A novel class of polymorphic toxins in Bacteroidetes

Jana, Biswanath; Salomon, Dor; Bosis, Eran

doi:10.26508/lsa.201900631

Cited by 10 publications

(10 citation statements)

References 43 publications

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“…and are virulence factors for some pathogens ( 38 ). T9SSs may also secrete antibacterial polymorphic toxins ( 39 ), and it is possible that the Rhs proteins encoded by Apibacter spp. genomes play a role in interbacterial antagonism.…”

Section: Resultsmentioning

confidence: 99%

Evolution of Interbacterial Antagonism in Bee Gut Microbiota Reflects Host and Symbiont Diversification

Steele

Moran

2021

mSystems

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Gram-negative bacteria frequently possess type VI secretion systems (T6SSs), protein complexes that are able to inject toxic proteins into nearby cells. Many aspects of T6SS structure and function have been characterized for model species, but less is known about the evolutionary processes that shape T6SS and effector (toxin) diversity in host-associated microbial communities. The bee gut microbiota is a simple community that has codiversified with bees for >80 million years. This study investigated how complements of T6SSs and effectors within the bee microbiota changed as bacteria and their hosts diversified into isolated species. We used protein homology to survey 198 isolate genomes of 9 Gram-negative species for genes encoding T6SS structural components; Rhs toxins, which are common T6SS effectors; and VgrG proteins, which are structural components associated with specific toxins. T6SS loci were present in 5 species clusters found only in bees, namely Apibacter spp., Gilliamella spp., Frischella perrara, “Candidatus Schmidhempelia bombi,” and Snodgrassella alvi. The distribution of T6SS loci suggests that at least 3 were present in the microbiota of the common ancestor of social bees and that loss of these genes in some bacterial lineages was linked to both host and bacterial speciation. Isolates differed enormously in repertoires of Rhs and VgrG proteins. We found that bacterial species employ different mechanisms for toxin acquisition and diversification and that species and strains sometimes lose the T6SS entirely, likely causing shifts in competitive dynamics within these communities. IMPORTANCE Antagonistic interactions between bacteria affect diversity and dynamics of host-associated communities, including gut communities that are linked to host health. In many bacterial communities, including human and honey bee gut microbiotas, antagonism is mediated by type VI secretion systems (T6SSs) that deliver lethal toxins to competing strains. In this study, we explored how T6SSs and associated toxins have evolved in the simple, host-specific gut microbiota of honey bees and bumble bees. Using comparative genomics, we explored the conservation, recombination, horizontal transfer, and loss of T6SSs and effectors during 80 million years of evolution of this bee-associated community. We find that that patterns of T6SS loss and retention are linked to differences in biology across host species, while trends in effector diversification are mostly specific to bacterial lineages.

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Section: Resultsmentioning

confidence: 99%

Evolution of Interbacterial Antagonism in Bee Gut Microbiota Reflects Host and Symbiont Diversification

Steele

Moran

2021

mSystems

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“…In addition to a PAAR domain, the PAAR-encoding gene (A7P61_RS17080) also encodes RhsA repeats and a C-terminal extension that harbors a putative antibacterial toxin domain. Homologs of this C-terminal domain are found in diverse Proteobacteria , where they are fused to PAAR and RhsA domains, and in Firmicutes , where they are fused to TANFOR domains, which were recently shown to carry polymorphic toxins (e.g., WP_066428025) (Quentin et al ., 2018; Jana et al ., 2020). Therefore, the PAAR protein appears to be a specialized effector.…”

Section: Resultsmentioning

confidence: 99%

A dynamic antibacterial T6SS in Pantoea agglomerans pv. betae delivers a lysozyme-like effector to antagonize competitors

