메뉴 건너뛰기




Volumn 9, Issue 4, 2007, Pages 846-858

Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla

Author keywords

[No Author keywords available]

Indexed keywords

CAROTENOID; PROTEORHODOPSIN; RHODOPSIN; SEA WATER; UNCLASSIFIED DRUG;

EID: 33947101507     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2006.01203.x     Document Type: Article
Times cited : (85)

References (53)
  • 2
    • 0030818333 scopus 로고    scopus 로고
    • Genetics of eubacterial carotenoid biosynthesis: A colorful tale
    • Armstrong, G.A. (1997) Genetics of eubacterial carotenoid biosynthesis: a colorful tale. Annu Rev Microbiol 51: 629-659.
    • (1997) Annu Rev Microbiol , vol.51 , pp. 629-659
    • Armstrong, G.A.1
  • 3
  • 4
    • 8744235102 scopus 로고    scopus 로고
    • Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
    • 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.
    • (2004) Genome Res , vol.14 , pp. 2221-2234
    • Baliga, N.S.1    Bonneau, R.2    Facciotti, M.T.3    Pan, M.4    Glusman, G.5    Deutsch, E.W.6
  • 6
    • 0034665853 scopus 로고    scopus 로고
    • Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea
    • Beja, 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.
    • (2000) Science , vol.289 , pp. 1902-1906
    • Beja, O.1    Aravind, L.2    Koonin, E.V.3    Suzuki, M.T.4    Hadd, A.5    Nguyen, L.P.6
  • 7
    • 0034554741 scopus 로고    scopus 로고
    • Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage
    • Beja, 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.
    • (2000) Environ Microbiol , vol.2 , pp. 516-529
    • Beja, O.1    Suzuki, M.T.2    Koonin, E.V.3    Aravind, L.4    Hadd, A.5    Nguyen, L.P.6
  • 9
    • 0035989637 scopus 로고    scopus 로고
    • Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family
    • Bernardet, J.F., Nakagawa, Y., and Holmes, B. (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52: 1049-1070.
    • (2002) Int J Syst Evol Microbiol , vol.52 , pp. 1049-1070
    • Bernardet, J.F.1    Nakagawa, Y.2    Holmes, B.3
  • 10
    • 6944240079 scopus 로고    scopus 로고
    • Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment
    • Bielawski, J., Dunn, K., Sabehi, G., and Beja, O. (2004) Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proc Natl Acad Sci USA 101: 14824-14829.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 14824-14829
    • Bielawski, J.1    Dunn, K.2    Sabehi, G.3    Beja, O.4
  • 11
    • 4544235395 scopus 로고    scopus 로고
    • Archaeal phylogeny based on proteins of the transcription and translation machineries: Tackling the Methanopyrus kandleri paradox
    • Brochier, C., Forterre, P., and Gribaldo, S. (2004) Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol 5: R17.
    • (2004) Genome Biol , vol.5
    • Brochier, C.1    Forterre, P.2    Gribaldo, S.3
  • 13
    • 0033617475 scopus 로고    scopus 로고
    • Cryptochromes: Blue light receptors for plants and animals
    • Cashmore, A.R., Jarillo, J.A., Wu, Y.-J., and Liu, D. (1999) Cryptochromes: blue light receptors for plants and animals. Science 284: 760-765.
    • (1999) Science , vol.284 , pp. 760-765
    • Cashmore, A.R.1    Jarillo, J.A.2    Wu, Y.-J.3    Liu, D.4
  • 14
    • 31544483932 scopus 로고    scopus 로고
    • Community genomics among stratified microbial assemblages in the ocean's interior
    • DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
    • (2006) Science , vol.311 , pp. 496-503
    • DeLong, E.F.1    Preston, C.M.2    Mincer, T.3    Rich, V.4    Hallam, S.J.5    Frigaard, N.U.6
  • 15
    • 32344444896 scopus 로고    scopus 로고
