Large-scale discovery of candidate type VI secretion effectors with antibacterial activity

Geller, Alexander Martin; Zlotkin, David; Levy, Asaf

doi:10.1101/2021.10.07.463556

Cited by 4 publications

(9 citation statements)

References 83 publications

(74 reference statements)

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“…At the phylum level, T6SS genes have been detected in genomes belonging to fewer than ten of the over 100 currently classified phyla (Fig. 3a) [1,[10][11][12][13][14]79]. The T6SS is therefore a trait present only in a small fraction of phyla.…”

Section: Presence and Absence Of T6sss Across Bacterial Taxamentioning

confidence: 99%

“…Another soil bacterium, Myxococcus xanthus, uses its T6SS to attack sibling cells under starvation, thereby maintaining a population of healthy, well-fed cells [49]. While there are free-living bacteria with the T6SS, comparative studies suggest that the T6SS is less common among free-living bacteria and more prominent among complex microbial communities, with even higher prominence among host-associated microbial communities [14,20]. Some T6SS-positive bacteria are associated with eukaryotic hosts as members of the microbiomes of plants and animals (Fig.…”

Section: T6sss Are Prevalent In Bacteria Across Ecosystems and Clinic...mentioning

confidence: 99%

“…Experimental evidence has been published for T6SS-positive members of the Proteobacteria [1] and Bacteroidetes [11], while only bioinformatics-derived evidence exists for T6SS in Acidobacteria , Deferribacteres , Nitrospirae , Planctomycetes , Gemmatimonates and Cyanobacteria [11–13]. A very recent analysis in preprint by Geller and colleagues also identified T6SS genes in genomes from Actinobacteria , Verrucomicrobia , Candidatus Aminicenantes and Candidatus Eisenbacteria, which requires further validation [14]. All validated T6SS-positive phyla described to date have a diderm and are Gram-negative.…”

Section: Presence and Absence Of T6sss Across Bacterial Taxamentioning

confidence: 99%

“…Within each phylum, only a fraction of bacteria are T6SS-positive [12,14]. Generally, less than half of the analysed genomes within a given phylum are T6SS-positive [12].…”

Section: Presence and Absence Of T6sss Across Bacterial Taxamentioning

confidence: 99%

“…The constantly growing number of sequenced bacterial genomes and the development of customized bioinformatics tools have enabled large-scale analyses of T6SS genes across bacteria [10][11][12][13][14]. Ready-to-use applications allow the screening of genomes for the presence of T6SS genes [15].…”

Section: Introductionmentioning

confidence: 99%

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Presence and absence of type VI secretion systems in bacteria

et al. 2022

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The type VI secretion system (T6SS) is a molecular puncturing device that enables Gram-negative bacteria to kill competitors, manipulate host cells and take up nutrients. Who would want to miss such superpowers? Indeed, many studies show how widespread the secretion apparatus is among microbes. However, it is becoming evident that, on multiple taxonomic levels, from phyla to species and strains, some bacteria lack a T6SS. Here, we review who does and does not have a type VI secretion apparatus and speculate on the dynamic process of gaining and losing the secretion system to better understand its spread and distribution across the microbial world.

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Section: Presence and Absence Of T6sss Across Bacterial Taxamentioning

confidence: 99%

Section: T6sss Are Prevalent In Bacteria Across Ecosystems and Clinic...mentioning

confidence: 99%

Section: Presence and Absence Of T6sss Across Bacterial Taxamentioning

confidence: 99%

“…Within each phylum, only a fraction of bacteria are T6SS-positive [12,14]. Generally, less than half of the analysed genomes within a given phylum are T6SS-positive [12].…”

Section: Presence and Absence Of T6sss Across Bacterial Taxamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Presence and absence of type VI secretion systems in bacteria

et al. 2022

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Killing in the name of: T6SS structure and effector diversity

Allsopp

Bernal

2023

Microbiology

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The life of bacteria is challenging, to endure bacteria employ a range of mechanisms to optimize their environment, including deploying the type VI secretion system (T6SS). Acting as a bacterial crossbow, this system delivers effectors responsible for subverting host cells, killing competitors and facilitating general secretion to access common goods. Due to its importance, this lethal machine has been evolutionarily maintained, disseminated and specialized to fulfil these vital functions. In fact, T6SS structural clusters are present in over 25 % of Gram-negative bacteria, varying in number from one to six different genetic clusters per organism. Since its discovery in 2006, research on the T6SS has rapidly progressed, yielding remarkable breakthroughs. The identification and characterization of novel components of the T6SS, combined with biochemical and structural studies, have revealed fascinating mechanisms governing its assembly, loading, firing and disassembly processes. Recent findings have also demonstrated the efficacy of this system against fungal and Gram-positive cells, expanding its scope. Ongoing research continues to uncover an extensive and expanding repertoire of T6SS effectors, the genuine mediators of T6SS function. These studies are shedding light on new aspects of the biology of prokaryotic and eukaryotic organisms. This review provides a comprehensive overview of the T6SS, highlighting recent discoveries of its structure and the diversity of its effectors. Additionally, it injects a personal perspective on avenues for future research, aiming to deepen our understanding of this combative system.

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A pangenomic atlas reveals that eco-evolutionary dynamics shape plant pathogen type VI secretion systems

Aoun,

Georgoulis,

Avalos

et al. 2023

Preprint

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Soil-borne Ralstonia solanacearum species complex (RSSC) bacteria disrupt rhizosphere and endophytic microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped pathogen T6SS biology, we analyzed the T6SS gene content and architecture across the RSSC pangenome and their evolutionarily relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem pathogenic RSSC bacteria and Acidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,069 auxiliary ("aux") T6SS toxin clusters across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Secondary replicons like megaplasmids often evolve more rapidly than the more evolutionarily stable chromosome. Although the single ancestral T6SS was broadly conserved in the RSSC, the T6SS was convergently lost in atypical lineages with vectored transmission. Overall, our data suggest dynamic interplay between the lifestyle of soil-transmitted RSSC lineages and the evolution of T6SSs with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.

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Large-scale discovery of candidate type VI secretion effectors with antibacterial activity

Cited by 4 publications

References 83 publications

Presence and absence of type VI secretion systems in bacteria

Presence and absence of type VI secretion systems in bacteria

Killing in the name of: T6SS structure and effector diversity

A pangenomic atlas reveals that eco-evolutionary dynamics shape plant pathogen type VI secretion systems

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