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OJBTM
Online
Journal of
Bioinformatics ©
Volume 14 (2): 235-257, 2013.
In silico
proteins of Flavobacterium columnare
as
therapeutic candidates for columnaris disease in fish.
S.
Murali1,
Sanath Kumar2, K. V.
Rajendran3
and Shrinivas Jahageerdar4*
1,4 Fish
Genetics
and Biotechnology Division, CIFE, 2Fisheries
Resource, Harvest and Post Harvest
Management Division, CIFE, 3
Aquatic Environment and Health Management Division, CIFE,
Mumbai, India
ABSTRACT
Murali
S, Kumar
S,
Rajendran
KV,
Jahageerdar
S., In silico proteins of Flavobacterium columnare
as
therapeutic candidates for columnaris
disease in fish,
Onl J Bioinform.,
14 (2): 235-257, 2013
Flavobacterium columnare,
the causative agent of columnaris
disease, is a major
fish pathogen responsible for severe economic losses to the
aquaculture
industry. In this
study, the complete
genomes of the pathogen F.
columnare and one of its
host Danio rerio (zebra fish)
were subjected to comparative genomic analysis to
identify the proteins essential for pathogen’s survival, but
non-homologous to
the host, so that these can be used as potential drug targets.
Our study
revealed 1826 proteins in F. columnare,
which are non-homologous to the
proteins in zebrafish
genome. Further screening of these proteins to determine their
essentiality was
done through Database of Essential Genes (DEG), which revealed
238 proteins as
essential to F. columnare.
These essential proteins were further analyzed to predict the
metabolic
pathways in which they are involved using the Kyoto
Encyclopedia of Genes and
Genomes (KEGG) pathways database. Of the identified proteins,
39 are involved
in genetic information processing, 37 in amino acid
metabolism, 23 in glycan
biosynthesis, 22 in metabolism of co-factors and vitamins, 16
in carbohydrate
metabolism, 16 in environmental information processing, 14 in
nucleotide
metabolism, 12 in energy metabolism, 10 in other amino acid
synthesis, 6 in
lipid metabolism and 8 in cellular processes and signaling. Two essential outer membrane proteins were also
identified in the study.
These
proteins may be the potential targets for controlling the
pathogen through
identification of effective antimicrobial agents, requiring
further study and characterization
in the laboratory.
Keywords:
Flavobacterium columnare,
columnaris disease, essential
proteins, outer membrane
proteins