    • Photolyases and cryptochromes: Common mechanisms of DNA repair and light-driven signaling?
    • Essen, L.O. (2006) Photolyases and cryptochromes: common mechanisms of DNA repair and light-driven signaling? Curr Opin Struct Biol 16: 51-59.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 51-59
    • Essen, L.O.1
  • 16
    • 32844465575 scopus 로고    scopus 로고
    • Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea
    • Frigaard, N.U., Martinez, A., Mincer, T.J., and DeLong, E.F. (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847-850.
    • (2006) Nature , vol.439 , pp. 847-850
    • Frigaard, N.U.1    Martinez, A.2    Mincer, T.J.3    DeLong, E.F.4
  • 23
    • 33646260901 scopus 로고    scopus 로고
    • Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota
    • Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M., and DeLong, E.F. (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4: 520-536.
    • (2006) PLoS Biol , vol.4 , pp. 520-536
    • Hallam, S.J.1    Mincer, T.J.2    Schleper, C.3    Preston, C.M.4    Roberts, K.5    Richardson, P.M.6    DeLong, E.F.7
  • 24
    • 0034660609 scopus 로고    scopus 로고
    • Bacterial cryptochrome and photolyase: Characterization of two photolyase-like genes of Synechocystis sp. PCC6803
    • Hitomi, K., Okamoto, K., Daiyasu, H., Miyashita, H., Iwai, S., Toh, H., et al. (2000) Bacterial cryptochrome and photolyase: characterization of two photolyase-like genes of Synechocystis sp. PCC6803. Nucleic Acids Res 28: 2353-2362.
    • (2000) Nucleic Acids Res , vol.28 , pp. 2353-2362
    • Hitomi, K.1    Okamoto, K.2    Daiyasu, H.3    Miyashita, H.4    Iwai, S.5    Toh, H.6
  • 25
    • 0037346546 scopus 로고    scopus 로고
    • Demonstration of a sensory rhodopsin in eubacteria
    • Jung, K.-H., Trivedi, V.D., and Spudich, J.L. (2003) Demonstration of a sensory rhodopsin in eubacteria. Mol Microbiol 47: 1513-1522.
    • (2003) Mol Microbiol , vol.47 , pp. 1513-1522
    • Jung, K.-H.1    Trivedi, V.D.2    Spudich, J.L.3
  • 26
    • 0030970352 scopus 로고    scopus 로고
    • Expression of an exogenous isopentenyl diphosphate isomerase gene enhances isoprenoid biosynthesis in Escherichia coli
    • Kajiwara, S., Fraser, P.D., Kondo, K., and Misawa, N. (1997) Expression of an exogenous isopentenyl diphosphate isomerase gene enhances isoprenoid biosynthesis in Escherichia coli. Biochem J 324: 421-426.
    • (1997) Biochem J , vol.324 , pp. 421-426
    • Kajiwara, S.1    Fraser, P.D.2    Kondo, K.3    Misawa, N.4
  • 27
    • 0035970116 scopus 로고    scopus 로고
    • An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190
    • Kaneda, K., Kuzuyama, T., Takagi, M., Hayakawa, Y., and Seto, H. (2001) An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190. Proc Natl Acad Sci USA 98: 932-937.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 932-937
    • Kaneda, K.1    Kuzuyama, T.2    Takagi, M.3    Hayakawa, Y.4    Seto, H.5
  • 28
    • 0035980822 scopus 로고    scopus 로고
    • Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120
    • Kaneko, T., Nakamura, Y., Wolk, C.P., Kuritz, T., Sasamoto, S., Watanabe, A., et al. (2001) Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res 8: 205-213.
    • (2001) DNA Res , vol.8 , pp. 205-213
    • Kaneko, T.1    Nakamura, Y.2    Wolk, C.P.3    Kuritz, T.4    Sasamoto, S.5    Watanabe, A.6
  • 29
    • 0034780910 scopus 로고    scopus 로고
    • Horizontal gene transfer in prokaryotes: Quantification and classification
    • Koonin, E.V., Makarova, K.S., and Aravind, L. (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55: 709-742.
