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Volumn 11, Issue SUPPL. 11, 2010, Pages

Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION ANALYSIS; COMPLETE GENOMES; GUANINE CYTOSINES; HABITAT CONDITIONS; HYPOTHETICAL PROTEIN; PROKARYOTIC SPECIES; TEMPERATURE RANGE; TRANSPORT SYSTEMS;

EID: 78651414000     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S11-S7     Document Type: Article
Times cited : (33)

References (51)
  • 1
    • 0038451426 scopus 로고    scopus 로고
    • Todar's Online Textbook of Bacteriology
    • Todar K
    • Todar's Online Textbook of Bacteriology. 2008, Todar K.
    • (2008)
  • 3
    • 61449245428 scopus 로고    scopus 로고
    • Effect of tempeature on growth parameters of psychrophilic bacteria and yeasts
    • Margesin R. Effect of tempeature on growth parameters of psychrophilic bacteria and yeasts. Extremophiles 2009, 13(2):257-262.
    • (2009) Extremophiles , vol.13 , Issue.2 , pp. 257-262
    • Margesin, R.1
  • 5
    • 0028163820 scopus 로고
    • Influence of temperature on growth rate and competition between two psychrotolerant Antarctic bacteria: low temperature diminishes affinity for substrate uptake
    • 201591, 8031092
    • Nedwell D, Rutter M. Influence of temperature on growth rate and competition between two psychrotolerant Antarctic bacteria: low temperature diminishes affinity for substrate uptake. Appl Environ Microbiol 1994, 60(6):1984-1992. 201591, 8031092.
    • (1994) Appl Environ Microbiol , vol.60 , Issue.6 , pp. 1984-1992
    • Nedwell, D.1    Rutter, M.2
  • 6
    • 0033043681 scopus 로고    scopus 로고
    • Temperature dependence of inorganic nitrogen uptake:reduced affinity for nitrate at suboptimal temperatures in both algae and bacteria
    • Reay D, Nedwell D, Priddle J, Ellis-Evans J. Temperature dependence of inorganic nitrogen uptake:reduced affinity for nitrate at suboptimal temperatures in both algae and bacteria. Applied and Environmental Microbiology 1999, 65(6):2577-2584.
    • (1999) Applied and Environmental Microbiology , vol.65 , Issue.6 , pp. 2577-2584
    • Reay, D.1    Nedwell, D.2    Priddle, J.3    Ellis-Evans, J.4
  • 7
    • 0036405341 scopus 로고    scopus 로고
    • Temperature effect on entrainment, phase shifting, and amplitude of circadian clocks and its molecular bases
    • Rensing L, Ruoff P. Temperature effect on entrainment, phase shifting, and amplitude of circadian clocks and its molecular bases. Chronobiol Int 2002, 19(5):807-64.
    • (2002) Chronobiol Int , vol.19 , Issue.5 , pp. 807-864
    • Rensing, L.1    Ruoff, P.2
  • 8
    • 0037193983 scopus 로고    scopus 로고
    • Low-temperature sensors in bacteria
    • 1692996, 12171652
    • Eriksson S, Hurme R, Rhen M. Low-temperature sensors in bacteria. Philos Trans R Soc Lond B Biol Sci 2002, 357(1423):887-893. 1692996, 12171652.
    • (2002) Philos Trans R Soc Lond B Biol Sci , vol.357 , Issue.1423 , pp. 887-893
    • Eriksson, S.1    Hurme, R.2    Rhen, M.3
  • 9
    • 0242290154 scopus 로고    scopus 로고
    • Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content
    • Singer G, Hickey D. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 2003, 317(1-2):39-47.
    • (2003) Gene , vol.317 , Issue.1-2 , pp. 39-47
    • Singer, G.1    Hickey, D.2
  • 10
    • 19644401538 scopus 로고    scopus 로고
    • Genomic and proteomic adaptations to growth at high temperature
    • 545586, 15461805
    • Hickey D, Singer G. Genomic and proteomic adaptations to growth at high temperature. Genome Biology 2004, 5:117. 545586, 15461805.
    • (2004) Genome Biology , vol.5 , pp. 117
    • Hickey, D.1    Singer, G.2
  • 11
    • 33846519263 scopus 로고    scopus 로고
    • Protein and DNA sequence determinants of thermophilic adaptation
    • 1769408, 17222055
    • Zeldovich K, Berezovsky I, Shakhnovich E. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol 2007, 3:e5. 1769408, 17222055.
