Amino acid and codon usage profiles

Adaptive changes in the frequency of amino acids and codons

Hani Goodarzi, Noorossadat Torabi, Hamed Shateri Najafabadi, Marco Archetti

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

In the work presented, the changes in codon and amino acid contents have been studied as a function of environmental conditions by comparing pairs of homologs in a group of extremophilic/non-extremophilic genomes. Our results obtained based on such analysis highlights a number of notable observations: (i) the overall preference of amino acid usages in the proteins of a given organism is significantly affected by major environmental factors. The changes in amino acid preferences (amino acid usage profiles) in an extremophile compared to its non-extremophile relative recurs in the organisms of similar extreme habitats. (ii) On the other hand, changes in codon usage preferences in these extremophilic/non-extremophilic pairs, lack such persistency not only in different genome-pairs but also in the individual genes of a specific pair. (iii) We have noted a correlation between cellular function and codon usage profiles of the genes in the studied pairs. (iv) Based on this correlation, we could obtain a decent prediction of cellular functions solely based on codon usage profile data. (v) Comparisons made between two sets of randomly generated genomes suggest that different patterns of codon usage changes in genes of different functional categories result in a partial resistance towards the changes in the concentration of a given amino acid. This buffering capacity might explain the observed differences in codon usage trends in genes of different functions. In the end, we suggest codon usage and amino acid profiles as powerful tools that can be utilized to improve function predictions and genome-environment mappings.

Original languageEnglish (US)
Pages (from-to)30-41
Number of pages12
JournalGene
Volume407
Issue number1-2
DOIs
StatePublished - Jan 15 2008

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Codon
Amino Acids
Genome
Genes
Chromosome Mapping
Ecosystem
Proteins

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Goodarzi, Hani ; Torabi, Noorossadat ; Najafabadi, Hamed Shateri ; Archetti, Marco. / Amino acid and codon usage profiles : Adaptive changes in the frequency of amino acids and codons. In: Gene. 2008 ; Vol. 407, No. 1-2. pp. 30-41.
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Amino acid and codon usage profiles : Adaptive changes in the frequency of amino acids and codons. / Goodarzi, Hani; Torabi, Noorossadat; Najafabadi, Hamed Shateri; Archetti, Marco.

In: Gene, Vol. 407, No. 1-2, 15.01.2008, p. 30-41.

Research output: Contribution to journalArticle

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