- Article -
| In Silico Biology 9, 0001 (2008); ©2008, Bioinformation Systems e.V. |
Temperature influences synonymous codon and amino acid usage biases in the phages infecting extremely thermophilic prokaryotes
Keya Sau* and Arpan Deb
Department of Biotechnology, Haldia Institute of Technology, PO - HIT, Dist- Purba Medinipur, WB, India
* Corresponding author
Email: keya_sau@yahoo.co.in
Edited by E. Wingender; received April 10, 2008; revised September 09, 2008; accepted November 01, 2008; published December 16, 2008
Abstract
To see the effect of temperature on the codon and amino acid usage in phages, codon and amino acid usage of 13 phages of extremely thermophilic prokaryotes were compared with that of 14 phages of mesophilic prokaryotes. Correspondence analysis on RSCU values of two groups of phage genomes clearly shows that phages are separated along the second major axis according to their growth temperature, whereas, they are separated along the first major axis according to their GC content. Correspondence analysis on RAAU values of two groups of phages clearly shows that protein encoding genes of the phages along the second major axis are highly correlated with the GRAVY, aromaticity and cysteine content. Moreover, correspondence analysis on the regular and irregular structures of proteins of phages infecting extremely thermophilic prokaryotes reveals that temperature is one of the factors responsible for most significant differentiation of codon and amino acid usages variation in these phages.
Keywords: relative synonymous codon usage (RSCU), relative amino acid usage (RAAU), correspondence analysis (CA), frequency of G+C at the synonymous third codon positions (GC3s), covalently closed circular (ccc) DNA, GRAVY, aromaticity, cysteine content, thermophilic prokaryotes, mesophilic prokaryotes