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

Lakshminarayan M Iyer,Dapeng Zhang,Robson F de Souza,L Aravind,Vivek Anantharaman

doi:10.1186/1745-6150-7-18

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 interactions between bacteria. These systems provide insights regarding the emergence of key systems at different points in eukaryotic evolution, such as ADP ribosylation, interaction of myosin VI with cargo proteins, mediation of apoptosis, hyphal heteroincompatibility, hedgehog signaling, arthropod toxins, cell-cell interaction molecules like teneurins and different signaling messengers.ReviewersThis article was reviewed by AM, FE and IZ.

Highlights

Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts
One of the most common features of this central region is the presence of RHS (Recombination hot spot)/YD or filamentous hemagglutinin (FilH) repeats which form extended fibrous or filamentous structures that help in displaying the C-terminal toxin domain on the cell-surface [17,18,37,45,55,56]
With the above domain-architecture template (Figure 1), we identified an initial set of exemplars, which were used in sequence similarity searches to identify homologs that were similar over most of their length but differing in their C-terminal-most domains – a hallmark of polymorphic toxins (Figure 1B). This enabled us to precisely define the boundaries of the C-terminal toxin domains and use them as seeds in iterative sequence profile searches with the PSI-BLAST and JACKHMMER programs

Summary

Introduction

Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. Production and deployment of “chemical armaments” is one of the most common strategies in inter-organismal conflict Such molecules, namely toxins or antibiotics, are observed at practically every level of biological organization ranging from multicellular organisms like animals and plants, through bacteria, all the way down to intra-genomic selfish elements [1,2,3,4]. Namely toxins or antibiotics, are observed at practically every level of biological organization ranging from multicellular organisms like animals and plants, through bacteria, all the way down to intra-genomic selfish elements [1,2,3,4] These molecules span an entire biochemical spectrum from diffusible small molecules (e.g. antibiotics) to some of the largest proteins in the biological world (secreted bacterial toxins) [5,6]. It is becoming increasingly clear that proteinaceous toxins are a common feature of biological conflicts at every organizational level [7]: 1) In antagonistic interactions between different multicellular eukaryotes, such as the castor bean ricin, Aspergillus sarcin and various snake venom proteins [2,3,8,9]. 2) Action by multicellular organisms against their pathogens (e.g. anti-microbial peptide toxins and defensive RNases such as RNaseA and RNase L [10,11,12,13]). 3) Action of pathogenic and symbiotic bacteria directed against their hosts (e.g. the cholera toxin and the shiga toxin [4,14]). 4) Interspecific conflict in bacteria [15]. 5) Conflict between bacterial sibling strains of the same species, namely contact dependent inhibition systems and related secreted toxins [16,17,18,19]. 6) Inter-genomic conflicts between cellular genomes and selfish replicons residing in the same cell (e.g. classical bacteriocins and plasmid addiction toxins [20]). 7) Intra-genomic conflicts between selfish elements and the host genome (restriction-modification systems [21] and genomic toxin-antitoxin systems [22,23,24])

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Results

Conclusion