New players in the toxin field: polymorphic toxin systems in bacteria

Abstract

Bacteria have evolved numerous strategies to increase their competitiveness and fight against each other. Indeed, a large arsenal of antibacterial weapons is available in order to inhibit the proliferation of competitor cells. Polymorphic toxin systems (PTS), recently identified by bioinformatics in all major bacterial lineages, correspond to such a system primarily involved in conflict between related bacterial strains. They are typically composed of a secreted multidomain toxin, a protective immunity protein, and multiple cassettes encoding alternative toxic domains. The C-terminal domains of polymorphic toxins carry the toxic activity, whereas the N-terminal domains are related to the trafficking mode. In silico analysis of PTS identified over 150 distinct toxin domains, including putative nuclease, deaminase, or peptidase domains. Immunity genes found immediately downstream of the toxin genes encode small proteins that protect bacteria against their own toxins or against toxins secreted by neighboring cells. PTS encompass well-known colicins and pyocins, contact-dependent growth inhibition systems which include CdiA and Rhs toxins and some effectors of type VI secretion systems. We have recently characterized the MafB toxins, a new family of PTS deployed by pathogenic Neisseria spp. Many other putative PTS have been identified by in silico predictions but have yet to be characterized experimentally. However, the high number of these systems suggests that PTS have a fundamental role in bacterial biology that is likely to extend beyond interbacterial competition.

FIG 1

Definition and discovery of polymorphic toxins. (A) General organization of a typical locus encoding a polymorphic toxin with its cognate immunity protein (Imm). A gene encoding a protein involved in the secretion of the toxin can be found upstream of the toxin gene (such as cdiB) and orphan modules encoding alternate toxic domains (CT), and their cognate immunity proteins can be found downstream of the toxin gene. A homologous region possibly involved in recombination between the toxin gene and the orphan module is colored in dark green. (B) Schema illustrating the possibility for a given N-terminal region to be fused to distinct toxic domains (Tox) and for a given toxic domain to be fused to distinct N-terminal regions. (C) In silico discovery of polymorphic toxins and their immunity proteins. By analyzing genetic neighborhood of SUKH genes, Zhang et al. (3) discovered that genes encoding various nucleasic toxic activities were located immediately upstream of SUKH genes. SUKH genes are depicted as red arrows labeled SUKH, and toxin genes encoding various toxic activities are depicted as white arrows with ends of different colors labeled Tox (upper panel). The lower panel shows that the analysis of the genetic neighborhood of toxin genes enabled the discovery of additional genes encoding immunity proteins which are not part of the SUKH superfamily. These immunity genes are depicted as red arrows labeled “Imm.” Immunity proteins are encoded by small ORFs that may contain a domain of the SUKH superfamily (e.g., SUKH-1, SUKH-2, SUKH-3…) or a domain of another family (e.g., Imm1, Imm2, Imm3…).

FIG 2

Overview of the polymorphic toxin families. (A) Simplified schematic representation of the domain organization found in several well-characterized families of polymorphic toxins. Domains constituting the conserved N-terminal region of polymorphic toxins are depicted as blue boxes irrespective of their family. Toxic domains of the variable C-terminal region are depicted as green boxes irrespective of their toxic activity. The secretion system involved in the secretion of the toxin is indicated. T5SS, type V secretion system; T6SS, type VI secretion system; SP, signal peptide; Hemag activity, hemagglutination activity domain, also called a “TPS domain” (PF05860); fil hemag repeats, filamentous hemagglutinin repeats (PF13332); RHS repeat ass core domain, RHS repeat-associated core domain (IPR022385). (B) Domain architectures found in colicins. Colicins usually contain three domains: an N-terminal translocation domain allowing translocation into target cells (blue boxes), a central domain involved in receptor recognition (gray boxes), and a C-terminal cytotoxic domain (green boxes). The short name of the corresponding domain from the Interpro database is written inside the blue and gray boxes. Cloacin_T_dom, cloacin translocation domain (IPR016128); colicin_R_dom, colicin receptor domain (IPR024566); channel_colicin_N, channel-forming colicin, N-terminal domain (IPR014739); channel_colicin_cen, channel-forming colicin, central receptor recognition domain (IPR014740). The toxic activity of the C-terminal domain is indicated in the green boxes as follows: 16S RNase (IPR009105), DNase (IPR024622), tRNase (IPR021964), Pore forming (pore-forming domain; IPR000293). Col, colicin. (C) Simplified schematic representation of the 3 classes of MafB toxins. Class 1 MafBs contain a VSGDF motif at the end of the N-terminal conserved domain and an optional bacterial intein-like (BIL) domain. Class 2 MafBs contain a VKYDT motif at the end of the N-terminal conserved domain. Class 3 MafBs contain a DWVKN motif at the end of the N-terminal conserved domain. Domains in panels A, B, and C are not depicted to scale.