In silico Analysis of Synonymous Codon Usage Pattern of Rhizobium etli CFN 42

Autor: Dhananjaya P. Singh, Mohammad Samir Farooqi, K. K. Chaturvedi, Naveen Sharma, Dwijesh Chandra Mishra, Anil Rai, R. K. Sanjukta
Rok vydání: 2014
Předmět:
Zdroj: Proceedings of the National Academy of Sciences, India Section B: Biological Sciences. 86:385-393
ISSN: 2250-1746
0369-8211
DOI: 10.1007/s40011-014-0457-x
Popis: Understanding the extent and pattern of codon bias and the forces affecting codon usage are the key steps towards elucidating choice of codons at the level of individual genes. In the present study, codon usage pattern among 3,703 genes of nitrogen fixing bacterium, Rhizobium etli CFN 42 was analyzed. The study aims to identify the factors responsible for codon usage bias and highly expressed genes of this bacterium. Multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation among the genes. Correlation analysis suggested that the axis has strong significant positive correlation with GC3s i.e. GC content at the third codon position. A significant negative correlation between effective number of codons and GC3s content was observed suggesting that the codon usage was affected by gene nucleotide composition. These findings suggested mutational role as the major factor in shaping codon usage bias among the genes. Further, correspondence analysis of Relative Synonymous Codon Usage revealed cluster of highly expressed genes. Notably, 26 codons were determined as the ‘optimal codons’ that were significantly more frequent among the highly expressed genes tested by χ2 test (P < 0.01). Such results may add value to the efforts of developing bio-fertilizers based on symbiotic or non-symbiotic bacteria for improving soil fertility.
Databáze: OpenAIRE
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