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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
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 pathogenís 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