Growth rate-optimised tRNA abundance and codon usage 1 1Edited by J. H. Miller

Berg, Otto G.; Kurland, C. G.

doi:10.1006/jmbi.1997.1142

Cited by 106 publications

(78 citation statements)

References 10 publications

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“…On one hand, enhancing the accuracy of translation provides economy of energy consumption, which may increase the cell growth rate and, in turn, fitness (Bulmer 1991). On the other hand, enhancing the speed of translation could maintain the pool of free ribosomes and thus optimize the growth rate (Kurland et al 1996) and, finally, fitness (Bulmer 1991;Berg and Kurland 1997). Hence, selection for speed and accuracy of protein synthesis explains how codon usage may act on the growth rate and then on fitness in many species including C. elegans.…”

Section: Does Codon Usage Improve the Accuracy The Speed Of Translatmentioning

confidence: 99%

Synonymous Codon Usage, Accuracy of Translation, and Gene Length in Caenorhabditis elegans

2001

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Abstract. In many unicellular organisms, invertebrates, and plants, synonymous codon usage biases result from a coadaptation between codon usage and tRNAs abundance to optimize the efficiency of protein synthesis. However, it remains unclear whether natural selection acts at the level of the speed or the accuracy of mRNAs translation. Here we show that codon usage can improve the fidelity of protein synthesis in multicellular species. As predicted by the model of selection for translational accuracy, we find that the frequency of codons optimal for translation is significantly higher at codons encoding for conserved amino acids than at codons encoding for nonconserved amino acids in 548 genes compared between Caenorhabditis elegans and Homo sapiens. Although this model predicts that codon bias correlates positively with gene length, a negative correlation between codon bias and gene length has been observed in eukaryotes. This suggests that selection for fidelity of protein synthesis is not the main factor responsible for codon biases. The relationship between codon bias and gene length remains unexplained. Exploring the differences in gene expression process in eukaryotes and prokaryotes should provide new insights to understand this key question of codon usage.

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Section: Does Codon Usage Improve the Accuracy The Speed Of Translatmentioning

confidence: 99%

Synonymous Codon Usage, Accuracy of Translation, and Gene Length in Caenorhabditis elegans

2001

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“…tRNA gene copy number correlates generally well with codon use in some species (Dong et al 1996;Berg and Kurland 1997;Percudani et al 1997;Duret 2000;see Plotkin and Kudla 2011). Although codon bias may reflect differently in different species, that which is most clearly supported is correlation with translation efficiency of mRNAs (Sharp et al 1986;Sorensen et al 1989;Plotkin and Kudla 2011).…”

Section: Introductionmentioning

confidence: 99%

tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote

Iben

Maraia²

2012

RNA

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ABSTRACTtRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of wholegenome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced relative to the other yeasts, while genes for synonymous wobble iso-acceptors are amplified, indicating wobble use not apparent in any other eukaryote. We identified a subset of japonicus-specific wobbles that improves correlation of codon use and tRNA gene content in japonicus. We conclude that tgCNV is high among Schizo species and occurs in related laboratory strains of S. pombe (and expectedly other species), and tRNAome-codon analyses can provide insight into species-specific wobble decoding.

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“…Despite many proposals, no single satisfactory explanation of skews and their diversity exists (7). Bacterial codon usage also seems complicated and multifactorial; there is evidence for translational selection resulting from uneven expression of the tRNAs (8,9), optimization of tRNA pools to the existing codon usage (10,11), and evidence for the primary role of neutral mutational pressure rather than selection (12,13). Importantly, these mechanisms by themselves do not explain diversity.…”

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confidence: 99%

“…During synthesis, a polymerase (DNA or RNA polymerase, ribosome) moves along a template and translates it to a product sequence by discriminating between competing adaptors (tRNAs for translation, dNTPs for replication, NTPs for transcription). The optimal allocation of different adaptors depends on template letter usage, as suggested for translation (10,11,15,16), whereas selection and mutation pressure on letter usage depend on resource allocation (8,9,16). …”

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confidence: 99%

Genome rhetoric and the emergence of compositional bias

Vetsigian

Goldenfeld

2009

Proc. Natl. Acad. Sci. U.S.A.

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Genomes exhibit diverse patterns of species-specific GC content, GC and AT skews, codon bias, and mutation bias. Despite intensive investigations and the rapid accumulation of sequence data, the causes of these a priori different genome biases have not been agreed on and seem multifactorial and idiosyncratic. We show that these biases can arise generically from an instability of the coevolutionary dynamics between genome composition and resource allocation for translation, transcription, and replication. Thus, we offer a unifying framework for understanding and analyzing different genome biases. We develop a test of multistability of nucleotide composition of completely sequenced genomes and reveal a bistability for Borrelia burgdorferi, a genome with pronounced replication-related biases. These results indicate that evolution generates rhetoric, it improves the efficiency of the genome's communication with the cell without modifying the message, and this leads to bias.skew ͉ GC content ͉ codon bias ͉ multistability ͉ coevolution

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Growth rate-optimised tRNA abundance and codon usage 1 1Edited by J. H. Miller

Cited by 106 publications

References 10 publications

Synonymous Codon Usage, Accuracy of Translation, and Gene Length in Caenorhabditis elegans

Synonymous Codon Usage, Accuracy of Translation, and Gene Length in Caenorhabditis elegans

tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote

Genome rhetoric and the emergence of compositional bias

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