    • (2007) PLoS Comput Biol , vol.3
    • Zeldovich, K.1    Berezovsky, I.2    Shakhnovich, E.3
  • 12
    • 33344467805 scopus 로고    scopus 로고
    • Optimal growth temperature of prokaryotes correlates with class II amino acid composition
    • Klipcan L, Safro I, Temkin B, Safro M. Optimal growth temperature of prokaryotes correlates with class II amino acid composition. FEBS Letters 2006, 580(6):1672-1676.
    • (2006) FEBS Letters , vol.580 , Issue.6 , pp. 1672-1676
    • Klipcan, L.1    Safro, I.2    Temkin, B.3    Safro, M.4
  • 14
    • 0033170850 scopus 로고    scopus 로고
    • Adaptation of proteins from hyperthermophiles to high pressure and high temperature
    • Robb F, Clark D. Adaptation of proteins from hyperthermophiles to high pressure and high temperature. J Mol Microbiol Biotechnol 1999, 1:101-5.
    • (1999) J Mol Microbiol Biotechnol , vol.1 , pp. 101-105
    • Robb, F.1    Clark, D.2
  • 15
    • 35549012368 scopus 로고    scopus 로고
    • Correlation between structure and temperature in prokaryotic metabolic networks
    • 2045116, 17711568
    • Takemoto K, Nacher J, T A. Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinformatics 2007, 8:303. 2045116, 17711568.
    • (2007) BMC Bioinformatics , vol.8 , pp. 303
    • Takemoto, K.1    Nacher, J.2    T, A.3
  • 16
    • 0041909570 scopus 로고    scopus 로고
    • Bacterial cold shock responses
    • Weber M, Marahiel M. Bacterial cold shock responses. Sci Prog 2003, 86(Pt 1-2):9-75.
    • (2003) Sci Prog , vol.86 , Issue.1-2 , pp. 9-75
    • Weber, M.1    Marahiel, M.2
  • 17
    • 34248147423 scopus 로고    scopus 로고
    • Thermosensors in eubacteria: role and evolution
    • Wolfgang S. Thermosensors in eubacteria: role and evolution. Journal of biosciences 2007, 32(3):549-57.
    • (2007) Journal of biosciences , vol.32 , Issue.3 , pp. 549-557
    • Wolfgang, S.1
  • 18
    • 60549112198 scopus 로고    scopus 로고
    • Temperature sensors of eubacteria
    • Schumann W. Temperature sensors of eubacteria. Adv Appl Microbiol 2009, 67:213-56.
    • (2009) Adv Appl Microbiol , vol.67 , pp. 213-256
    • Schumann, W.1
  • 19
    • 4344666232 scopus 로고    scopus 로고
    • Correlations between genomic GC levels and optimal growth temperatures in prokaryotes
    • Musto H, Naya H, Zavala A, Romero H, Alvarez-Valin F, Bernardi G. Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett 2004, 573(1-3):73-77.
    • (2004) FEBS Lett , vol.573 , Issue.1-3 , pp. 73-77
    • Musto, H.1    Naya, H.2    Zavala, A.3    Romero, H.4    Alvarez-Valin, F.5    Bernardi, G.6
  • 20
    • 7644238105 scopus 로고    scopus 로고
    • Correlations between genomic GC levels and optimal growth temperatures are not 'robust'
    • Marashi S, Ghalanbor Z. Correlations between genomic GC levels and optimal growth temperatures are not 'robust'. Biochemical and Biophysical Research Communications 2004, 325:381-383.
    • (2004) Biochemical and Biophysical Research Communications , vol.325 , pp. 381-383
    • Marashi, S.1    Ghalanbor, Z.2
  • 21
    • 12344322489 scopus 로고    scopus 로고
    • Correlations between genomic GC levels and optimal growth temperatures: some comments
    • Basak S, Mandal S, Ghosh T. Correlations between genomic GC levels and optimal growth temperatures: some comments. Biochem. Biophys. Res. Commun. 2005, 327:969-970.
    • (2005) Biochem. Biophys. Res. Commun. , vol.327 , pp. 969-970
    • Basak, S.1    Mandal, S.2    Ghosh, T.3
  • 22
    • 33644622447 scopus 로고    scopus 로고
    • On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors
    • Wang H, Susko E, Roger A. On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors. Biochem. Biophys. Res. Commun. 2006, 342(3):681-684.
    • (2006) Biochem. Biophys. Res. Commun. , vol.342 , Issue.3 , pp. 681-684
    • Wang, H.1    Susko, E.2    Roger, A.3
  • 23
    • 0036574857 scopus 로고    scopus 로고
    • A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein
    • Forterre P. A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 2002, 18(5):236-7.
