Viruses inhibit TIR gcADPR signalling to overcome bacterial defence

Article Multidisciplinary Sciences

Bacterial gasdermins reveal an ancient mechanism of cell death

Alex G. Johnson et al.

Summary: Gasdermin proteins play important roles in immune regulation and induction of cell death in human cells by forming membrane pores. Similar proteins encoded by bacteria have been found to defend against phages and execute cell death.

SCIENCE (2022)

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Article Biochemistry & Molecular Biology

TIR domains of plant immune receptors are 2′,3′-cAMP/cGMP synthetases mediating cell death

Dongli Yu et al.

Summary: This study reveals that plant Toll/interleukin-1 receptor (TIR) proteins not only have NADase function, but also act as 2',3'-cAMP/cGMP synthetases. These cyclic nucleotide monophosphates (cNMPs) play a critical role in plant immune responses.

CELL (2022)

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Article Multidisciplinary Sciences

Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity

Samuel J. Hobbs et al.

Summary: CBASS and Pycsar are bacterial defense systems against phages, and phages have developed anti-CBASS and anti-Pycsar proteins to counteract these defenses. These proteins degrade cyclic nucleotide signals that activate host immunity. Acb1 and Apyc1 are identified as founding members of distinct families of immune evasion proteins, and they block downstream effector activation, protecting phages from CBASS and Pycsar defense.

NATURE (2022)

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Article Cell Biology

Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition

James S. Weagley et al.

Summary: This study characterized bacterial TIR protein domains and found that TIR NADases activity in bacterial strains resulted in a specific metabolite, v-cADPR-x. The research highlighted the correlation between acute malnutrition and decreased fecal levels of TIR genes encoding the generation of v-cADPR-x as well as decreased levels of the metabolite itself.

CELL REPORTS (2022)

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Review Multidisciplinary Sciences

Shared TIR enzymatic functions regulate cell death and immunity across the tree of life

Kow Essuman et al.

Summary: This article presents the research on the TIR domain in animal, plant, bacterial, and archaeal systems, revealing its diverse functions and enzymatic activities in immune systems. It provides important guidance for future interventions.

SCIENCE (2022)

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Article Multidisciplinary Sciences

TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity

Aolin Jia et al.

Summary: In this study, the researchers discovered the enzymatic activity of TIR proteins, which can catalyze the ribosylation of ADP to ATP and ADPR. This enzymatic activity plays a role in activating the immune branch in plants.

SCIENCE (2022)

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Article Multidisciplinary Sciences

Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity

Shijia Huang et al.

Summary: This article investigates the role of TIR domain in plant receptors in catalyzing the production of pRib-AMP and pRib-ADP, and finds that these molecules play a crucial role in plant immune signaling, involving the participation of other proteins.

SCIENCE (2022)

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Article Multidisciplinary Sciences

Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling

Mohammad K. Manik et al.

Summary: This study reveals the production process of cADPR isomers and identifies 3'cADPR as an antiviral agent in bacteria and an immune-suppressing signaling molecule in plants.

SCIENCE (2022)

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Article Microbiology

Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion

Jeremy Garb et al.

Summary: DSR proteins defend bacteria from phage infection by degrading NAD(+) and acting as active NADases, with DSR2 directly identifying phage proteins. Some phages express anti-DSR2 proteins to block bacterial immunity. This study establishes the general role of SIR2 domains in bacterial immunity against phages.

NATURE MICROBIOLOGY (2022)

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Article Multidisciplinary Sciences

Prokaryotic viperins produce diverse antiviral molecules

Aude Bernheim et al.

Summary: Eukaryotic viperins originated from a clade of bacterial and archaeal proteins that protect against phage infection. These proteins produce modified ribonucleotides to combat viruses. Prokaryotic viperins can inhibit T7 phage infection by blocking viral polymerase-dependent transcription.

NATURE (2021)

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Article Biochemical Research Methods

clinker & clustermap.js: automatic generation of gene cluster comparison figures

Cameron L. M. Gilchrist et al.

Summary: Genes involved in biological pathways are often found in gene clusters, and comparing these clusters can provide valuable insights into their function and evolutionary history. To simplify the tedious process of comparing and visualizing gene cluster similarity, a Python tool called clinker and a companion JavaScript library called clustermap.js have been developed to automatically generate accurate, interactive, publication-quality gene cluster comparison figures from sequence files.

