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Volumn 27, Issue 9, 2010, Pages 2129-2140

The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria

Author keywords

anticodon; codon usage; modified nucleotides; translational selection; tRNA

Indexed keywords

TRANSFER RNA;

EID: 77955955750     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq102     Document Type: Article
Times cited : (60)

References (60)
  • 1
    • 1242309517 scopus 로고    scopus 로고
    • Survey and summary decoding the genome: A modified view
    • Agris PF. 2004. Survey and summary decoding the genome: a modified view. Nucleic Acids Res. 32:223-238
    • (2004) Nucleic Acids Res. , vol.32 , pp. 223-238
    • Agris, P.F.1
  • 2
    • 46449083572 scopus 로고    scopus 로고
    • Bringing order to translation: The contributions of transfer RNA anticodon-domain modifications
    • Agris PF. 2008. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep. 9:629-635
    • (2008) EMBO Rep. , vol.9 , pp. 629-635
    • Agris, P.F.1
  • 3
    • 77955937498 scopus 로고
    • Synonymous codon usage in Drosophila mela-nogaster: Natural selection and translational accuracy
    • Akashi H. 1994. Synonymous codon usage in Drosophila mela-nogaster: natural selection and translational accuracy. Genetics 164:1291-1303
    • (1994) Genetics , vol.164 , pp. 1291-1303
    • Akashi, H.1
  • 4
    • 0024415902 scopus 로고
    • Codon recognition patterns as deduced from sequences of the complete set of transfer RNAs species in Mycoplasma capricolum
    • Andachi Y, Yamao F, Muto A, Osawa S. 1989. Codon recognition patterns as deduced from sequences of the complete set of transfer RNAs species in Mycoplasma capricolum. J Mol Biol. 209:37-54
    • (1989) J Mol Biol. , vol.209 , pp. 37-54
    • Andachi, Y.1    Yamao, F.2    Muto, A.3    Osawa, S.4
  • 9
    • 0025941139 scopus 로고
    • The selection-mutation-drift theory of synonymous codon usage
    • Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907
    • (1991) Genetics , vol.129 , pp. 897-907
    • Bulmer, M.1
  • 10
    • 66649105285 scopus 로고    scopus 로고
    • Evolution of pathogenicity and sexual reproduction in eight Candida genomes
    • (51 co-authors)
    • Butler G, Rasmussen MD, Lin MF, Santos MAS, et al. (51 co-authors). 2009. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459:657-662
    • (2009) Nature , vol.459 , pp. 657-662
    • Butler, G.1    Rasmussen, M.D.2    Lin, M.F.3    Mas, S.4
  • 11
    • 0002090634 scopus 로고    scopus 로고
    • Modified nucleosides in translation
    • In: Grosjean H, Benne R, editors Washington (DC) ASM Press
    • Curran JF. 1998. Modified nucleosides in translation. In: Grosjean H, Benne R, editors. Modification and editing of RNA. Washington (DC): ASM Press. p. 493-516
    • (1998) Modification and Editing of RNA , pp. 493-516
    • Curran, J.F.1
  • 12
    • 0024962419 scopus 로고
    • Rates of aminoacyl-tRNA selection at 29 sense codons in vivo
    • Curran JF, Yarus M. 1989. Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J Mol Biol. 209:65-77
    • (1989) J Mol Biol. , vol.209 , pp. 65-77
    • Curran, J.F.1    Yarus, M.2
  • 13
    • 33747886005 scopus 로고    scopus 로고
    • The ribosome's response to codon-anticodon mismatches
    • Daviter T, Gromadski KB, Rodnina MV. 2006. The ribosome's response to codon-anticodon mismatches. Biochimie 88:1001-1011
    • (2006) Biochimie , vol.88 , pp. 1001-1011
    • Daviter, T.1    Gromadski, K.B.2    Rodnina, M.V.3
  • 14
    • 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 CG. 1996. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 260:649-663
    • (1996) J Mol Biol. , vol.260 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 15
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on codong-sequence evolution
    • Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on codong-sequence evolution. Cell 134:341-342
    • (2008) Cell , vol.134 , pp. 341-342
    • Drummond, D.A.1    Wilke, C.O.2
  • 16
    • 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. 2000. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 16:287-289
    • (2000) Trends Genet. , vol.16 , pp. 287-289
    • Duret, L.1
  • 17
    • 0038179369 scopus 로고    scopus 로고
