Actinorhodopsins: Proteorhodopsin-like gene sequences found predominantly in non-marine environments

Environmental Microbiology

Volumn 10, Issue 4, 2008, Pages 1039-1056

  Sharma, Adrian K ^a   Zhaxybayeva, Olga ^a   Papke, R Thane ^b   Doolittle, W Ford ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DNA BINDING PROTEIN; FRESH WATER; RADA PROTEIN, BACTERIA; RECA PROTEIN; RECA PROTEIN, ACINETOBACTER CALCOACETICUS; RHODOPSIN; UNCLASSIFIED DRUG;

ACTINOBACTERIA; ARTICLE; ECUADOR; GENETICS; ION TRANSPORT; METABOLISM; MICROBIOLOGY; PANAMA; PHYLOGENY; UNITED STATES;

ACTINOBACTERIA; BACTERIAL PROTEINS; DELAWARE; DNA-BINDING PROTEINS; ECUADOR; FRESH WATER; ION PUMPS; MARYLAND; PANAMA CANAL ZONE; PHYLOGENY; REC A RECOMBINASES; RHODOPSINS, MICROBIAL; SOIL MICROBIOLOGY; WATER MICROBIOLOGY;

ACTINOBACTERIA;

EID: 40949103188     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01525.x     Document Type: Article

References (50)

1. Allgaier, M. Grossart, H.P. (2006) Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany. Appl Environ Microbiol 72: 3489 3497.
2. Baliga, N.S., Bonneau, R., Facciotti, M.T., Pan, M., Glusman, G., Deutsch, E.W., et al. (2004) Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14: 2221 2234.
3. Beja, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902 1906.
4. Beja, O., Spudich, E.N., Spudich, J.L., Leclerc, M. DeLong, E.F. (2001) Proteorhodopsin phototrophy in the ocean. Nature 411: 786 789.
5. Benlloch, S., Lopez-Lopez, A., Casamayor, E.O., Ovreas, L., Goddard, V., Daae, F.L., et al. (2002) Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environ Microbiol 4: 349 360.
6. Bogomolni, R.A. Spudich, J.L. (1982) Identification of a third rhodopsin-like pigment in phototactic Halobacterium halobium. Proc Natl Acad Sci USA 79: 6250 6254.
7. Bryant, D.A. Frigaard, N.U. (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol 14: 488 496.
8. Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics 14: 755 763.
9. Edgar, R.C. (2004) muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792 1797.
10. Elifantz, H., Malmstrom, R.R., Cottrell, M.T. Kirchman, D.L. (2005) Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary. Appl Environ Microbiol 71: 7799 7805.
11. Frigaard, N.U., Martinez, A., Mincer, T.J. DeLong, E.F. (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847 850.
12. Furutani, Y., Bezerra, A.G., Jr, Waschuk, S., Sumii, M., Brown, L.S. Kandori, H. (2004) FTIR spectroscopy of the K photointermediate of Neurospora rhodopsin: structural changes of the retinal, protein, and water molecules after photoisomerization. Biochemistry 43: 9636 9646.
13. Garrett, C. (1972) Tidal resonance in the Bay of Fundy and Gulf of Maine. Nature 238: 441 443.
14. Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242 1245.
15. Gomez-Consarnau, L., Gonzalez, J.M., Coll-Llado, M., Gourdon, P., Pascher, T., Neutze, R., et al. (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445: 210 213.
16. Good, I.J. (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237 264.
17. Guindon, S. Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696 704.
18. Guindon, S., Lethiec, F., Duroux, P. Gascuel, O. (2005) phyml Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33: W557 W559.
19. Hallam, S.J., Putnam, N., Preston, C.M., Detter, J.C., Rokhsar, D., Richardson, P.M. DeLong, E.F. (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 1457 1462.
20. Hanada, S., Takaichi, S., Matsuura, K. Nakamura, K. (2002) Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 52: 187 193.
21. Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J. Goodman, R.M. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5: R245 R249.
22. Hartmann, R., Sickinger, H.D. Oesterhelt, D. (1980) Anaerobic growth of halobacteria. Proc Natl Acad Sci USA 77: 3821 3825.
23. Ihara, K., Umemura, T., Katagiri, I., Kitajima-Ihara, T., Sugiyama, Y., Kimura, Y. Mukohata, Y. (1999) Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation. J Mol Biol 285: 163 174.
24. Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G. Gibson, T.J. (1998) Multiple sequence alignment with clustal x. Trends Biochem Sci 23: 403 405.
25. Jung, K.H., Trivedi, V.D. Spudich, J.L. (2003) Demonstration of a sensory rhodopsin in eubacteria. Mol Microbiol 47: 1513 1522.
26. Kirchman, D.L., Dittel, A.I., Malmstrom, R.R. Cottrell, M.T. (2005) Biogeography of major bacterial groups in the Delaware estuary. Limnol Oceanogr 50: 1697 1706.
27. Legault, B.A., Lopez-Lopez, A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodriguez-Valera, F. Papke, R.T. (2006) Environmental genomics of 'Haloquadratum walsbyi' in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 7: 171.
28. McCarren, J. DeLong, E.F. (2007) Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla. Environ Microbiol 9: 846 858.
29. Martinez, A., Bradley, A.S., Waldbauer, J.R., Summons, R.E. DeLong, E.F. (2007) Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci USA 104: 5590 5595.
30. Matsuno-Yagi, A. Mukohata, Y. (1977) Two possible roles of bacteriorhodopsin; a comparative study of strains of Halobacterium halobium differing in pigmentation. Biochem Biophys Res Commun 78: 237 243.
31. Morris, R.M., Rappe, M.S., Connon, S.A., Vergin, K.L., Siebold, W.A., Carlson, C.A. Giovannoni, S.J. (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806 810.
32. Nakamura, Y., Kaneko, T., Sato, S., Mimuro, M., Miyashita, H., Tsuchiya, T., et al. (2003) Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids (supplement). DNA Res 10: 181 201.
33. Nesbo, C.L., Boucher, Y., Dlutek, M. Doolittle, W.F. (2005) Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environ Microbiol 7: 2011 2026.
34. Oesterhelt, D. Stoeckenius, W. (1973) Functions of a new photoreceptor membrane. Proc Natl Acad Sci USA 70: 2853 2857.
35. Partha, R., Krebs, R., Caterino, T.L. Braiman, M.S. (2005) Weakened coupling of conserved arginine to the proteorhodopsin chromophore and its counterion implies structural differences from bacteriorhodopsin. Biochim Biophys Acta 1708: 6 12.
36. Pernthaler, J., Glockner, F.O., Unterholzner, S., Alfreider, A., Psenner, R. Amann, R. (1998) Seasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake. Appl Environ Microbiol 64: 4299 4306.
37. Rusch, D.B., Halpern, A.L., Sutton, G., Heidelberg, K.B., Williamson, S., Yooseph, S., et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5: e77.
38. Sabehi, G., Kirkup, B.C., Rozenberg, M., Stambler, N., Polz, M.F. Béjà, O. (2007) Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern mediterranean and the Sargasso Seas. ISME J 1: 48 55.
39. Sabehi, G., Loy, A., Jung, K.H., Partha, R., Spudich, J.L., Isaacson, T., et al. (2005) New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol 3: e273.
40. Schloss, P.D. Handelsman, J. (2005) Introducing dotur, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501 1506.
41. Schmidt, H.A., Strimmer, K., Vingron, M. von Haeseler, A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502 504.
42. Schobert, B. Lanyi, J.K. (1982) Halorhodopsin is a light-driven chloride pump. J Biol Chem 257: 10306 10313.
43. Sharma, A.K., Spudich, J.L. Doolittle, W.F. (2006) Microbial rhodopsins: functional versatility and genetic mobility. Trends Microbiol 14: 463 469.
44. Sharma, A.K., Walsh, D.A., Bapteste, E., Rodriguez-Valera, F., Ford Doolittle, W. Papke, R.T. (2007) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol 7: 79.
45. Spudich, J.L. Jung, K.-H. (2005) Microbial Rhodopsins: Phylogenetic and Functional Diversity. Weinheim, Germany: Wiley-VCH.
46. Spudich, E.N. Spudich, J.L. (1982) Control of transmembrane ion fluxes to select halorhodopsin-deficient and other energy-transduction mutants of Halobacterium halobium. Proc Natl Acad Sci USA 79: 4308 4312.
47. Spudich, J.L., Yang, C.S., Jung, K.H. Spudich, E.N. (2000) Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol 16: 365 392.
48. Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37 43.
49. Warnecke, F., Sommaruga, R., Sekar, R., Hofer, J.S. Pernthaler, J. (2005) Abundances, identity, and growth state of actinobacteria in mountain lakes of different UV transparency. Appl Environ Microbiol 71: 5551 5559.
50. Yooseph, S., Sutton, G., Rusch, D.B., Halpern, A.L., Williamson, S.J., Remington, K., et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16.