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Volumn 101, Issue 6, 2013, Pages 362-367

Non-random arrangement of synonymous codons in archaea coding sequences

Author keywords

Archaeal genes; Codon; Genetic selection; MRNA translation; Regulation of gene expression

Indexed keywords

TRANSFER RNA;

EID: 84877927738     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2013.04.008     Document Type: Article
Times cited : (11)

References (37)
  • 1
    • 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. 1981, 151:389-409.
    • (1981) J. Mol. Biol. , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 2
    • 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. 1985, 2:13-34.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 3
    • 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. 1986, 14:7737-7749.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 7737-7749
    • Sharp, P.M.1    Li, W.H.2
  • 4
    • 0034237669 scopus 로고    scopus 로고
    • TRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
    • Duret L. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 2000, 16:287-289.
    • (2000) Trends Genet. , vol.16 , pp. 287-289
    • Duret, L.1
  • 8
    • 79551481541 scopus 로고    scopus 로고
    • Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis
    • Emery L.R., Sharp P.M. Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis. Biol. Lett. 2011, 7:131-135.
    • (2011) Biol. Lett. , vol.7 , pp. 131-135
    • Emery, L.R.1    Sharp, P.M.2
  • 9
    • 79960863042 scopus 로고    scopus 로고
    • Optimal codon identities in bacteria: implications from the conflicting results of two different methods
    • Wang B., et al. Optimal codon identities in bacteria: implications from the conflicting results of two different methods. PLoS One 2011, 6:e22714.
    • (2011) PLoS One , vol.6
    • Wang, B.1
  • 10
    • 17444449538 scopus 로고    scopus 로고
    • Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
    • Percudani R., Pavesi A., Ottonello S. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol. 1997, 268:322-330.
    • (1997) J. Mol. Biol. , vol.268 , pp. 322-330
    • Percudani, R.1    Pavesi, A.2    Ottonello, S.3
  • 11
    • 8744310123 scopus 로고    scopus 로고
    • Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
    • Rocha E.P. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 2004, 14:2279-2286.
    • (2004) Genome Res. , vol.14 , pp. 2279-2286
    • Rocha, E.P.1
  • 12
    • 77955955750 scopus 로고    scopus 로고
    • The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria
    • Ran W., Higgs P.G. The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria. Mol. Biol. Evol. 2010, 27:2129-2140.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 2129-2140
    • Ran, W.1    Higgs, P.G.2
  • 13
    • 54149105223 scopus 로고    scopus 로고
    • Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage
    • Higgs P.G., Ran W. Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage. Mol. Biol. Evol. 2008, 25:2279-2291.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 2279-2291
    • Higgs, P.G.1    Ran, W.2
  • 15
    • 77951734603 scopus 로고    scopus 로고
    • A role for codon order in translation dynamics
    • Cannarozzi G., et al. A role for codon order in translation dynamics. Cell 2010, 141:355-367.
    • (2010) Cell , vol.141 , pp. 355-367
    • Cannarozzi, G.1
  • 16
    • 77951715627 scopus 로고    scopus 로고
    • An evolutionarily conserved mechanism for controlling the efficiency of protein translation
    • Tuller T., et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 2010, 141:344-354.
    • (2010) Cell , vol.141 , pp. 344-354
    • Tuller, T.1
  • 17
    • 84863281523 scopus 로고    scopus 로고
    • Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency
    • Shao Z.Q., Zhang Y.M., Feng X.Y., Wang B., Chen J.Q. Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency. PLoS One 2012, 7:e33547.
    • (2012) PLoS One , vol.7
    • Shao, Z.Q.1    Zhang, Y.M.2    Feng, X.Y.3    Wang, B.4    Chen, J.Q.5
  • 18
    • 71849108697 scopus 로고    scopus 로고
    • Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes
    • Grosjean H., de Crecy-Lagard V., Marck C. Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett. 2010, 584:252-264.
    • (2010) FEBS Lett. , vol.584 , pp. 252-264
    • Grosjean, H.1    de Crecy-Lagard, V.2    Marck, C.3
  • 19
    • 84859174156 scopus 로고    scopus 로고
    • A role for tRNA modifications in genome structure and codon usage
    • Novoa E.M., Pavon-Eternod M., Pan T., Ribas de Pouplana L. A role for tRNA modifications in genome structure and codon usage. Cell 2012, 149:202-213.
    • (2012) Cell , vol.149 , pp. 202-213
    • Novoa, E.M.1    Pavon-Eternod, M.2    Pan, T.3    Ribas de Pouplana, L.4
