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Volumn 77, Issue 24, 2011, Pages 8676-8686

Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134

Author keywords

[No Author keywords available]

Indexed keywords

ANAPLEROTIC ENZYMES; CARBON AND NITROGEN; FLAVOBACTERIUM; GENOME ANALYSIS; GENOMICS; LOW CONCENTRATIONS; MARINE BACTERIUM; PHOTOHETEROTROPHIC; PROMOTER SEQUENCES; PROTEORHODOPSIN; RECALCITRANT ORGANIC MATTER; SOURCES OF ENERGY;

EID: 83155176272     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06152-11     Document Type: Article
Times cited : (43)

References (82)
  • 1
    • 9144253359 scopus 로고    scopus 로고
    • Application of comparative genomics in the identification and analysis of novel families of membraneassociated receptors in bacteria
    • Anantharaman, V., and L. Aravind. 2003. Application of comparative genomics in the identification and analysis of novel families of membraneassociated receptors in bacteria. BMC Genomics 4:34.
    • (2003) BMC Genomics , vol.4 , pp. 34
    • Anantharaman, V.1    Aravind, L.2
  • 2
    • 0024319453 scopus 로고
    • Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch binding sites and periplasmic starch-degrading enzymes
    • Anderson, K. L., and A. A. Salyers. 1989. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch binding sites and periplasmic starch-degrading enzymes. J. Bacteriol. 171: 3192-3198.
    • (1989) J. Bacteriol. , vol.171 , pp. 3192-3198
    • Anderson, K.L.1    Salyers, A.A.2
  • 3
    • 0024336683 scopus 로고
    • Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron
    • Anderson, K. L., and A. A. Salyers. 1989. Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron. J. Bacteriol. 171:3199-3204.
    • (1989) J. Bacteriol. , vol.171 , pp. 3199-3204
    • Anderson, K.L.1    Salyers, A.A.2
  • 4
    • 33750907710 scopus 로고    scopus 로고
    • Whole genome analysis of the marine Bacteroidetes "Gramella forsetii" reveals adaptations to degradation of polymeric organic matter
    • Bauer, M. M., et al. 2006. Whole genome analysis of the marine Bacteroidetes "Gramella forsetii" reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8:2201-2213.
    • (2006) Environ. Microbiol. , vol.8 , pp. 2201-2213
    • Bauer, M.M.1
  • 5
    • 0000288758 scopus 로고
    • The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes
    • M.P. Starr, H. Stolp, H. G. Trüper, A. Balows, and H. G. Schlegel (ed.), Springer-Verlag, Berlin, Germany
    • Baumann, P., and L. Baumann. 1981. The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes, p. 1302-1331. In M. P. Starr, H. Stolp, H. G. Trüper, A. Balows, and H. G. Schlegel (ed.), The prokaryotes. Springer-Verlag, Berlin, Germany.
    • (1981) The prokaryotes , pp. 1302-1331
    • Baumann, P.1    Baumann, L.2
  • 6
    • 0034665853 scopus 로고    scopus 로고
    • Bacterial rhodopsin: evidence for a new type of phototrophy in the sea
    • Béjà, O., et al. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902-1906.
    • (2000) Science , vol.289 , pp. 1902-1906
    • Béjà, O.1
  • 7
    • 45649085030 scopus 로고    scopus 로고
    • Plant carbohydrate scavenging through TonBdependent receptors: a feature shared by phytopathogenic and aquatic bacteria
    • Blanvillain, S., et al. 2007. Plant carbohydrate scavenging through TonBdependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One 2:e224.
    • (2007) PLoS One , vol.2
    • Blanvillain, S.1
  • 8
    • 77649282211 scopus 로고    scopus 로고
    • Relationship between operon preference and functional properties of persistent genes in bacterial genomes
    • Bratlie, M. S., J. Johansen, and F. Drabløs. 2010. Relationship between operon preference and functional properties of persistent genes in bacterial genomes. BMC Genomics 11:71.
