A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

Abstract

The use of nucleases as toxins for defense, offense or addiction of selfish elements is widely encountered across all life forms. Using sensitive sequence profile analysis methods, we characterize a novel superfamily (the SUKH superfamily) that unites a diverse group of proteins including Smi1/Knr4, PGs2, FBXO3, SKIP16, Syd, herpesviral US22, IRS1 and TRS1, and their bacterial homologs. Using contextual analysis we present evidence that the bacterial members of this superfamily are potential immunity proteins for a variety of toxin systems that also include the recently characterized contact-dependent inhibition (CDI) systems of proteobacteria. By analyzing the toxin proteins encoded in the neighborhood of the SUKH superfamily we predict that they possess domains belonging to diverse nuclease and nucleic acid deaminase families. These include at least eight distinct types of DNases belonging to HNH/EndoVII- and restriction endonuclease-fold, and RNases of the EndoU-like and colicin E3-like cytotoxic RNases-folds. The N-terminal domains of these toxins indicate that they are extruded by several distinct secretory mechanisms such as the two-partner system (shared with the CDI systems) in proteobacteria, ESAT-6/WXG-like ATP-dependent secretory systems in Gram-positive bacteria and the conventional Sec-dependent system in several bacterial lineages. The hedgehog-intein domain might also release a subset of toxic nuclease domains through auto-proteolytic action. Unlike classical colicin-like nuclease toxins, the overwhelming majority of toxin systems with the SUKH superfamily is chromosomally encoded and appears to have diversified through a recombination process combining different C-terminal nuclease domains to N-terminal secretion-related domains. Across the bacterial superkingdom these systems might participate in discriminating `self’ or kin from `non-self’ or non-kin strains. Using structural analysis we demonstrate that the SUKH domain possesses a versatile scaffold that can be used to bind a wide range of protein partners. In eukaryotes it appears to have been recruited as an adaptor to regulate modification of proteins by ubiquitination or polyglutamylation. Similarly, another widespread immunity protein from these toxin systems, namely the suppressor of fused (SuFu) superfamily has been recruited for comparable roles in eukaryotes. In animal DNA viruses, such as herpesviruses, poxviruses, iridoviruses and adenoviruses, the ability of the SUKH domain to bind diverse targets has been deployed to counter diverse anti-viral responses by interacting with specific host proteins.

Bacterial killing via a type IV secretion system

“…Many of these proteins carry domains that may work to kill or inhibit growth of other organisms. 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).…”

“…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 .…”

Unraveling the essential role of CysK in CDI toxin activation

“…Although CysK is critical for CdiA-CT EC536 nuclease activity, related toxins from Gram-positive bacteria probably do not require extrinsic activation because purified Tox28 domain from R. lactaris has tRNase activity in vitro. Ntox28 domains are typically found at the C terminus of proteins that mediate interbacterial competition (4,(29)(30)(31). For example, the R. lactaris Tox28 Rlac domain is part of a larger EC536 were treated with formaldehyde, and cross-linked nucleoprotein complexes were purified by Ni 2+ -affinity chromatography.…”

“…Further, the Ntox28 homolog from Geobacillus sp. strain Y412MC10 (GYMC10_1092) is linked to an N-terminal ESAT-6-like domain, which is predicted to guide export through type VII secretion systems (4,29). Given that all Ntox28 domains function in intercellular competition, perhaps the mechanism of toxin delivery into Gram-negative bacteria accounts for the relative instability of CdiA-CT EC536 .…”

Activation of contact-dependent antibacterial tRNase toxins by translation elongation factors

“…Upon binding receptor, CdiA transfers its C-terminal toxin domain (CdiA-CT) into the target bacterium through an incompletely understood translocation mechanism (4,5). Genome and protein database surveys show that CdiA effectors carry a wide variety of distinct toxins (1,(6)(7)(8). CDI + cells protect themselves from self-intoxication by producing CdiI immunity proteins, which bind specifically to cognate CdiA-CT domains and neutralize their toxic activities.…”