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In Silico Biology 7, 0030 (2007); ©2007, Bioinformation Systems e.V.  



Evaluation of codon bias perspectives in phage therapy of Mycobacterium tuberculosis by multivariate analysis

Ashutosh Ranjan, Ambrish Sharan Vidyarthi and Raju Poddar*

Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi-835215, India

* Corresponding author
   Email: rpoddar@bitmesra.ac.in


Edited by H. Michael; received December 06, 2006; revised and accepted April 26, 2007; published June 12, 2007


Abstract

To reveal the relative synonymous codon usage and base composition variation in bacteriophages, six mycobacteriophages were used as a model system here and both parameters in these phages and their host bacteria, Mycobacterium tuberculosis, have been determined and compared. As expected for GC-rich genomes, there are predominantly G and C ending codons in all 6 phages. Both Nc plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in the 6 phages. Further analysis indicates that among 6 Mycobacterium phages Che9c, Bxz1 and TM4 may be extremely virulent in nature as most of their genes have high translation efficiency. Based on our data we suggest that the genes of above three phages are expressed rapidly by host's translation machinery. The information might be used to select the extremely virulent Mycobacterium tuberculosis phages suitable for phage therapy.


Keywords: relative synonymous codon usage, correspondence analysis, translational selection, multivariate statistical analysis, Mycobacterium tuberculosis