Carobbi

Nepi

Fridman

et al. 2021

Preprint

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The type VI secretion system (T6SS) is deployed by numerous Gram-negative bacteria to deliver toxic effectors into neighboring cells. The genome of Pantoea agglomerans pv. betae (Pab) phytopathogenic bacteria contains a gene cluster (T6SS1) predicted to encode a complete T6SS. Using secretion and competition assays, we found that T6SS1 in Pab is a functional antibacterial system that allows this pathogen to outcompete rival plant-associated bacteria found in its natural environment. Computational analysis of the T6SS1 gene cluster revealed that antibacterial effector and immunity proteins are encoded within three dynamic genomic islands that harbor arrays of orphan immunity genes or toxin and immunity cassettes. Functional analysis demonstrated that the specialized antibacterial effector VgrG contains a C-terminal catalytically active glucosaminidase domain that is used to degrade prey peptidoglycan. Moreover, we confirmed that a bicistronic unit at the end of the T6SS1 cluster encodes a novel antibacterial T6SS effector and immunity pair. Together, these results demonstrate that Pab T6SS1 is an antibacterial system delivering a lysozyme-like effector to eliminate competitors, and indicate that this bacterium contains novel T6SS effectors.Significance StatementIn this work, we describe the identification of a Pantoea agglomerans T6SS as an antibacterial determinant used by this phytopathogen to outcompete bacterial rivals. Furthermore, we provide an in-depth analysis of the T6SS gene cluster and the putative effector and immunity genes that comprise it, and we propose explanations for its dynamic evolution and effector diversification in Pantoea strains. Lastly, we experimentally validate two predicted effector and immunity pairs, and we demonstrate that one is a potent lysozyme-like toxin.

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“…Polymorphic toxins are multi-domain proteins involved primarily in inter-bacterial competition that were discovered nearly a decade ago 14 . In recent years it is becoming clear that polymorphic toxins play important roles in various bacteria, archaea and temperate phages, and their toxins can serve as DNAses, RNAses, rRNA ADP-ribosylating and membrane depolarization enzymes, metallopeptidase, and cell wall biosynthesis inhibitors [9][10][11]13,15,18,20,[46][47][48][49][50][51][52] . Here, we developed a new algorithm to predict novel toxin domains (PTs) located at the C-terminus of polymorphic toxin proteins across over 100,000 genomes from the microbial world.…”

Section: Discussionmentioning

confidence: 99%

Systematic Discovery of Antibacterial and Antifungal Bacterial Toxins

Nachmias

Dotan

Shalom

et al. 2021

Preprint

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Microbes employ a large diversity of toxins to kill competing microbes or eukaryotic host cells. Polymorphic toxins are a class of protein toxins abundant in Nature and secreted through various secretion systems. Polymorphic toxins have a modular protein architecture with a toxin domain found at the protein C-terminus. The discovery of microbial toxins is important to improve our understanding of microbial ecology and infectious diseases. Here, we developed a computational approach to discover novel toxin domains of polymorphic toxins and applied it to 105,438 microbial genomes. We validated nine short novel toxins (“PTs”) that lead to bacterial cell death; one of them also kills yeast. For four toxins, we also identified a cognate immunity gene (“PIM”) that protects the toxin producing cell from toxicity. Additionally, we found that the novel PTs are encoded by ~2.2% of the sequenced bacteria, including numerous Gram-negative and -positive pathogens. We explored two avenues to determine the mechanism of action of these nine PTs. First, we used fluorescence microscopy to observe severe changes in cell size, membrane and chromosome morphology upon expression of the novel toxins. We then identified putative catalytic sites of these toxins, which, upon mutation, abolished their harmful activities. Thus, using this unique hybrid computational-experimental pipeline, we were able to expand the microbial toxins repertoire significantly. These new potent toxins likely play essential roles in inter-microbial competition in Nature and can be utilized in various biotechnological and clinical applications.

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A novel class of polymorphic toxins in Bacteroidetes

Cited by 10 publications

References 43 publications

Evolution of Interbacterial Antagonism in Bee Gut Microbiota Reflects Host and Symbiont Diversification

Evolution of Interbacterial Antagonism in Bee Gut Microbiota Reflects Host and Symbiont Diversification

A dynamic antibacterial T6SS in Pantoea agglomerans pv. betae delivers a lysozyme-like effector to antagonize competitors

Systematic Discovery of Antibacterial and Antifungal Bacterial Toxins

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