    • (2001) Annu Rev Microbiol , vol.55 , pp. 709-742
    • Koonin, E.V.1    Makarova, K.S.2    Aravind, L.3
  • 30
    • 0037394552 scopus 로고    scopus 로고
    • Diversity of the biosynthesis of the isoprene units
    • Kuzuyama, T., and Seto, H. (2003) Diversity of the biosynthesis of the isoprene units. Nat Prod Rep 20: 171-183.
    • (2003) Nat Prod Rep , vol.20 , pp. 171-183
    • Kuzuyama, T.1    Seto, H.2
  • 31
    • 0038391981 scopus 로고    scopus 로고
    • Diversification and spectral tuning in marine proteorhodopsins
    • 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.
    • (2003) EMBO J , vol.22 , pp. 1725-1731
    • Man, D.1    Wang, W.2    Sabehi, G.3    Aravind, L.4    Post, A.F.5    Massana, R.6
  • 32
    • 29144485325 scopus 로고    scopus 로고
    • The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea
    • Mongodin, E.F., Nelson, K.E., Daugherty, S., DeBoy, R.T., Wister, J., Khouri, H., et al. (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci USA 102: 18147-18152.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 18147-18152
    • Mongodin, E.F.1    Nelson, K.E.2    Daugherty, S.3    DeBoy, R.T.4    Wister, J.5    Khouri, H.6
  • 33
    • 12444292075 scopus 로고    scopus 로고
    • Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids
    • 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. DNA Res 10: 137-145.
    • (2003) DNA Res , vol.10 , pp. 137-145
    • Nakamura, Y.1    Kaneko, T.2    Sato, S.3    Mimuro, M.4    Miyashita, H.5    Tsuchiya, T.6
  • 34
    • 28644452091 scopus 로고    scopus 로고
    • Lateral gene transfer and phylogenetic assignment of environmental fosmid clones
    • Nesbo, C.L., Boucher, Y., Dlutek, M., and Doolittle, W.F. (2005) Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environ Microbiol 7: 2011-2026.
    • (2005) Environ Microbiol , vol.7 , pp. 2011-2026
    • Nesbo, C.L.1    Boucher, Y.2    Dlutek, M.3    Doolittle, W.F.4
  • 35
    • 0038009383 scopus 로고    scopus 로고
    • Novel dinoflagellate clock-related genes identified through microarray analysis
    • Okamoto, O.K., and Hastings, J.W. (2003) Novel dinoflagellate clock-related genes identified through microarray analysis. J Phycol 39: 519-526.
    • (2003) J Phycol , vol.39 , pp. 519-526
    • Okamoto, O.K.1    Hastings, J.W.2
  • 36
    • 0642312313 scopus 로고    scopus 로고
    • Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
    • Omelchenko, M.V., Makarova, K.S., Wolf, Y.I., Rogozin, I.B., and Koonin, E.V. (2003) Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol 4: R55.
    • (2003) Genome Biol , vol.4
    • Omelchenko, M.V.1    Makarova, K.S.2    Wolf, Y.I.3    Rogozin, I.B.4    Koonin, E.V.5
  • 37
    • 0035937192 scopus 로고    scopus 로고
    • brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum
    • Peck, R.F., Echavarri-Erasun, C., Johnson, E.A., Ng, W.V., Kennedy, S.P., Hood, L., et al. (2001) brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum. J Biol Chem 276: 5739-5744.
    • (2001) J Biol Chem , vol.276 , pp. 5739-5744
    • Peck, R.F.1    Echavarri-Erasun, C.2    Johnson, E.A.3    Ng, W.V.4    Kennedy, S.P.5    Hood, L.6
  • 38
    • 1842531691 scopus 로고    scopus 로고
    • New insights into the evolutionary history of type 1 rhodopsins
    • Ruiz-Gonzalez, M.X., and Marin, I. (2004) New insights into the evolutionary history of type 1 rhodopsins. J Mol Evol 58: 348-358.
    • (2004) J Mol Evol , vol.58 , pp. 348-358
    • Ruiz-Gonzalez, M.X.1    Marin, I.2
  • 42
    • 23944505538 scopus 로고    scopus 로고
    • New insights into metabolic properties of marine bacteria encoding proteorhodopsins
