Metaproteomics

Metaproteomics (also Community Proteomics, Environmental Proteomics, or Community Proteogenomics) is the study of all protein samples recovered directly from environmental sources. Metaproteomics is used to classify experiments that deal with all the genes and proteins identified from complex communities, where individuals cannot be binned into species or organisms types. The metaproteomics approach is comparable to gene-centric environmental genomics, or metagenomics.[1][2]

Origin of the term

The term "metaproteomics" was proposed by Francisco Rodríguez-Valera to describe the genes and/or proteins most abundantly expressed in environmental samples.[3] The term was derived from "metagenome". Wilmes and Bond proposed the term "metaproteomics" for the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time.[4] At the same time, the terms "microbial community proteomics" and "microbial community proteogenomics" are sometimes used interchangeably for different types of experiments and results.

Proteomics of microbial community

The first proteomics experiment was conducted with the invention of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE).[5][6] The 1980s and 1990s saw the development of mass spectrometry and mass spectrometry based proteomics. The current proteomics of microbial community makes use of both gel-based (one-dimensional and two-dimensional) and non-gel liquid chromatography based separation, where both rely on mass spectrometry based peptide identification.

While proteomics is largely a discovery-based approach that is followed by other molecular or analytical techniques to provide a full picture of the subject system, it is not limited to simple cataloging of proteins present in a sample. With the combined capabilities of "top-down" and "bottom-up" approaches, proteomics can pursue inquiries ranging from quantitation of gene expression between growth conditions (whether nutritional, spatial, temporal, or chemical) to protein structural information.[1]

A metaproteomics study of the human oral microbiome found 50 bacterial genera using shotgun proteomics. The results agreed with the Human Microbiome Project, a metagenomic based approach.[7]

See also

References

  1. 1 2 Dill BD, et al. (2010). "Metaproteomics: Techniques and Applications". Environmental Molecular Microbiology. Caister Academic Press. ISBN 978-1-904455-52-3.
  2. ↑ Marco, D (editor) (2010). Metagenomics: Theory, Methods and Applications. Caister Academic Press. ISBN 978-1-904455-54-7.
  3. ↑ Rodriguez-Valera, F. 2004. Environmental genomics, the big picture? FEMS Microbiol. Lett. 231:153-158.
  4. ↑ Wilmes, P., and P. L. Bond. 2006. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 14:92-97.
  5. ↑ O'Farrell, P. H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007–4021 (1974).
  6. ↑ Klose, J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231–243 (1975).
  7. ↑ Grassl, Niklas; Kulak, Nils Alexander; Pichler, Garwin; Geyer, Philipp Emanuel; Jung, Jette; Schubert, Sören; Sinitcyn, Pavel; Cox, Juergen; Mann, Matthias (2016-01-01). "Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome". Genome Medicine. 8 (1): 44. doi:10.1186/s13073-016-0293-0. ISSN 1756-994X. PMC 4841045Freely accessible. PMID 27102203.
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