Trends in the codon usage patterns of Chromohalobacter salexigens genes |
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Authors: | Rajkumari Sanjukta Mohammad Samir Farooqi Naveen Sharma Anil Rai Dwijesh Chandra Mishra Dhananjaya P Singh |
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Institution: | 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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Abstract: | 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. |
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Keywords: | Codon usage pattern Correspondence analysis Relative synonymous codon usage Mutational bias Halophilic bacteria |
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