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Volumn 101, Issue 2, 2004, Pages 155-161

Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales

Author keywords

Base pair; bp; CA; Correspondence analysis; Effective number of codons; ENC; GC3S; Relative synonymous codon usage; RSCU; SARSCoV; Severe acute respiratory syndrome Coronavirus; The frequency of G+C at the synonymous third position of sense codons

Indexed keywords

ARTERIVIRUS; ARTICLE; CODON USAGE; CONTROLLED STUDY; CORRELATION ANALYSIS; CORRESPONDENCE ANALYSIS; GENE FUNCTION; GENETIC ANALYSIS; GENETIC VARIABILITY; NIDOVIRALES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SARS CORONAVIRUS; SPECIES DIVERSITY; VIRAL GENETICS; VIRUS GENE; VIRUS TRANSCRIPTION;

EID: 1642412614     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2004.01.006     Document Type: Article
Times cited : (185)

References (41)
  • 1
    • 0037454366 scopus 로고    scopus 로고
    • Outbreak of severe acute respiratory syndrome in Hong Kong Special Administrative Region: Case report
    • Chan-Yeung M., Yu W.C. Outbreak of severe acute respiratory syndrome in Hong Kong Special Administrative Region: case report. Brit. Med. J. 326:2003;850-852.
    • (2003) Brit. Med. J. , vol.326 , pp. 850-852
    • Chan-Yeung, M.1    Yu, W.C.2
  • 2
    • 0344653653 scopus 로고    scopus 로고
    • Codon usage and gene function are related in sequences of Arabidopsis thaliana
    • Chiapello H., Lisacek F., Caboche M., Henaut A. Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene. 209:1998;GC1-GC38.
    • (1998) Gene , vol.209 , pp. 1-GC38
    • Chiapello, H.1    Lisacek, F.2    Caboche, M.3    Henaut, A.4
  • 3
    • 0033565223 scopus 로고    scopus 로고
    • Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases
    • Chiapello H., Ollivier E., Landes-Devauchelle C., Nitschke P., Risler J.L. Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases. Nucleic Acids Res. 27:1999;2848-2851.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2848-2851
    • Chiapello, H.1    Ollivier, E.2    Landes-Devauchelle, C.3    Nitschke, P.4    Risler, J.L.5
  • 4
    • 0032884346 scopus 로고    scopus 로고
    • Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure
    • Chiusano M.L., D'Onofrio G., Alvarez-Valin F., Jabbari K., Colonna G., Bernardi G. Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure. Gene. 238:1999;23-31.
    • (1999) Gene , vol.238 , pp. 23-31
    • Chiusano, M.L.1    D'Onofrio, G.2    Alvarez-Valin, F.3    Jabbari, K.4    Colonna, G.5    Bernardi, G.6
  • 5
    • 0034736516 scopus 로고    scopus 로고
    • Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code
    • Chiusano M.L., Alvarez-Valin F., Di Giulio M., D'Onofrio G., Ammirato G., Colonna G., Bernardi G. Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene. 261:2000;63-69.
    • (2000) Gene , vol.261 , pp. 63-69
    • Chiusano, M.L.1    Alvarez-Valin, F.2    Di Giulio, M.3    D'Onofrio, G.4    Ammirato, G.5    Colonna, G.6    Bernardi, G.7
  • 6
    • 0034666040 scopus 로고    scopus 로고
    • Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
    • Coghlan A., Wolfe K.H. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast. 16:2000;1131-1145.
    • (2000) Yeast , vol.16 , pp. 1131-1145
    • Coghlan, A.1    Wolfe, K.H.2
  • 7
    • 0031694427 scopus 로고    scopus 로고
    • An evaluation of measures of synonymous codon usage bias
    • Comeron J.M., Aguade M. An evaluation of measures of synonymous codon usage bias. J. Mol. Evol. 47:1998;268-274.
    • (1998) J. Mol. Evol. , vol.47 , pp. 268-274
    • Comeron, J.M.1    Aguade, M.2
  • 9
    • 0038445498 scopus 로고    scopus 로고
    • Case clusters of the severe acute respiratory syndrome
    • Drazen J.M. Case clusters of the severe acute respiratory syndrome. New Engl. J. Med. 348:2003;e6-e7.
    • (2003) New Engl. J. Med. , vol.348 , pp. 6-e7
    • Drazen, J.M.1
  • 10
    • 0034696628 scopus 로고    scopus 로고
    • A functional significance for codon third bases
    • Epstein R.J., Lin K., Tan T.W. A functional significance for codon third bases. Gene. 245:2000;291-298.