    • Selective charging of tRNA isoacceptors explains patterns of codon usage
    • Elf J, Nilsson D, Tenson T, Ehrenberg M. 2003. Selective charging of tRNA isoacceptors explains patterns of codon usage. Science 300:1718-1722
    • (2003) Science , vol.300 , pp. 1718-1722
    • Elf, J.1    Nilsson, D.2    Tenson, T.3    Ehrenberg, M.4
  • 18
    • 31544454704 scopus 로고    scopus 로고
    • A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity
    • Gromadski KB, Daviter T, Rodnina MV. 2006. A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol Cell. 21:369-377
    • (2006) Mol Cell. , vol.21 , pp. 369-377
    • Gromadski, K.B.1    Daviter, T.2    Rodnina, M.V.3
  • 19
    • 71849108697 scopus 로고    scopus 로고
    • Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes
    • Grosjean H, de Crécy-Lagard V, Marck C. 2010. Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett. 584:252-264
    • (2010) FEBS Lett. , vol.584 , pp. 252-264
    • Grosjean, H.1    De Crécy-Lagard, V.2    Marck, C.3
  • 20
    • 0032553438 scopus 로고    scopus 로고
    • Lyswith hypomodified derivatives of 5-methylaminomethyl 2-thiouridine in the wobble position
    • Hagervall TG, Pomerantz SC, McCloskey JA. 1998. Reduced misreading of asparagine codons by Escherichia coli tRNALyswith hypomodified derivatives of 5-methylaminomethyl 2-thiouridine in the wobble position. J Mol Biol. 284:33-42
    • (1998) J Mol Biol. , vol.284 , pp. 33-42
    • Hagervall, T.G.1    Pomerantz, S.C.2    McCloskey, J.A.3
  • 21
    • 67449137928 scopus 로고    scopus 로고
    • A four-column theory for the origin of the genetic code: Tracing the evolutionary pathways that gave rise to an optimized code
    • Higgs PG. 2009. A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biol Direct. 4:16.
    • (2009) Biol Direct. , vol.4 , pp. 16
    • Higgs, P.G.1
  • 22
    • 54149105223 scopus 로고    scopus 로고
    • Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage
    • Higgs PG, Ran W. 2008. Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage. Mol Biol Evol. 25:2279-2291
    • (2008) Mol Biol Evol. , vol.25 , pp. 2279-2291
    • Higgs, P.G.1    Ran, W.2
  • 23
    • 0019474499 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
    • Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 146:1-21
    • (1981) J Mol Biol. , vol.146 , pp. 1-21
    • Ikemura, T.1
  • 24
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 2:13-34
    • (1985) Mol Biol Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 25
    • 38949118287 scopus 로고    scopus 로고
    • Codon usage in mitochondrial genomes: Distinguishing context-dependent mutation from translational selection
    • Jia WL, Higgs PG. 2008. Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol Biol Evol. 25:339-351
    • (2008) Mol Biol Evol. , vol.25 , pp. 339-351
    • Jia, W.L.1    Higgs, P.G.2
  • 27
    • 0032882170 scopus 로고    scopus 로고
    • Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs
    • Kanaya S, Yamada Y, Kudo Y, Ikemura T. 1999. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs. Gene 238:143-155
    • (1999) Gene , vol.238 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 28
    • 33845995459 scopus 로고    scopus 로고
    • Codon reading by tRNAAla with modified uridine in the wobble position
    • Kothe U, Rodnina MV. 2007. Codon reading by tRNAAla with modified uridine in the wobble position. Mol Cell 25:167-174
    • (2007) Mol Cell , vol.25 , pp. 167-174
    • Kothe, U.1    Rodnina, M.V.2
  • 29
    • 33845895536 scopus 로고    scopus 로고
    • The frequency of translational misreading errors in E. coli is largely determined by tRNA competition
    • Kramer E, Farabaugh PJ. 2007. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA 13:87-96
    • (2007) RNA , vol.13 , pp. 87-96
    • Kramer, E.1    Farabaugh, P.J.2
  • 30
    • 0042492708 scopus 로고    scopus 로고
    • The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo
    • Krüger MK, Pedersen S, Hagervall TG, Sorensen MA. 1998. The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo,. J Mol Biol. 284:621-631
    • (1998) J Mol Biol. , vol.284 , pp. 621-631
    • Krüger, M.K.1    Pedersen, S.2    Hagervall, T.G.3    Sorensen, M.A.4
  • 31
    • 13444291526 scopus 로고    scopus 로고
    • Codon bias as a factor in regulating expression via translation rate in the human genome