  • 20
    • 79955142868 scopus 로고    scopus 로고
    • Proteinortho: detection of (co-)orthologs in large-scale analysis
    • Lechner M., et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinforma. 2011, 12:124.
    • (2011) BMC Bioinforma. , vol.12 , pp. 124
    • Lechner, M.1
  • 21
    • 80055104018 scopus 로고    scopus 로고
    • MorePhyML: improving the phylogenetic tree space exploration with PhyML 3
    • Criscuolo A. morePhyML: improving the phylogenetic tree space exploration with PhyML 3. Mol. Phylogenet. Evol. 2011, 61:944-948.
    • (2011) Mol. Phylogenet. Evol. , vol.61 , pp. 944-948
    • Criscuolo, A.1
  • 22
    • 84875202216 scopus 로고    scopus 로고
    • Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus
    • Shao Z.Q., Zhang Y.M., Pan X.Z., Wang B., Chen J.Q. Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus. PLoS One 2013, 8:e60116.
    • (2013) PLoS One , vol.8
    • Shao, Z.Q.1    Zhang, Y.M.2    Pan, X.Z.3    Wang, B.4    Chen, J.Q.5
  • 23
    • 0036225678 scopus 로고    scopus 로고
    • The genome of M. acetivorans reveals extensive metabolic and physiological diversity
    • Galagan J.E., et al. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 2002, 12:532-542.
    • (2002) Genome Res. , vol.12 , pp. 532-542
    • Galagan, J.E.1
  • 24
    • 58149189877 scopus 로고    scopus 로고
    • GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    • Chan P.P., Lowe T.M. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009, 37:D93-D97.
    • (2009) Nucleic Acids Res. , vol.37
    • Chan, P.P.1    Lowe, T.M.2
  • 27
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • Dong H., Nilsson L., Kurland C.G. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 1996, 260:649-663.
    • (1996) J. Mol. Biol. , vol.260 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 28
    • 84859219968 scopus 로고    scopus 로고
    • Balanced codon usage optimizes eukaryotic translational efficiency
    • Qian W., Yang J.R., Pearson N.M., Maclean C., Zhang J. Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet. 2012, 8:e1002603.
    • (2012) PLoS Genet. , vol.8
    • Qian, W.1    Yang, J.R.2    Pearson, N.M.3    Maclean, C.4    Zhang, J.5
  • 29
    • 0024415902 scopus 로고
    • Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria
    • Andachi Y., Yamao F., Muto A., Osawa S. Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria. J. Mol. Biol. 1989, 209:37-54.
    • (1989) J. Mol. Biol. , vol.209 , pp. 37-54
    • Andachi, Y.1    Yamao, F.2    Muto, A.3    Osawa, S.4
  • 30
    • 0034788470 scopus 로고    scopus 로고
    • Queuosine modification of tRNA: a case for convergent evolution
    • Morris R.C., Elliott M.S. Queuosine modification of tRNA: a case for convergent evolution. Mol. Genet. Metab. 2001, 74:147-159.
    • (2001) Mol. Genet. Metab. , vol.74 , pp. 147-159
    • Morris, R.C.1    Elliott, M.S.2
  • 31
    • 0003634460 scopus 로고    scopus 로고
    • Structural basis of base exchange by tRNA-guanine transglycosylases
    • ASM Press, Washington (DC), H. Grosjean, R. Benne (Eds.)
    • Romier C., Ficner R., Suck D. Structural basis of base exchange by tRNA-guanine transglycosylases. Modification and Editing of RNA 1998, 493-516. ASM Press, Washington (DC). H. Grosjean, R. Benne (Eds.).
    • (1998) Modification and Editing of RNA , pp. 493-516
    • Romier, C.1    Ficner, R.2    Suck, D.3
  • 32
    • 58149191272 scopus 로고    scopus 로고
    • TRNAdb 2009: compilation of tRNA sequences and tRNA genes
    • Juhling F., et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2009, 37:D159-D162.
    • (2009) Nucleic Acids Res. , vol.37
    • Juhling, F.1
  • 35
    • 33845995459 scopus 로고    scopus 로고
    • Codon reading by tRNAAla with modified uridine in the wobble position
    • Kothe U., Rodnina M.V. Codon reading by tRNAAla with modified uridine in the wobble position. Mol. Cell 2007, 25:167-174.
    • (2007) Mol. Cell , vol.25 , pp. 167-174
    • Kothe, U.1    Rodnina, M.V.2
  • 36
    • 36248950665 scopus 로고    scopus 로고
    • The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons
    • Nasvall S.J., Chen P., Bjork G.R. The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. RNA 2007, 13:2151-2164.
    • (2007) RNA , vol.13 , pp. 2151-2164
    • Nasvall, S.J.1    Chen, P.2    Bjork, G.R.3
  • 37
    • 0018955991 scopus 로고
    • A novel link between the biosynthesis of aromatic amino acids and transfer RNA modification in Escherichia coli
    • Bjork G.R. A novel link between the biosynthesis of aromatic amino acids and transfer RNA modification in Escherichia coli. J. Mol. Biol. 1980, 140:391-410.
    • (1980) J. Mol. Biol. , vol.140 , pp. 391-410
    • Bjork, G.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.