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OJBTM
Online Journal of Bioinformatics ©
Volume 14 (1): 14-31, 2013.
Statistical analysis of codon
usage in extremely halophilic bacterium, Salinibacter
ruber DSM 13855
Sanjukta RK1 , Farooqi
MS1, Sharma N1 , Rai
N Mishra DC2, Rai A, Singh DP3
and Chaturvedi KK1
Centre
for Agricultural Bioinformatics, Indian Agricultural Statistics Research
Institute, Pusa, New Delhi Central Drug Research
Institute, Jhankipuram, Lucknow, National Bureau of
Agriculturally Important Microorganisms, Mau Nath Bhanjan, India
ABSTRACT
Sanjukta
RK, Farooqi MS, Sharma N, Rai N, Mishra DC, Rai A, Singh DP, Chaturvedi KK., Statistical Analysis of codon usage in
extremely halophilic bacterium, Salinibacter ruber DSM 13855, Online J Bioinform.,
14(1): 15-31, 2013.
Synonymous codons are randomly distributed among genes, a phenomenon termed as
codon usage bias. Understanding the extent and pattern of codon bias; the
forces affecting codon usage are the key steps towards elucidating the adaptive
choice of codon at the level of individual genes. Herein, trends in codon usage
bias in a set of 1450 genes in Salinibacter
ruber, an extremely halophilic bacterium have
been evaluated. Notably, synonymous codon usage varies considerably among genes
of this bacterium. Base composition (mutational bias) particularly C- and
G-ending codons predominate with greater preference of ‘C’ at synonymously
variable sites. The effect of natural selection acting at the level of
translation has been observed. Certain genes with a high codon bias have been
identified by multivariate statistical approach and investigations through
various codon bias indices. These genes appearto be highly expressed, and their codon usage seems
to have been shaped by selection favouring a limited
number of translationally optimal codons.
A subset
of 27 optimal codons seems to be preferentially used in highly expressed genes.
The frequency
of these codons appears to be correlated with the level of gene expression, and
may be a useful indicator in the case of genes (or open reading frames) whose
expression levels are unknown.
Keywords:
synonymous codon usage, mutational bias, multivariate statistical