On the Organizational Dynamics of the Genetic Code

Handle URI:
http://hdl.handle.net/10754/552438
Title:
On the Organizational Dynamics of the Genetic Code
Authors:
Zhang, Zhang; Yu, Jun
Abstract:
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.
KAUST Department:
Plant Stress Genomics Research Lab; Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
On the Organizational Dynamics of the Genetic Code 2011, 9 (1-2):21 Genomics, Proteomics & Bioinformatics
Journal:
Genomics, Proteomics & Bioinformatics
Issue Date:
7-Jun-2011
DOI:
10.1016/S1672-0229(11)60004-1
Type:
Article
ISSN:
16720229
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S1672022911600041
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorZhang, Zhangen
dc.contributor.authorYu, Junen
dc.date.accessioned2015-05-07T13:23:10Zen
dc.date.available2015-05-07T13:23:10Zen
dc.date.issued2011-06-07en
dc.identifier.citationOn the Organizational Dynamics of the Genetic Code 2011, 9 (1-2):21 Genomics, Proteomics & Bioinformaticsen
dc.identifier.issn16720229en
dc.identifier.doi10.1016/S1672-0229(11)60004-1en
dc.identifier.urihttp://hdl.handle.net/10754/552438en
dc.description.abstractThe 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.en
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S1672022911600041en
dc.rightsArchived with thanks to Genomics, Proteomics & Bioinformatics. http://creativecommons.org/licenses/by-nc-sa/3.0/en
dc.subjectgenetic codeen
dc.subjectcodonen
dc.subjectGC contenten
dc.subjectpurine contenten
dc.subjectorganizational dynamicsen
dc.subjectcompositional dynamicsen
dc.titleOn the Organizational Dynamics of the Genetic Codeen
dc.typeArticleen
dc.contributor.departmentPlant Stress Genomics Research Laben
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalGenomics, Proteomics & Bioinformaticsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, Chinaen
kaust.authorZhang, Zhangen
kaust.authorYu, Junen
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