Topic
Codon Adaptation Index
About: Codon Adaptation Index is a research topic. Over the lifetime, 340 publications have been published within this topic receiving 25337 citations.
Papers published on a yearly basis
Papers
TL;DR: A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed, useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons ofCodon usage in different organisms.
Abstract: A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.
3,842 citations
TL;DR: A simple measure is presented that quantifies how far the codon usage of a gene departs from equal usage of synonymous codons, Nc, which provides an intuitively meaningful measure of the extent of codon preference in a gene.
2,212 citations
TL;DR: Examination of silent substitutions and tRNA populations in Enterobacteriaceae revealed that the evolutionary constraint imposed by tRNA content on codon usage decelerated rather than accelerated the silent-substitution rate, at least insofar as pairs of taxonomically related organisms were examined.
Abstract: Choices of synonymous codons in unicellular organisms are here reviewed, and differences in synonymous codon usages between Escherichia coli and the yeast Saccharomyces cerevisiae are attributed to differences in the actual populations of isoaccepting tRNAs. There exists a strong positive correlation between codon usage and tRNA content in both organisms, and the extent of this correlation relates to the protein production levels of individual genes. Codon-choice patterns are believed to have been well conserved during the course of evolution. Examination of silent substitutions and tRNA populations in Enterobacteriaceae revealed that the evolutionary constraint imposed by tRNA content on codon usage decelerated rather than accelerated the silent-substitution rate, at least insofar as pairs of taxonomically related organisms were examined. Codon-choice patterns of multicellular organisms are briefly reviewed, and diversity in G+C percentage at the third position of codons in vertebrate genes--as well as a possible causative factor in the production of this diversity--is discussed.
1,893 citations
TL;DR: Extreme codon bias is seen for the Saccharomyces cerevisiae genes for the fermentative alcohol dehydrogenase isozyme I (ADH-I) and glyceraldehyde-3-phosphate dehydrogenased genes and a similar phenomenon is observed in the codon preferences of highly expressed genes in Escherichia coli.
1,644 citations
TL;DR: The finding that the frequency of usage of optimal codons is closely correlated with the production levels of individual genes was discussed from an evolutionary viewpoint.
1,500 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2022 | 1 |
| 2021 | 25 |
| 2020 | 33 |
| 2019 | 17 |
| 2018 | 26 |
| 2017 | 15 |