In silico identification and characterization of novel drug targets and outer membrane proteins in the fish pathogen Edwardsiella tarda
Mohammed Neema, Iddya Karunasagar, Indrani Karunasagar
UNESCO Microbial Resource Centre for Marine Biotechnology, Department of Fishery Microbiology, Karnataka Veterinary Animal and Fisheries Sciences University, College of Fisheries, Mangalore, Karnataka, India
Abstract: The complete genome of the fish pathogen Edwardsiella tarda and the host Danio rerio (zebrafish) was subjected to subtractive genome analysis with the objective of identifying potential drug targets and vaccine candidates. The homologous proteins were excluded to prevent any chance of cytotoxic cross-reaction with the host. The nonparalogous proteins were analyzed for sequence homology with the Database of Essential Genes to determine the essentiality of the proteins for the bacteria. These essential proteins were further analyzed to predict the metabolic pathways in which they were involved. Cellular localization analysis was carried out to determine the possibility of the protein being present in the outer membrane. Outer membrane proteins may play an important role in the interaction with hosts and in bacterial pathogenicity. The study identified 171 of 3986 proteins as potential drug targets. The study also identified seven novel outer membrane proteins.
Keywords: subtractive genomics, CD-HIT, DEG, KEGG, homology modelling, Edwardsiella tarda, OMPs
© 2011 The Author(s). This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution - Non Commercial (unported, v3.0) License. By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms.