Document Detail


Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons.
MedLine Citation:
PMID:  17977670     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Hani Goodarzi; Noorossadat Torabi; Hamed Shateri Najafabadi; Marco Archetti
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2007-10-05
Journal Detail:
Title:  Gene     Volume:  407     ISSN:  0378-1119     ISO Abbreviation:  Gene     Publication Date:  2008 Jan 
Date Detail:
Created Date:  2007-12-18     Completed Date:  2008-03-20     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  7706761     Medline TA:  Gene     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  30-41     Citation Subset:  IM    
Affiliation:
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. goodarzi@princeton.edu
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MeSH Terms
Descriptor/Qualifier:
Adaptation, Physiological
Amino Acids / genetics*
Bacteria / genetics
Base Sequence
Codon / genetics*
Genetic Code / genetics*
Genome / genetics*
Molecular Sequence Data
Multigene Family
Neural Networks (Computer)
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Codon

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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