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Volumn 397, Issue 1-2, 2007, Pages 136-142

Comparative analysis of predicted gene expression among deep-sea genomes

Author keywords

Deep sea microbes; G + C content; Hydrostatic pressure; Optimal growth temperature; Predicted highly expressed

Indexed keywords

RIBOSOME PROTEIN; TRANSCRIPTION FACTOR;

EID: 34250832787     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2007.04.023     Document Type: Article
Times cited : (14)

References (40)
  • 1
    • 33744760821 scopus 로고    scopus 로고
    • Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice
    • Auman A.J., Breezee J.L., Gosink J.J., Kampfer P., and Staley J.T. Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice. Int. J. Syst. Evol. Microbiol. 56 (2006) 1001-1007
    • (2006) Int. J. Syst. Evol. Microbiol. , vol.56 , pp. 1001-1007
    • Auman, A.J.1    Breezee, J.L.2    Gosink, J.J.3    Kampfer, P.4    Staley, J.T.5
  • 2
    • 0037171156 scopus 로고    scopus 로고
    • Pressure effects on in vivo microbial processes
    • Bartlett D.H. Pressure effects on in vivo microbial processes. Biochim. Biophys. Acta 1595 (2002) 367-381
    • (2002) Biochim. Biophys. Acta , vol.1595 , pp. 367-381
    • Bartlett, D.H.1
  • 3
    • 16044367245 scopus 로고    scopus 로고
    • Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
    • Bult C.J., et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273 (1996) 1058-1073
    • (1996) Science , vol.273 , pp. 1058-1073
    • Bult, C.J.1
  • 4
    • 0034693042 scopus 로고    scopus 로고
    • Structural and genomic correlates of hyperthermostability
    • Cambillau C., and Claverie J.M. Structural and genomic correlates of hyperthermostability. J. Biol. Chem. 275 (2000) 32383-32386
    • (2000) J. Biol. Chem. , vol.275 , pp. 32383-32386
    • Cambillau, C.1    Claverie, J.M.2
  • 5
    • 0037346631 scopus 로고    scopus 로고
    • An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi
    • Cohen G.N., et al. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol. 47 (2003) 1495-1512
    • (2003) Mol. Microbiol. , vol.47 , pp. 1495-1512
    • Cohen, G.N.1
  • 6
    • 14744303570 scopus 로고    scopus 로고
    • A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code
    • Di Giulio M. A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code. Gene 346 (2005) 1-6
    • (2005) Gene , vol.346 , pp. 1-6
    • Di Giulio, M.1
  • 7
    • 19444366761 scopus 로고    scopus 로고
    • Gene expression analysis of six GC-rich Gram-negative phytopathogens
    • Fu Q.S., Li F., and Chen L.L. Gene expression analysis of six GC-rich Gram-negative phytopathogens. Biochem. Biophys. Res. Commun. 332 (2005) 380-387
    • (2005) Biochem. Biophys. Res. Commun. , vol.332 , pp. 380-387
    • Fu, Q.S.1    Li, F.2    Chen, L.L.3
  • 8
    • 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. 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 (2004) 18036-18041
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 18036-18041
    • Hou, S.1
  • 9
    • 0033816775 scopus 로고    scopus 로고
    • Predicted highly expressed genes of diverse prokaryotic genomes
    • Karlin S., and Mrazek J. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182 (2000) 5238-5250
    • (2000) J. Bacteriol. , vol.182 , pp. 5238-5250
    • Karlin, S.1    Mrazek, J.2
  • 10
    • 0031720281 scopus 로고    scopus 로고
    • Codon usages in different gene classes of the Escherichia coli genome
    • Karlin S., Mrazek J., and Campbell A.M. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29 (1998) 1341-1355
    • (1998) Mol. Microbiol. , vol.29 , pp. 1341-1355
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 11
    • 0034888743 scopus 로고    scopus 로고
    • Characterizations of highly expressed genes of four fast-growing bacteria
    • Karlin S., Mrazek J., Campbell A., and Kaiser D. Characterizations of highly expressed genes of four fast-growing bacteria. J. Bacteriol. 183 (2001) 5025-5040
    • (2001) J. Bacteriol. , vol.183 , pp. 5025-5040
    • Karlin, S.1    Mrazek, J.2    Campbell, A.3    Kaiser, D.4
  • 13
    • 1942469359 scopus 로고    scopus 로고
    • Comparative analysis of gene expression among low G + C gram-positive genomes
