title: Comprehensive analysis of prokaryotic mechanosensation genes: their characteristics in codon usage.
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 overrepresentation 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.
authors.affiliation: School of Medicine, Xi'an Jiaotong University, Xi'an, People's Republic of China.
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Hong
authors.initials: H
authors.lastname: Yan
authors.forename: Kong-Nan
authors.initials: KN
authors.lastname: Zhao
authors.forename: Boris
authors.initials: B
authors.lastname: Martinac
authors.forename: Guang B
authors.initials: GB
authors.lastname: Liu
mesh_terms: D001419:Bacteria / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D020862:GC Rich Sequence / Q000235:genetics; D040542:Mechanotransduction, Cellular / Q000235:genetics*; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA
chemical_list: D003062:Codon