In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors

Abstract

Bacterial type VI secretion systems (T6SSs) are contractile nanomachines that deliver proteinic substrates into target prokaryotic or eukaryotic cells and the surrounding milieu. The genus Campylobacter encompasses 39 recognized species and 13 subspecies, with many belonging to a group known as ‘emerging Campylobacter pathogens’. Within Campylobacter , seven species have been identified to harbour a complete T6SS cluster but have yet to be comparatively assessed. In this study, using systematic bioinformatics approaches and the T6SS-positive Campylobacter jejuni 488 strain as a reference, we explored the genus-wide prevalence, similarity and make-up of the T6SS amongst 372 publicly available ‘complete’ Campylobacter genomes. Our analyses predict that approximately one-third of Campylobacter species possess a T6SS. We also putatively report the first identification of a T6SS in four species: Campylobacter cuniculorum, Campylobacter helveticus, Campylobacter armoricus and Campylobacter ornithocola . The Campylobacter T6SSs cluster into three distinct organizations (I–III), of which two break down into further variants. Thirty T6SS-containing genomes were found to harbour more than one vgrG gene, with Campylobacter lari strain NCTC 11845 possessing five. Analysis of the C. jejuni Pathogenicity Island-1 confirmed its conservation amongst T6SS-positive C. jejuni strains, as well as highlighting its diverse genetic composition, including additional putative effector–immunity pairs (e.g. PoNe and DUF1911 domains). Effector–immunity pairs were also observed neighbouring vgrGs in several other Campylobacter species, in addition to putative genes encoding nucleases, lysozymes, ATPases and a ferric ATP-binding cassette uptake system. These observations highlight the diverse genetic make-up of the T6SS within Campylobacter and provide further evidence of its role in pathogenesis.

Heterogeneity and Compositional Diversities of Campylobacter jejuni Outer Membrane Vesicles (OMVs) Drive Multiple Cellular Uptake Processes

“…Among them, proteins specifically associated with bacterial defense mechanisms, energy production and conversion, and cell wall biogenesis are noteworthy. In addition, we identified a key protein of the bacterial T6SS, VgrG, which is the puncturing spike of the machinery. − This is in line with prevoius studies showing the ability of OMVs carriage of bacterial secretion system-associated proteins, however, in Helicobacter pylori …”

Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains

“…and Robinson et al. and included the CC and ST of every C. jejuni strain from Chile sequenced to date ( van Vliet et al., 2021 ; Robinson et al., 2022 ). The analysis corroborated the global representation of CC-464, CC-353, CC-573, and CC-403 ( Figure 6A ).…”

“…A recent bioinformatic survey identified that Campylobacter T6SS gene clusters could be classified into three distinct cluster organizations (types I, II, and III). Analysis of T6SS genetic organization revealed that each of the T6SS gene clusters identified belonged to the T6SS group I-a, the same T6SS group as the T6SS of the Brazilian type strain 488 (Robinson et al, 2021;Robinson et al, 2022). In addition, we analyzed each ORF of the chromosomally encoded T6SS gene clusters in strains CFSAN122719 and CFSAN122739 and found a novel putative effector/immunity module (ORFs Z_00322 and Z_00323) in the variable region of the T6SS gene cluster of strain CFSAN122739 (Figure 6C).…”

“…In C. jejuni , the T6SS contribute to a variety of in vitro and in vivo phenotypes, ranging from host cell adherence, cellular invasion, resistance to bile salts or oxidative stress, and interbacterial competition to the ability to colonize both mouse and chicken in vivo infection models efficiently ( Lertpiriyapong et al., 2012 ; Bleumink-Pluym et al., 2013 ; Liaw et al., 2019 ). No T6SS effector protein has been fully characterized for Campylobacter , but recent bioinformatic analyzes of the genome of C. jejuni strain 488 have predicted the presence of at least 15 effector candidates ( Robinson et al., 2021 ; Robinson et al., 2022 ).…”

Campylobacter jejuni virulence factors: update on emerging issues and trends

“…In addition, the T6SS was shown to play a major role in bacterial inter-species competition, whereby T6SS-positive strains of C. jejuni outcompeted E. coli within the same niche [ 60 ]. While the Hcp has been characterised well as both a structural and effector protein in C. jejuni T6SS [ 57 ], very little is known about the roles of other effectors of the C. jejuni T6SS and their specific functions during infection, although recent bioinformatic studies have identified several putative T6SS effectors, including nucleases and an NAD + -glycohydrolase [ 61 , 62 ], which opens avenues for further investigation of their functions.…”