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

Article

Chen, Rong, Yan, Hong, Zhao, Kong-Nan, Martinac, Boris and Liu, Guang B.. 2007. "Comprehensive analysis of prokaryotic mechanosensation genes: their characteristics in codon usage." DNA Sequence. 18 (4), pp. 269-278. https://doi.org/10.1080/10425170601136564
Article Title

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

ERA Journal ID2330
Article CategoryArticle
AuthorsChen, Rong (Author), Yan, Hong (Author), Zhao, Kong-Nan (Author), Martinac, Boris (Author) and Liu, Guang B. (Author)
Journal TitleDNA Sequence
Journal Citation18 (4), pp. 269-278
Number of Pages10
Year2007
PublisherTaylor & Francis
Place of PublicationLondon, United Kingdom
ISSN1042-5179
1029-2365
Digital Object Identifier (DOI)https://doi.org/10.1080/10425170601136564
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.

KeywordsGC nucleotide composition; mechanosensitive channel genes; principal component analysis; relative synonymous codon usage
ANZSRC Field of Research 2020310508. Genome structure and regulation
320701. Medical bacteriology
320603. Medical molecular engineering of nucleic acids and proteins
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Byline AffiliationsXi'an Jiaotong University, China
University of Queensland
Centre for Systems Biology
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