    • 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.
    • (2005) PLoS Biol , vol.3
    • Sabehi, G.1    Loy, A.2    Jung, K.-H.3    Partha, R.4    Spudich, J.L.5    Isaacson, T.6
  • 43
    • 0028332220 scopus 로고
    • Carotenoid biosynthesis in microorganisms and plants
    • Sandmann, G. (1994) Carotenoid biosynthesis in microorganisms and plants. Eur J Biochem 223: 7-24.
    • (1994) Eur J Biochem , vol.223 , pp. 7-24
    • Sandmann, G.1
  • 44
    • 0036896020 scopus 로고    scopus 로고
    • Molecular evolution of carotenoid biosynthesis from bacteria to plants
    • Sandmann, G. (2002) Molecular evolution of carotenoid biosynthesis from bacteria to plants. Physiol Planta 116: 431-440.
    • (2002) Physiol Planta , vol.116 , pp. 431-440
    • Sandmann, G.1
  • 45
    • 29144522344 scopus 로고    scopus 로고
    • Diversity of carotenoid synthesis gene clusters from environmental Enterobacteriaceae strains
    • Sedkova, N., Tao, L., Rouviere, P.E., and Cheng, Q. (2005) Diversity of carotenoid synthesis gene clusters from environmental Enterobacteriaceae strains. Appl Environ Microbiol 71: 8141-8146.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8141-8146
    • Sedkova, N.1    Tao, L.2    Rouviere, P.E.3    Cheng, Q.4
  • 46
    • 0037173051 scopus 로고    scopus 로고
    • Two rhodopsins mediate phototaxis to low- and highintensity light in Chlamydomonas reinhardtii
    • Sineshchekov, O.A., Jung, K.-H., and Spudich, J.L. (2002) Two rhodopsins mediate phototaxis to low- and highintensity light in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 99: 8689-8694.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8689-8694
    • Sineshchekov, O.A.1    Jung, K.-H.2    Spudich, J.L.3
  • 47
    • 0034519206 scopus 로고    scopus 로고
    • Retinylidene proteins: Structures and functions from archaea to humans
    • 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.
    • (2000) Annu Rev Cell Dev Biol , vol.16 , pp. 365-392
    • Spudich, J.L.1    Yang, C.S.2    Jung, K.H.3    Spudich, E.N.4
  • 48
    • 0035208354 scopus 로고    scopus 로고
    • Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton
    • Suzuki, M.T., Beja, O., Taylor, L.T., and DeLong, E.F. (2001) Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 3: 323-331.
    • (2001) Environ Microbiol , vol.3 , pp. 323-331
    • Suzuki, M.T.1    Beja, O.2    Taylor, L.T.3    DeLong, E.F.4
  • 49
    • 12244263975 scopus 로고    scopus 로고
    • Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay
    • Suzuki, M.T., Preston, C.M., Beja, O., de la Torre, J.R., Steward, G.F., and DeLong, E.F. (2004) Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb Ecol 48: 473-488.
    • (2004) Microb Ecol , vol.48 , pp. 473-488
    • Suzuki, M.T.1    Preston, C.M.2    Beja, O.3    de la Torre, J.R.4    Steward, G.F.5    DeLong, E.F.6
  • 50
    • 33645464254 scopus 로고    scopus 로고
    • RibAlign: A software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
    • Teeling, H., and Gloeckner, F.O. (2006) RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. BMC Bioinformatics 7: 66.
    • (2006) BMC Bioinformatics , vol.7 , pp. 66
    • Teeling, H.1    Gloeckner, F.O.2
  • 53
    • 0035085816 scopus 로고    scopus 로고
    • Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
    • Wolf, Y.I., Rogozin, I.B., Kondrashov, A.S., and Koonin, E.V. (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 11: 356-372.
    • (2001) Genome Res , vol.11 , pp. 356-372
    • Wolf, Y.I.1    Rogozin, I.B.2    Kondrashov, A.S.3    Koonin, E.V.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.