codon usage

codon usage

the frequency with which a particular organism uses the available CODONS in genes. The majority of AMINO ACIDS are coded for by more than one codon (see GENETIC CODE and there are marked preferences for the use of the alternative codons amongst different species. For example, in bacteria CCG is the preferred codon for the amino acid proline, rather than CCU, CCC or CCA. Codon usage can affect the efficiency of translation, particularly when cloned heterologous genes are being expressed. If the cloned gene contains a large number of unfavoured codons the tRNA molecules of the host may not effectively recognize them, so reducing translation and hence the amount of protein synthesized.

ORF SCANNING takes codon usage into account to facilitate the location of genes, since real EXONS are likely to display a bias for certain codons, whereas runs of chance triplets will not. Codon usage is also called codon bias.

References in periodicals archive ?
were sequenced, their genomic structure examined, and their genome organization, arrangement and codon usage analyzed.
Mutation bias is the driving force of codon usage in the gallus gallus genome.
We rely on our preliminary results that show a striking dichotomy in codon usage: genes involved in cellular proliferation have distinct codon usage compared to genes involved in differentiation and other multi-cellular process.
The codons of the gene must also be optimized for the organism due to codon usage bias.
Phage apparently don't really 'care' about the codon usage of the host.
The most representative signatures include G + C content, dinucleotide biases, codon usage, mobility genes (including transposases and integrases), and tRNA genes [14, 15].
Codon optimization was carried out by considering codon usage table for Gossypium hirsutum [gbpln]: 557 CDS's (190383 codons) from NCBI- GenBank codon usage data base.
Recently, they have realized that this is not the case and that differences in synonymous codon usage have a significant impact on cellular processes, so scientists have advanced a wide variety of ideas about the role that these variations play.
This bias exists among the 61 amino acid codons found in mRNA molecules, and the levels of aminoacyl-tRNAs seem to correlate with the frequency of codon usage [3,4].
Virus mutant spectra under the selective pressure of monoclonal antibodies: codon usage constraints limit capsid variability.