    • (2002) Trends Genet , vol.18 , Issue.5 , pp. 236-237
    • Forterre, P.1
  • 24
    • 0038583819 scopus 로고    scopus 로고
    • Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures
    • Nakashima H, Fukuchi S, Nishikawa K. Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J. Biochem 2003, 133(4):507-513.
    • (2003) J. Biochem , vol.133 , Issue.4 , pp. 507-513
    • Nakashima, H.1    Fukuchi, S.2    Nishikawa, K.3
  • 25
    • 43249115309 scopus 로고    scopus 로고
    • Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
    • 2289840, 18421372
    • Bohlin J, Skjerve E, Ussery D. Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes. PLoS Computational Biology 2008, 4:e1000057. 2289840, 18421372.
    • (2008) PLoS Computational Biology , vol.4
    • Bohlin, J.1    Skjerve, E.2    Ussery, D.3
  • 26
    • 0030900384 scopus 로고    scopus 로고
    • Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes
    • Galtier N, Lobry J. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 1997, 44(6):632-6.
    • (1997) J Mol Evol , vol.44 , Issue.6 , pp. 632-636
    • Galtier, N.1    Lobry, J.2
  • 28
    • 0003962869 scopus 로고
    • Engineering Statistics
    • New York: MacMillan
    • Hogg R, Ledolter J. Engineering Statistics. 1987, New York: MacMillan.
    • (1987)
    • Hogg, R.1    Ledolter, J.2
  • 29
    • 0003898205 scopus 로고    scopus 로고
    • A guide to chi-squared testing
    • Wiley, New York, 047155779X
    • Greenwood P, Nikulin M. A guide to chi-squared testing. 1996, Wiley, New York, 047155779X.
    • (1996)
    • Greenwood, P.1    Nikulin, M.2
  • 30
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • 2808910, 19880382
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360. 2808910, 19880382.
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 31
    • 77953810073 scopus 로고    scopus 로고
    • Association analysis of the general environmental conditions and prokaryotes' gene distributions in various functional groups
    • (doi:10.1016/j.ygeno.2010.03.007)
    • Wu H, Moore E. Association analysis of the general environmental conditions and prokaryotes' gene distributions in various functional groups. Genomics 2010, (doi:10.1016/j.ygeno.2010.03.007).
    • (2010) Genomics
    • Wu, H.1    Moore, E.2
  • 34
    • 33847073796 scopus 로고    scopus 로고
    • Achieving 80% Ten-fold Cross-validated Accuracy for Secondary Structure Prediction by Large-scale Training
    • Dor O, Zhou Y. Achieving 80% Ten-fold Cross-validated Accuracy for Secondary Structure Prediction by Large-scale Training. PROTEINS: Structure, Function, and Bioinformatics 2007, 66:838-845.
    • (2007) PROTEINS: Structure, Function, and Bioinformatics , vol.66 , pp. 838-845
    • Dor, O.1    Zhou, Y.2
  • 36
    • 0342794791 scopus 로고
    • Motility of Erwinia amylovora
    • Raymundo A, Ries S. Motility of Erwinia amylovora. Phytopathology 1981, 71:45-49.
    • (1981) Phytopathology , vol.71 , pp. 45-49
    • Raymundo, A.1    Ries, S.2
  • 37
    • 0017758317 scopus 로고
    • Temperature effects on bacterial movement
    • 242732, 339831
    • Schneider WJ, Doetsch R. Temperature effects on bacterial movement. Appl Environ Microbiol 1977, 34(6):695-700. 242732, 339831.
    • (1977) Appl Environ Microbiol , vol.34 , Issue.6 , pp. 695-700
    • Schneider, W.J.1    Doetsch, R.2
  • 38
    • 0029839359 scopus 로고    scopus 로고
    • Temperature-induced switching of the bacterial flagellar motor
    • 1233691, 8889199
    • Turner L, Caplan S, Berg H. Temperature-induced switching of the bacterial flagellar motor. Biophys J 1996, 71(4):2227-33. 1233691, 8889199.
    • (1996) Biophys J , vol.71 , Issue.4 , pp. 2227-2233
    • Turner, L.1    Caplan, S.2    Berg, H.3
  • 39
    • 25844517671 scopus 로고    scopus 로고
    • Characteristics of styrene degradation by Rhodococcus pyridinovorans isolated from a biofilter
    • Junga I, Park C. Characteristics of styrene degradation by Rhodococcus pyridinovorans isolated from a biofilter. Chemosphere 2005, 61(4):451-456.
