Insights into virulence: structure classification of the Vibrio parahaemolyticus RIMD mobilome

Abstract

Vibrio parahaemolyticus ( Vpar ) is a major cause of seafood-related gastroenteritis. A pandemic strain, RIMD2210633 (RIMD), has emerged from ancestors due to virulence mechanisms acquired through horizontal gene transfer (HGT). Mobile genetic elements play an essential role in RIMD pathogenicity, but they evolve rapidly and are challenging for sequence-based homology detection and functional inference. Guided by the Evolutionary Classification of protein Domains (ECOD), we utilized structure-assisted homology detection of high-quality AlphaFold models for RIMD proteins to augment their functional interpretation. This approach detected 7,107 domains from 3,970 RIMD proteins and classified them into the ECOD hierarchy, providing functional insights into 80% of the proteome. RIMD proteins originating from HGT were identified by comparison against 86 complete proteomes of other Vpar strains. The resulting RIMD mobilome is enriched with phage markers and bacterial defense domains. Evolutionary classification of known HGT proteins suggests they provide selective advantages against the human host, phage, and other stresses. Compared to a pre-pandemic strain, we found fast-evolving proteins with potential involvement in RIMD virulence and phage avoidance. These findings provide vital insights into bacterial evolution, pathogenic mechanisms, and adaptation strategies while offering testable hypotheses for experimental studies and an online resource for future investigation of the RIMD proteome. IMPORTANCE The pandemic Vpar strain RIMD causes seafood-borne illness worldwide. Previous comparative genomic studies have revealed pathogenicity islands in RIMD that contribute to the success of the strain in infection. However, not all virulence determinants have been identified, and many of the proteins encoded in known pathogenicity islands are of unknown function. Based on the EOCD database, we used evolution-based classification of structure models for the RIMD proteome to improve our functional understanding of virulence determinants acquired by the pandemic strain. We further identify and classify previously unknown mobile protein domains as well as fast evolving residue positions in structure models that contribute to virulence and adaptation with respect to a pre-pandemic strain. Our work highlights key contributions of phage in mediating seafood born illness, suggesting this strain balances its avoidance of phage predators with its successful colonization of human hosts.