Marine metaproteomics: Current status and future directions

Journal of Proteomics

Volumn 97, Issue , 2014, Pages 27-35

  Wang, Da Zhi ^a   Xie, Zhang Xian ^a   Zhang, Shu Feng ^a  

^a XIAMEN UNIVERSITY   (China)

Author keywords

Biogeochemical cycle; Ecological function; Marine ecosystem; Metaproteomics; Microbial community

Indexed keywords

ORGANIC MATTER;

GENE EXPRESSION; HABITAT; MARINE BIOLOGY; MARINE ENVIRONMENT; MARINE SPECIES; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METAGENOMICS; METAPROTEOMICS; MICROBIAL COMMUNITY; NONHUMAN; OCEANOGRAPHY; PHYSIOLOGICAL PROCESS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS; ELECTROSPRAY MASS SPECTROMETRY; ENERGY TRANSFER; MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTON MOTIVE FORCE; TIME OF FLIGHT MASS SPECTROMETRY;

BIOGEOCHEMICAL CYCLE; ECOLOGICAL FUNCTION; MARINE ECOSYSTEM; METAPROTEOMICS; MICROBIAL COMMUNITY;

AQUATIC ORGANISMS; METAGENOME; METAGENOMICS; PROTEOMICS; WATER MICROBIOLOGY;

EID: 84892888848     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.08.024     Document Type: Review

References (51)