    • (2010) BMC Genomics , vol.11 , pp. 71
    • Bratlie, M.S.1    Johansen, J.2    Drabløs, F.3
  • 9
    • 26444465087 scopus 로고    scopus 로고
    • Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis
    • Braun, T. F., M. K. Khubbar, D. A. Saffarini, and M. J. McBride. 2005. Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis. J. Bacteriol. 187:6943-6952.
    • (2005) J. Bacteriol. , vol.187 , pp. 6943-6952
    • Braun, T.F.1    Khubbar, M.K.2    Saffarini, D.A.3    McBride, M.J.4
  • 10
    • 58149200943 scopus 로고    scopus 로고
    • The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics
    • Cantarel, B. L., et al. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37:D233-238.
    • (2009) Nucleic Acids Res. , vol.37
    • Cantarel, B.L.1
  • 11
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 12
    • 0021273677 scopus 로고
    • Isolation and characterization of nonspreading mutants of the gliding bacterium Cytophaga johnsoniae
    • Chang, L. E., J. L. Pate, and R. J. Betzig. 1984. Isolation and characterization of nonspreading mutants of the gliding bacterium Cytophaga johnsoniae. J. Bacteriol. 159:26-35.
    • (1984) J. Bacteriol. , vol.159 , pp. 26-35
    • Chang, L.E.1    Pate, J.L.2    Betzig, R.J.3
  • 13
    • 34447513132 scopus 로고    scopus 로고
    • Mutational analysis of the ompA promoter from Flavobacterium johnsoniae
    • Chen, S., M. Bagdasarian, M. G. Kaufman, A. K. Bates, and E. D. Walker. 2007. Mutational analysis of the ompA promoter from Flavobacterium johnsoniae. J. Bacteriol. 189:5108-5118.
    • (2007) J. Bacteriol. , vol.189 , pp. 5108-5118
    • Chen, S.1    Bagdasarian, M.2    Kaufman, M.G.3    Bates, A.K.4    Walker, E.D.5
  • 14
    • 0027801562 scopus 로고
    • Phylogenetic diversity of aggregate-attached versus free-living marine bacterial assemblages
    • DeLong, E., D. G. Franks, and A. L. Alldredge. 1993. Phylogenetic diversity of aggregate-attached versus free-living marine bacterial assemblages. Limnol. Oceanogr. 38:924-934.
    • (1993) Limnol. Oceanogr. , vol.38 , pp. 924-934
    • DeLong, E.1    Franks, D.G.2    Alldredge, A.L.3
  • 15
    • 34247519181 scopus 로고    scopus 로고
    • Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay
    • Dulebohn, D., J. Choy, T. Sundermeier, N. Okan, and A. W. Karzai. 2007. Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry 46:4681-4693.
    • (2007) Biochemistry , vol.46 , pp. 4681-4693
    • Dulebohn, D.1    Choy, J.2    Sundermeier, T.3    Okan, N.4    Karzai, A.W.5
  • 16
    • 44949157290 scopus 로고    scopus 로고
    • A probabilistic model of local sequence alignment that simplifies statistical significance estimation
    • Eddy, S. R. 2008. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol. 4:e1000069.
    • (2008) PLoS Comput. Biol. , vol.4
    • Eddy, S.R.1
  • 17
    • 0032544080 scopus 로고    scopus 로고
    • Identification of an UP element consensus sequence for bacterial promoters
    • Estrem, S. T., T. Gaal, W. Ross, and R. L. Gourse. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. U. S. A. 95:9761-9766.
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 9761-9766
    • Estrem, S.T.1    Gaal, T.2    Ross, W.3    Gourse, R.L.4
  • 19
    • 51549120596 scopus 로고    scopus 로고
    • The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
    • Ganesan, H., A. S. Rakitianskaia, C. F. Davenport, B. Tümmler, and O. N. Reva. 2008. The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 9:333.
