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
Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli.
TL;DR: The correspondence analysis showed that in 13 species the major trend of synonymous codon usage was highly correlated with gene expression level as assessed by the “Codon Adaptation Index” (CAI) values, and major factors shaping codon and amino acid usage variation Lactobacillus sakei 23K were investigated.
Journal ArticleDOI
Theoretical methods for identifying important functional genes in bacterial genomes
TL;DR: This review attempts to summarize current computational methods in identifying the above functional genes from bacterial genomes, which is of significant importance in exploring the bacterial genomes.
Patent
Fluorescent proteins from aquatic species
TL;DR: In this article, four new fluorescent proteins were derived from two wild-type fluorescent proteins: a red fluorescent protein (RFP) that was isolated from Actinodiscus or Discosoma sp. 1 and a green fluorescent proteins (GFP) isolated from Montastraea cavernosa.
Journal ArticleDOI
Analysis of codon usage bias of chloroplast genomes in Gynostemma species
Journal ArticleDOI
Native cysteine residues are dispensable for the structure and function of all five yeast mitotic septins
Natalia de Val,Michael A. McMurray,Lisa H. Lam,Chris C.-S. Hsiung,Aurélie Bertin,Eva Nogales,Eva Nogales,Eva Nogales,Jeremy Thorner +8 more
TL;DR: Budding yeast septins assemble into hetero‐octamers and filaments required for cytokinesis and display assembly properties in vitro indistinguishable from wild‐type, and recombinant Cys‐less sePTins—or where one of the Cys-less septin contained a single Cys introduced at a new site—displayed assembly properties at defined locations indistinguishable fromWild‐type.
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