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Computational Molecular Biology
2014, Vol.4, No.2, 18-25 http://cmb.sophiapublisher.com
Research Report
Open Access
GC2 Biology Dictates Gene Expressivity in
Camellia sinensis
Supriyo Chakraborty , Prosenjit Paul
Department of Biotechnology, Assam University, Silchar-788011, Assam, India
Corresponding Author email: supriyoch_2008@rediffmail.com;
Author
Computational Molecular Biology, 2014, Vol.4, No.2 doi: 10.5376/cmb.2014.04.0002
Copyright
© 2014 Chakraborty and Paul. This is an open access article published under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
The effectiveness of the gene expression is influenced by the nature of codons used throughout the coding sequence (cds)
of the gene. This is due to the fact that most genes and organisms do not use synonymous codons uniformly. Certain synonymous
codons are used preferentially and this phenomenon is called codon usage bias (CUB). We analyzed normalized AT and GC
frequency at each codon site. We observed that the correlations between gene expression (measured by CAI) and GC content at any
codon site were very weak except GC2s showed moderate positive correlation with gene expression. We also measured the
correlations between CAI and AT content at three codon sites. AT2s showed moderate negative correlation with gene expression. We
further observed a strong correlation between RCBS (a measure of gene expression) and cds length indicating that natural selection is
probably operating in favor of shorter genes to be expressed at higher level. For this analysis, we initially downloaded 350 coding
sequences of
Camellia sinensis
, out of which only ten cds were found to begin with the initiator codon ATG, and length as exact
multiple of three bases and devoid of N (any unknown base). Our analysis on these ten cds revealed that the second position of
synonymous codons in
Camellia sinensis
possibly plays a more prominent role than the third position in determining the gene
expressivity as evident from the CUB and the correlation analyses.
Keywords
Gene expression; Relative codon usage bias (RCBS); Codon adaptation index (CAI); Codon usage bias (CUB)
Introduction
The effectiveness of the gene expression is influenced
by the nature of codons used throughout the gene.
Since the course of evolution, there are few genes in a
coding sequence which remains unchanged, i.e.
conserved throughout. This is due to the fact that most
genes and organisms do not use synonymous codons
uniformly; certain synonymous codons are used
preferentially, a phenomenon called codon usage
bias (CUB).
Codon bias, the unequal usage of synonymous codons,
varies widely between species and in some cases, it
has also been reported that there is significant
variation of codon usage bias among different genes
within the same organism (Bernardi, 1993). Previous
codon usage analyses showed that codon usage bias is
very complicated and associated with various
biological factors, such as gene expression level
(Gouy and Gautier, 1982; Sharp and Li, 1986; Sharp
et al., 1986; Sharp and Li, 1987), gene length (Bains,
1987; Eyre-Walker, 1996), gene translation initiation
signal (Ma, 2002), protein amino acid composition
(Lobry and Gautier, 1994), protein structure
(D'Onofrio et al., 2002), tRNA abundance (Ikemura,
1981, 1982), mutation frequency and patterns (Sueoka,
1999), and GC composition (Sueoka and Kawanishi,
2000). The influence of GC bias has a major impact
on codon bias, resulting in a close association between
GC% at the third codon position, also called GC3 and
GC bias (Sueoka, 1988). As all amino acids (with the
exception methionine and tryptophan) allow
GC-changing synonymous substitutions in the third
position, this has led to a common belief that the
use of synonymous G/C-ending codons should
increase in frequency with increasing GC bias,
while usage of A/T-ending codons should decrease
(Wan et al., 2004).
Preferred citation for this article:
Chakraborty and Paul, 2014, GC2 Biology Dictates Gene Expressivity in
Camellia sinensis
, Computational Molecular Biology, Vol.4, No.2 10-17 (doi:
10.5376/cmb.2014.04.0002)
Received: 27 Dec., 2013
|
Accepted: 15 Jan., 2014
|
Published: 27 Feb., 2014
Computational
Molecular Biology