Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems.
Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems.
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DOI：
10.1093/nar/gkad317
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发表时间：
2023-06-09
影响因子：
14.9
通讯作者：
Bondy-Denomy, Joseph
中科院分区：
文献类型：
--
作者：
Johnson, Matthew C.;Laderman, Eric;Huiting, Erin;Zhang, Chi;Davidson, Alan;Bondy-Denomy, Joseph
细菌使用多种抗噬菌体免疫系统，包括CRISPR-Cas和限制性内切酶。抗噬菌体系统发现和注释工具的最新进展已经发现了许多独特的系统，通常编码在水平转移的防御岛中，这些防御岛可以水平转移。在这里，我们开发了用于防御系统的隐马尔可夫模型（Hidden Markov Models，简称HMRM），并在NCBI数据库上查询了微生物基因组。在具有>200个完全测序的基因组的30个物种中，我们的分析发现铜绿假单胞菌表现出最大的抗噬菌体系统多样性，如通过香农熵测量的。使用网络分析来确定抗噬菌体系统的共同邻居，我们确定了两个核心防御热点位点（cDHS 1和cDHS 2）。cDHS 1高达224 kb（中位数：26 kb），在分离株之间具有超过30个不同免疫系统的不同排列，而cDHS 2具有24个不同系统（中位数：6 kb）。这两个cDHS区域在大多数铜绿假单胞菌分离株中被占据。大多数cDHS基因是未知的功能，可能代表新的抗噬菌体系统，我们验证了一种新的抗噬菌体系统（Shango）通常编码在cDHS 1。识别免疫岛侧翼的核心基因可以简化免疫系统的发现，并可能代表携带抗噬菌体系统的各种MGE的流行着陆点。核心防御热点是细菌基因组的区域，其中多个抗噬菌体免疫系统在核心基因之间编码。
Bacteria use a diverse arsenal of anti-phage immune systems, including CRISPR-Cas and restriction enzymes. Recent advances in anti-phage system discovery and annotation tools have unearthed many unique systems, often encoded in horizontally transferred defense islands, which can be horizontally transferred. Here, we developed Hidden Markov Models (HMMs) for defense systems and queried microbial genomes on the NCBI database. Out of the 30 species with >200 completely sequenced genomes, our analysis found Pseudomonas aeruginosa exhibits the greatest diversity of anti-phage systems, as measured by Shannon entropy. Using network analysis to identify the common neighbors of anti-phage systems, we identified two core defense hotspot loci (cDHS1 and cDHS2). cDHS1 is up to 224 kb (median: 26 kb) with varied arrangements of more than 30 distinct immune systems across isolates, while cDHS2 has 24 distinct systems (median: 6 kb). Both cDHS regions are occupied in a majority of P. aeruginosa isolates. Most cDHS genes are of unknown function potentially representing new anti-phage systems, which we validated by identifying a novel anti-phage system (Shango) commonly encoded in cDHS1. Identifying core genes flanking immune islands could simplify immune system discovery and may represent popular landing spots for diverse MGEs carrying anti-phage systems. Core defense hotspots are regions of a bacterial genome where multiple anti-phage immune systems are encoded between core genes.
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影响因子：
28.3
作者：
Millman A;Melamed S;Amitai G;Sorek R
通讯作者：
Sorek R
DOI：
10.1126/science.aba0372
发表时间：
2020-08-28
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gao L;Altae-Tran H;Böhning F;Makarova KS;Segel M;Schmid-Burgk JL;Koob J;Wolf YI;Koonin EV;Zhang F
通讯作者：
Zhang F
影响因子：
14.9
作者：
Grissa, Ibtissem;Vergnaud, Gilles;Pourcel, Christine
通讯作者：
Pourcel, Christine
影响因子：
30.3
作者：
Millman, Adi;Melamed, Sarah;Sorek, Rotem
通讯作者：
Sorek, Rotem
影响因子：
3.7
作者：
Abby SS;Néron B;Ménager H;Touchon M;Rocha EP
通讯作者：
Rocha EP