    • (2000) Gene , vol.245 , pp. 291-298
    • Epstein, R.J.1    Lin, K.2    Tan, T.W.3
  • 12
    • 0033168465 scopus 로고    scopus 로고
    • Isochores result from mutation not selection
    • Francino H.P., Ochman H. Isochores result from mutation not selection. Nature. 400:1999;30-31.
    • (1999) Nature , vol.400 , pp. 30-31
    • Francino, H.P.1    Ochman, H.2
  • 13
    • 0034193767 scopus 로고    scopus 로고
    • Studies on codon usage in Entamoeba histolytica
    • Ghosh T.C., Gupta S.K., Majumdar S. Studies on codon usage in Entamoeba histolytica. Int. J. Parasitol. 30:2000;715-722.
    • (2000) Int. J. Parasitol. , vol.30 , pp. 715-722
    • Ghosh, T.C.1    Gupta, S.K.2    Majumdar, S.3
  • 14
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10:1982;7055-7074.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 17
    • 0034708361 scopus 로고    scopus 로고
    • Studies on the relationships between the synonymous codon usage and protein secondary structural units
    • Gupta S.K., Majumdar S., Bhattacharya T.K., Ghosh T.C. Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem. Biophys. Res. Commun. 269:2000;692-696.
    • (2000) Biochem. Biophys. Res. Commun. , vol.269 , pp. 692-696
    • Gupta, S.K.1    Majumdar, S.2    Bhattacharya, T.K.3    Ghosh, T.C.4
  • 18
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
    • Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151:1981;389-409.
    • (1981) J. Mol. Biol. , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 19
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:1985;13-34.
    • (1985) Mol. Biol. Evol , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 21
    • 0037372775 scopus 로고    scopus 로고
    • The extent of codon usage bias in human RNA viruses and its evolutionary origin
    • Jenkins G.M., Holmes E.C. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 92:2003;1-7.
    • (2003) Virus Res. , vol.92 , pp. 1-7
    • Jenkins, G.M.1    Holmes, E.C.2
  • 22
    • 0030569016 scopus 로고    scopus 로고
    • What drives codon choices in human genes?
    • Karlin S., Mrazek J. What drives codon choices in human genes? J. Mol. Biol. 262:1996;459-472.
    • (1996) J. Mol. Biol. , vol.262 , pp. 459-472
    • Karlin, S.1    Mrazek, J.2
  • 24
    • 0033828846 scopus 로고    scopus 로고
    • Codon usage in nucleopolyhedroviruses
    • Levin D.B., Whittome B. Codon usage in nucleopolyhedroviruses. J. Gen. Virol. 81:2000;2313-2325.
    • (2000) J. Gen. Virol. , vol.81 , pp. 2313-2325
    • Levin, D.B.1    Whittome, B.2
  • 25
    • 0026709809 scopus 로고
    • Evolution of codon usage patterns: The extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae
    • Lloyd A.T., Sharp P.M. Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Nucleic Acids Res. 20:1992;5289-5295.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 5289-5295
    • Lloyd, A.T.1    Sharp, P.M.2
  • 26
    • 0036267948 scopus 로고    scopus 로고
    • Cluster analysis of the codon use frequency of MHC genes from different species
    • Ma J.M., Zhou T., Gu W.J., Sun X., Lu Z.H. Cluster analysis of the codon use frequency of MHC genes from different species. Biosystems. 65:2002;199-207.
    • (2002) Biosystems , vol.65 , pp. 199-207
    • Ma, J.M.1    Zhou, T.2    Gu, W.J.3    Sun, X.4    Lu, Z.H.5
  • 27
    • 0033539907 scopus 로고    scopus 로고
    • Compositional correlation studies among the three different codon positions in 12 bacterial genomes
    • Majumdar S., Gupta S.K., Sundararaj V.S., Ghosh T.C. Compositional correlation studies among the three different codon positions in 12 bacterial genomes. Biochem. Biophys. Res. Commun. 266:1999;66-71.
    • (1999) Biochem. Biophys. Res. Commun. , vol.266 , pp. 66-71
    • Majumdar, S.1    Gupta, S.K.2    Sundararaj, V.S.3    Ghosh, T.C.4
  • 28
    • 0035012056 scopus 로고    scopus 로고
    • Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans
    • Marais G., Duret L. Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J. Mol. Evol. 52:2001;275-280.
    • (2001) J. Mol. Evol. , vol.52 , pp. 275-280
    • Marais, G.1    Duret, L.2
  • 30
    • 0038823524 scopus 로고    scopus 로고