    • Karlin S., Theriot J., and Mrazek J. Comparative analysis of gene expression among low G + C gram-positive genomes. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 6182-6187
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 6182-6187
    • Karlin, S.1    Theriot, J.2    Mrazek, J.3
  • 15
    • 0037336256 scopus 로고    scopus 로고
    • Molecular analysis of the multiple GroEL proteins of Chlamydiae
    • Karunakaran K.P., et al. Molecular analysis of the multiple GroEL proteins of Chlamydiae. J. Bacteriol. 185 (2003) 1958-1966
    • (2003) J. Bacteriol. , vol.185 , pp. 1958-1966
    • Karunakaran, K.P.1
  • 16
    • 0031196960 scopus 로고    scopus 로고
    • The molecular biology of barophilic bacteria
    • Kato C., and Bartlett D.H. The molecular biology of barophilic bacteria. Extremophiles 1 (1997) 111-116
    • (1997) Extremophiles , vol.1 , pp. 111-116
    • Kato, C.1    Bartlett, D.H.2
  • 17
    • 0033563504 scopus 로고    scopus 로고
    • Statistical properties of open reading frames in complete genome sequences
    • Li W. Statistical properties of open reading frames in complete genome sequences. Comput. Chem. 23 (1999) 283-301
    • (1999) Comput. Chem. , vol.23 , pp. 283-301
    • Li, W.1
  • 18
    • 0032519913 scopus 로고    scopus 로고
    • Distribution of the pressure-regulated operons in deep-sea bacteria
    • Li L., Kato C., Nogi Y., and Horikoshi K. Distribution of the pressure-regulated operons in deep-sea bacteria. FEMS. Microbiol. Lett. 159 (1998) 159-166
    • (1998) FEMS. Microbiol. Lett. , vol.159 , pp. 159-166
    • Li, L.1    Kato, C.2    Nogi, Y.3    Horikoshi, K.4
  • 19
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strands of bacteria
    • Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13 (1996) 660-665
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 20
    • 0036796799 scopus 로고    scopus 로고
    • Synonymous codon usage is subject to selection in thermophilic bacteria
    • Lynn D.J., Singer G.A., and Hickey D.A. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30 (2002) 4272-4277
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4272-4277
    • Lynn, D.J.1    Singer, G.A.2    Hickey, D.A.3
  • 21
    • 25144435959 scopus 로고    scopus 로고
    • The most deviated codon position in AT-rich bacterial genomes: a function related analysis
    • Ma B.G., and Chen L.L. The most deviated codon position in AT-rich bacterial genomes: a function related analysis. J. Biomol. Struct. Dyn. 23 (2005) 143-149
    • (2005) J. Biomol. Struct. Dyn. , vol.23 , pp. 143-149
    • Ma, B.G.1    Chen, L.L.2
  • 22
    • 33645294354 scopus 로고    scopus 로고
    • CvP-bias as an index to predict the life style of last common ancestor
    • Ma B.G., Song Q.S., and Zhang H.Y. CvP-bias as an index to predict the life style of last common ancestor. J. Biomol. Struct. Dyn. 23 (2006) 555-558
    • (2006) J. Biomol. Struct. Dyn. , vol.23 , pp. 555-558
    • Ma, B.G.1    Song, Q.S.2    Zhang, H.Y.3
  • 23
    • 0043011009 scopus 로고    scopus 로고
    • Comparative genomics of Archaea: how much have we learned in six years, and what's next?
    • Makarova K.S., and Koonin E.V. Comparative genomics of Archaea: how much have we learned in six years, and what's next?. Genome Biol. 4 (2003) 115
    • (2003) Genome Biol. , vol.4 , pp. 115
    • Makarova, K.S.1    Koonin, E.V.2
  • 24
    • 0035027423 scopus 로고    scopus 로고
    • Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus
    • McDonald J.H. Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus. Mol. Biol. Evol. 18 (2001) 741-749
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 741-749
    • McDonald, J.H.1
  • 25
    • 0032737311 scopus 로고    scopus 로고
    • Patterns of temperature adaptation in proteins from Methanococcus and Bacillus
    • McDonald J.H., Grasso A.M., and Rejto L.K. Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol. Biol. Evol. 16 (1999) 1785-1790
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1785-1790
    • McDonald, J.H.1    Grasso, A.M.2    Rejto, L.K.3
  • 26
    • 0032584101 scopus 로고    scopus 로고
    • Strand compositional asymmetry in bacterial and large viral genomes
    • Mrazek J., and Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 3720-3725
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 3720-3725
    • Mrazek, J.1    Karlin, S.2
  • 29
    • 0036754289 scopus 로고    scopus 로고
    • The general stress protein Ctc of Bacillus subtilis is a ribosomal protein
    • Schmalisch M., Langbein I., and Stulke J. The general stress protein Ctc of Bacillus subtilis is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4 (2002) 495-501
    • (2002) J. Mol. Microbiol. Biotechnol. , vol.4 , pp. 495-501
    • Schmalisch, M.1    Langbein, I.2    Stulke, J.3
  • 30
    • 0023650543 scopus 로고
    • The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp P.M., and Li W.H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 (1987) 1281-1295
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 31
    • 33748749355 scopus 로고    scopus 로고
    • Piezophilic adaptation: a genomic point of view
    • Simonato F., et al. Piezophilic adaptation: a genomic point of view. J. Biotechnol. 126 (2006) 11-25
    • (2006) J. Biotechnol. , vol.126 , pp. 11-25
    • Simonato, F.1
  • 32
    • 0037007150 scopus 로고    scopus 로고
    • The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
    • Slesarev A.I., et al. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 4644-4649
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 4644-4649
    • Slesarev, A.I.1
  • 33
    • 0037931826 scopus 로고    scopus 로고
    • Genomic correlates of hyperthermostability, an update
    • Suhre K., and Claverie J.M. Genomic correlates of hyperthermostability, an update. J. Biol. Chem. 278 (2003) 17198-17202
    • (2003) J. Biol. Chem. , vol.278 , pp. 17198-17202
    • Suhre, K.1    Claverie, J.M.2
  • 34
    • 12744268746 scopus 로고    scopus 로고
    • Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus
    • Takami H., et al. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res. 32 (2004) 6292-6303
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6292-6303
    • Takami, H.1
  • 35
    • 0037106449 scopus 로고    scopus 로고
    • Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments
    • Takami H., Takaki Y., and Uchiyama I. Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res. 30 (2002) 3927-3935
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3927-3935
    • Takami, H.1    Takaki, Y.2    Uchiyama, I.3
  • 36
    • 20044393188 scopus 로고    scopus 로고
    • Life at depth: Photobacterium profundum genome sequence and expression analysis
    • Vezzi A., et al. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307 (2005) 1459-1461
    • (2005) Science , vol.307 , pp. 1459-1461
    • Vezzi, A.1
  • 38
    • 0029762245 scopus 로고    scopus 로고
    • Isolation and characterization of the structural gene for OmpL, a pressure-regulated porin-like protein from the deep-sea bacterium Photobacterium species strain SS9
    • Welch T.J., and Bartlett D.H. Isolation and characterization of the structural gene for OmpL, a pressure-regulated porin-like protein from the deep-sea bacterium Photobacterium species strain SS9. J. Bacteriol. 178 (1996) 5027-5031
    • (1996) J. Bacteriol. , vol.178 , pp. 5027-5031
    • Welch, T.J.1    Bartlett, D.H.2
  • 39
    • 0031779823 scopus 로고    scopus 로고
    • Identification of a regulatory protein required for pressure-responsive gene expression in the deep-sea bacterium Photobacterium species strain SS9
    • Welch T.J., and Bartlett D.H. Identification of a regulatory protein required for pressure-responsive gene expression in the deep-sea bacterium Photobacterium species strain SS9. Mol. Microbiol. 27 (1998) 977-985
    • (1998) Mol. Microbiol. , vol.27 , pp. 977-985
    • Welch, T.J.1    Bartlett, D.H.2
  • 40
    • 0027370350 scopus 로고
    • Stress response of Escherichia coli to elevated hydrostatic pressure
    • Welch T.J., Farewell A., Neidhardt F.C., and Bartlett D.H. Stress response of Escherichia coli to elevated hydrostatic pressure. J. Bacteriol. 175 (1993) 7170-7177
    • (1993) J. Bacteriol. , vol.175 , pp. 7170-7177
    • Welch, T.J.1    Farewell, A.2    Neidhardt, F.C.3    Bartlett, D.H.4


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