Diversity and distribution of Type VI Secretion System gene clusters in bacterial plasmids

Abstract

Type VI Secretion System (T6SS) is a nanomolecular apparatus that allows the delivery of effector molecules through the cell envelope of a donor bacterium to prokaryotic and/or eukaryotic cells, playing a role in the bacterial competition, virulence, and host interaction. T6SS is patchily distributed in bacterial genomes, suggesting an association with horizontal gene transfer (HGT). In fact, T6SS gene loci are eventually found within genomic islands (GIs), and there are some reports in plasmids and integrative and conjugative elements (ICEs). The impact that T6SS may have on bacteria fitness and the lack of evidence on its spread mechanism led us to question whether plasmids could represent a key mechanism in the spread of T6SS in bacteria. Therefore, we performed an in-silico analysis to reveal the association between T6SS and plasmids. T6SS was mined on 30,660 plasmids from NCBI based on the presence of at least six T6SS core proteins. T6SS was identified in 330 plasmids, all belonging to the same type (T6SSⁱ), mainly in Proteobacteria (328/330), particularly in Rhizobium and Ralstonia. Interestingly, most genomes carrying T6SS-harboring plasmids did not encode T6SS in their chromosomes, and, in general, chromosomal and plasmid T6SSs did not form separate clades.

Figure 1

Pie chart of bacterial sources from which sequences were obtained. ND, no data.

Figure 2

Phylogenetic relationship of plasmid T6SS based on TssB core component protein and maximum likelihood method. The sequences are divided into four types (T6SS^i-iv) and six subtypes (i1, i2, i3, i4a, i4b, and i5) by colored backgrounds. The chromosomal reference sequences have black circles adjacent to their labels. The red branch represents sequences assigned to the i3 subtype, but which are not grouped with the i3 reference sequences. The colored blocks closest to the tree represent the bacterial families from which the sequences were obtained. The predicted mobility of the plasmids harboring the T6SS gene clusters is indicated by the outer colored blocks. Bootstrap values above 70 are shown as red circles in the middle of the branches.

Figure 3

Genetic architecture of T6SS gene loci of different type i subtypes.