Computational Molecular Biology 2015, Vol.5, No.6, 1-4
1
Research Report Open Access
Comparative study of Codon usage pattern and compositional distribution between
whole genome and virulence gene set of
Vibrio cholera N16961
.
Sushanta Deb, Surajit Basak
Department of Molecular Biology and Bioinformatics, Tripura University, Suryamaninagar, India
Corresponding author email
Computational Molecular Biology, 2015, Vol.5, No.6 doi: 10.5376/cmb.2015.05.0006
Received: 31 Aug., 2015
Accepted: 12 Oct., 2015
Published: 16 Nov., 2015
Copyright
©
2015
Deb and Basak, 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.
Preferred citation for this article:
Deb S. and Basak S., 2015, Comparative study of Codon usage pattern and compositional distribution between whole genome and virulence gene set of Vibrio
cholera N16961., Computational Molecular Biology, Vol.5, No.6 1-4 (doi
Abstract
Vibrio cholerae
is the pathogenic organism causes cholera, a severe diarrheal disease. Occurs frequently in southern Asia.
Vibrio cholerae
has both pathogenic and nonpathogenic strains that vary in their virulence gene content. Great variety of strains and
biotypes of
Vibrio cholerae
are found. These varieties are involve in shuffling of different pathogenic factors among them such as
receiving and transferring genes for toxins, colonization factors, antibiotic resistance, capsular polysaccharides which giving
resistance to chlorine 7 and new surface antigens, such as the 0139 lip polysaccharide and O antigen capsule. Different mode of
transfer of these virulence gene i.e. lateral and horizontal transfer by phase, collection of pathogenic genes and other accessory
genetic element, pave the way to understand how bacterial pathogen develop its Pathogenicity and become a new strain. To provide a
insights into the genetic features and the relationship between the overall codon usage pattern of virulence gene set (VGS).We
measure the GC content of VGS which shows that there is no any difference between GC content of whole genome and VGS .It also
has been found that GC content shows the similar distribution among the CDS of both whole genome and Virulence gene set. A
correlation analysis between the A3s, T3s, G3s, C3s, and GC3s, the ENC values, and the nucleotide contents (A%, T%, G%, C%, and
GC %) indicated that mutational bias plays role in shaping the VGS codon usage bias.
Keywords
Codon usage pattern; whole genome; virulence gene; Vibrio cholera
Introduction
Strains of the El Tor biotype causes sporadic
infections and cholera epidemics as early as 1910, this
biotype emerged in 1961 to cause the 7
th
pandemic
which in turn causes the global elimination of
classical biotype strains as a cause of disease. The
Gram negative,
Vibrio cholerae
El Tor N16961
possesses a complete genomic sequence of is
4,033,460 base pairs (bp). The whole genome of
Vibrio cholerae
El Tor N16961 is divided in to two
circular chromosomes of 2,961,146 bp and 1,072,314
bp. The total 3,885 open reading frames were encoded
by the whole genome of
vibrio cholera
. Major part of
recognizable genes which plays a chief role in cell
functions (such as DNA duplication, transcription,
protein synthesis and cell-wall biosynthesis) and
pathogenicity (for example, toxins, surface antigens
and adhesions) are resides on the primary
chromosome. The
V. cholerae
genomic sequence open
the scope for understanding how a free-living,
environmental organism evolved to become a
significant human bacterial pathogen.
Pathogenic bacteria uses a lot of mechanisms to cause
disease in human hosts. Bacterial pathogens have a
wide range of molecules that bind host cell targets to
produce different type of host responses. The
molecular mechanism of pathogenic bacteria to
interact with the host unique to every pathogens or
conserved throughout the several different species.
The availability of complete genome sequences for
several bacterial pathogens facilitates to reveal the
mystery behind the molecular strategy used by
bacteria to infect host. The “horizontal gene transfer”
is one of the major factor which changes the genomic
feature of bacterial genome in a fast and dramatic way.
Recent studies have shown that horizontal gene
transfer plays an important role in the molecular
evolution of novel bacterial pathogens. There is a
section which may contain large blocks of virulence
determinants (adhesions, invasions, toxins, antibiotic
