数字农科院2.0

Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements

文献类型： 外文期刊

作者： Tesson, Florian;Huiting, Erin;Wei, Linlin;Ren, Jie;Johnson, Matthew;Planel, Remi;Cury, Jean;Feng, Yue;Bondy-Denomy, Joseph;Bernheim, Aude

作者机构：

期刊名称： NUCLEIC ACIDS RESEARCH

ISSN： 0305-1048

年卷期： 2024 年

页码：

收录情况： SCIE（2024版）

摘要： The co-evolution of prokaryotes, phages and mobile genetic elements (MGEs) has driven the diversification of defense and anti-defense systems alike. Anti-defense proteins have diverse functional domains, sequences and are typically small, creating a challenge to detect anti-defense homologs across prokaryotic and phage genomes. To date, no tools comprehensively annotate anti-defense proteins within a desired sequence. Here, we developed 'AntiDefenseFinder'-a free open-source tool and web service that detects 156 anti-defense systems of one or more proteins in any genomic sequence. Using this dataset, we identified 47 981 anti-defense systems distributed across prokaryotes and their viruses. We found that some genes co-localize in 'anti-defense islands', including Escherichia coli T4 and Lambda phages, although many appear standalone. Eighty-nine per cent anti-defense systems localize only or preferentially in MGE. However, >80% of anti-Pycsar protein 1 (Apyc1) resides in nonmobile regions of bacterial genomes. Evolutionary analysis and biochemical experiments revealed that Apyc1 likely originated in bacteria to regulate cyclic nucleotide (cNMP) signaling, but phage co-opted Apyc1 to overcome cNMP-utilizing defenses. With the AntiDefenseFinder tool, we hope to facilitate the identification of the full repertoire of anti-defense systems in MGEs, the discovery of new protein functions and a deeper understanding of host-pathogen arms race. [GRAPHICS] .

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