Metagenomics and the protein universe

Current Opinion in Structural Biology

Volumn 21, Issue 3, 2011, Pages 398-403

  Godzik, Adam ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; DNA PURIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GRAM NEGATIVE BACTERIUM; HUMAN; LACTOBACILLUS ACIDOPHILUS; METAGENOMICS; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN STRUCTURE; REVIEW; SACCHAROPHAGUS DEGRADANS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SULFUROSPIRILLUM DELEYIANUM; TREE OF LIFE;

ANIMALS; DATABASES, PROTEIN; HUMANS; METAGENOMICS; PROTEINS; PROTEOMICS;

EID: 79958071293     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2011.03.010     Document Type: Review

References (38)

1. Curtis T.P., Sloan W.T., Scannell J.W. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 2002, 99:10494-10499.
2. Schloss P.D., Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev 2004, 68:686-691.
3. Tettelin H., Masignani V., Cieslewicz M.J., Donati C., Medini D., Ward N.L., Angiuoli S.V., Crabtree J., Jones A.L., Durkin A.S., et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial " pan-genome" Proc Natl Acad Sci U S A 2005, 102:13950-13955.
4. Mira A., Martin-Cuadrado A.B., D'Auria G., Rodriguez-Valera F. The bacterial pan-genome: a new paradigm in microbiology. Int Microbiol 2010, 13:45-57.
5. Sogin M.L., Morrison H.G., Huber J.A., Mark Welch D., Huse S.M., Neal P.R., Arrieta J.M., Herndl G.J. Microbial diversity in the deep sea and the underexplored " rare biosphere" Proc Natl Acad Sci U S A 2006, 103:12115-12120.
6. Finn R.D., Mistry J., Tate J., Coggill P., Heger A., Pollington J.E., Gavin O.L., Gunasekaran P., Ceric G., Forslund K., et al. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-222.
7. Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Das U., Daugherty L., Duquenne L., et al. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-D215.
8. Andreeva A., Howorth D., Chandonia J.M., Brenner S.E., Hubbard T.J., Chothia C., Murzin AG Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 2008, 36:D419-D425.
9. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004, 68:669-685.
10. National Research Council (U.S.), Committee on Metagenomics: Challenges and Functional Applications, National Academies Press (U.S.) The new science of metagenomics: revealing the secrets of our microbial planet 2007, vol. xii. National Academies Press, Washington, DC, 158 pp.
11. The Universal Protein Resource (UniProt) in 2010 Nucleic Acids Res 2010, 38:D142-D148.
12. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Res 2008, 36:D25-30.
13. Bandeira N., Clauser K.R., Pevzner P.A. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics 2007, 6:1123-1134.
14. Hugenholtz P., Kyrpides N.C. A changing of the guard. Environ Microbiol 2009, 11:551-553.
15. Pace N.R. Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 2009, 73:565-576.
16. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74.
17. Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007, 5:e77.
18. Gill S.R., Pop M., Deboy R.T., Eckburg P.B., Turnbaugh P.J., Samuel B.S., Gordon J.I., Relman D.A., Fraser-Liggett C.M., Nelson K.E. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359.
19. Kurokawa K., Itoh T., Kuwahara T., Oshima K., Toh H., Toyoda A., Takami H., Morita H., Sharma V.K., Srivastava T.P., et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007, 14:169-181.
20. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
21. Peterson J., Garges S., Giovanni M., McInnes P., Wang L., Schloss J.A., Bonazzi V., McEwen J.E., Wetterstrand K.A., Deal C., et al. The NIH Human Microbiome Project. Genome Res 2009, 19:2317-2323.
22. Sun S., Chen J., Li W., Altintas I., Lin A., Peltier S., Stocks K., Allen E.E., Ellisman M., Grethe J., et al. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res 2011, 39:D546-D551.
23. Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N.N., Kunin V., Goodwin L., Wu M., Tindall B.J., et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009, 462:1056-1060.
24. Yooseph S., Sutton G., Rusch D.B., Halpern A.L., Williamson S.J., Remington K., Eisen J.A., Heidelberg K.B., Manning G., Li W., et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 2007, 5:e16.
25. Ellrott K., Jaroszewski L., Li W., Wooley J.C., Godzik A. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PLoS Comput Biol 2010, 6:e1000798.
26. Levitt M. Nature of the protein universe. Proc Natl Acad Sci U S A 2009, 106:11079-11084.
27. Chubb D., Jefferys B.R., Sternberg M.J., Kelley L.A. Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe. Bioinformatics 2010, 26:2664-2671.
28. Joachimiak A. High-throughput crystallography for structural genomics. Curr Opin Struct Biol 2009, 19:573-584.
29. Hall R.S., Fedorov A.A., Marti-Arbona R., Fedorov E.V., Kolb P., Sauder J.M., Burley S.K., Shoichet B.K., Almo S.C., Raushel F.M. The hunt for 8-oxoguanine deaminase. J Am Chem Soc 2010, 132:1762-1763.
30. Xiang D.F., Patskovsky Y., Xu C., Meyer A.J., Sauder J.M., Burley S.K., Almo S.C., Raushel F.M. Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes. Biochemistry 2009, 48:3730-3742.
31. Xiang D.F., Xu C., Kumaran D., Brown A.C., Sauder J.M., Burley S.K., Swaminathan S., Raushel F.M. Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. Biochemistry 2009, 48:4567-4576.
32. Li W., Wooley J.C., Godzik A. Probing metagenomics by rapid cluster analysis of very large datasets. PLoS One 2008, 3:e3375.
33. Das D., Kozbial P., Axelrod H.L., Miller M.D., McMullan D., Krishna S.S., Abdubek P., Acosta C., Astakhova T., Burra P., et al. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60Å resolution. Proteins 2009, 75:296-307.
34. Sciara G., Kendrew S.G., Miele A.E., Marsh N.G., Federici L., Malatesta F., Schimperna G., Savino C., Vallone B. The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis. EMBO J 2003, 22:205-215.
35. Jaroszewski L., Li Z., Krishna S.S., Bakolitsa C., Wooley J., Deacon A.M., Wilson I.A., Godzik A. Exploration of uncharted regions of the protein universe. PLoS Biol 2009, 7:e1000205.
36. Dessailly B.H., Redfern O.C., Cuff A.L., Orengo C.A. Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification. Structure 2010, 18:1522-1535.
37. Elsliger M.A., Deacon A.M., Godzik A., Lesley S.A., Wooley J., Wuthrich K., Wilson I.A. The JCSG high-throughput structural biology pipeline. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010, 66:1137-1142.
38. Henshaw J., Horne-Bitschy A., van Bueren A.L., Money V.A., Bolam D.N., Czjzek M., Ekborg N.A., Weiner R.M., Hutcheson S.W., Davies G.J., et al. Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains. J Biol Chem 2006, 281:17099-17107.