BIOINFORMATICS (2021)

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Article Biochemistry & Molecular Biology

Cyclic CMP and cyclic UMP mediate bacterial immunity against phages

Nitzan Tal et al.

Summary: This study identifies the roles of cyclic pyrimidines cCMP and cUMP as immunity signaling molecules in bacterial defense against viruses. A family of bacterial pyrimidine cyclase enzymes was discovered to specifically synthesize these molecules following phage infection, activating immune effectors for antiviral response. Defense systems encoding pyrimidine cyclases, known as Pycsar, are widespread in prokaryotes, providing a clear biological function for cCMP and cUMP in bacterial immunity.

CELL (2021)

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Article Multidisciplinary Sciences

Antiviral activity of bacterial TIR domains via immune signalling molecules

Gal Ofir et al.

Summary: The TIR domain plays a crucial role in animal and plant immune systems, triggering cell death and participating in the bacterial antiviral defence system Thoeris. Research findings suggest that TIR-domain proteins in bacteria recognize infection and produce signalling molecules to execute cell death, similar to the roles of these proteins in plants.

NATURE (2021)

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Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.

NUCLEIC ACIDS RESEARCH (2021)

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Article Microbiology

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Stephen Nayfach et al.

Summary: By mining deposited human stool metagenomes, nearly 190,000 draft-quality DNA virus genomes were recovered to create the Metagenomic Gut Virus catalogue, improving virus detection in stool metagenomes and revealing diverse retroelements with potential involvement in the molecular arms race between phages and their bacterial hosts.

NATURE MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity

Januka S. Athukoralage et al.

NATURE (2020)

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Review Biochemistry & Molecular Biology

Toll-like Receptors and the Control of Immunity

Katherine A. Fitzgerald et al.

CELL (2020)

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Review Genetics & Heredity

Enzymatic Functions for Toll/Interleukin-1 Receptor Domain Proteins in the Plant Immune System

Adam M. Bayless et al.

FRONTIERS IN GENETICS (2020)

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Article Multidisciplinary Sciences

Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+ degradation

Donghyun Ka et al.

NATURE COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

STING cyclic dinucleotide sensing originated in bacteria

Benjamin R. Morehouse et al.

NATURE (2020)

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Article Biochemistry & Molecular Biology

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

I-Min A. Chen et al.

NUCLEIC ACIDS RESEARCH (2019)

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Article Multidisciplinary Sciences

Viral and metazoan poxins are cGAMP-specific nucleases that restrict cGAS-STING signalling

James B. Eaglesham et al.

NATURE (2019)

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Article Multidisciplinary Sciences

Bacterial cGAS-like enzymes synthesize diverse nucleotide signals

Aaron T. Whiteley et al.

NATURE (2019)

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Article Multidisciplinary Sciences

Cyclic GMP-AMP signalling protects bacteria against viral infection

Daniel Cohen et al.

NATURE (2019)

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Article Multidisciplinary Sciences

TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death

Li Wan et al.

SCIENCE (2019)

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Article Multidisciplinary Sciences

NAD+ cleavage activity by animal an plant TIR domains in cell death pathways

Shane Horsefield et al.

SCIENCE (2019)

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Article Biochemical Research Methods

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Dorothee Liebschner et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2019)

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Article Biochemistry & Molecular Biology

Structure of the Human cGAS-DNA Complex Reveals Enhanced Control of Immune Surveillance

Wen Zhou et al.

CELL (2018)

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Article Multidisciplinary Sciences

Systematic discovery of antiphage defense systems in the microbial pangenome

Shany Doron et al.

SCIENCE (2018)

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Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

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A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

Jason M. Peters et al.

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

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Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

Michael Baym et al.

PLOS ONE (2015)

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A new set of highly efficient, tag-cleaving proteases for purifying recombinant proteins

Steffen Frey et al.

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

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Linking Crystallographic Model and Data Quality

P. Andrew Karplus et al.

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MolProbity: all-atom structure validation for macromolecular crystallography

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Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

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Applications of the Restriction Free (RF) cloning procedure for molecular manipulations and protein expression

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Coot:: model-building tools for molecular graphics

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Viruses inhibit TIR gcADPR signalling to overcome bacterial defence

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