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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
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