Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered

Abstract

Bacteria encode multiple protein secretion systems that are crucial for interaction with the environment and with hosts. In recent years, attention has focused on type VI secretion systems (T6SSs), which are specialized transporters widely encoded in Proteobacteria. The myriad of processes associated with these secretion systems could be explained by subclasses of T6SS, each involved in specialized functions. To assess diversity and predict function associated with different T6SSs, comparative genomic analysis of 34 Pseudomonas genomes was performed. This identified 70 T6SSs, with at least one locus in every strain, except for Pseudomonas stutzeri A1501. By comparing 11 core genes of the T6SS, it was possible to identify five main Pseudomonas phylogenetic clusters, with strains typically carrying T6SSs from more than one clade. In addition, most strains encode additional vgrG and hcp genes, which encode extracellular structural components of the secretion apparatus. Using a combination of phylogenetic and meta-analysis of transcriptome datasets it was possible to associate specific subsets of VgrG and Hcp proteins with each Pseudomonas T6SS clade. Moreover, a closer examination of the genomic context of vgrG genes in multiple strains highlights a number of additional genes associated with these regions. It is proposed that these genes may play a role in secretion or alternatively could be new T6S effectors.

Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung

“…The variable loci were associated with type III secretion systems and effectors, type VI secretion systems and effectors, and pyoverdine siderophore biosynthesis. These structures vary among strains (37)(38)(39)(40). This finding suggests that Nanostring analysis of some transcripts across different genotypes requires the inclusion of probes that target multiple alleles, as demonstrated here for fliC, and/or DNA sequence analysis to confirm the target sequence will hybridize to the probe.…”

Vibrio cholerae VttR A and VttR B Regulatory Influences Extend beyond the Type 3 Secretion System Genomic Island

“…Recent reports suggest that Hcp and VgrG proteins are both structural and effector components of T6SSs (47,48). RPKM values for hcp-1 and hcp-2 were at least 2.5-fold lower in the ⌬vttR A and ⌬vttR B strains than in the parental strain.…”

The Hcp proteins fused with diverse extended-toxin domains represent a novel pattern of antibacterial effectors in type VI secretion systems

“…Commonly, these 'orphan' hcp and vgrG genes are always encoded in the proximity of putative effector genes. 30,31 Further studies demonstrated that in T6SS-dependent delivery, the antibacterial effectors are loaded onto the secretion complex by interaction with PAAR/VgrG or by binding to the inner surface of the Hcp tube. 3 Notably, some VgrG and PAAR proteins can carry antibacterial extension domains, thus acting as secreted T6SS effectors.…”

“…56 The donor and recipient strains (Nal R ) were mixed together at a ratio of 3:1 after the cultures were normalized to an OD 600nm of 0.5. The mixture was then spotted on the nitrocellulose membrane placed on low-salt LB agar for 6 h incubation at 30 C. The bacterial spots were then resuspended, serially diluted in PBS and visualized on plates (eosin-methylene blue medium) containing 50 mg/ ml Nal to compare the survivals of the recipient cells co-incubated with different donor strains.…”