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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