    • (2008) BMC Bioinformatics , vol.9 , pp. 333
    • Ganesan, H.1    Rakitianskaia, A.S.2    Davenport, C.F.3    Tümmler, B.4    Reva, O.N.5
  • 20
    • 33747858422 scopus 로고    scopus 로고
    • GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
    • Gao, F., and C. T. Zhang. 2006. GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences, Nucleic Acids Res. 34:W686-W691.
    • (2006) Nucleic Acids Res , vol.34
    • Gao, F.1    Zhang, C.T.2
  • 21
    • 27744438187 scopus 로고    scopus 로고
    • Proteorhodopsin in the ubiquitous marine bacterium SAR11
    • Giovannoni, S. J., et al. 2005. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438:82-85.
    • (2005) Nature , vol.438 , pp. 82-85
    • Giovannoni, S.J.1
  • 22
    • 33746605947 scopus 로고    scopus 로고
    • A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes
    • Goldberg, S. M. D., et al. 2006. A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. U. S. A. 103:11240-11245.
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 11240-11245
    • Goldberg, S.M.D.1
  • 23
    • 33846238031 scopus 로고    scopus 로고
    • Light stimulates growth of proteorhodopsin- containing marine Flavobacteria
    • Gómez-Consarnau, L., et al. 2007. Light stimulates growth of proteorhodopsin- containing marine Flavobacteria. Nature 445:210-213.
    • (2007) Nature , vol.445 , pp. 210-213
    • Gómez-Consarnau, L.1
  • 24
    • 77951706049 scopus 로고    scopus 로고
    • Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation
    • Gómez-Consarnau, L., et al. 2010. Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol. 8:e1000358.
    • (2010) PLoS Biol. , vol.8
    • Gómez-Consarnau, L.1
  • 25
    • 47249148362 scopus 로고    scopus 로고
    • Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)
    • González, J. M., et al. 2008. Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc. Natl. Acad. Sci. U. S. A. 105:8724-8729.
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 8724-8729
    • González, J.M.1
  • 26
    • 0034835047 scopus 로고    scopus 로고
    • Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons
    • Häse, C. C., N. D. Fedorova, M. Y. Galperin, and P. A. Dibrov. 2001. Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons. Microbiol. Mol. Biol. Rev. 65:353-370.
    • (2001) Microbiol. Mol. Biol. Rev. , vol.65 , pp. 353-370
    • Häse, C.C.1    Fedorova, N.D.2    Galperin, M.Y.3    Dibrov, P.A.4
  • 27
    • 54949108618 scopus 로고    scopus 로고
    • Heme uptake by Microscilla marina and evidence for heme uptake systems in the genomes of diverse marine bacteria
    • Hopkinson, B. M., K. L. Roe, and K. A. Barbeau. 2008. Heme uptake by Microscilla marina and evidence for heme uptake systems in the genomes of diverse marine bacteria. Appl. Environ. Microbiol. 74:6263-6270.
    • (2008) Appl. Environ. Microbiol. , vol.74 , pp. 6263-6270
    • Hopkinson, B.M.1    Roe, K.L.2    Barbeau, K.A.3
  • 28
    • 19944428969 scopus 로고    scopus 로고
    • Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy
    • Hou, S., et al. 2004. Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc. Natl. Acad. Sci. U. S. A. 101:18036-18041.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 18036-18041
    • Hou, S.1
  • 29
    • 77954273729 scopus 로고    scopus 로고
    • Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping
    • Johnson, E. T., et al. 2010. Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping. Appl. Environ. Microbiol. 76:4123-4129.
    • (2010) Appl. Environ. Microbiol. , vol.76 , pp. 4123-4129
    • Johnson, E.T.1
  • 30
    • 0041341888 scopus 로고    scopus 로고
    • Prediction of lipoprotein signal peptides in Gram-negative bacteria
    • Juncker, A. S., et al. 2003. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. 12:1652-1662.
    • (2003) Protein Sci. , vol.12 , pp. 1652-1662
    • Juncker, A.S.1
  • 31
    • 0033816775 scopus 로고    scopus 로고
    • Predicted highly expressed genes of diverse prokaryotic genomes
    • Karlin, S., and J. Mrázek. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182:5238-5250.
