A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains.
A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains.
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DOI：
10.1073/pnas.2102212119
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发表时间：
2022-02-08
影响因子：
11.1
通讯作者：
Atkinson GC
中科院分区：
文献类型：
--
作者：
Kurata T;Saha CK;Buttress JA;Mets T;Brodiazhenko T;Turnbull KJ;Awoyomi OF;Oliveira SRA;Jimmy S;Ernits K;Delannoy M;Persson K;Tenson T;Strahl H;Hauryliuk V;Atkinson GC
毒素-抗毒素系统是细菌和噬菌体基因组中神秘而多样的元素。我们发现抗毒素蛋白结构域具有显着的多功能性，该结构域已经进化到可以中和数十种不同的毒素结构域。我们发现携带该结构域的抗毒素（Panacea）与其同源毒素形成复合物，表明存在直接中和机制，并且 Panacea 可以进化为仅通过两个氨基酸取代即可中和非同源和非同源毒素。这提出了该结构域可能是具有重大生物技术和医学潜力的适应性通用或半通用蛋白质中和剂的可能性。毒素-抗毒素（TA）基因对普遍存在于微生物染色体基因组和质粒以及温带噬菌体中。它们充当调节开关，毒素通过损害多种重要的细胞靶标来限制细菌和古细菌的生长，而抗毒素则抵消毒性作用。为了揭示微生物和噬菌体中以前未知的 TA 多样性，我们使用计算工具 FlaGs（用于侧翼基因）分析了基因组邻域的保守性，该工具允许高通量检测类似 TA 的操纵子。着眼于广泛但实验表征不足的抗毒素结构域 DUF4065，我们的计算机分析表明，含有 DUF4065 的蛋白质在假定的 TA 样操纵子中作为广泛分布的抗毒素成分，具有数十个具有多个不同折叠的不同毒性结构域。鉴于 DUF4065 的多功能性，我们以希腊万能治疗女神的名字命名该域 Panacea（以及包含该域的蛋白质 PanA）。我们通过实验验证了九个 PanA 中和的 TA 对。虽然大多数经过验证的 PanA 中和毒素充当翻译抑制剂或膜破坏剂，但来自伯克霍尔德氏菌原噬菌体的假定核苷酸环化酶毒素会损害转录和翻译，并诱导 RelA 依赖性核苷酸报警素 (p)ppGpp 的积累。我们发现，含有 Panacea 的抗毒素与其多种同源毒素形成复合物，这是 II 型 TA 系统采用的直接中和机制的特征。最后，通过定向进化，我们选择了可以中和非同源TA毒素的PanA变体，从而通过实验证明了这种过度混杂的抗毒素结构域的进化可塑性。
Toxin–antitoxin systems are enigmatic and diverse elements of bacterial and bacteriophage genomes. We have uncovered remarkable versatility in an antitoxin protein domain that has evolved to neutralize dozens of different toxin domains. We find that antitoxins carrying this domain—Panacea—form complexes with their cognate toxins, indicating a direct neutralization mechanism, and that Panacea can be evolved to neutralize a noncognate and nonhomologous toxin with just two amino acid substitutions. This raises the possibility that this domain could be an adaptable universal or semi-universal protein neutralizer with significant biotechnological and medical potential. Toxin–antitoxin (TA) gene pairs are ubiquitous in microbial chromosomal genomes and plasmids as well as temperate bacteriophages. They act as regulatory switches, with the toxin limiting the growth of bacteria and archaea by compromising diverse essential cellular targets and the antitoxin counteracting the toxic effect. To uncover previously uncharted TA diversity across microbes and bacteriophages, we analyzed the conservation of genomic neighborhoods using our computational tool FlaGs (for flanking genes), which allows high-throughput detection of TA-like operons. Focusing on the widespread but poorly experimentally characterized antitoxin domain DUF4065, our in silico analyses indicated that DUF4065-containing proteins serve as broadly distributed antitoxin components in putative TA-like operons with dozens of different toxic domains with multiple different folds. Given the versatility of DUF4065, we have named the domain Panacea (and proteins containing the domain, PanA) after the Greek goddess of universal remedy. We have experimentally validated nine PanA-neutralized TA pairs. While the majority of validated PanA-neutralized toxins act as translation inhibitors or membrane disruptors, a putative nucleotide cyclase toxin from a Burkholderia prophage compromises transcription and translation as well as inducing RelA-dependent accumulation of the nucleotide alarmone (p)ppGpp. We find that Panacea-containing antitoxins form a complex with their diverse cognate toxins, characteristic of the direct neutralization mechanisms employed by Type II TA systems. Finally, through directed evolution, we have selected PanA variants that can neutralize noncognate TA toxins, thus experimentally demonstrating the evolutionary plasticity of this hyperpromiscuous antitoxin domain.
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影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
影响因子：
16
作者：
Jankevicius, Gytis;Ariza, Antonio;Ahel, Marijan;Ahel, Ivan
通讯作者：
Ahel, Ivan
影响因子：
64.8
作者：
HASELTIN.WA;BLOCK, R;GILBERT, W
通讯作者：
GILBERT, W
通过混杂中间体发展出新的蛋白质 - 蛋白质相互作用特异性。
影响因子：
64.5
作者：
Aakre CD;Herrou J;Phung TN;Perchuk BS;Crosson S;Laub MT
通讯作者：
Laub MT
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