Cryo-EM structure of the RADAR supramolecular anti-phage defense complex

Duncan-Lowey, Brianna; Tal, Nitzan; Johnson, Alex G.; Rawson, Shaun; Mayer, Megan L.; Doron, Shany; Millman, Adi; Melamed, Sarah; Fedorenko, Taya; Kacen, Assaf; Brandis, Alexander; Mehlman, Tevie; Amitai, Gil; Sorek, Rotem; Kranzusch, Philip J.

doi:10.1016/j.cell.2023.01.012

Cited by 37 publications

(21 citation statements)

References 55 publications

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“…For systems and subsystems where protein accessions were impossible to retrieve, we selected another representative. Recent studies demonstrated that many systems function as complexes 4,8,10,39,40 . To provide insight on the possible complexes, all possible dimers (homo and heterodimers) were computed for each system.…”

Section: Resultsmentioning

confidence: 99%

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

Tesson,

Planel,

Egorov

et al. 2024

Preprint

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In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To facilitate the exploration of mechanistic, ecological, and evolutionary aspects related to antiphage defense systems, we released DefenseFinder in 2021 (Tesson et al., 2022). DefenseFinder is a bioinformatic program designed for the systematic identification of all known antiphage defense mechanisms. The initial release of DefenseFinder v1.0.0 included 60 systems. Over the past three years, the number of antiphage systems incorporated into DefenseFinder has grown to 152. The increasing number of known systems makes it a challenge to enter the field and makes the interpretation of detections of antiphage systems difficult. Moreover, the rapid development of sequence-based predictions of structures offers novel possibilities of analysis and should be easily available. To overcome these challenges, we present a hub of resources on defense systems including 1) a search tool (DefenseFinder as a web service) 2) a knowledge base, and 3) precomputed databases (results of DefenseFinder ran on RefSeq database, predicted structure database computed with AlphaFold). These pages can be freely accessed for users as a starting point on their journey to better understand a given system. We anticipate that these resources will foster the use of bioinformatics in the study of antiphage systems and will serve the community of researchers who study antiphage systems. This resource is available at: https://defensefinder.mdmlab.fr.

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Section: Resultsmentioning

confidence: 99%

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

Tesson,

Planel,

Egorov

et al. 2024

Preprint

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“…We speculate that the three AAA-neutralised TA pairs are also Abi phage defence systems. AlphaFold2 modelling does not give a convincing interface for AAA antitoxins and their toxins (pDockQ score of 0.24-0.35), which may be because phage defence AAA-containing systems form large multimeric complexes, as is seen with AAA-containing RADAR [66, 67].…”

Section: Resultsmentioning

confidence: 99%

The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems

Ernits

Saha

Brodiazhenko

et al. 2023

Preprint

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Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and neutralising antitoxin. Using our tool NetFlax (standing for Network-FlaGs for toxins and antitoxins) we have performed a large-scale bioinformatic analysis of proteinaceous TAs, revealing interconnected clusters constituting a core network of TA-like gene pairs. To understand the structural basis of toxin neutralisation by antitoxins, we have predicted the structures of 3,419 complexes with AlphaFold2. Together with mutagenesis and functional assays, our structural predictions provide insights into the neutralising mechanism of the hyperpromiscuous Panacea antitoxin domain. In antitoxins composed of standalone Panacea, the domain mediates direct toxin neutralisation, while in multidomain antitoxins the neutralisation is mediated by other domains, such as PAD1, Phd-C and ZFD. We hypothesise that Panacea acts as a sensor that regulates TA activation. We have experimentally validated 16 new NetFlax TA systems. We used functional domain annotations and with metabolic labelling assays to predict their potential mechanisms of toxicity (such as disruption of membrane integrity, inhibition of cell division and abrogation of protein synthesis) as well as biological functions (such as antiphage defence). The interactive version of the NetFlax TA network that includes structural predictions can be accessed at http://netflax.webflags.se/.

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“…A possible scenario is that the phage-associated signal is transmitted from HerA to the large domain of SIR2, based on the observation that the large domain of SIR2 is responsible for SIR2-HerA complex formation (Figure 4A-B). Coupling diverse enzymes to provide protection from phage appears to be a prevalent strategy for bacterial immunity (Duncan-Lowey et al , 2023; Gao et al ., 2020; Gao et al , 2023). HerA ATPase/helicase works in concert with the NurA nuclease in archaea and some bacteria for DNA end resection during the repair of double-stranded DNA breaks (White & Allers, 2018; Yang et al , 2023).…”

Section: Discussionmentioning

confidence: 99%

Structural basis for the concerted antiphage activity in the SIR2-HerA system

Yu,

Liao,

Zhang

et al. 2023

Preprint

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Recently, a novel two-gene bacterial defense system against phages, encoding a SIR2 NADase and a HerA translocase, has been identified. However, the molecular mechanism of the bacterial SIR2-HerA immune system remains unclear. Here, we determine the cryo-EM structures of SIR2, HerA and their complex in different functional states. The SIR2 proteins oligomerize into a dodecameric ring-shaped structure consisting of two layers of interlocked hexamers, in which each SIR2 unit exhibits an auto-inhibited conformation. Distinct from the canonical AAA+ proteins, the HerA hexamer in this antiphage system adopts a split spiral arrangement, resembling the substrate-binding state, which is stabilized by a unique C-terminal extension. SIR2 and HerA proteins assemble into a ∼ 1.1 MDa torch-shaped complex to fight against phage infection. Importantly, disruption of the interactions between SIR2 and HerA largely abolishes the antiphage activity. Interestingly, HerA binding alters the oligomer state of SIR2, switching from a 12-mer state to a 14-mer state. On the other hand, binding of SIR2 stimulates the ATPase activity of HerA. Together, our study not only provides a structural basis for the functional communications between SIR2 and HerA proteins, but also unravels a novel concerted antiviral mechanism through nucleotide (NAD+and ATP) depletion.

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Cryo-EM structure of the RADAR supramolecular anti-phage defense complex

Cited by 37 publications

References 55 publications

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems

Structural basis for the concerted antiphage activity in the SIR2-HerA system

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