Document Detail


On the organizational dynamics of the genetic code.
MedLine Citation:
PMID:  21641559     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides-adenine, thymine, guanine and cytosine-according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.
Authors:
Zhang Zhang; Jun Yu
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Genomics, proteomics & bioinformatics     Volume:  9     ISSN:  2210-3244     ISO Abbreviation:  Genomics Proteomics Bioinformatics     Publication Date:  2011 Apr 
Date Detail:
Created Date:  2011-06-06     Completed Date:  2011-08-24     Revised Date:  2013-04-17    
Medline Journal Info:
Nlm Unique ID:  101197608     Medline TA:  Genomics Proteomics Bioinformatics     Country:  China    
Other Details:
Languages:  eng     Pagination:  21-9     Citation Subset:  IM    
Copyright Information:
Copyright © 2011 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.
Affiliation:
Plant Stress Genomics Research Center, Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / genetics
Archaea / genetics*
Bacteria / genetics*
Base Composition
Evolution, Molecular*
Genetic Code*
Genome, Archaeal
Genome, Bacterial
Nucleotides / chemistry*,  genetics
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Nucleotides

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


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