Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes

Abstract

BackgroundThe recently described Type VI Secretion System (T6SS) represents a new paradigm of protein secretion in bacteria. A number of bioinformatic studies have been conducted to identify T6SS gene clusters in the available bacterial genome sequences. According to these studies, Salmonella harbors a unique T6SS encoded in the Salmonella Pathogenicity Island 6 (SPI-6). Since these studies only considered few Salmonella genomes, the present work aimed to identify novel T6SS loci by in silico analysis of every genome sequence of Salmonella available.ResultsThe analysis of sequencing data from 44 completed or in progress Salmonella genome projects allowed the identification of 3 novel T6SS loci. These clusters are located in differentially-distributed genomic islands we designated SPI-19, SPI-20 and SPI-21, respectively. SPI-19 was identified in a subset of S. enterica serotypes including Dublin, Weltevreden, Agona, Gallinarum and Enteritidis. In the later, an internal deletion eliminated most of the island. On the other hand, SPI-20 and SPI-21 were restricted to S. enterica subspecies arizonae (IIIa) serotype 62:z4,z23:-. Remarkably, SPI-21 encodes a VgrG protein containing a C-terminal extension similar to S-type pyocins of Pseudomonas aeruginosa. This is not only the first evolved VgrG described in Salmonella, but also the first evolved VgrG including a pyocin domain described so far in the literature. In addition, the data indicate that SPI-6 T6SS is widely distributed in S. enterica and absent in serotypes Enteritidis, Gallinarum, Agona, Javiana, Paratyphi B, Virchow, IIIa 62:z4,z23:- and IIIb 61:1,v:1,5,(7). Interestingly, while some serotypes harbor multiple T6SS (Dublin, Weltvreden and IIIa 62:z4,z23:-) others do not encode for any (Enteritidis, Paratyphi B, Javiana, Virchow and IIIb 61:1,v:1,5,(7)). Comparative and phylogenetic analyses indicate that the 4 T6SS loci in Salmonella have a distinct evolutionary history. Finally, we identified an orphan Hcp-like protein containing the Hcp/COG3157 domain linked to a C-terminal extension. We propose to designate this and related proteins as "evolved Hcps".ConclusionAltogether, our data suggest that (i) the Salmonella T6SS loci were acquired by independent lateral transfer events and (ii) evolved to contribute in the adaptation of the serotypes to different lifestyles and environments, including animal hosts. Notably, the presence of an evolved VgrG protein related to pyocins suggests a novel role for T6SS in bacterial killing. Future studies on the roles of the identified T6SS loci will expand our knowledge on Salmonella pathogenesis and host specificity.

Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut

“…The genome of S. Typhimurium encodes a T6SS within the Salmonella pathogenicity island 6 (SPI-6) locus that is well conserved among S. enterica serovars (33). In addition to the structural components of the T6SS, the SPI-6 locus encodes two Hcp subunits, Hcp1 and Hcp2 (33), as well as Tae4, an antibacterial amidase with homologs in other bacteria (34) (Fig.…”

“…In addition to the structural components of the T6SS, the SPI-6 locus encodes two Hcp subunits, Hcp1 and Hcp2 (33), as well as Tae4, an antibacterial amidase with homologs in other bacteria (34) (Fig. S1).…”

VgrG C terminus confers the type VI effector transport specificity and is required for binding with PAAR and adaptor–effector complex

“…In addition to its assembly into homohexameric hollow ring structures, Hcp can function as a chaperone and receptor for certain effectors bound to its inner cavity for transport across double membranes (23). Some unusually large Hcp proteins harboring putative catalytic domains, and therefore possibly having effector functions, have yet to be characterized (24).…”

Type VI Secretion System-Associated Gene Clusters Contribute to Pathogenesis of Salmonella enterica Serovar Typhimurium

“…For some T6SS-harboring organisms, the core gene encoding the tailspike protein encodes a fusion protein that allows the translocation of an effector domain (43). However, in S. Typhimurium and other T6SS-harboring organisms, no evolved tailspike protein is present (5). In addition to the core genes, organisms that possess a T6SS typically encode less-well-conserved, T6SS-associated genes that differ extensively in their number and location throughout the genome, and some of these genes have been reported to act as effector or regulatory proteins (2,14,43).…”

“…enterica also encode a T6SS within Salmonella pathogenicity island 6 (SPI-6), while two other classes of T6SS have been described in S. bongori and S. enterica subsp. arizonae at SPI-2 and SPI-6, respectively (5,17,46). The S. enterica subsp.…”