Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity
Paul M. Sharp,Elizabeth Cowe,Desmond G. Higgins,Denis C. Shields,Kenneth H. Wolfe,Frank Wright +5 more
Reads0
Chats0
TLDR
These trends for codon usage are illustrated for six species whereCodon usage has been examined in detail, by presenting the pooled codon used for the 10% of genes at either end of the major trend.Abstract:
The genetic code is degenerate, but alternative synonymous codons are generally not used with equal frequency. Since the pioneering work of Grantham's group it has been apparent that genes from one species often share similarities in codon frequency; under the "genome hypothesis" there is a species-specific pattern to codon usage. However, it has become clear that in most species there are also considerable differences among genes. Multivariate analyses have revealed that in each species so far examined there is a single major trend in codon usage among genes, usually from highly biased to more nearly even usage of synonymous codons. Thus, to represent the codon usage pattern of an organism it is not sufficient to sum over all genes as this conceals the underlying heterogeneity. Rather, it is necessary to describe the trend among genes seen in that species. We illustrate these trends for six species where codon usage has been examined in detail, by presenting the pooled codon usage for the 10% of genes at either end of the major trend. Closely-related organisms have similar patterns of codon usage, and so the six species in Table 1 are representative of wider groups. For example, with respect to codon usage, Salmonella typhimurium closely resembles E. coli, while all mammalian species so far examined (principally mouse, rat and cow) largely resemble humans.read more
Citations
More filters
Journal ArticleDOI
Regeneration and functional incorporation of bacteriorhodopsin in membranes of fission yeast but not inE. coli
Journal ArticleDOI
Looking into the genome of Thermosynechococcus elongatus thermophilic cyanobacteria with codon selection and usage perspective
TL;DR: Findings showed cumulative role of translational selection, translational accuracy and gene expression levels with mutational bias as key player in codon selection pattern of this organism.
Journal ArticleDOI
Bio-informatique (5) : phylogénie et évolution moléculaires
TL;DR: The phylogenie moleculaire as discussed by the authors reconfigures the relations of parente entre sequences of nucleotides ou d'acides amines, and is used to understand the evolution of the genome.
Proceedings ArticleDOI
Genome analysis of Rhizobium species using codon usage bias tools
Niyati Rai,Dwijesh Chandra Mishra,Sanjeev Kumar,Anil Rai,K. K. Chaturvedi,S. B. Lal,Anil Kumar,Mohammad Samir Farooqi,P. G. Majumdar,Sunil Archak +9 more
TL;DR: The overall codon usage analysis showed that codons ending with G and C are preferred more in the rhizobium genome than codon ending with A and T, which revealed that compositional constraints along with translational selection are the major cause ofcodon usage bias.
The bifunctional flavokinase/FAD synthetase from Streptomyces davawensis produces inactive flavin cofactors and is not involved in resistance to the antibiotic roseoflavin
TL;DR: It was hypothesized that a flavokinase/FAD synthetase (RibC) highly specific for riboflavin may be present in S. davawensis, which would not allow the formation of toxic RoFMN/RoFAD.
Related Papers (5)
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
Paul M. Sharp,Wen-Hsiung Li +1 more