Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction.

Luca Robinson,Arnoud H. M. van Vliet,Ozan Gundogdu,Janie Liaw,Dong Xia,Nicolae Corcionivoschi,Zahra Omole,Abderrahman Hachani

doi:10.3389/fmicb.2021.694824

Abstract

The Type VI Secretion System (T6SS) has important roles relating to bacterial antagonism, subversion of host cells, and niche colonisation. Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis worldwide and is a commensal coloniser of birds. Although recently discovered, the T6SS biological functions and identities of its effectors are still poorly defined in C. jejuni. Here, we perform a comprehensive bioinformatic analysis of the C. jejuni T6SS by investigating the prevalence and genetic architecture of the T6SS in 513 publicly available genomes using C. jejuni 488 strain as reference. A unique and conserved T6SS cluster associated with the Campylobacter jejuni Integrated Element 3 (CJIE3) was identified in the genomes of 117 strains. Analyses of the T6SS-positive 488 strain against the T6SS-negative C. jejuni RM1221 strain and the T6SS-positive plasmid pCJDM202 carried by C. jejuni WP2-202 strain defined the “T6SS-containing CJIE3” as a pathogenicity island, thus renamed as Campylobacter jejuni Pathogenicity Island-1 (CJPI-1). Analysis of CJPI-1 revealed two canonical VgrG homologues, CJ488_0978 and CJ488_0998, harbouring distinct C-termini in a genetically variable region downstream of the T6SS operon. CJPI-1 was also found to carry a putative DinJ-YafQ Type II toxin-antitoxin (TA) module, conserved across pCJDM202 and the genomic island CJIE3, as well as several open reading frames functionally predicted to encode for nucleases, lipases, and peptidoglycan hydrolases. This comprehensive in silico study provides a framework for experimental characterisation of T6SS-related effectors and TA modules in C. jejuni.

Highlights

Bacterial secretion systems, classified from Type I to X according to their genetic and structural organisation and composition, are protein transport machineries enabling niche colonisation, interaction with host cells, and bacterial antagonism (Costa et al, 2015; Palmer et al, 2021)
We investigated the prevalence and genomic organisation of the T6SS in 513 publicly available C. jejuni genomes through screening of the major T6SS components, previously characterised T6SS effectors, and the integrative element Campylobacter jejuni Integrated Element 3 (CJIE3)
We identified a number of putative T6SS effectors and predicted toxin-antitoxin (TA) modules carried by the Campylobacter jejuni Pathogenicity Island-1 (CJPI-1) pathogenicity island (PAI)

Summary

Introduction

Bacterial secretion systems, classified from Type I to X according to their genetic and structural organisation and composition, are protein transport machineries enabling niche colonisation, interaction with host cells, and bacterial antagonism (Costa et al, 2015; Palmer et al, 2021). Despite the multiple roles of T6SSs in complex ecosystems, the genes encoding the T6SS core components are highly conserved into genomic clusters (Coulthurst, 2019). The machinery is characterised by a puncturing spike (VgrG) that structurally resembles the bacteriophage T4 gp27/gp proteins (typically sharpened by a Proline-Alanine-AlanineArginine (PAAR) protein), a contractile sheath (formed by the complex TssB and TssC) encasing a needle-like tube (Hcp/TssD) and capped by a core component (TssA) in the cytoplasm. The TssBC sheath propels the VgrGPAAR complex and associated effectors into target cells or the external milieu (Coulthurst, 2019). The contracted sheath can be depolymerised by the ATPase ClpV/TssH and released TssB and TssC subunits are recycled for assembly (Kapitein et al, 2013; Zoued et al, 2014)

Methods

Results

Conclusion