Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Buttigieg, Pier Luigi ^a,b   Hankeln, Wolfgang ^a   Kostadinov, Ivaylo ^c   Kottmann, Renzo ^a   Yilmaz, Pelin ^a   Duhaime, Melissa Beth ^d   Glöckner, Frank Oliver ^a,b  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b JACOBS UNIVERSITY BREMEN   (Germany)

^c INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^d UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; PFAM PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; DNA METABOLISM; DNA REPAIR; GENOME ANALYSIS; MARINE ENVIRONMENT; MARINE SPECIES; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOBIOLOGY; PREDICTION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN TARGETING; SIGNAL TRANSDUCTION;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CYANOBACTERIA; ECOSYSTEM; IRON; METAGENOME; METAGENOMICS; PHOTOSYNTHESIS; PROTEIN INTERACTION DOMAINS AND MOTIFS; SEAWATER;

EID: 84875045322     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050869     Document Type: Article

References (47)

1. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-222.
2. Bateman A, Coggill P, Finn RD, (2010) DUFs: families in search of function. Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1148-1152.
3. Roberts RJ, (2004) Identifying protein function-a call for community action. PLoS Biol 2: E42.
4. Galperin MY, Koonin EV, (2010) From complete genome sequence to "complete" understanding? Trends Biotechnol 28: 398-406.
5. Deng H, McMahon SA, Eustáquio AS, Moore BS, Naismith JH, et al. (2009) Mechanistic insights into water activation in SAM hydroxide adenosyltransferase (duf-62). Chembiochem 10: 2455-2459.
6. Weinitschke S, Denger K, Cook AM, Smits THM, (2007) The DUF81 protein TauE in Cupriavidus necator H16, a sulfite exporter in the metabolism of C2 sulfonates. Microbiology 153: 3055-3060.
7. Goonesekere NCW, Shipely K, O'Connor K, (2010) The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. Comput Biol Chem 34: 210-214.
8. Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, et al. (2009) Exploration of uncharted regions of the protein universe. PLoS Biol 7: e1000205.
9. Wooley JC, Godzik A, Friedberg I, (2010) A primer on metagenomics. PLoS Comput Biol 6 (2) (): e1000667.
10. Gilbert JA, Dupont CL, (2011) Microbial metagenomics: Beyond the genome. Ann Rev Mar Sci 3: 347-371.
11. Delmont TO, Malandain C, Prestat E, Larose C, Monier J-M, et al. (2011) Metagenomic mining for microbiologists. ISME J 5: 1837-1843.
12. Merico D, Gfeller D, Bader GD, (2009) How to visually interpret biological data using networks. Nat Biotechnol 27: 921-924.
13. Breitling R, Vitkup D, Barrett MP, (2008) New surveyor tools for charting microbial metabolic maps. Nat Rev Microbiol 6: 156-161.
14. Fuhrman J, Steele J, (2008) Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquat Microb Ecol 53: 69-81.
15. Fuhrman JA, (2009) Microbial community structure and its functional implications. Nature 459: 193-199.
16. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: 398-431.
17. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-301.
18. Fuchs G, (2011) Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Ann Rev Microbiol 65: 631-658.
19. Martinez A, Tyson GW, Delong EF, (2009) Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environ Microbiol 12: 222-238.
20. Villarreal-Chiu JF, Quinn JP, McGrath JW, (2012) The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment. Front Microbiol 3: 19.
21. Kujawinski EB, (2011) The impact of microbial metabolism on marine dissolved organic matter. Ann Rev Mar Sci 3: 567-599.
22. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L, (2009) Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Mol Biosyst 5: 1636-1660.
23. Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, et al. (2006) Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol 4: e234.
24. K-ichi Miyazono, Shirokane M, Sawano Y, Tanokura M, (2009) Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3. Proteins 74: 256-260.
25. Wittkop T, Emig D, Truss A, Albrecht M, Böcker S, et al. (2011) Comprehensive cluster analysis with Transitivity Clustering. Nat Protoc 6: 285-295.
26. Polz MF, Hunt DE, Preheim SP, Weinreich DM, (2006) Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc B 361: 2009-2021.
27. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, et al. (2009) The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci USA 106: 15527-15533.
28. Seligmann H, (2003) Cost-minimization of amino acid usage. J Mol Evol 56: 151-161.
29. Meador JA, Baldwin AJ, Catala P, Jeffrey WH, Joux F, et al. (2009) Sunlight-induced DNA damage in marine micro-organisms collected along a latitudinal gradient from 70°N to 68°S. Photochem Photobiol 85: 412-420.
30. Milligan JR, Aguilera JA, Ly A, Tran NQ, Hoang O, et al. (2003) Repair of oxidative DNA damage by amino acids. Nucleic Acids Res 31: 6258-6263.
31. Fernandes AP, Holmgren A, (2004) Glutaredoxins: glutathione-dependent redox enzymes with functions far beyond a simple thioredoxin backup system. Antioxid Redox Signal 6: 63-74.
32. Rouhier N, Lemaire SD, Jacquot J-P, (2008) The role of glutathione in photosynthetic organisms: emerging functions for glutaredoxins and glutathionylation. Annu Rev Plant Biol 59: 143-166.
33. Toulza E, Tagliabue A, Blain S, Piganeau G, (2012) Analysis of the Global Ocean Sampling (GOS) project for trends in iron uptake by surface ocean microbes. PLoS ONE 7: e30931.
34. Lash LH, Jones P, (1984) Renal glutathione transport: Characteristics of the sodium-dependent system in the basal-lateral membrane. J Biol Chem 259: 14508-14514.
35. Kannan R, Yi JR, Tang D, Li Y, Ziokovic BV, et al. (1996) Evidence for the existence of a sodium-dependent glutathione (GSH) transporter. J Biol Chem 271: 9754-9758.
36. DeLong EF, Béjà O, (2010) The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol 8: e1000359.
37. Slamovits CH, Okamoto N, Burri L, James ER, Keeling PJ, (2011) A bacterial proteorhodopsin proton pump in marine eukaryotes. Nat Commun 2: 183.
38. Börnke F (2008) Protein Interaction Networks. In: Junker BH, Schreiber F, editors. Analysis of Biological Networks. Hoboken, NJ, USA: John Wiley & Sons, Inc. pp. 207-232.
39. Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, et al. (2011) A holistic approach to marine eco-systems biology. PLoS Biol 9: e1001177.
40. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.
41. Roberts RJ, Chang Y-C, Hu Z, Rachlin JN, Anton BP, et al. (2011) COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res 39: D11-14.
42. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M, (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5: e75.
43. Markowitz VM, Chen I-M, Palaniappan K, Chu K, Szeto E, et al. (2010) The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res 38: D382-390.
44. Csardi G, Nepusz T, (2006) The igraph software package for complex network research. InterJournal Complex Sy pp. 1695.
45. Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
46. Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, et al. (2010) Partitioning biological data with transitivity clustering. Nat Methods 7: 419-420.
47. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, et al. (2011) clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics 12: 436.