    • Lavner Y, Kotlar D. 2005. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345:127-138
    • (2005) Gene , vol.345 , pp. 127-138
    • Lavner, Y.1    Kotlar, D.2
  • 32
    • 45749090511 scopus 로고    scopus 로고
    • Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon
    • Lehmann J, Libchaber A. 2008. Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon. RNA 14:1264-1269
    • (2008) RNA , vol.14 , pp. 1264-1269
    • Lehmann, J.1    Libchaber, A.2
  • 33
    • 0023064998 scopus 로고
    • Models of nearly neutral mutation with particular implications for nonrandom usage of synonymous codons
    • Li WH. 1987. Models of nearly neutral mutation with particular implications for nonrandom usage of synonymous codons. J Mol Evol. 24:337-345
    • (1987) J Mol Evol. , vol.24 , pp. 337-345
    • Li, W.H.1
  • 34
    • 0027530123 scopus 로고
    • The nucleotide in position 32 of the tRNA anticodon loop determines abilityofanticodon UCCtodiscriminate among glycine codons
    • Lustig F, Borén T, Claesson C, Simonsson C, Barciszewska M, Lagerkvist U. 1993. The nucleotide in position 32 of the tRNA anticodon loop determines abilityofanticodon UCCtodiscriminate among glycine codons,. Proc Natl Acad Sci\USA. 90:3343-3347
    • (1993) Proc Natl Acad Sci\USA. , vol.90 , pp. 3343-3347
    • Lustig, F.1    Borén, T.2    Claesson, C.3    Simonsson, C.4    Barciszewska, M.5    Lagerkvist, U.6
  • 35
    • 0345306751 scopus 로고    scopus 로고
    • The origins of genome complexity
    • Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302:1401-1404
    • (2003) Science , vol.302 , pp. 1401-1404
    • Lynch, M.1    Conery, J.S.2
  • 36
    • 0022036496 scopus 로고
    • His influences in vivo decoding properties
    • Meier F, Suter B, Grosjean H, Keith G, Kubli E. 1985. Queuosine modification of the wobble base in tRNAHis influences in vivo decoding properties. EMBO J. 4:823-827
    • (1985) EMBO J. , vol.4 , pp. 823-827
    • Meier, F.1    Suter, B.2    Grosjean, H.3    Keith, G.4    Kubli, E.5
  • 37
    • 49349113285 scopus 로고    scopus 로고
    • Ribosome collisions and translational efficiency: Optimization by codon usage and mRNA destabilization
    • Mitarai N, Sneppen K, Pedersen S. 2008. Ribosome collisions and translational efficiency: optimization by codon usage and mRNA destabilization. J Mol Biol. 382:236-245
    • (2008) J Mol Biol. , vol.382 , pp. 236-245
    • Mitarai, N.1    Sneppen, K.2    Pedersen, S.3
  • 38
  • 39
    • 0034788470 scopus 로고    scopus 로고
    • Queuosine modification of tRNA: A case for convergent evolution
    • Morris RC, Elliott MS. 2001. Queuosine modification of tRNA: a case for convergent evolution. Mol Genet Metab. 74:147-159
    • (2001) Mol Genet Metab. , vol.74 , pp. 147-159
    • Morris, R.C.1    Elliott, M.S.2
  • 40
    • 39449087192 scopus 로고    scopus 로고
    • Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure
    • Moura G, Pinheiro M, Arrais J, Gomes AC, Carreto L, Freitas A, Oliveira JL, Santos MAS. 2007. Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS One. 2(9):e847.
    • (2007) PLoS One. , vol.2 , Issue.9
    • Moura, G.1    Pinheiro, M.2    Arrais, J.3    Gomes, A.C.4    Carreto, L.5    Freitas, A.6    Oliveira, J.L.7    Mas, S.8
  • 41
    • 36248950665 scopus 로고    scopus 로고
    • The wobble hypothesis revisited: Uridine-5-oxyacetic acid is critical for reading of G-ending codons
    • Näsvall SJ, Chen P, Björk R. 2007. The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. RNA 13:2151-2164
    • (2007) RNA , vol.13 , pp. 2151-2164
    • Näsvall, S.J.1    Chen, P.2    Björk, R.3
  • 42
    • 33747889715 scopus 로고    scopus 로고
    • Multiple stages in codon-anticodon recognition: Double-trigger mechanisms and geometric constraints
    • Ninio J. 2006. Multiple stages in codon-anticodon recognition: double-trigger mechanisms and geometric constraints. Biochimie 88:963-992
    • (2006) Biochimie , vol.88 , pp. 963-992
    • Ninio, J.1
  • 44
    • 1842686227 scopus 로고    scopus 로고
    • Val are important for trans-location
    • Phelps SS, Malkiewicz A, Agris PF, Joseph S. 2004. Modified nucleotides in tRNALys and tRBAVal are important for trans-location. J Mol Biol. 338:439-444