    • (2000) J. Bacteriol. , vol.182 , pp. 5238-5250
    • Karlin, S.1    Mrázek, J.2
  • 32
    • 0034888743 scopus 로고    scopus 로고
    • Characterizations of highly expressed genes of four fast-growing bacteria
    • Karlin, S., J. Mrázek, A. Campbell, and D. Kaiser. 2001. Characterizations of highly expressed genes of four fast-growing bacteria. J. Bacteriol. 183: 5025-5040.
    • (2001) J. Bacteriol. , vol.183 , pp. 5025-5040
    • Karlin, S.1    Mrázek, J.2    Campbell, A.3    Kaiser, D.4
  • 33
    • 18844446950 scopus 로고    scopus 로고
    • Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes
    • Karlin, S., L. Brocchieri, A. Campbell, M. Cyert, and J. Mrázek. 2005. Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. Proc. Natl. Acad. Sci. U. S. A. 102:7309-7314.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 7309-7314
    • Karlin, S.1    Brocchieri, L.2    Campbell, A.3    Cyert, M.4    Mrázek, J.5
  • 35
    • 80052340733 scopus 로고    scopus 로고
    • Complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae
    • Klippel, B., et al. 2011. Complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae. J. Bacteriol. 193:4545-4546.
    • (2011) J. Bacteriol , vol.193 , pp. 4545-4546
    • Klippel, B.1
  • 36
    • 0031840359 scopus 로고    scopus 로고
    • Bioenergetics of marine bacteria
    • Kogure, K. 1998. Bioenergetics of marine bacteria. Curr. Opin. Biotechnol. 9:278-282.
    • (1998) Curr. Opin. Biotechnol. , vol.9 , pp. 278-282
    • Kogure, K.1
  • 37
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S., et al. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12.
    • (2004) Genome Biol. , vol.5
    • Kurtz, S.1
  • 38
    • 71249149524 scopus 로고    scopus 로고
    • Lightdependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal water
    • Lami, R., M. T. Cottrell, B. J. Campbell, and D. L. Kirchman. 2009. Lightdependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal water. Environ. Microbiol. 11:3201-3209.
    • (2009) Environ. Microbiol. , vol.11 , pp. 3201-3209
    • Lami, R.1    Cottrell, M.T.2    Campbell, B.J.3    Kirchman, D.L.4
  • 39
    • 0016139829 scopus 로고
    • Salt-dependent properties of proteins from extremely halophilic bacteria
    • Lanyi, J. K. 1974. Salt-dependent properties of proteins from extremely halophilic bacteria. Bacteriol. Rev. 38:272-290.
    • (1974) Bacteriol. Rev. , vol.38 , pp. 272-290
    • Lanyi, J.K.1
  • 40
    • 36448991500 scopus 로고    scopus 로고
    • CLUSTAL W and CLUSTAL X version 2.0
    • Larkin, M. A., et al. 2007. CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 23:2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 41
    • 0034306448 scopus 로고    scopus 로고
    • Gene context conservation of a higher order than operons
    • Lathe, W. C., B. Snel, and P. Bork. 2000. Gene context conservation of a higher order than operons. Trends Biochem. Sci. 25:474-479.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 474-479
    • Lathe, W.C.1    Snel, B.2    Bork, P.3
  • 42
    • 0242440314 scopus 로고    scopus 로고
    • Gene organization: selection, selfishness, and serendipity
    • Lawrence, J. G. 2003. Gene organization: selection, selfishness, and serendipity. Annu. Rev. Microbiol. 57:419-440.
    • (2003) Annu. Rev. Microbiol. , vol.57 , pp. 419-440
    • Lawrence, J.G.1
  • 44
    • 0034769801 scopus 로고    scopus 로고
    • Bacterial gliding motility: multiple mechanisms for cell movement over surfaces
    • McBride, M. J. 2001. Bacterial gliding motility: multiple mechanisms for cell movement over surfaces. Annu. Rev. Microbiol. 55:49-75.
