Systematic discovery of antiphage defense systems in the microbial pangenome

Shany Doron; Sarah Melamed; Gal Ofir; Azita Leavitt; Anna Lopatina; Mai Keren; Gil Amitai; Rotem Sorek

doi:10.1126/science.aar4120

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Systematic discovery of antiphage defense systems in the microbial pangenome

Journal article

Peer reviewed

Systematic discovery of antiphage defense systems in the microbial pangenome

Shany Doron, Sarah Melamed, Gal Ofir, Azita Leavitt, Anna Lopatina, Mai Keren, Gil Amitai and Rotem Sorek

Science (American Association for the Advancement of Science), Vol.359(6379), eaar4120

25/Jan/2018

DOI: https://doi.org/10.1126/science.aar4120

PMID: 29371424

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Abstract

The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that known and unknown defense systems are located in "defense islands" in microbial genomes. Here, we comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities. We report nine previously unknown antiphage systems and one antiplasmid system that are widespread in microbes and strongly protect against foreign invaders. These include systems that adopted components of the bacterial flagella and condensin complexes. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.

Bacillus subtilis - genetics

Bacillus subtilis - immunology

Bacillus subtilis - virology

Bacteriophages - immunology

Bacteriophages - pathogenicity

Escherichia coli - genetics

Escherichia coli - immunology

Escherichia coli - virology

Genes, Bacterial - physiology

Genome, Bacterial

Multigene Family

Details

Title: Systematic discovery of antiphage defense systems in the microbial pangenome
Creators: Shany Doron - 972WIS_INST___111
Sarah Melamed - 972WIS_INST___111
Gal Ofir - 972WIS_INST___111
Azita Leavitt - 972WIS_INST___111
Anna Lopatina - 972WIS_INST___111
Mai Keren - 972WIS_INST___111
Gil Amitai - 972WIS_INST___111
Rotem Sorek (Corresponding Author) - 972WIS_INST___111
Resource Type: Journal article
Publication Details: Science (American Association for the Advancement of Science), Vol.359(6379), eaar4120; 25/Jan/2018
Language: English
DOI: https://doi.org/10.1126/science.aar4120
PMID: 29371424
Grants: Beyond CRISPR: Systematic characterization of novel anti-phage defense systems in the microbial pan-genome, 681203, European Research Council (Belgium, Brussels) - ERC
Grant note: We thank H. Sberro, O. Zuqert, O. Cohen, S. Mintzer, R. Shenhav, Z. Erez, D. Dar, M. Voichek, and N. Tal for useful discussion during the course of this study. We also thank M. Voichek for assistance with RNA-seq and S. Silverman for help with phage isolation. R.S. was supported, in part, by the Israel Science Foundation (personal grant 1360/16 and I-CORE grant 1796/12), the European Research Council (ERC) (grant ERC-CoG 681203), the Abisch-Frenkel Foundation, the David and Fela Shapell Family Foundation, the Benoziyo Advancement of Science grant, the Minerva Foundation, and the Pasteur-Weizmann Council. Assembled phage genomes and raw reads were deposited in the European Nucleotide Archive (ENA) under study accession PRJEB23070. Competing interests: R.S. is a scientific cofounder and advisor of BiomX Ltd. S.D., S.M., G.A., A. Leavitt, and R.S. are inventors on U.S. provisional patent application 62/586,911. S.D., S.M., G.O., and R.S. are inventors on U.S. provisional patent applications 62/512,216 and 62/512,219.
Record Identifier: 993338515803596

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