    • (2005) Chemosphere , vol.61 , Issue.4 , pp. 451-456
    • Junga, I.1    Park, C.2
  • 40
    • 0018134985 scopus 로고
    • Dioxygen and temperature dependence of ubiquinone formation in Escherichia coli: studies of cells charged with 2-octaprenyl phenol
    • Knoell H, Kraft R, Knappe J. Dioxygen and temperature dependence of ubiquinone formation in Escherichia coli: studies of cells charged with 2-octaprenyl phenol. Eur J Biochem 1978, 90:107-12.
    • (1978) Eur J Biochem , vol.90 , pp. 107-112
    • Knoell, H.1    Kraft, R.2    Knappe, J.3
  • 41
    • 0028832670 scopus 로고
    • Depression of streptomycin production by Streptomyces griseus at elevated growth temperature studies using gene fusions
    • Deeble V, Lindley H, Fazeli M, Cove J, Baumberg S. Depression of streptomycin production by Streptomyces griseus at elevated growth temperature studies using gene fusions. Microbiohgy 1995, 141:2511-2518.
    • (1995) Microbiohgy , vol.141 , pp. 2511-2518
    • Deeble, V.1    Lindley, H.2    Fazeli, M.3    Cove, J.4    Baumberg, S.5
  • 42
    • 13944254408 scopus 로고    scopus 로고
    • S-adenosylhomocysteine hydrolase from the archaeon Pyrococcus furiosus: biochemical characterization and analysis of protein structure by comparative molecular modeling
    • Porcelli M, Moretti M, Concilio L, Forte S, Merlino A, Graziano G, Cacciapuoti G. S-adenosylhomocysteine hydrolase from the archaeon Pyrococcus furiosus: biochemical characterization and analysis of protein structure by comparative molecular modeling. Proteins 2005, 58(4):815-25.
    • (2005) Proteins , vol.58 , Issue.4 , pp. 815-825
    • Porcelli, M.1    Moretti, M.2    Concilio, L.3    Forte, S.4    Merlino, A.5    Graziano, G.6    Cacciapuoti, G.7
  • 43
    • 0034175750 scopus 로고    scopus 로고
    • The question of DNA repair in hyper-thermophilic archaea
    • Grogan D. The question of DNA repair in hyper-thermophilic archaea. Trends Microbiol 2000, 8:180-185.
    • (2000) Trends Microbiol , vol.8 , pp. 180-185
    • Grogan, D.1
  • 44
    • 84874758501 scopus 로고    scopus 로고
    • cgi?&dataset=.A..z.......&dataset=.G..5.......£&gmin=0.000015&gmax=0.000171&absc=&gds=1848&idref=1540&annot=lhr
    • cgi?&dataset=.A..z.......&dataset=.G..5.......£&gmin=0.000015&gmax=0.000171&absc=&gds=1848&idref=1540&annot=lhr., http://www.ncbi.nlm.nih.gov/geo/gds/profileGraph
  • 45
    • 84874759518 scopus 로고    scopus 로고
    • cgi?&dataset=.M..z....AE.&dataset=.J..0....DG. £&gmin=0.000007&gmax=0.000130&absc=&gds=1848&idref=1004&annot=argK
    • cgi?&dataset=.M..z....AE.&dataset=.J..0....DG. £&gmin=0.000007&gmax=0.000130&absc=&gds=1848&idref=1004&annot=argK., http://www.ncbi.nlm.nih.gov/geo/gds/profileGraph
  • 47
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package (Version 3.2)
    • Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 49
    • 33746265929 scopus 로고    scopus 로고
    • Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments
    • Kendall M, Liu Y, Sieprawska-Lupa M, Stetter K, Whitman W, Boone D. Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol 2006, 56:1525-1529.
    • (2006) Int J Syst Evol Microbiol , vol.56 , pp. 1525-1529
    • Kendall, M.1    Liu, Y.2    Sieprawska-Lupa, M.3    Stetter, K.4    Whitman, W.5    Boone, D.6
  • 50
    • 67349173563 scopus 로고    scopus 로고
    • The Exiguobacterium genus: biodiversity and biogeography
    • Vishnivetskaya T, Kathariou S, Tiedje J. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 2009, 13(3):541-555.
    • (2009) Extremophiles , vol.13 , Issue.3 , pp. 541-555
    • Vishnivetskaya, T.1    Kathariou, S.2    Tiedje, J.3
  • 51
    • 55749087868 scopus 로고    scopus 로고
    • Large-scale reconstruction and phylogenetic analysis of metabolic environments
    • 2567166, 18787117
    • Borenstein E, Kupiec M, E FMR. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci 2008, 105:14482-14487. 2567166, 18787117.
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 14482-14487
    • Borenstein, E.1    Kupiec, M.2    E, F.M.R.3


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