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

Abstract

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, encompassing isolates of different biotypes, serotypes, OMP-types and hosts of origin and provides insights into the potential roles of these diverse proteins in host-pathogen interactions. The study has identified key OMPs likely to be involved in disease pathogenesis and makes a significant contribution to furthering our understanding of the cell-surface composition of this important fish pathogen that will be relevant to the development of improved vaccines and therapeutics.

Overcoming Fish Defences: The Virulence Factors of Yersinia ruckeri

“…Sixteen OMPs were exclusively assigned to Y. ruckeri isolates from rainbow trout, including, e.g., filamentous hemagglutinin, metallopeptidases, a siderophore receptor and components of the T3SS that were predicted to be involved in adhesion to host cells, iron uptake and intracellular survival, respectively. Five proteins were exclusive for Y. ruckeri isolates of Atlantic salmon and these included proteins involved in autotransport, phospholipid-hydrolyzing enzymes and proteins involved in uptake of the ruckerbactin [146].…”

Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection

“…Against the phylogenetic background so derived, we then wished to explore the molecular evolution and diversity of the OmpA and OmpF proteins in the same isolates with a view to further understanding their potential roles in host-adaptation and virulence. OmpA and OmpF form the basis of the Y. ruckeri OMP-typing scheme 42 , were two of the most abundant OMPs identified in our previous proteomic analysis 15 , and are known to play various roles, via variation in their surface-exposed loops, in pathogenesis in other pathogens 51,[63][64][65][66][67][68][69][70][71][72][73] .…”

Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective

“…The iron metal is essential for bacteria [ 27 ], as shown in Vibrio spp., which was able to trap iron [ 125 ], and by Aeromonas salmonicida [ 206 ]. The outer membrane proteins, important for virulence by Y. ruckeri on Atlantic salmon and rainbow trout were identified in different isolates [ 109 ]. As parasites go through various life stages different proteins are needed in each one of them.…”