    • (2001) Annu. Rev. Microbiol. , vol.55 , pp. 49-75
    • McBride, M.J.1
  • 45
    • 2642529310 scopus 로고    scopus 로고
    • Cytophaga-Flavobacterium gliding motility
    • McBride, M. J. 2004. Cytophaga-Flavobacterium gliding motility. J. Mol. Microbiol. Biotechnol. 7:63-71.
    • (2004) J. Mol. Microbiol. Biotechnol. , vol.7 , pp. 63-71
    • McBride, M.J.1
  • 46
    • 70350508238 scopus 로고    scopus 로고
    • Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis
    • McBride, M. J., et al. 2009. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl. Environ. Microbiol. 75:6864-6875.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 6864-6875
    • McBride, M.J.1
  • 47
    • 0027770723 scopus 로고
    • In a class of its own-the RNA polymerase sigma factor sigma 54 (sigma N)
    • Merrick, M. J. 1993. In a class of its own-the RNA polymerase sigma factor sigma 54 (sigma N). Mol. Microbiol. 10:903-909.
    • (1993) Mol. Microbiol. , vol.10 , pp. 903-909
    • Merrick, M.J.1
  • 48
    • 0037561991 scopus 로고    scopus 로고
    • GenDB: an open source genome annotation system for prokaryote genomes
    • Meyer, F., et al. 2003. GenDB: an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31:2187-2195.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2187-2195
    • Meyer, F.1
  • 49
    • 77951497989 scopus 로고    scopus 로고
    • Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction
    • Morris, R. M., et al. 2010. Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J. 4:673-685.
    • (2010) ISME J. , vol.4 , pp. 673-685
    • Morris, R.M.1
  • 50
    • 41949087859 scopus 로고    scopus 로고
    • SprB is a cell surface component of the Flavobacterium johnsoniae gliding motility machinery
    • Nelson, S. S., S. Bollampalli, and M. J. McBride. 2008. SprB is a cell surface component of the Flavobacterium johnsoniae gliding motility machinery. J. Bacteriol. 190:2851-2857.
    • (2008) J. Bacteriol. , vol.190 , pp. 2851-2857
    • Nelson, S.S.1    Bollampalli, S.2    McBride, M.J.3
  • 51
    • 0037109119 scopus 로고    scopus 로고
    • Use and misuse of correspondence analysis in codon usage studies
    • Perriere, G., and J. Thioulouse. 2002. Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res. 30:4548-4555.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4548-4555
    • Perriere, G.1    Thioulouse, J.2
  • 52
    • 8744282719 scopus 로고    scopus 로고
    • Changes in bacterioplankton composition under different phytoplankton regimens
    • Pinhassi, J., et al. 2004. Changes in bacterioplankton composition under different phytoplankton regimens. Appl. Environ. Microbiol. 70:6753-6766.
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 6753-6766
    • Pinhassi, J.1
  • 54
    • 0037512192 scopus 로고
    • Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit P in Escherichia coli
    • Post, L. E., G. D. Strycharz, M. Nomura, H. Lewis, and P. P. Dennis. 1979. Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit P in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 76:1697-1701.
    • (1979) Proc. Natl. Acad. Sci. U. S. A. , vol.76 , pp. 1697-1701
    • Post, L.E.1    Strycharz, G.D.2    Nomura, M.3    Lewis, H.4    Dennis, P.P.5
  • 55
    • 0027469984 scopus 로고
    • Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis
    • Preisig, O., D. Anthamatten, and H. Hennecke. 1993. Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis. Proc. Natl. Acad. Sci. U. S. A. 90:3309-3313.
    • (1993) Proc. Natl. Acad. Sci. U. S. A. , vol.90 , pp. 3309-3313
    • Preisig, O.1    Anthamatten, D.2    Hennecke, H.3
  • 56
    • 38549144165 scopus 로고    scopus 로고
    • HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
    • Puigbò, P., A. Romeu, and S. Garcia-Vallvé. 2008. HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res. 36:D524-D527.
