Factors
Affecting Codon Usage in Yersinia pestis
HOU Zhuo-Cheng, YANG Ning*
(
College of Animal Science and Technology, China Agricultural University,
Beijing 100094, China )
Abstract The
complete genome of Yersinia pestis which was the causative agent of the
systemic invasive infectious disease classically referred as plague, had been
recently sequenced. In order to have a further insight into the synonymous
codon usage evolution, factors shaping synonymous codon usage pattern of
Yersinia pestis were analyzed in this paper. The coding sequences larger than
or equal to 300 bp were used in codon usage analysis. Though “G”+”C”
content in Y. pestis genome was slightly lower (47.64%), the highly
expressed genes tended to use “C” or “G” at synonymous
sites compared with lowly expressed genes. Conversely, lowly expressed genes
tended to prefer “A” or “T” at synonymous positions. Gene
expression level was strongly correlated with the first axis of the
correspondence analysis (COA) (R=0.63, P<0.0001). By the analyses of the
codon usage pattern of highly and lowly expressed genes, it was confirmed that
gene expression level was partially responsible for the codon usage bias.
GC-skew analysis showed that codon usage suffered replication-transcriptional
selection. Codon adaptation index (CAI), frequency of "C"+"G"
at the synonymous third position of codon (GC3s) and the effective number of
codons (Nc) values showed some differences among different gene length groups. "G"+"C"
content of genes was strongly correlated with the first axis of the COA (R=0.72,
P<0.0001). It could be concluded that gene expressivity,
replication-transcriptional selection, gene length and gene composition
constraints were the main affecting factors of codon usage variation in Y.
pestis.
Key words codon
usage; correspondence analysis; gene expression level; coding sequence length;
Yersinia pestis
*Corresponding author: Tel, 86-10-628927141; Fax, 86-10-62891351; e-mail, [email protected]