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Studies on Synonymous Codon and Amino Acid Usage Biases in the Broad-Host Range Bacteriophage KVP40  

Sau Keya (Department of Mathematics, Jadavpur University)
Gupta Sanjib Kumar (Bioinformatics Centre)
Sau Subrata (Department of Biochemistry, Bose Institute)
Mandal Subhas Chandra (Department of Mathematics, Jadavpur University)
Ghosh Tapash Chandra (Bioinformatics Centre)
Publication Information
Journal of Microbiology / v.45, no.1, 2007 , pp. 58-63 More about this Journal
Abstract
In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/protein-coding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be AT-rich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.
Keywords
relative synonymous codon usage (RSCU); amino acid usage; correspondence analysis; phage KVP40; GRAVY; mean molecular weight;
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