    • (2008) Nucleic Acids Res. , vol.36
    • Puigbò, P.1    Romeu, A.2    Garcia-Vallvé, S.3
  • 57
    • 34547579086 scopus 로고    scopus 로고
    • OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
    • Puigbò, P., E. Guzmán, A. Romeu, and S. Garcia-Vallvé. 2007. OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res. 35:W126-W131.
    • (2007) Nucleic Acids Res. , vol.35
    • Puigbò, P.1    Guzmán, E.2    Romeu, A.3    Garcia-Vallvé, S.4
  • 58
    • 77950888128 scopus 로고    scopus 로고
    • The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation
    • Qin, Q.-L., et al. 2010. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 11:247.
    • (2010) BMC Genomics , vol.11 , pp. 247
    • Qin, Q.-L.1
  • 60
    • 77952279613 scopus 로고    scopus 로고
    • Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea
    • Riedel, T., et al. 2010. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl. Environ. Microbiol. 76:3187-3197.
    • (2010) Appl. Environ. Microbiol. , vol.76 , pp. 3187-3197
    • Riedel, T.1
  • 61
    • 0033951021 scopus 로고    scopus 로고
    • Dynamics of bacterial community composition and activity during a mesocosm diatom bloom
    • Riemann, L., G. F. Steward, and F. Azam. 2000. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol. 66:578-587.
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 578-587
    • Riemann, L.1    Steward, G.F.2    Azam, F.3
  • 62
    • 0037052935 scopus 로고    scopus 로고
    • Connected gene neighborhoods in prokaryotic genomes
    • Rogozin, I. B., et al. 2002. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 30:2212-2223.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 2212-2223
    • Rogozin, I.B.1
  • 63
    • 0028889420 scopus 로고
    • Conjugative transposons: an unusual and diverse set of integrated gene transfer elements
    • Salyers, A. A., N. B. Shoemaker, A. M. Stevens, and L. Y. Li. 1995. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol. Rev. 59:579-590.
    • (1995) Microbiol. Rev. , vol.59 , pp. 579-590
    • Salyers, A.A.1    Shoemaker, N.B.2    Stevens, A.M.3    Li, L.Y.4
  • 64
    • 0023650543 scopus 로고
    • The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M., and W. H. Li. 1987. The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 65
  • 66
    • 58149505604 scopus 로고    scopus 로고
    • Discovering functional novelty in metagenomes: examples from light-mediated processes
    • Singh, A. H., T. Doerks, I. Letunic, J. Raes, and P. Bork. 2009. Discovering functional novelty in metagenomes: examples from light-mediated processes. J. Bacteriol. 191:32-41.
    • (2009) J. Bacteriol. , vol.191 , pp. 32-41
    • Singh, A.H.1    Doerks, T.2    Letunic, I.3    Raes, J.4    Bork, P.5
  • 67
    • 0031821181 scopus 로고    scopus 로고
    • Genetic elements of Bacteroides species: a moving story
    • Smith, C. J., G. D. Tribble, and D. P. Bayley. 1998. Genetic elements of Bacteroides species: a moving story. Plasmid 40:12-29.
    • (1998) Plasmid , vol.40 , pp. 12-29
    • Smith, C.J.1    Tribble, G.D.2    Bayley, D.P.3
  • 68
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 69
    • 79955856835 scopus 로고    scopus 로고
    • Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration
    • Steindler, L., M. S. Schwalbach, D. P. Smith, F. Chan, and S. J. Giovannoni. 2011. Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration. PLoS One 6:e19725.
    • (2011) PLoS One , vol.6
    • Steindler, L.1    Schwalbach, M.S.2    Smith, D.P.3    Chan, F.4    Giovannoni, S.J.5
  • 70
    • 34547492897 scopus 로고    scopus 로고
    • Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
    • Stepanauskas, R., and M. E. Sieracki. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc. Natl. Acad. Sci. U. S. A. 104:9052-9057.
