Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas

ISME Journal

Volumn 1, Issue 1, 2007, Pages 48-55

  Sabehi, Gazalah ^a   Kirkup, Benjamin C ^b   Rozenberg, Mira ^a   Stambler, Noga ^c   Polz, Martin F ^b   Béjá, Oded ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b USA   (United States)

^c BAR ILAN UNIVERSITY   (Israel)

Author keywords

Flavobacteria; Proteorhodopsin; Retinal; SAR11; SAR86; Spectral tuning

Indexed keywords

PROTEORHODOPSIN; RHODOPSIN; SEA WATER; UNCLASSIFIED DRUG;

ADAPTATION; ARTICLE; ATLANTIC OCEAN; COMPARATIVE STUDY; MEDITERRANEAN SEA; METABOLISM; PHYSIOLOGY; PROTEOBACTERIA; SEASON; SPECIES DIFFERENCE;

ADAPTATION, PHYSIOLOGICAL; ATLANTIC OCEAN; MEDITERRANEAN SEA; PROTEOBACTERIA; RHODOPSIN; SEASONS; SEAWATER; SPECIES SPECIFICITY;

FLAVOBACTERIA;

EID: 34248191374     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2007.10     Document Type: Article

References (34)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990). Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP et al. (2000). Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902-1906.
3. Béjà O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. (2001). Proteorhodopsin phototrophy in the ocean. Nature 411: 786-789.
4. Bielawski JP, Dunn KA, Sabehi G, Béjà O. (2004). Darwinian adaptation of proteorhodopsin to different light intensities in the environment. Proc Natl Acad Sci USA 141: 14824-14829.
5. Colwell RK. (2005). EstimateS: statistical estimation of species richness and shared species from samples, version 7.5. http://purl.oclc.org/estimat.
6. de la Torre JR, Christianson L, Béjà O, Suzuki MT, Karl D, Heidelberg JF et al. (2003). Proteorhodopsin genes are widely distributed among divergent bacterial taxa. Proc Natl Acad Sci USA 100: 12830-12835.
7. Felsenstein J. (1989). PHYLIP-phylogeny interference package (version 3.2). Cladistics 5: 164-166.
8. Frigaard N-U, Martinez A, Mincer TJ, DeLong EF. (2006). Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847-850.
9. Giovannoni SJ, Rappé M. (2000). Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman DL (ed). Microbial Ecology of the Oceans. John Wiley & Sons Inc.: New York, NY, USA, pp 47-84.
10. Giovannoni SJ, Bibbs L, Cho J-C, Stapels MD, Desiderio R, Vergin KL et al. (2005a). Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438: 82-85.
11. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D et al. (2005b). Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.
12. Gómez-Consarnau L, González JM, Coll-Lladó M, Gourdon P, Pascher T, Neutze R et al. (2007). Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445: 210-213.
13. Gordon DA, Giovannoni SJ. (1996). Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific Oceans. Appl Environ Microbiol 62: 1171-1177.
14. Klepac-Ceraj V, Ceraj I, Polz MF. (2006). CLUSTERER: extendable java application for sequence grouping and cluster analyses. Online J Bioinf 7: 15-21.
15. Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R et al. (2003). Diversification and spectral tuning in marine proteorhodopsins. EMBO J 22: 1725-1731.
16. Martinez A, Bradley AS, Waldbauer J, Summons RE, DeLong EF. (2007). Proteorhodopsin photosystem gene expression enables photophosphorylation in heterologous host. Proc Natl Acad Sci USA, 10.1073/pnas.0611470104.
17. Massana R, Murray AE, Preston CM, DeLong ED. (1997). Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl Environ Microbiol 63: 50-56.
18. McCarren J, DeLong EF. (2007). Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla. Environ Microbiol 9: 846-858.
19. Okamoto OK, Hastings aJW. (2003). Novel dinoflagellate clock-related genes identified through microarray analysis. J Phycol 39: 519-526.
20. Sabehi G, Béjà O, Suzuki MT, Preston CM, DeLong EF. (2004). Different SAR86 subgroups harbour divergent proteorhodopsins. Environ Microbiol 6: 903-910.
21. Sabehi G, Massana R, Bielawski JP, Rosenberg M, DeLong EF, Béjà O. (2003). Novel proteorhodopsin variants from the Mediterranean and Red Seas. Environ Microbiol 5: 842-849.
22. Sabehi G, Loy A, Jung KH, Partha R, Spudich JL, Isaacson T et al. (2005). New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol 3: e273.
23. Schloss PD, Handelsman J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
24. Schloss PD, Larget BR, Handelsman J. (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-5492.
25. Sharma AK, Spudich JL, Doolittle WE (2006). Microbial rhodopsins: functional versatility and genetic mobility. Trends Microbiol 14: 463-469.
26. Spudich JL, Yang CS, Jung KH, Spudich EN. (2000). Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol 16: 365-392.
27. Stingl U, Desiderio RA, Cho J-C, Vergin KL, Giovannoni SJ. (2007). The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microbiol, doi:10.1128/AEM.02559-06.
28. Stomp M, Huisman J, De Jongh F, Veraart AJ, Gerla D, Rijkeboer M et al. (2004). Adaptive divergence in pigment composition promotes phytoplankton biodiversity. Nature 432: 104-107.
29. Suzuki MT, Giovannoni SJ. (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
30. Swofford DL. (2002). PAUP*. Phylogenetic analysis using parsimony (*and other methods). PAUP*, Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates: Sunderland, MA, USA.
31. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
32. Thurman HV, Trujillo AP. (1999). Essentials of Oceanography. Prentice Hall: NJ, USA.
33. Venter JC, Remington K, Heidelberg J, Halpern AL, Rusch D, Eisen JA et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
34. Walter JM, Greenfield D, Bustamante C, Liphardt J. (2007). Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci USA 104: 2408-2412.