Skip to main content

Metabolomics of Mycobacterium tuberculosis

  • Protocol
  • First Online:
Mycobacteria Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1285))

Abstract

Enzymes fuel the biochemical activities of all cells. Their substrates and products thus offer a potential window into the physiologic state of a cell. Metabolomics focuses on the global, or systems-level, study of small molecules in a given biological system and thus provided an experimental tool with which to study cellular physiology on a global biochemical scale. While metabolomic studies of Mycobacterium tuberculosis are still in their infancy, recent studies have begun to deliver unique insights into the composition, organization, activity, and regulation of M. tuberculosis’ physiologic network. Here, we outline practical methods for the culture, collection, and analysis of metabolomic samples from Mycobacterium tuberculosis that emphasize minimal sample perturbation, broad and native metabolite recovery, and sensitive, biologically agnostic metabolite detection.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Patti GJ, Yanes O, Siuzdak G (2012) Innovation: metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 13(4):263–269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Reaves ML, Rabinowitz JD (2011) Metabolomics in systems microbiology. Curr Opin Biotechnol 22(1):17–25

    Article  CAS  PubMed  Google Scholar 

  3. Rhee KY, Carvalho LP, Bryk R, Ehrt S, Marrero J, Park SW, Schnappinger D, Venugopal A, Nathan C (2011) Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier. Trends Microbiol 7:307–314

    Article  Google Scholar 

  4. Saghatelian A, Cravatt BF (2005) Global strategies to integrate the proteome and metabolome. Curr Opin Chem Biol 9(1):62–68

    Article  CAS  PubMed  Google Scholar 

  5. de Carvalho LP, Zhao H, Dickinson CE, Arango NM, Lima CD, Fischer SM, Ouerfelli O, Nathan C, Rhee KY (2010) Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase. Chem Biol 17(4):323–332

    Article  PubMed  PubMed Central  Google Scholar 

  6. Larrouy-Maumus G, Biswas T, Hunt DM, Kelly G, Tsodikov OV, de Carvalho LP (2013) Discovery of a glycerol 3-phosphate phosphatase reveals glycerophospholipid polar head recycling in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 110(28):11320–11325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. de Carvalho LP, Fischer SM, Marrero J, Nathan C, Ehrt S, Rhee KY (2010) Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates. Chem Biol 17(10):1122–1131

    Article  PubMed  Google Scholar 

  8. Eoh H, Rhee KY (2013) Multifunctional essentiality of succinate metabolism in adaptation to hypoxia in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 110(16):6554–6559. doi:10.1073/pnas.1219375110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Marrero J, Rhee KY, 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(21):9819–9824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Marrero J, Trujillo C, Rhee KY, Ehrt S (2013) Glucose phosphorylation is required for Mycobacterium tuberculosis persistence in mice. PLoS Pathog 9(1):e1003116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Eoh H, Rhee KY (2014) Methylcitrate cycle defines the bactericidal essentiality of isocitrate lyase for survival of Mycobacterium tuberculosis on fatty acids. Proc Natl Acad Sci U S A 111(13):4976–4981

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chakraborty S, Gruber T, Barry CE 3rd, Boshoff HI, Rhee KY (2013) Para-aminosalicylic acid acts as an alternative substrate of folate metabolism in Mycobacterium tuberculosis. Science 339(6115):88–91

    Article  CAS  PubMed  Google Scholar 

  13. Kwon YK, Higgins MB, Rabinowitz JD (2010) Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli. ACS Chem Biol 5(8):787–795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kwon YK, Lu W, Melamud E, Khanam N, Bognar A, Rabinowitz JD (2008) A domino effect in antifolate drug action in Escherichia coli. Nat Chem Biol 4(10):602–608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Villas-Boas SG, Mas S, Akesson M, Smedsgaard J, Nielsen J (2005) Mass spectrometry in metabolome analysis. Mass Spectrom Rev 24(5):613–646

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kyu Rhee .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Nandakumar, M., Prosser, G.A., de Carvalho, L.P.S., Rhee, K. (2015). Metabolomics of Mycobacterium tuberculosis . In: Parish, T., Roberts, D. (eds) Mycobacteria Protocols. Methods in Molecular Biology, vol 1285. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2450-9_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2450-9_6

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2449-3

  • Online ISBN: 978-1-4939-2450-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics