Centre of Excellence for Bacterial Stress Response and Persistence, Section for Functional Genomics, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
mBio. 2021 Jun 29;12(3):e0105821. doi: 10.1128/mBio.01058-21. Epub 2021 Jun 1.
Toxin-antitoxin modules function in the genetic stability of mobile genetic elements, bacteriophage defense, and antibiotic tolerance. A gain-of-function mutation of the Escherichia coli K-12 module can induce antibiotic tolerance in a subpopulation of bacterial cells, a phenomenon known as persistence. HipA is a Ser/Thr kinase that phosphorylates and inactivates glutamyl tRNA synthetase, inhibiting cellular translation and inducing the stringent response. Additional characterized HipA homologues include HipT from pathogenic E. coli O127 and YjjJ of E. coli K-12, which are encoded by tricistronic and monocistronic operons, respectively. The apparent diversity of HipA homologues in bacterial genomes inspired us to investigate overall phylogeny. Here, we present a comprehensive phylogenetic analysis of the Hip kinases in bacteria and archaea that expands on this diversity by revealing seven novel kinase families. Kinases of one family, encoded by monocistronic operons, consist of an N-terminal core kinase domain, a HipS-like domain, and a HIRAN (HIP116 Rad5p N-terminal) domain. HIRAN domains bind single- or double-stranded DNA ends. Moreover, five types of bicistronic kinase operons encode putative antitoxins with HipS-HIRAN, HipS, γδ-resolvase, or Stl repressor-like domains. Finally, our analysis indicates that reversion of gene order happened independently several times during evolution. Bacterial multidrug tolerance and persistence are problems of increasing scientific and medical significance. The first gene discovered to confer persistence was , encoding the kinase toxin of the toxin-antitoxin (TA) module of E. coli. HipA-homologous kinases phosphorylate and thereby inactivate specific tRNA synthetases, thus inhibiting protein translation and cell proliferation. Here, we present a comprehensive phylogenetic analysis of bacterial Hip kinases and discover seven new families with novel operon structures and domains. Overall, Hip kinases are encoded by TA modules with at least 10 different genetic organizations, 7 of which have not been described before. These results open up exciting avenues for the experimental analysis of the superfamily of Hip kinases.
毒素-抗毒素模块在移动遗传元件的遗传稳定性、噬菌体防御和抗生素耐药性中发挥作用。大肠杆菌 K-12 模块的功能获得性突变可以诱导细菌细胞亚群产生抗生素耐药性，这种现象称为持续存在。HipA 是一种丝氨酸/苏氨酸激酶，可使谷氨酰-tRNA 合成酶磷酸化失活，抑制细胞翻译并诱导严格反应。其他特征明确的 HipA 同源物包括致病性大肠杆菌 O127 的 HipT 和大肠杆菌 K-12 的 YjjJ，它们分别由三顺反子和单顺反子操纵子编码。细菌基因组中 HipA 同源物的明显多样性促使我们研究整体系统发育。在这里，我们对细菌和古细菌中的 Hip 激酶进行了全面的系统发育分析，通过揭示七个新的激酶家族扩展了这种多样性。一个家族的激酶，由单顺反子操纵子编码，由 N 端核心激酶结构域、HipS 样结构域和 HIRAN（HIP116 Rad5p N 端）结构域组成。HIRAN 结构域结合单链或双链 DNA 末端。此外，五种类型的双顺反子激酶操纵子编码具有 HipS-HIRAN、HipS、γδ-核酸内切酶或 Stl 阻遏物样结构域的假定抗毒素。最后，我们的分析表明，在进化过程中，基因顺序的反转独立发生了多次。细菌多药耐药性和持续存在是科学和医学意义日益增加的问题。第一个被发现赋予持续存在的基因是 ，它编码大肠杆菌 毒素-抗毒素（TA）模块的激酶毒素。HipA 同源激酶磷酸化并因此失活特定的 tRNA 合成酶，从而抑制蛋白质翻译和细胞增殖。在这里，我们对细菌 Hip 激酶进行了全面的系统发育分析，并发现了七个具有新的操纵子结构和结构域的新家族。总体而言，Hip 激酶由至少 10 种不同遗传结构的 TA 模块编码，其中 7 种以前没有描述过。这些结果为 Hip 激酶超家族的实验分析开辟了令人兴奋的途径。
