A novel variant of theListeria monocytogenestype VII secretion system EssC component is associated with an Rhs toxin
Authors: Bowran Kieran , Garrett Stephen R. , Vliet Arnoud H. M. van , Palmer Tracy 
Published: February 2023

The Type VIIb protein secretion system (T7SSb) is found in Bacillota (firmicute) bacteria and has been shown to mediate interbacterial competition. EssC is a membrane-bound ATPase that is a critical component of the T7SSb and plays a key role in substrate recognition. Prior analysis of available genome sequences of the foodborne bacterial pathogenListeria monocytogeneshas shown that although the T7SSb was encoded as part of the core genome, EssC could be found as one of seven different sequence variants. While each sequence variant was associated with a specific suite of candidate substrate proteins encoded immediately downstream ofessC, many LXG-domain proteins were encoded across multipleessCsequence variants. Here we have extended this analysis using a diverse collection of 37,930L. monocytogenesgenomes. We have identified a rare eighth variant of EssC present in tenL. monocytogenesLineage III genomes. These genomes also encode a large toxin of the rearrangement hotspot (Rhs) repeat family adjacent toessC8, along with a probable immunity protein and three small accessory proteins. We have further identified nine novel LXG-domain proteins, and four additional chromosomal hotspots acrossL. monocytogenesgenomes where LXG proteins can be encoded. The eightL. monocytogenesEssC variants were also found in otherListeriaspecies, with additional novel EssC types also identified. Across the genus, species frequently encoded multiple EssC types, indicating that T7SSb diversity is a primary feature of the genusListeria.

DATA SUMMARY

All genome sequences used in this study are available via Genbank, and the assembly accession numbers are provided in Table S1. This file also lists relevant metadata (name, source category, country, year and clonal complex).

IMPACT STATEMENT

Listeria monocytogenesis a soil-borne saprophytic bacterium and a food-borne pathogen of humans. Decomposing plant matter and the human GI tract are rich in diverse microbial species and to colonise these nichesL. monocytogenesmust be able to compete with other bacteria. The type VII secretion system (T7SS) of Bacillota has been shown to secrete protein toxins that target other bacteria. In this study we have analysed a diverse collection ofL. monocytogenesgenome sequences to study the diversity of theListeriaT7SS and its putative effector proteins. We show that the EssC component of theL. monocytogenesT7SS is highly diverse, clustering into one of eight sequence variants. Each EssC variant is associated with a specific toxin candidate, and the EssC8 variant T7SS likely secretes a novel rearrangement hotspot (Rhs) repeat toxin. We also identify multiple new LXG-families of T7SS toxins and describe genomic hotspots where they are encoded. We find no link between EssC variants and clinical outcome. In agreement with this, analysis of EssC variability in available genomes of otherListeriaspecies showed that all eightL. monocytogenesEssC variants are present in non-monocytogenesListeriaspecies.