Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

Abstract

BackgroundProteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific conflicts. They are characterized by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. Prior analysis revealed a striking diversity of nuclease and deaminase domains among the toxin modules. We systematically investigated polymorphic toxin systems using comparative genomics, sequence and structure analysis.ResultsPolymorphic toxin systems are distributed across all major bacterial lineages and are delivered by at least eight distinct secretory systems. In addition to type-II, these include type-V, VI, VII (ESX), and the poorly characterized “Photorhabdus virulence cassettes (PVC)”, PrsW-dependent and MuF phage-capsid-like systems. We present evidence that trafficking of these toxins is often accompanied by autoproteolytic processing catalyzed by HINT, ZU5, PrsW, caspase-like, papain-like, and a novel metallopeptidase associated with the PVC system. We identified over 150 distinct toxin domains in these systems. These span an extraordinary catalytic spectrum to include 23 distinct clades of peptidases, numerous previously unrecognized versions of nucleases and deaminases, ADP-ribosyltransferases, ADP ribosyl cyclases, RelA/SpoT-like nucleotidyltransferases, glycosyltranferases and other enzymes predicted to modify lipids and carbohydrates, and a pore-forming toxin domain. Several of these toxin domains are shared with host-directed effectors of pathogenic bacteria. Over 90 families of immunity proteins might neutralize anywhere between a single to at least 27 distinct types of toxin domains. In some organisms multiple tandem immunity genes or immunity protein domains are organized into polyimmunity loci or polyimmunity proteins. Gene-neighborhood-analysis of polymorphic toxin systems predicts the presence of novel trafficking-related components, and also the organizational logic that allows toxin diversification through recombination. Domain architecture and protein-length analysis revealed that these toxins might be deployed as secreted factors, through directed injection, or via inter-cellular contact facilitated by filamentous structures formed by RHS/YD, filamentous hemagglutinin and other repeats. Phyletic pattern and life-style analysis indicate that polymorphic toxins and polyimmunity loci participate in cooperative behavior and facultative ‘cheating’ in several ecosystems such as the human oral cavity and soil. Multiple domains from these systems have also been repeatedly transferred to eukaryotes and their viruses, such as the nucleo-cytoplasmic large DNA viruses.ConclusionsAlong with a comprehensive inventory of toxins and immunity proteins, we present several testable predictions regarding active sites and catalytic mechanisms of toxins, their processing and trafficking and their role in intra-specific and inter-specific interac...

The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device

“…However, the entomopathogenic bacterium Yersinia entomophaga contains a related Tc locus that includes an A component encoded by two ORFs (yenA1 and yenA2), a single B gene (yenB) and two C genes (yenC1 and yenC2), 10 the products of which associate independently with the A and B proteins, giving rise to two Tcs from one genetic locus. The C proteins of this and other Tcs are similar to the "polymorphic toxins" described by Zhang et al 11 as they have a conserved RHS-repeat-containing amino-terminal region and a variable carboxyterminal region 10 . The carboxy-terminal regions (CTRs) of the Y. entomophaga C proteins are predicted to have different toxic activities: the C1 CTR is homologous to cytotoxic necrotising factor 1 (CNF1) from Escherichia coli 12 , whereas the C2 CTR is homologous to the deaminase YwqJ from Bacillus subtilis 13 .…”

“…It is therefore tempting to speculate that the function of the B/C shell, and of RHS-and YD-repeat proteins more generally, may be to encapsulate unfolded proteins. There is support for this idea in the observation that many polymorphic toxins have predicted proteases as their toxic components, which would need to be contained in an inactive state to prevent proteolysis of the shell itself 11 . As the pore formed by the A subunit has not yet been visualised in an active conformation, it remains unknown whether the translocating conformation of the toxin contains an open pore wide enough to allow the passage of the folded protein.…”

Bacterial killing via a type IV secretion system

“…Especially abundant are lipase domains 34 and domains involved in binding or modification of PG, found exclusively in bacterial cell walls 35 41 , the AHH domain likely involved in killing bacteria via its putative nuclease activity 42 and DUF2235 (ref. 43), a putative hydrolase recently found to be present in T6SS effectors 44 (Table 1). Both Zeta toxin and AHH domains are found in toxin-antitoxin systems where they are inhibited by specific immunity proteins 41,42 .…”

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

“…In HCO 3 À grown co-cultures (Supplementary Table S4), Shewanella W3-18-1 displayed increased transcript abundances of genes encoding secreted or outer membrane proteins including a lipase (SputW3181_ 1613), several proteases (sapSH, Sputw3181_3341, Sputw3181_3384 and SputW3181_0531) and a polymorphic toxin (Sputw3181_0994), which together may be involved in cell envelope lysis and degradation of surface structures (Zhang et al, 2012). Similarly, the elevated mRNA levels of 4-alphaglucanotransferase gene (malQ) can potentially allow for carbohydrate utilization, while DNA can be broken down by the putative extracellular endonuclease (exeS).…”