Trends in the codon usage patterns of Chromohalobacter salexigens genes



Rajkumari Sanjukta1*, Mohammad Samir Farooqi1*, Naveen Sharma1, Anil Rai1, Dwijesh Chandra Mishra1 & Dhananjaya P Singh2



1Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110 012; 2National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, UP 275 101


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Received September 22, 2012; Accepted October 06, 2012; Published November 13, 2012



Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage (RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to develop salt-tolerant crops of agronomic value.



Codon usage pattern, Correspondence analysis, Relative synonymous codon usage, Mutational bias, Halophilic bacteria.



Sanjukta et al. Bioinformation 8(22): 1087-1095 (2012)

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P Kangueane






Biomedical Informatics



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