Proteorhodopsin genes in giant viruses

Biology Direct

Volumn 7, Issue , 2012, Pages

  Yutin, Natalya ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; PHAEOCYSTIS GLOBOSA VIRUS; PROTISTA;

PROTEORHODOPSIN; RHODOPSIN; VIRUS PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; GENETICS; HAPTOPHYTA; HORIZONTAL GENE TRANSFER; METABOLISM; MOLECULAR GENETICS; PHYCODNAVIRIDAE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIROLOGY;

AMINO ACID SEQUENCE; GENE TRANSFER, HORIZONTAL; HAPTOPHYTA; MOLECULAR SEQUENCE DATA; PHYCODNAVIRIDAE; PHYLOGENY; RHODOPSIN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; VIRAL PROTEINS;

EID: 84866914570     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-7-34     Document Type: Article

References (32)

1. Agol VI, Gmyl AP. Viral security proteins: counteracting host defences. Nat Rev Microbiol 2010, 8(12):867-878. 10.1038/nrmicro2452, 21060318.
2. Wei H, Zhou MM. Viral-encoded enzymes that target host chromatin functions. Biochim Biophys Acta 2010, 1799(3-4):296-301. 2923641, 19716451.
3. de Souza RF, Iyer LM, Aravind L. Diversity and evolution of chromatin proteins encoded by DNA viruses. Biochim Biophys Acta 2010, 1799(3-4):302-318. 3243496, 19878744.
4. Werden SJ, Rahman MM, McFadden G. Poxvirus host range genes. Adv Virus Res 2008, 71:135-171.
5. Bugert JJ, Darai G. Poxvirus homologues of cellular genes. Virus Genes 2000, 21(1-2):111-133.
6. Alperovitch-Lavy A, Sharon I, Rohwer F, Aro EM, Glaser F, Milo R, Nelson N, Beja O. Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. Environ Microbiol 2011, 13(1):24-32. 10.1111/j.1462-2920.2010.02304.x, 20649642.
7. Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin EV, Wolf YI, et al. Photosystem I gene cassettes are present in marine virus genomes. Nature 2009, 461(7261):258-262. 10.1038/nature08284, 19710652.
8. Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol 2006, 4(8):e234. 10.1371/journal.pbio.0040234, 1484495, 16802857.
9. Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 2005, 438(7064):86-89. 10.1038/nature04111, 16222247.
10. Bragg JG, Chisholm SW. Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene. PLoS One 2008, 3(10):e3550. 10.1371/journal.pone.0003550, 2570332, 18958282.
11. Yau S, Lauro FM, DeMaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Gibson JA, et al. Virophage control of antarctic algal host-virus dynamics. Proc Natl Acad Sci U S A 2011, 108(15):6163-6168. 10.1073/pnas.1018221108, 3076838, 21444812.
12. Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. Proteorhodopsin phototrophy in the ocean. Nature 2001, 411(6839):786-789. 10.1038/35081051, 11459054.
13. Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 2000, 289(5486):1902-1906. 10.1126/science.289.5486.1902, 10988064.
14. Moran MA, Miller WL. Resourceful heterotrophs make the most of light in the coastal ocean. Nat Rev Microbiol 2007, 5(10):792-800. 10.1038/nrmicro1746, 17828280.
15. Spudich JL, Yang CS, Jung KH, Spudich EN. Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol 2000, 16:365-392. 10.1146/annurev.cellbio.16.1.365, 11031241.
16. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007, 5(3):e77. 10.1371/journal.pbio.0050077, 1821060, 17355176.
17. Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich EN, Spudich JL, Beja O. Diversification and spectral tuning in marine proteorhodopsins. EMBO J 2003, 22(8):1725-1731. 10.1093/emboj/cdg183, 154475, 12682005.
18. Atamna-Ismaeel N, Finkel OM, Glaser F, Sharon I, Schneider R, Post AF, Spudich JL, von Mering C, Vorholt JA, Iluz D, et al. Microbial rhodopsins on leaf surfaces of terrestrial plants. Environ Microbiol 2012, 14(1):140-146. 10.1111/j.1462-2920.2011.02554.x, 21883799.
19. Jung KH. The distinct signaling mechanisms of microbial sensory rhodopsins in Archaea, Eubacteria and Eukarya. Photochem Photobiol 2007, 83(1):63-69. 10.1562/2006-03-20-IR-853, 16968113.
20. Frigaard NU, Martinez A, Mincer TJ, DeLong EF. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 2006, 439(7078):847-850. 10.1038/nature04435, 16482157.
21. Slamovits CH, Okamoto N, Burri L, James ER, Keeling PJ. A bacterial proteorhodopsin proton pump in marine eukaryotes. Nat Commun 2011, 2:183.
22. Lin S, Zhang H, Zhuang Y, Tran B, Gill J. Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. Proc Natl Acad Sci U S A 2010, 107(46):20033-20038. 10.1073/pnas.1007246107, 2993343, 21041634.
23. Okamoto OK, Hastings JW. Novel dinoflagellate clock-related genes identified through microarray analysis. J Phycol 2003, 39:519-526.
24. Fuhrman JA, Schwalbach MS, Stingl U. Proteorhodopsins: an array of physiological roles?. Nat Rev Microbiol 2008, 6(6):488-494.
25. DeLong EF, Beja O. The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol 2010, 8(4):e1000359. 10.1371/journal.pbio.1000359, 2860490, 20436957.
26. Brussard CPG, Bratbak G, Baudoux AC, Ruardij P. Phaeocystis and its interaction with viruses. Biogeochemistry 2007, 83:201-215.
27. Ugalde JA, Podell S, Narasingarao P, Allen EE. Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biol Direct 2011, 6:52. 10.1186/1745-6150-6-52, 3198991, 21985229.
28. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
29. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
30. Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV. The deep archaeal roots of eukaryotes. Mol Biol Evol 2008, 25(8):1619-1630. 10.1093/molbev/msn108, 2464739, 18463089.
31. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5(3):e9490. 10.1371/journal.pone.0009490, 2835736, 20224823.
32. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305(3):567-580. 10.1006/jmbi.2000.4315, 11152613.