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Metaproteomics of Freshwater Microbial Communities

  • David A. Russo
  • Narciso Couto
  • Andrew P. Beckerman
  • Jagroop PandhalEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1977)

Abstract

Recent advances in metaproteomics have provided us a link between genomic expression and functional characterization of environmental microbial communities. Therefore, the large-scale identification of proteins expressed by environmental microbiomes allows an unprecedented view of their in situ metabolism and function. However, one of the main challenges in metaproteomics remains the lack of robust analytical pipelines. This is especially true for aquatic environments with low protein concentrations and the presence of compounds that are known to interfere with traditional sample preparation pipelines and downstream LC-MS/MS analyses. In this chapter, a semiquantitative method that spans from sample preparation to functional annotation is provided. This method has been shown to provide in-depth and representative results of both the eukaryotic and prokaryotic fractions of freshwater microbiomes.

Key words

Algae Bioinformatics Environmental sample Functional analysis Mass spectrometry Metaproteomics Microbial community Protein extraction Shotgun proteomics 

Notes

Acknowledgments

The authors would like to thank the Natural Environment Research Council (NE/J024767/1) and the Technology Strategy Board for funding this work.

References

  1. 1.
    Leary DH, Hervey WJ 4th, Li RW et al (2012) Method development for metaproteomic analyses of marine biofilms. Anal Chem 84(9):4006–4013.  https://doi.org/10.1021/ac203315nCrossRefPubMedGoogle Scholar
  2. 2.
    Leary DH, Hervey WJ 4th, Deschamps JR et al (2013) Which metaproteome? The impact of protein extraction bias on metaproteomic analyses. Mol Cell Probes 27(5–6):193–199.  https://doi.org/10.1016/j.mcp.2013.06.003CrossRefPubMedGoogle Scholar
  3. 3.
    Teeling H, Fuchs BM, Becher D et al (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336(6081):608–611.  https://doi.org/10.1126/science.1218344CrossRefPubMedGoogle Scholar
  4. 4.
    Schneider T, Riedel K (2010) Environmental proteomics: analysis of structure and function of microbial communities. Proteomics 10(4):785–798.  https://doi.org/10.1002/pmic.200900450CrossRefPubMedGoogle Scholar
  5. 5.
    Motoyama A, Yates JR (2008) Multidimensional LC separations in shotgun proteomics. Anal Chem 80(19):7187–7193.  https://doi.org/10.1021/ac8013669CrossRefPubMedGoogle Scholar
  6. 6.
    Bereszczak JZ, Brancia FL (2009) Offline and online liquid chromatography mass spectrometry in quantitative proteomics. Comb Chem High Throughput Screen 12(2):185–193.  https://doi.org/10.2174/138620709787315418CrossRefPubMedGoogle Scholar
  7. 7.
    Fenn JB, Mann M, Meng CK et al (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246(4926):64–71.  https://doi.org/10.1126/science.2675315CrossRefPubMedGoogle Scholar
  8. 8.
    Hillenkamp F, Karas M, Beavis RC et al (1991) Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal Chem 63(24):1193A–1203A.  https://doi.org/10.1021/ac00024a716CrossRefPubMedGoogle Scholar
  9. 9.
    Yates JR, Ruse CI, Nakorchevsky A (2009) Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng 11:49–79.  https://doi.org/10.1146/annurev-bioeng-061008-124934CrossRefPubMedGoogle Scholar
  10. 10.
    Muth T, Benndorf D, Reichl U et al (2013) Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. Mol BioSyst 9(4):578–585.  https://doi.org/10.1039/c2mb25415hCrossRefPubMedGoogle Scholar
  11. 11.
    Perkins DN, Pappin DJ, Creasy DM et al (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551–3567.  https://doi.org/10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2CrossRefPubMedGoogle Scholar
  12. 12.
    Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20(9):1466–1467.  https://doi.org/10.1093/bioinformatics/bth092CrossRefPubMedGoogle Scholar
  13. 13.
    Pible O, Armengaud J (2015) Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0. Proteomics 15(20):3418–3423.  https://doi.org/10.1002/pmic.201500104CrossRefPubMedGoogle Scholar
  14. 14.
    Russo DA, Couto N, Beckerman AP et al (2016) A metaproteomic analysis of the response of a freshwater microbial community under nutrient enrichment. Front Microbiol 7:1172.  https://doi.org/10.3389/fmicb.2016.01172CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Jagtap P, Goslinga J, Kooren JA et al (2013) A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics 13(8):1352–1357.  https://doi.org/10.1002/pmic.201200352CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Apweiler R, Bairoch A, Wu CH et al (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32(database issue):D115–D119.  https://doi.org/10.1093/nar/gkh131CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Tatusov R, Fedorova N, Jackson J et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4(1):1–14.  https://doi.org/10.1186/1471-2105-4-41CrossRefGoogle Scholar
  18. 18.
    Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25(1):25–29.  https://doi.org/10.1038/75556CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28(1):27–30.  https://doi.org/10.1093/nar/28.1.27CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Ogunseitan OA (1993) Direct extraction of proteins from environmental samples. J Microbiol Meth 17(4):273–281.  https://doi.org/10.1016/0167-7012(93)90056-NCrossRefGoogle Scholar
  21. 21.
    Kalb VF Jr, Bernlohr RW (1977) A new spectrophotometric assay for protein in cell extracts. Anal Biochem 82:362–371.  https://doi.org/10.1016/0003-2697(77)90173-7CrossRefPubMedGoogle Scholar
  22. 22.
    Ishihama Y, Oda Y, Tabata T et al (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4(9):1265–1272.  https://doi.org/10.1074/mcp.M500061-MCP200CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • David A. Russo
    • 1
  • Narciso Couto
    • 2
  • Andrew P. Beckerman
    • 3
  • Jagroop Pandhal
    • 2
    Email author
  1. 1.Department of Plant and Environmental SciencesUniversity of CopenhaganCopenhaganDenmark
  2. 2.Department of Chemical and Biological EngineeringThe University of SheffieldSheffieldUK
  3. 3.Department of Animal and Plant SciencesThe University of SheffieldSheffieldUK

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