Comprehensive analysis of prokaryotic mechanosensation genes: their characteristics in codon usage

Chen, Rong and Yan, Hong and Zhao, Kong-Nan and Martinac, Boris and Liu, Guang B. (2007) Comprehensive analysis of prokaryotic mechanosensation genes: their characteristics in codon usage. Mitochondrial DNA, 18 (4). pp. 269-278. ISSN 1042-5179

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Abstract

In the present study, we examined GC nucleotide composition, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI) and gene length for 308 prokaryotic mechanosensitive ion channel (MSC) genes from six evolutionary groups: Euryarchaeota, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, and Gammaproteobacteria. Results showed that: (1) a wide variation of over representation of nucleotides exists in the MSC genes; (2) codon usage bias varies considerably among the MSC genes; (3) both nucleotide constraint and gene length play an important role in shaping codon usage of the bacterial MSC genes; and (4) synonymous codon usage of prokaryotic MSC genes is phylogenetically conserved. Knowledge of codon usage in prokaryotic MSC genes may benefit from the study of the MSC genes in eukaryotes in which few MSC genes have been identified and functionally analysed.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Deposited in accordance with the copyright policy of the publisher.
Depositing User: Ms Debbie White
Faculty / Department / School: Historic - Faculty of Sciences - Department of Biological and Physical Sciences
Date Deposited: 11 Oct 2007 01:15
Last Modified: 02 Jul 2013 22:47
Uncontrolled Keywords: GC nucleotide composition; mechanosensitive channel genes; principal component analysis; relative synonymous codon usage
Fields of Research (FOR2008): 06 Biological Sciences > 0604 Genetics > 060407 Genome Structure and Regulation
11 Medical and Health Sciences > 1108 Medical Microbiology > 110801 Medical Bacteriology
10 Technology > 1004 Medical Biotechnology > 100403 Medical Molecular Engineering of Nucleic Acids and Proteins
Socio-Economic Objective (SEO2008): E Expanding Knowledge > 97 Expanding Knowledge > 970106 Expanding Knowledge in the Biological Sciences
Identification Number or DOI: doi: 10.1080/10425170601136564
URI: http://eprints.usq.edu.au/id/eprint/2864

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