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]
Similarly, metaproteomics approaches have been used in larger clinical studies linking the bacterial proteome with human health. A recent paper used shotgun proteomics to characterize the vaginal microbiome, identifying 188 unique bacterial species in 688 women profiled[8]. This study linked vaginal microbiome groups to the efficacy of topical antiretroviral drugs to prevent HIV acquisition in women, which was attributed to bacterial metabolism of the drug in vivo. In addition, metaproteomic approaches have been used to study other aspects of the vaginal microbiome, including the immunological and inflammatory consequences of vaginal microbial dysbiosis[9], as well as the influence of hormonal contraceptives on the vaginal microbiome[10].
See also
References
- Dill BD, et al. (2010). "Metaproteomics: Techniques and Applications". Environmental Molecular Microbiology. Caister Academic Press. ISBN 978-1-904455-52-3.
- Marco, D (editor) (2010). Metagenomics: Theory, Methods and Applications. Caister Academic Press. ISBN 978-1-904455-54-7.CS1 maint: extra text: authors list (link)
- Rodriguez-Valera, F. 2004. Environmental genomics, the big picture? FEMS Microbiol. Lett. 231:153-158.
- Wilmes, P., and P. L. Bond. 2006. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 14:92-97.
- O'Farrell, P. H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007–4021 (1974).
- 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).
- 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 4841045. PMID 27102203.
- Klatt, Nichole R.; Cheu, Ryan; Birse, Kenzie; Zevin, Alexander S.; Perner, Michelle; Noël-Romas, Laura; Grobler, Anneke; Westmacott, Garrett; Xie, Irene Y.; Butler, Jennifer; Mansoor, Leila; McKinnon, Lyle R.; Passmore, Jo-Ann S.; Abdool Karim, Quarraisha; Abdool Karim, Salim S.; Burgener, Adam D. (1 June 2017). "Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women". Science. 356 (6341): 938–945. doi:10.1126/science.aai9383. hdl:10413/15137. PMID 28572388.
- Zevin, Alexander S.; Xie, Irene Y.; Birse, Kenzie; Arnold, Kelly; Romas, Laura; Westmacott, Garrett; Novak, Richard M.; McCorrister, Stuart; McKinnon, Lyle R.; Cohen, Craig R.; Mackelprang, Romel; Lingappa, Jairam; Lauffenburger, Doug A.; Klatt, Nichole R.; Burgener, Adam D. (22 September 2016). "Microbiome Composition and Function Drives Wound-Healing Impairment in the Female Genital Tract". PLOS Pathogens. 12 (9): e1005889. doi:10.1371/journal.ppat.1005889. PMC 5033340. PMID 27656899.
- Birse, Kenzie D.; Romas, Laura M.; Guthrie, Brandon L.; Nilsson, Peter; Bosire, Rose; Kiarie, James; Farquhar, Carey; Broliden, Kristina; Burgener, Adam D. (23 December 2016). "Genital injury signatures and microbiome alterations associated with depot medroxyprogesterone acetate usage and intravaginal drying practices". Journal of Infectious Diseases. 215 (4): 590–598. doi:10.1093/infdis/jiw590. PMC 5388302. PMID 28011908.