Major codon preference: theme and variations

Kurland, C. G.

doi:10.1042/bst0210841

Cited by 38 publications

(30 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Since tRNA expression levels and tRNA gene copy number are correlated (Ikemura 1981a,b;Bennetzen and Hall 1982;Kurland 1993;Kanaya et al 1999), we decided to investigate whether the variation in gene copy number observed for some tRNA genes along the lineages analyzed has had an effect on the codon usage of the genomes involved. In order to achieve this goal, the S-values (dos Reis et al 2004) for the coadaptation between genomic tRNAs and codon usage was computed for each genome, and the process was carried out using modern and ancestral tRNA sets (see Materials and Methods).…”

Section: Adaptation Of Codon Usage To the Ancestral Trna Setmentioning

confidence: 99%

“…It has been suggested that cellular tRNA content might be rate-limiting during protein translation (Kurland 1993). For example, in certain organisms like Escherichia coli or the baker's yeast, it has been observed that highly expressed genes use a subset of optimal codons that match the most abundant tRNAs within the cell (Ikemura 1981a;Bennetzen and Hall 1982).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Archaeology and evolution of transfer RNA genes in the Escherichia coli genome

Withers

Wernisch²,

Reis³

2006

RNA

View full text Add to dashboard Cite

Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat neglected area of molecular evolution. Escherichia coli, the first phylogenetic species for which more than two different strains have been sequenced, provides an invaluable framework to study the evolution of tRNA genes. In this work, a detailed analysis of the tRNA structure of the genomes of Escherichia coli strains K12, CFT073, and O157:H7, Shigella flexneri 2a 301, and Salmonella typhimurium LT2 was carried out. A phylogenetic analysis of these organisms was completed, and an archaeological map depicting the main events in the evolution of tRNA genes was drawn. It is shown that duplications, deletions, and horizontal gene transfers are the main factors driving tRNA evolution in these genomes. On average, 0.64 tRNA insertions/duplications occur every million years (Myr) per genome per lineage, while deletions occur at the slower rate of 0.30 per million years per genome per lineage. This work provides a first genomic glance at the problem of tRNA evolution as a repetitive process, and the relationship of this mechanism to genome evolution and codon usage is discussed.

show abstract

Section: Adaptation Of Codon Usage To the Ancestral Trna Setmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Archaeology and evolution of transfer RNA genes in the Escherichia coli genome

Withers

Wernisch²,

Reis³

2006

RNA

View full text Add to dashboard Cite

show abstract

“…The nature of gene codon choices varies considerably from organism to organism; for recent reviews, see Andersson and Kurland (1990), Kurland (1993) and Sharp and Matassi (1994). Pronounced differences in codon usage raise questions about the mechanisms producing and maintaining these differences.…”

Section: Introductionmentioning

confidence: 99%

“…Codon/anticodon interaction strength (e.g. Kurland, 1993), site-specific codon biases (e.g. Maynard-Smith and Smith, 1996), time of replication (e.g.…”

Section: Introductionmentioning

confidence: 99%

Codon usages in different gene classes of the Escherichia coli genome

Karlin¹,

Mrázek²,

Campbell

1998

Molecular Microbiology

207

152

View full text Add to dashboard Cite

SummaryA new measure for assessing codon bias of one group of genes with respect to a second group of genes is introduced. In this formulation, codon bias correlations for Escherichia coli genes are evaluated for level of expression, for contrasts along genes, for genes in different 200 kb (or longer) contigs around the genome, for effects of gene size, for variation over different function classes, for codon bias in relation to possible lateral transfer and for dicodon bias for some gene classes. Among the function classes, codon biases of ribosomal proteins are the most deviant from the codon frequencies of the average E. coli gene. Other classes of 'highly expressed genes' (e.g. amino acyl tRNA synthetases, chaperonins, modification genes essential to translation activities) show less extreme codon biases. Consistently for genes with experimentally determined expression rates in the exponential growth phase, those of highest molar abundances are more deviant from the average gene codon frequencies and are more similar in codon frequencies to the average ribosomal protein gene. Independent of gene size, the codon biases in the 5Ј third of genes deviate by more than a factor of two from those in the middle and 3Ј thirds. In this context, there appear to be conflicting selection pressures imposed by the constraints of ribosomal binding, or more generally the early phase of protein synthesis (about the first 50 codons) may be more biased than the complete nascent polypeptide. In partitioning the E. coli genome into 10 equal lengths, pronounced differences in codon site 3 GþC frequencies accumulate. Genes near to oriC have 5% greater codon site 3 GþC frequencies than do genes from the ter region. This difference also is observed between small (100-300 codons) and large (>800 codons) genes. This result contrasts with that for eukaryotic genomes (including human, Caenorhabditis elegans and yeast) where long genes tend to have site 3 more AT rich than short genes. Many of the above results are special for E. coli genes and do not apply to genes of most bacterial genomes. A gene is defined as alien (possibly horizontally transferred) if its codon bias relative to the average gene exceeds a high threshold and the codon bias relative to ribosomal proteins is also appropriately high. These are identified, including four clusters (operons). The bulk of these genes have no known function.

show abstract

“…Other contributing factors include interaction between codons and anticodons (18), efficacy of replication (19) and usage of codon pairs (20).…”

mentioning

confidence: 99%