State Key Laboratory of Microbial Technology
Shandong University
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The prokaryotic antimicrobial toxin is a protein that can transfer between competing cells and inhibit other microbial cell growth. Antimicrobial toxins help secreting cells win competitive advantages in intraspecific or interspecific conflicts and are a critical factor in the pathogenicity of many pathogens that threaten human health (Chassaing, et al., 2018; Garcia-Bayona, et al., 2018; Ruhe, et al., 2020). Antimicrobial toxin production is ubiquitous in microbial communities. Many organisms are armed with multiple antimicrobial toxins: some kill strains of the same species, and others kill strains across species, genera, families, and orders (Peterson, et al., 2020). The arsenal of prokaryotic antimicrobial toxins is extremely diverse (Granato, et al., 2019; Klein, et al., 2020).
Antimicrobial toxins can be broadly classified into two categories: diffusible molecules that are released into the extracellular milieu, and toxin proteins that are delivered directly to the target cell via cell-to-cell contact through a variety of secretion systems (Chassaing, et al., 2018; Garcia-Bayona, et al., 2018). A striking feature of antimicrobial toxins is that a given N-terminal region can be found fused to distinct toxic domains, and a given toxic domain can be found fused to distinct N-terminal regions (Jamet, et al., 2015; Zhang, et al., 2012). Another striking feature is that the loci encoding an antimicrobial toxin also encode an immunity protein (Chassaing, et al., 2018). Immunity proteins are usually encoded immediately downstream of the antimicrobial toxin gene; this organization protects the producing cell from either autointoxication or toxin produced by clonemates (Zhang, et al., 2012).
A large number of genes in prokaryotic genomes are expected to encode antimicrobial toxins, immunity proteins and related secretion systems, but experimentally verifying antimicrobial toxin activities and mechanisms of action remains a significant challenge (Geller, et al., 2021; Jamet, et al., 2018; Zhang, et al., 2012). Most of the known antimicrobial toxins have enzymatic activities and can disrupt critical molecular structures of target cells in very small amounts (Ruhe, et al., 2020). These antimicrobial toxins can be nucleases that target DNA or RNA, phospholipases or pore-forming toxins that target cell membranes, glycoside hydrolases or proteases that degrade cell walls, NADases that disrupt cellular energy balance, ADP-ribosyltransferases that target tubulin-like proteins to prevent cell division, and so on (Ruhe, et al., 2020; Zhang, et al., 2012).
Here, we have organized information on antimicrobial toxins and immunity proteins derived from the reported literature as the web-based resource PAT (prokaryotic antimicrobial toxin). This database focuses on diffusible proteinaceous toxins, and toxins deployed by contact-dependent systems, including bacteriocin (molecular weight >10 kDa), type IV secretion system (T4SS) toxins, contact-dependent growth inhibition (CDI) toxins, type VI secretion system (T6SS) toxins, type VII secretion system (T7SS) toxins, extracellular contractile injection system (eCIS) toxins, outer membrane exchange (OME) toxins, MafB toxins and WapA toxins.
“Bacteriocin” is a broad term used to describe a very heterogeneous group of diffusible bacterially produced peptides or protein antibacterial toxins (Ruhe, et al., 2020). These include small peptide toxins that are often posttranslationally modified (PTM), large proteins, and R-type bacteriocins. Bacteriocins are ubiquitous, with evidence of their production across all major groups of bacteria and many archaea. In contrast to antibiotics, bacteriocins typically have a narrow killing spectrum, targeting close relatives of the producing strain. This range is most often dictated by the requirement for a specific cell-surface receptor on the target cell that mediates attachment and sometimes import into the cell. Bacteriocins use a variety of mechanisms to kill sensitive cells, including pore-formation, inhibition of cell-wall synthesis, degradation of peptidoglycan, inhibition of protein synthesis, nuclease activity, and gyrase inhibition (Chassaing, et al., 2018). PAT covers antimicrobial proteins with a molecular weight greater than 10 kDa, including colicins and colicin-like bacteriocins produced by gram-negative bacteria, class III bacteriocins produced by gram-positive bacteria, but excluding antimicrobial peptides and multiprotein complexes.
T4SSs can transfer DNA, proteins, and protein-DNA complexes into neighboring cells in a contact-dependent manner (Garcia-Bayona, et al., 2018). This ATP-dependent multiprotein complex has a translocation channel that spans the whole cell envelope and an extracellular pilus involved in conjugative DNA transfers between bacteria or translocation of effectors largely into eukaryotic cells (Klein, et al., 2020). A T4SS of the plant pathogen Xanthomonas citri was shown to secrete toxic effectors into bacterial cells and was shown to antagonize two different Proteobacterial species.
The first contact-dependent antagonistic system, cdiBAI, was characterized in E. coli. The CDI phenotype was established to be mediated by the cdiBAI gene cluster (Jamet, et al., 2015). The CdiA adhesin consists of three domains: a large conserved N-terminal domain (NtD) with a triple-stranded beta-helix structure, a receptor-binding domain (RBD), and a smaller C-terminal effector domain (CdiA-CT). CdiA is secreted through CdiB, a β-barrel outer membrane protein. Upon contact with the target, CdiA autoproteolytically cleaves its effector part, CdiA-CT, which translocates into the competitor cell, leading to disruption of intracellular processes (Granato, et al., 2019). Due to its peculiar structure, CdiA was named “toxin-on-a-stick”. Immunity to its own toxin is provided by CdiI, a small protein located on the inner membrane, where it can form a tight complex with CdiA-CT.
The T6SS is a dynamic contractile protein nanomachine, evolutionarily related to bacteriophage tails, which delivers protein effectors in a contact-dependent manner into diverse cellular types, including eukaryotic host cells and rival bacteria and fungi (Chassaing, et al., 2018). The T6SS gene cluster encodes at least 13 conserved core components for apparatus assembly and other less conserved accessory proteins and effectors. It functions as a contractile tail machine comprising a contractile sheath and an expelled puncturing device consisting of an Hcp tube topped by a spike complex of VgrG and PAAR proteins. Contraction of the sheath propels the tube out of the bacterial cell into a target cell and leads to the injection of toxic proteins. Different bacteria use the T6SS for specific roles according to the niche and versatility of the organism (Garcia-Bayona, et al., 2018). Effectors are present both as cargo (by non-covalent interactions with one of the core components) or specialized domains (fused to structural components).
The T7SS (Esx pathway) is widespread in Mycobacteria and other Gram-positive bacteria and exports substrates with a variety of biological roles, including antimicrobial toxins (Klein, et al., 2020). The Leu-Xaa-Gly (LXG) polymorphic toxins, broadly distributed in Firmicutes, were shown to be secreted as substrates of the T7SS to mediate interbacterial competition. The LXG architecture includes a conserved N-terminal (LXG domain) necessary for secretion, a middle domain of variable length, and a C-terminal variable toxin domain (Jamet, et al., 2018). The T7SS was shown to deliver LXG or non-LXG toxins to target cells of diverse Gram-positive species.
The eCIS is a cell-free protein delivery system that is prevalent in bacteria and archaea. The eCIS particle resembles the contractile tail of a T4 bacteriophage and is mostly encoded by an operon of 15-28 genes (Geller, et al., 2021). The effectors that have been studied were shown to perform enzymatic activities in the target eukaryotic cell, most of which led to cell toxicity. ECIS shares structural similarity with other contractile weapons such as the type VI secretion system (T6SS) and R-type pyocins but differ from these by being extracellular and by injecting effectors into the target cell instead of just perforating it, respectively.
OME in the social bacterium Myxococcus xanthus is regulated by a cell-surface receptor, TraA, which is polymorphic among different M. xanthus strains (Ruhe, et al., 2020). TraA interactions between cells lead to transient outer-membrane fusion and exchange of lipopolysaccharide, lipid, and lipoprotein. The polymorphic SitA lipoprotein toxins are delivered during OME, in which they are serially transferred between cells, killing those lacking the immunity protein (Garcia-Bayona, et al., 2018).
MafB proteins are polymorphic effectors encoded on five genomic islands in strains of Neisseria meningitidis and Neisseria gonorrhoeae (Ruhe, et al., 2020). MafB toxins are neutralized by specific immunity proteins encoded by mafI genes found immediately downstream of mafB genes. MafB proteins exhibit a signal peptide sequence, an N-terminal conserved domain of unknown function named DUF1020 (PF06255), and a C-terminal variable region (Jamet, et al., 2015). Toxin transfer is cell-contact or proximity dependent, although this has yet to be tested explicitly.
Bacillus subtilis is able to rapidly inhibit Bacillus megaterium growth by delivering WapA toxin (Jamet, et al., 2018). WapA was shown to be constantly exchanged among nearby B. subtilis cells, reducing viability in cells lacking the cognate wapI immunity gene; however, its exact delivery mechanism has not been elucidated (Ruhe, et al., 2020). WapA was shown to carry a secretion signal sequence in its N-terminus and to contain toxic activity in its C-terminus.
Chassaing B, Cascales E. Antibacterial weapons: targeted destruction in the microbiota. Trends in microbiology, 2018, 26(4): 329-338.
García-Bayona L, Comstock L E. Bacterial antagonism in host-associated microbial communities. Science, 2018, 361(6408): eaat2456.
Geller A M, Pollin I, Zlotkin D, et al. The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins. Nature communications, 2021, 12(1): 1-15.
Granato E T, Meiller-Legrand T A, Foster K R. The evolution and ecology of bacterial warfare. Current biology, 2019, 29(11): R521-R537.
Jamet A, Charbit A, Nassif X. Antibacterial toxins: gram-positive bacteria strike back!. Trends in microbiology, 2018, 26(2): 89-91.
Jamet A, Nassif X. New players in the toxin field: polymorphic toxin systems in bacteria. MBio, 2015, 6(3): e00285-15.
Klein T A, Ahmad S, Whitney J C. Contact-dependent interbacterial antagonism mediated by protein secretion machines. Trends in microbiology, 2020, 28(5): 387-400.
Peterson S B, Bertolli S K, Mougous J D. The central role of interbacterial antagonism in bacterial life. Current Biology, 2020, 30(19): R1203-R1214.
Ruhe Z C, Low D A, Hayes C S. Polymorphic toxins and their immunity proteins: diversity, evolution, and mechanisms of delivery. Annual review of microbiology, 2020, 74: 497-520.
Zhang D, de Souza R F, Anantharaman V, et al. Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biology direct, 2012, 7(1): 1-76.