    • (2004) J Mol Biol. , vol.338 , pp. 439-444
    • Phelps, S.S.1    Malkiewicz, A.2    Agris, P.F.3    Joseph, S.4
  • 45
    • 0023655732 scopus 로고
    • Missense misreading of asparagine codons as a function of codon identity and context
    • Precup J, Parker J. 1987. Missense misreading of asparagine codons as a function of codon identity and context. J Biol Chem. 23:11351-11355
    • (1987) J Biol Chem. , vol.23 , pp. 11351-11355
    • Precup, J.1    Parker, J.2
  • 46
    • 8744310123 scopus 로고    scopus 로고
    • Codon usage bias from the tRNA's point of view: Redundancy, specialization, and efficient decoding for trans-lational optimization
    • Rocha EPC. 2004. Codon usage bias from the tRNA's point of view: redundancy, specialization, and efficient decoding for trans-lational optimization. Genome Res. 14:2279-2286
    • (2004) Genome Res. , vol.14 , pp. 2279-2286
    • Epc, R.1
  • 47
    • 0034923932 scopus 로고    scopus 로고
    • Fidelity of aminoacyl-tRNA selection on the ribosome: Kinetic and structural mechanisms
    • Rodnina MV, Wintermeyer W. 2001. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu Rev Biochem. 70:415-435
    • (2001) Annu Rev Biochem. , vol.70 , pp. 415-435
    • Rodnina, M.V.1    Wintermeyer, W.2
  • 48
    • 0003634460 scopus 로고    scopus 로고
    • Structural basis of base exchange by tRNA-guanine transglycosylases
    • In: Grosjean H, Benne R, editors Washington (DC) ASM Press
    • Romier C, Ficner R, Suck D. 1998. Structural basis of base exchange by tRNA-guanine transglycosylases. In: Grosjean H, Benne R, editors. Modification and editing of RNA. Washington (DC): ASM Press. p. 493-516
    • (1998) Modification and Editing of RNA , pp. 493-516
    • Romier, C.1    Ficner, R.2    Suck, D.3
  • 49
    • 34250704167 scopus 로고    scopus 로고
    • The mechanisms of codon reassignments in mitochondrial genetic codes
    • Sengupta S, Yang X, Higgs PG. 2007. The mechanisms of codon reassignments in mitochondrial genetic codes. J Mol Evol. 64: 662-688
    • (2007) J Mol Evol. , vol.64 , pp. 662-688
    • Sengupta, S.1    Yang, X.2    Higgs, P.G.3
  • 50
    • 0023046211 scopus 로고
    • Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons
    • Sharp PM, Li WH. 1986. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 14:7737-7749
    • (1986) Nucleic Acids Res. , vol.14 , pp. 7737-7749
    • Sharp, P.M.1    Li, W.H.2
  • 52
    • 0025181355 scopus 로고
    • Switches in species-species codon preferences: The influence of mutation bias
    • Shields DC. 1990. Switches in species-species codon preferences: the influence of mutation bias. J Mol Evol. 31:71-80
    • (1990) J Mol Evol. , vol.31 , pp. 71-80
    • Shields, D.C.1
  • 53
    • 0026409389 scopus 로고
    • Absolute in vivo translation rates of individual codons in Escherichia coli
    • Sorensen MA, Pedersen S. 1991. Absolute in vivo translation rates of individual codons in Escherichia coli. J Mol Biol. 222:265-280
    • (1991) J Mol Biol. , vol.222 , pp. 265-280
    • Sorensen, M.A.1    Pedersen, S.2
  • 54
    • 33846786904 scopus 로고    scopus 로고
    • Synonymous codon usage in Escherichia coli: Selection for translational accuracy
    • Stoletzki N, Eyre-Walker A. 2006. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol. 24:374-381
    • (2006) Mol Biol Evol. , vol.24 , pp. 374-381
    • Stoletzki, N.1    Eyre-Walker, A.2
  • 55
    • 0035801515 scopus 로고    scopus 로고
    • Improvement of reading frame maintenance is a common function for several tRNA modifications
    • Urbonavicius J, Qian Q, Durand JMB, Hagervall TG, Björk GR. 2001. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J. 20: 4863-4873
    • (2001) EMBO J. , vol.20 , pp. 4863-4873
    • Urbonavicius, J.1    Qian, Q.2    Jmb, D.3    Hagervall, T.G.4    Björk, G.R.5
  • 56
  • 59
    • 0034822301 scopus 로고    scopus 로고
    • Genetic code variantions in mitochondria: TRNA as a major determinant of genetic code plasticity
    • Yokobori S, Suzuki T, Watanabe K. 2001. Genetic code variantions in mitochondria: tRNA as a major determinant of genetic code plasticity. J Mol Evol. 53:314-326
    • (2001) J Mol Evol. , vol.53 , pp. 314-326
    • Yokobori, S.1    Suzuki, T.2    Watanabe, K.3


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