Single-mode termination of phage transcriptions, disclosing bacterial adaptation for facilitated reinitiations

Prof. Sungchul Hohng's lab and other groups have recently found that the transcription termination mode is dual with decomposing and recycling terminations compatible at a single terminator in bacteria and budding yeast. Now, in this study by Prof. Hohng et al., the phage termination mode is discovered to be single only with decomposing termination. This reveals that the recycling termination is a bacterial gain and likely the adaptation that has been conserved at least in yeasts and possibly in all the organisms including the human.

Abstract: 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.

Online publication for Nucleic Acids Research on July 16, 2024

Article link: https://doi.org/10.1093/nar/gkae620