Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea.
Department of Biological Sciences, and KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
Nucleic Acids Res. 2024 Aug 27;52(15):9092-9102. doi: 10.1093/nar/gkae620.
Bacterial and bacteriophage RNA polymerases (RNAPs) have divergently evolved and share the RNA hairpin-dependent intrinsic termination of transcription. Here, we examined phage T7, T3 and SP6 RNAP terminations utilizing the single-molecule fluorescence assays we had developed for bacterial terminations. We discovered the phage termination mode or outcome is virtually single with decomposing termination. Therein, RNAP is displaced forward along DNA and departs both RNA and DNA for one-step decomposition, three-dimensional diffusion and reinitiation at any promoter. This phage displacement-mediated decomposing termination is much slower than readthrough and appears homologous with the bacterial one. However, the phage sole mode of termination contrasts with the bacterial dual mode, where both decomposing and recycling terminations occur compatibly at any single hairpin- or Rho-dependent terminator. In the bacterial recycling termination, RNA is sheared from RNA·DNA hybrid, and RNAP remains bound to DNA for one-dimensional diffusion, which enables facilitated recycling for reinitiation at the nearest promoter located downstream or upstream in the sense or antisense orientation. Aligning with proximity of most terminators to adjacent promoters in bacterial genomes, the shearing-mediated recycling termination could be bacterial adaptation for the facilitated reinitiations repeated at a promoter for accelerated expression and coupled at adjoining promoters for coordinated regulation.
细菌和噬菌体 RNA 聚合酶 (RNAP) 已经发生了分歧进化，并具有 RNA 发夹依赖性转录内在终止的共同特征。在这里，我们利用我们为细菌终止开发的单分子荧光测定法研究了噬菌体 T7、T3 和 SP6 的 RNAP 终止。我们发现噬菌体的终止模式或结果几乎是单一的，即分解终止。在此过程中，RNAP 沿 DNA 向前移位，并从 RNA 和 DNA 一步分解、三维扩散和在任何启动子处重新起始。这种噬菌体位移介导的分解终止比通读慢得多，与细菌的终止方式相似。然而，噬菌体的终止方式与细菌的双重终止方式形成对比，在任何单个发夹或 Rho 依赖性终止子处，这两种终止方式都可以兼容地发生。在细菌的回收终止中，RNA 从 RNA·DNA 杂交体上被剪切，RNAP 仍然与 DNA 结合进行一维扩散，这使得在下游或上游的最接近的启动子处进行重新起始变得更容易，无论是在正向还是反向。与细菌基因组中大多数终止子与相邻启动子的接近程度相一致，剪切介导的回收终止可能是细菌的一种适应机制，通过这种机制，在启动子处进行重复的快速起始和在相邻启动子处进行协调调节。