1. Kan J., Hanson T.E., Ginter J.M., Wang K., Chen F. Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Syst 2005, 1:7.
2. Pierre-Alain M., Christophe M., Séverine S., Houria A., Philippe L., Lionel R. Protein extraction and fingerprinting optimization of bacterial communities in natural environment. Microb Ecol 2007, 53:426-434.
3. Wilmes P., Bond P.L. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ Microbiol 2004, 6:911-920.
4. Ram R.J., VerBerkmoes N.C., Thelen M.P., Tyson G.W., Baker B.J., Blake R.C., et al. Community proteomics of a natural microbial biofilm. Science 2005, 308:1915-1920.
5. Williams M.A., Taylor E.B., Mula H.P. Metaproteomic characterization of a soil microbial community following carbon amendment. Soil Biol. Biochem. 2010, 42:1148-1156.
6. Wang H.B., Zhang Z.X., Li H., He H.B., Fang C.X., Zhang A.J., et al. Characterization of metaproteomics in crop rhizospheric soil. J Proteome Res 2010, 10:932-940.
7. Benndorf D., Vogt C., Jehmlich N., Schmidt Y., Thomas H., Woffendin G., et al. Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 2009, 20:737-750.
8. Bruneel O., Volant A., Gallien S., Chaumande B., Casiot C., Carapito C., et al. Characterization of the active bacterial community involved in natural attenuation processes in arsenic-rich creek sediments. Microb Ecol 2011, 61:793-810.
9. Ng C., DeMaere M.Z., Williams T.J., Lauro F.M., Raftery M., Gibson J.A., et al. Metaproteogenomic analysis of a dominant green sulphur bacterium from Ace Lake, Antartica. ISME J 2010, 4:1002-1019.
10. Habicht K.S., Miller M., Cox R.P., Frigaard N.U., Tonolla M., Peduzzi S., et al. Comparative proteomics and activity of a green sulfur bacterium through the water column of Lake Cadagno, Switzerland. Environ Microbiol 2011, 13:203-215.
11. Lauro F.M., DeMaere M.Z., Yau S., Brown M.V., Ng C., Wilkins D., et al. An integrative study of a meromictic lake ecosystem in Antarctica. ISME J 2011, 5:879-895.
12. Benndorf D., Balcke G.U., Harms H., von Bergen M. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 2007, 1:224-234.
13. Wilmes P., Wexler M., Bond P.L. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 2008, 3:e1778.
14. Jehmlich N., Kleinsteuber S., Vogt C., Benndorf D., Harms H., Schmidt F., et al. Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community. J Appl Microbiol 2010, 109:1937-1945.
15. Toyoda A., Iio W., Mitsumori M., Minato H. Isolation and identification of cellulose-binding proteins from sheep rumen contents. Appl Environ Microbiol 2009, 75:1667-1673.
16. Burnum K.E., Callister S.J., Nicora C.D., Purvine S.O., Hugenholtz P., Warnecke F., et al. Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J 2011, 5:161-164.
17. Verberkmoes N.C., Russell A.L., Shah M., Godzik A., Rosenquist M., Halfvarson J., et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J 2009, 3:179-189.
18. Rooijers K., Kolmeder C., Juste C., Dore J., de Been M., Boeren S., et al. An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 2011, 12:6.
19. Rudney J.D., Xie H., Rhodus N.L., Ondrey F.G., Griffin T.J. A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol Oral Microbiol 2010, 25:38-49.
20. DeLong E.F. Microbial community genomics in the ocean. Nat Rev Microbiol 2005, 3:459-469.
21. Yooseph S., Sutton G., Rusch D.B., Halpern A.L., Williamson S.J., Remington K., et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 2007, 5(3):e16.
22. Cottrell J.S., London U. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
23. Eng J.K., McCormack A.L., Yates J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5:976-989.
24. Ma B., Zhang K., Hendrie C., Liang C., Li M., Doherty-Kirby A., et al. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 2003, 17:2337-2342.
25. Tabb D.L., McDonald W.H., Yates J.R. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 2002, 1:21-26.
26. Craig R., Beavis R.C. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom 2003, 17:2310-2316.
27. Bernhardt J., Michalik S., Wollscheid B., Völker U., Schmidt F. Proteomics approaches for the analysis of enriched microbial subpopulations and visualization of complex functional information. Curr Opin Biotechnol 2013, 24:112-119.
28. Sowell S.M., Wilhelm L.J., Norbeck A.D., Lipton M.S., Nicora C.D., Barofsky D.F., et al. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 2009, 3:93-105.
29. Sowell S.M., Abraham P.E., Shah M., Verberkmoes N.C., Smith D.P., Barofsky D.F., et al. Environmental proteomics of microbial plankton in a highly productive coastal upwelling system. ISME J 2011, 5:856-865.
30. Dyhrman S.T., Haley S.T. Phosphorus scavenging in the unicellular marine diazotroph Crocosphaera watsonii. Appl Environ Microbiol 2006, 72:1452-1458.
31. Martiny A.C., Coleman M.L., Chisholm S.W. Phosphate acquisition genes in Prochlorococcus ecotypes: evidence for genome-wide adaptation. Proc Natl Acad Sci 2006, 103:12552-12557.
32. Morris R.M., Nunn B.L., Frazar C., Goodlett D.R., Ting Y.S., Rocap G. Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J 2010, 4:673-685.
33. Dong H.P., Wang D.Z., Xie Z.X., Dai M.H., Hong H.S. Metaproteomic characterization of high molecular weight dissolved organic matter in surface seawaters in the South China Sea. Geochim Cosmochim Acta 2013, 109:51-61.
34. Dong H.P., Wang D.Z., Dai M.H., Hong H.S. Characterization of particulate organic matter in the water column of the South China Sea using a shotgun proteomic approach. Limnol Oceanogr 2010, 55:1565-1578.
35. Wang D.Z., Dong H.P., Xie Z.X., Dai M.H., Hong H.S. Metaproteomic characterization of dissolved organic matter in the water column of the South China Sea. Limnol Oceanogr 2011, 56:1641-1652.
36. Moore E.K., Nunn B.L., Goodlett D.R., Harvey H.R. Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments. Geochim Cosmochim Acta 2012, 83:324-359.
37. Stokke R., Roalkvam I., Lanzen A., Haflidason H., Steen I.H. Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environ Microbiol 2012, 14:1333-1346.
38. Kleiner M., Wentrup C., Lott C., Teeling H., Wetzel S., Young J., et al. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci 2012, 10.1073/pnas.1121198109.
39. Teeling H., Fuchs B.M., Becher D., Klockow C., Gardebrecht A., Bennke C.M., et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 2012, 336:608-611.
40. Hettich R.L., Sharma R., Chourey K., Giannone R.J. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr Opin Microbiol 2012, 15:373-380.
41. Banfield J.F., Verberkmoes N.C., Hettich R.L., Thelen M.P. Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS 2005, 9:301-333.
42. Chen S., Rillig M.C., Wang W. Improving soil protein extraction for metaproteome analysis and glomalin-related soil protein detection. Proteomics 2009, 9:4970-4973.
43. Chourey K., Jansson J., VerBerkmoes N., Shah M., Chavarria K.L., Tom L.M., et al. Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res 2010, 9:6615-6622.
44. Abram F., Gunnigle E., O'Flaherty V. Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms. Electrophoresis 2009, 30:4149-4151.
45. Leary D.H., Hervey W.J., Li R.W., Deschamps J.R., Kusterbeck A.W., Vora G.J. Method development for metaproteomic analyses of marine biofilms. Anal Chem 2012, 84:4006-4013.
46. Dong H.P., Wang D.Z., Dai M.H., Chan L.L., Hong H.S. Shotgun proteomics: tools for analysis of marine particulate proteins. Limnol Oceanogr Methods 2009, 7:865-874.
47. Saijo S., Tanoue E. Characterization of particulate proteins in Pacific surface waters. Limnol Oceanogr 2004, 49:953-963.
48. Junqueira M., Spirin V., Balbuena T.S., Thomas H., Adzhubei I., Sunyaev S., et al. Protein identification pipeline for the homology-driven proteomics. J Proteomics 2008, 71:346-356.
49. Shevchenko A., Valcu C.-M., Junqueira M. Tools for exploring the proteomosphere. J Proteomics 2009, 72:137-144.
50. Wielsch N., Thomas H., Surendranath V., Waridel P., Frank A., Pevzner P., et al. Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches. J Proteome Res 2006, 5:2448-2456.
51. Mary I., Oliver A., Skipp P., Holland R., Topping J., Tarran G., et al. Metaproteomic and metagenomic analyses of defined oceanic microbial populations using microwave cell fixation and flow cytometric sorting. FEMS Microbiol Ecol 2010, 74:10-18.