    • The genome sequence of the SARS-associated Coronavirus
    • Marra M.A., Jones S.J., Astell C.R. The genome sequence of the SARS-associated Coronavirus. Science. 300:2003;1399-1404.
    • (2003) Science , vol.300 , pp. 1399-1404
    • Marra, M.A.1    Jones, S.J.2    Astell, C.R.3
  • 31
    • 0024322840 scopus 로고
    • Variation in G+C content and codon choice: Differences among synonymous codon groups in vertebrate genes
    • Martin A., Bertranpetit J., Oliver J.L., Medina J.R. Variation in. G+C content and codon choice: differences among synonymous codon groups in vertebrate genes Nucleic Acids Res. 17:1989;6181-6189.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 6181-6189
    • Martin, A.1    Bertranpetit, J.2    Oliver, J.L.3    Medina, J.R.4
  • 32
    • 0032169578 scopus 로고    scopus 로고
    • Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
    • McInerney J.O. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. U.S.A. 95:1998;10698-10703.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 10698-10703
    • McInerney, J.O.1
  • 33
    • 0032126484 scopus 로고    scopus 로고
    • Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli
    • Moriyama E.N., Powell J.R. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 26:1998;3188-3193.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3188-3193
    • Moriyama, E.N.1    Powell, J.R.2
  • 34
    • 0032493780 scopus 로고    scopus 로고
    • Specific correlations between relative synonymous codon usage and protein secondary structure
    • Oresic M., Shalloway D. Specific correlations between relative synonymous codon usage and protein secondary structure. J. Mol. Biol. 281:1998;31-48.
    • (1998) J. Mol. Biol. , vol.281 , pp. 31-48
    • Oresic, M.1    Shalloway, D.2
  • 35
    • 0037561920 scopus 로고    scopus 로고
    • Characterization of a novel Coronavirus associated with severe acute respiratory syndrome
    • Paul A.R., Steven O.M., Stephan S.M. Characterization of a novel Coronavirus associated with severe acute respiratory syndrome. Science. 300:2003;1394-1399.
    • (2003) Science , vol.300 , pp. 1394-1399
    • Paul, A.R.1    Steven, O.M.2    Stephan, S.M.3
  • 36
    • 0038083173 scopus 로고    scopus 로고
    • A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01)
    • Qin E.D., Zhu Q.Y., Yu M. A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). Chin. Sci. Bull. 48:2003;941-948.
    • (2003) Chin. Sci. Bull. , vol.48 , pp. 941-948
    • Qin, E.D.1    Zhu, Q.Y.2    Yu, M.3
  • 37
    • 0023046211 scopus 로고
    • Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons
    • Sharp P.M., Li W.H. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 14:1986;7737-7749.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 7737-7749
    • Sharp, P.M.1    Li, W.H.2
  • 38
    • 0023046874 scopus 로고
    • Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp P.M., Tuohy T.M., Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14:1986;5125-5143.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.M.2    Mosurski, K.R.3
  • 39
    • 0042164218 scopus 로고    scopus 로고
    • Unique and conserved features of genome and proteome of SARS-Coronavirus, an early split-off from the Coronavirus group 2 lineage
    • Snijder E.J., Bredenbeek P.J., Dobbe J.C. Unique and conserved features of genome and proteome of SARS-Coronavirus, an early split-off from the Coronavirus group 2 lineage. J. Mol. Biol. 331:2003;991-1004.
    • (2003) J. Mol. Biol. , vol.331 , pp. 991-1004
    • Snijder, E.J.1    Bredenbeek, P.J.2    Dobbe, J.C.3
  • 40
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • Wright F. The 'effective number of codons' used in a gene. Gene. 87:1990;23-29.
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 41
    • 0031697801 scopus 로고    scopus 로고
    • The relationship between synonymous codon usage and protein structure
    • Xie T., Ding D.F. The relationship between synonymous codon usage and protein structure. FEBS Lett. 434:1998;93-96.
    • (1998) FEBS Lett. , vol.434 , pp. 93-96
    • Xie, T.1    Ding, D.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.