casali, N., Bancroft, G. J., & Stoker, N. G. (2003). Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infection and Immunity, 71, 1134–1140.PubMedCrossRefGoogle Scholar
  36. Pheiffer, C., Betts, J. C., Flynn, H. R., Lukey, P. T., & van Helden, P. (2005). Protein expression by a Beijing strain differs from that of another clinical isolate and Mycobacterium tuberculosis H37Rv. Microbiology, 151(4), 1139–1150.PubMedCrossRefGoogle Scholar
  37. Qureshi, N., Sathyamoorthy, N., & Takayama, K. (1984). Biosynthesis of C30 to C56 fatty acids by an extract of Mycobacterium tuberculosis H37Ra. Journal of Bacteriology, 157(1), 46–52.PubMedGoogle Scholar
  38. Rad, M. E., Bifani, P., Martin, C., Kremer, K., Samper, S., Rauzier, J., et al. (2003). Mutations in putative mutator genes of Mycobacterium tuberculosis strains of the W-Beijing family. Emerging Infectious Diseases, 9, 838–845.CrossRefGoogle Scholar
  39. Ramakrishnan, T., Murthy, P. S., & Gopinathan, K. P. (1972). Intermediary metabolism of mycobacteria. Bacteriology Review, 36(1), 65–108.Google Scholar
  40. Ramos, J. L., Martínez-Bueno, M., Molina-Henares, A. J., Terán, W., Watanabe, K., Zhang, X., et al. (2005). The TetR family of transcriptional repressors. Microbiology and Molecular Biology Reviews, 69(2), 326–356.PubMedCrossRefGoogle Scholar
  41. Reed, M. B., Domenech, P., Manca, C., Su, H., Barczak, A. K., Kreiswirth, B. N., et al. (2004). A glyco-lipid of hypervirulent tuberculosis strains that inhibits the innate immune response. Nature, 431, 84–87.PubMedCrossRefGoogle Scholar
  42. Reed, M. B., Gagneux, S., DeRiemer, K., Small, P. M., & Barry, C. E, I. I. I. (2007). The W-Beijing lineage of Mycobacterium tuberculosis overproduces triglycerides and has the DosR dormancy regulon constitutively upregulated. Journal of Bacteriology, 189(7), 2583–2589.PubMedCrossRefGoogle Scholar
  43. Reitzer, L. (2003). Nitrogen assimilation and global regulation in Escherichia coli. Annual Review of Microbiology, 57, 155–176.PubMedCrossRefGoogle Scholar
  44. Rocha-Ramírez, L. M., Estrada-García, I., López-Marín, L. M., Segura-Salinas, E., Méndez-Aragón, P., Van Soolingen, D., et al. (2008). Mycobacterium tuberculosis lipids regulate cytokines, TLR-2/4 and MHC class II expression in human macrophages. Tuberculosis, 88(3), 212–220.PubMedCrossRefGoogle Scholar
  45. Samartzidou, H., & Delcour, A. H. (1998). E.coli PhoE porin has an opposite voltage-dependence to the homologous OmpF. EMBO Journal, 17(1), 93–100.PubMedCrossRefGoogle Scholar
  46. Sareen, D., Newton, G. L., Fahey, R. C., & Buchmeier, N. A. (2003). Mycothiol is essential for growth of Mycobacterium tuberculosis Erdman. Journal of Bacteriology, 185(22), 6736–6740.PubMedCrossRefGoogle Scholar
  47. Shi, L., Sohaskey, C. D., Pfeiffer, C., Datta, P., Parks, M., McFadden, J., et al. (2010). Carbon flux rerouting during Mycobacterium tuberculosis growth arrest. Molecular Microbiology, 78(5), 1199–1215.PubMedCrossRefGoogle Scholar
  48. Tsenova, L., Ellison, E., Harbacheuski, R., Moreira, A. L., Kurepina, N., Reed, M. B., et al. (2005). Virulence of selected Mycobacterium tuberculosis clinical isolates in the rabbit model of meningitis is dependent on phenolic glycolipid produced by the bacilli. Journal of Infectious Diseases, 192(1), 98–106.PubMedCrossRefGoogle Scholar
  49. Umbarger, H. E. (1978). Amino acid biosynthesis and its regulation. Annual Review Biochemistry., 47, 532–606.Google Scholar
  50. Van Soolingen, D., Qian, L., deHaas, P. E., Douglas, J. T., Traore, H., Portaels, F., et al. (1995). Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. Journal of Clinical Microbiology, 33, 3234–3238.PubMedGoogle Scholar
  51. Vercellone, A., Nigou, J., & Puzo, G. (1998). Relationships between the structure and the roles of lipoarabinomannans and related glycoconjugates in tuberculosis pathogenesis. Frontiers Bioscience, 3, 149–163.Google Scholar
  52. Voskuil, M. I., Schnappinger, D., Visconti, K. C., Harrell, M. I., Dolganov, G. M., Sherman, D. R., et al. (2003). Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. Journal of Experimental Medicine, 198, 705–713.PubMedCrossRefGoogle Scholar
  53. Warren, R., Richardson, M., Sampson, S., Hauman, J. H., Beyers, N., Donald, P. R., et al. (1996). Genotyping of Mycobacterium tuberculosis with additional markers enhances accuracy in epidemiological studies. Journal of Clinical Microbiology, 34(9), 2219–2224.PubMedGoogle Scholar
  54. Zheng, H., Lu, L., Wang, B., Pu, S., Zhang, X., Zhu, G., et al. (2008). Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv. PLoS ONE, 3(6), e2375.PubMedCrossRefGoogle Scholar
  55. Ziebart, K. T., Dixon, S. M., Avila, B., El-Badri, M. H., Guggenheim, K. G., Kurth, M. J., et al. (2010). Targeting multiple chorismate-utilizing enzymes with a single inhibitor: Validation of a three-stage design. Journal of Medicinal Chemistry, 53(9), 3718–3729.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Reinart J. Meissner-Roloff
    • 1
  • Gerhard Koekemoer
    • 2
  • Robert M. Warren
    • 3
  • Du Toit Loots
    • 1
    Email author
  1. 1.School for Physical and Chemical Sciences, Centre for Human MetabonomicsNorth-West UniversityPotchefstroomSouth Africa
  2. 2.Statistical ConsultingNorth-West UniversityPotchefstroomSouth Africa
  3. 3.DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, US/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health SciencesStellenbosch UniversityTygerbergSouth Africa

Personalised recommendations