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 9052-9057
    • Stepanauskas, R.1    Sieracki, M.E.2
  • 71
    • 34247488726 scopus 로고    scopus 로고
    • The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin
    • Stingl, U., R. A. Desiderio, J. C. Cho, K. L. Vergin, and S. J. Giovannoni. 2007. The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl. Environ. Microbiol. 73:2290-2296.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 2290-2296
    • Stingl, U.1    Desiderio, R.A.2    Cho, J.C.3    Vergin, K.L.4    Giovannoni, S.J.5
  • 72
    • 70349661794 scopus 로고    scopus 로고
    • Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114
    • Tang, K.-H., X. Feng, Y. J. Tang, and R. E. Blankenship. 2009. Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114. PLoS One 4:e7233.
    • (2009) PLoS One , vol.4
    • Tang, K.-H.1    Feng, X.2    Tang, Y.J.3    Blankenship, R.E.4
  • 73
    • 36248934750 scopus 로고    scopus 로고
    • Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too
    • van der Horst, M. A., J. Key, and K. J. Hellingwerf. 2007. Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too. Trends Microbiol. 15:554-562.
    • (2007) Trends Microbiol. , vol.15 , pp. 554-562
    • van der Horst, M.A.1    Key, J.2    Hellingwerf, K.J.3
  • 74
    • 11144354360 scopus 로고    scopus 로고
    • Environmental genome shotgun sequencing of the Sargasso Sea
    • Venter, J. C., et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
    • (2004) Science , vol.304 , pp. 66-74
    • Venter, J.C.1
  • 75
    • 33745828696 scopus 로고    scopus 로고
    • Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
    • Waack, S., et al. 2006. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7:142.
    • (2006) BMC Bioinformatics , vol.7 , pp. 142
    • Waack, S.1
  • 76
    • 0038477099 scopus 로고    scopus 로고
    • Utilization of iron/organic ligand complexes by marine bacterioplankton
    • Weaver, R. S., D. L. Kirchman, and D. A. Hutchins. 2003. Utilization of iron/organic ligand complexes by marine bacterioplankton. Aquat. Microb. Ecol. 31:227-239.
    • (2003) Aquat. Microb. Ecol. , vol.31 , pp. 227-239
    • Weaver, R.S.1    Kirchman, D.L.2    Hutchins, D.A.3
  • 77
    • 65449134335 scopus 로고    scopus 로고
    • Assembling the marine metagenome, one cell at a time
    • Woyke, T., et al. 2009. Assembling the marine metagenome, one cell at a time. PLoS One 4:e5299.
    • (2009) PLoS One , vol.4
    • Woyke, T.1
  • 78
    • 34249901582 scopus 로고    scopus 로고
    • Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii
    • Xie, G., et al. 2007. Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appl. Environ. Microbiol. 73:3536-3546.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 3536-3546
    • Xie, G.1
  • 79
    • 77958064380 scopus 로고    scopus 로고
    • Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron
    • Xu, Q., et al. 2010. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66:1297-1305.
    • (2010) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. , vol.66 , pp. 1297-1305
    • Xu, Q.1
  • 80
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • Yu, N. Y., et al. 2010. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes, Bioinformatics 26:1608-1615.
    • (2010) Bioinformatics , vol.26 , pp. 1608-1615
    • Yu, N.Y.1
  • 81
    • 33244469311 scopus 로고    scopus 로고
    • Segmentation algorithm for DNA sequences
    • Zhang, C.-T., F. Gao, and R. Zhang. 2005. Segmentation algorithm for DNA sequences. Phys. Rev. E 72:041917(1-6).
    • (2005) Phys. Rev. E , vol.72 , Issue.1-6 , pp. 041917
    • Zhang, C.-T.1    Gao, F.2    Zhang, R.3
  • 82
    • 68849120882 scopus 로고    scopus 로고
    • Photoheterotrophy in marine prokaryotes
    • Zubkov, M. V. 2009. Photoheterotrophy in marine prokaryotes. J. Plankton Res. 31:933-938.
    • (2009) J. Plankton Res. , vol.31 , pp. 933-938
    • Zubkov, M.V.1


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