Comparative bioinformatic and proteomic approaches to evaluate the outer membrane proteome of the fish pathogen Yersinia ruckeri

• Published in: Journal of Proteomics
• Main Authors: Ormsby, Michael J, Grahame, Edward, Burchmore, Richard, Davies, Robert L
• Other Authors: Biotechnology and Biological Sciences Research Council, University of Glasgow, orcid:0000-0002-3991-2336
• Format: Article in Journal/Newspaper
• Language: English
• Published: Elsevier 2019
• Subjects: Bioinformatics; Outer membrane; Proteomics; Yersinia ruckeri; Atlantic salmon; Salmo salar
• Online Access: http://hdl.handle.net/1893/33660; https://doi.org/10.1016/J.JPROT.2019.02.014; http://dspace.stir.ac.uk/retrieve/01746191-9a50-4f2c-a4ab-e42b5f34053d/1-s2.0-S187439191930065X-main.pdf

Yersinia ruckeri is the aetiological agent of enteric redmouth (ERM) disease and is responsible for significant economic losses in farmed salmonids. Enteric redmouth disease is associated primarily with rainbow trout (Oncorhynchus mykiss, Walbaum) but its incidence in Atlantic salmon (Salmo salar) is increasing. Outer membrane proteins (OMPs) of Gram-negative bacteria are located at the host-pathogen interface and play important roles in virulence. The outer membrane of Y. ruckeri is poorly characterised and little is known about its composition and the roles of individual OMPs in virulence. Here, we employed a bioinformatic pipeline to first predict the OMP composition of Y. ruckeri. Comparative proteomic approaches were subsequently used to identify those proteins expressed in vitro in eight representative isolates recovered from Atlantic salmon and rainbow trout. One hundred and forty-one OMPs were predicted from four Y. ruckeri genomes and 77 of these were identified in three or more genomes and were considered as “core” proteins. Gel-free and gel-based proteomic approaches together identified 65 OMPs in a single reference isolate and subsequent gel-free analysis identified 64 OMPs in the eight Atlantic salmon and rainbow trout isolates. Together, our gel-free and gel-based proteomic analyses identified 84 unique OMPs in Y. ruckeri. Significance: Yersinia ruckeri is an important pathogen of Atlantic salmon and rainbow trout and is of major economic significance to the aquaculture industry worldwide. Disease outbreaks are becoming more problematic in Atlantic salmon and there is an urgent need to investigate in further detail the cell-surface (outer membrane) composition of strains infecting each of these host species. Currently, the outer membrane of Y. ruckeri is poorly characterised and very little is known about the OMP composition of strains infecting each of these salmonid species. This study represents the most comprehensive comparative outer membrane proteomic analysis of Y. ruckeri to date, ...