Different SAR86 subgroups harbour divergent proteorhodopsins

Environmental Microbiology

Volumn 6, Issue 9, 2004, Pages 903-910

  Sabehi, Gazalah ^a   Béjà, Oded ^a   Suzuki, Marcelino T ^b   Preston, Christina M ^c   DeLong, Edward F ^d  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b UNIVERSITY OF MARYLAND CENTER FOR ENVIRONMENTAL SCIENCE   (United States)

^c MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA; PROTEORHODOPSIN; RETINAL; RHODOPSIN; RIBOSOME RNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BACTERIAL GENOME; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GAMMAPROTEOBACTERIA; GENE LIBRARY; GENETIC VARIABILITY; GENETICS; INDIAN OCEAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PACIFIC OCEAN; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

AMINO ACID SEQUENCE; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLUSTER ANALYSIS; DNA PRIMERS; GAMMAPROTEOBACTERIA; GENE LIBRARY; GENOME, BACTERIAL; INDIAN OCEAN; MOLECULAR SEQUENCE DATA; PACIFIC OCEAN; PHYLOGENY; RETINALDEHYDE; RHODOPSIN; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROTEOBACTERIA;

EID: 4344584482     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00676.x     Document Type: Article

References (25)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein data-base search programs. Nucleic Acids Res 25: 3389-3402.
2. Béjà, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., et al. (2000a) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902-1906.
3. Béjà, O., Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., et al. (2000b) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2: 516-529.
4. Béjà, O., Spudich, E.N., Spudich, J.L., Leclerc, M., and DeLong, E.F. (2001) Proteorhodopsin phototrophy in the ocean. Nature 411: 786-789.
5. Dioumaev, A.K., Brown, L.S., Shih, J., Spudich, E.N., Spudich, J.L., and Lanyi, J.K. (2002) Proton transfers in the photochemical reaction cycle of proteorhodopsin. Biochemistry 41: 5348-5358.
6. Eilers, H., Pernthaler, J., Glockner, F.O., and Amann, R. (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66: 3044-3051.
7. González, J.M., Simo, R., Massana, R., Covert, J.S., Casamayor, E.O., Pedrós-Alió, C., and Moran, M.A. (2000) Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol 66: 4237-4246.
8. Karl, D.M., and Lukas, R. (1996) The Hawaii ocean time-series (HOT) program: background, rationale and field implementation. Deep-Sea Res 43: 129-156.
9. Kelly, K.M., and Chistoserdov, A.Y. (2001) Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island). FEMS Microbiol Ecol 35: 85-95.
10. Lowe, T.M., and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
11. Man, D., Wang, W., Sabehi, G., Aravind, L., Post, A.F., Massana, R., et al. (2003) Diversification and spectral tuning in marine proteorhodopsins. EMBO J 22: 1725-1731.
12. Mullins, T.D., Britschgi, T.B., Krest, R.L., and Giovannoni, S.J. (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 40: 148-158.
13. Pernthaler, A., Pernthaler, J., and Amann, R. (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68: 3094-3101.
14. Rappé, M.S., Vergin, K., and Giovannoni, S.J. (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol Ecol 33: 219-232.
15. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A., and Barrell, B. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
16. Sabehi, G., Massana, R., Bielawski, J.P., Rosenberg, M., DeLong, E.F., and Béjà, O. (2003) Novel proteorhodopsin variants from the Mediterranean and Red Seas. Environ Microbiol 5: 842-849.
17. Seki, T., Isono, K., Ozaki, K., Tsukahara, Y., Shibata-Katsuta, Y., Ito, M., et al. (1998) The metabolic pathway of visual pigment chromophore formation. Eur J Biochem 257: 522-527.
18. Spudich, J.L., Yang, C.S., Jung, K.H., and Spudich, E.N. (2000) Retinylidene proteins: structures and functions from Archaea to humans. Annu Rev Cell Dev Biol 16: 365-392.
19. Stein, J.L., Marsh, T.L., Wu, K.Y., Shizuya, H., and DeLong, E.F. (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178: 591-599.
20. Suzuki, M.T., Preston, C.M., Chavez, F.P., and DeLong, E.F. (2001a) Quantitative mapping of bacterioplankton populations in seawater: field tests across an upwelling plume in Monterey Bay. Aquat Microbiol Ecol 24: 117-127.
21. Suzuki, M.T., Béjà, O., Taylor, L.T., and DeLong, E.F. (2001b) Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 3: 323-331.
22. Swofford, D.L. (2002) PAUP*. Phylogenetic Analysis Using Parsimony. Sunderland, MA, USA: Sinauer Associates.
23. de la Torre, J.R., Christianson, L., Béjà, O., Suzuki, M.T., Karl, D., Heidelberg, J.F., and DeLong, E.F. (2003) Proteorhodopsin genes are widely distributed among divergent bacterial taxa. Proc Natl Acad Sci USA 100: 12830-12835.
24. Venter, J.C., Remington, K., Heidelberg, J., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
25. Zubkov, M.V., Fuchs, B.M., Burkill, P.H., and Amann, R. (2001) Comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the Celtic Sea. Appl Environ Microbiol 67: 5210-5218.