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.

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References in periodicals archive ?
subtilis main codons based on Codon Usage Database (Kazusa DNA Research Institute, Japan; Website: http:// www.
Construction of Bacillus subtilis strain engineered for expression of porcine [beta]-defensin-2/cecropin P1 fusion antimicrobial peptides and its growth-promoting effect and antimicrobial activity
were sequenced, their genomic structure examined, and their genome organization, arrangement and codon usage analyzed.
Complete Mitochondrial Genome of Three Fish Species (Perciformes: Amblyopinae): Genome Description and Phylogenetic Relationships
NM_000515) was performed by Codon Usage Wrangler server at http://www.
Evaluation of recombinant human growth hormone secretion in E. coli. using the L-asparaginase II signal peptide
Mutation bias is the driving force of codon usage in the gallus gallus genome.
SITE-DIRECTED MUTAGENESIS OF THE BACTERIAL PHYTASE GENE COMPATIBLE FOR CHICKEN CODON PREFERENCES
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.
TRNAPROLIF: Control of translation efficiency in proliferating and differentiated mammalian cells
The codons of the gene must also be optimized for the organism due to codon usage bias.
Role of genetically modified crops in agriculture
Phage apparently don't really 'care' about the codon usage of the host.
Meaning of Genetic Code Gets Reassigned
The most representative signatures include G + C content, dinucleotide biases, codon usage, mobility genes (including transposases and integrases), and tRNA genes [14, 15].
A computational framework for tracing the origins of genomic islands in prokaryotes
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.
Interference of a Synthetic Rep Protein to Develop Resistance against Cotton Leaf Curl Disease
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.
'Snooze button' on biological clocks boosts cell adaptability
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].
Enhanced biological activity of recombinant human interferon alpha produced in Pichia pastoris using a codon-optimized synthetic cDNA
Virus mutant spectra under the selective pressure of monoclonal antibodies: codon usage constraints limit capsid variability.
Hepatitis A virus vaccine escape variants and potential new serotype emergence

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