Xun Wang, Monford Paul Abishek N, Heung Jin Jeon, Yonho Lee, Jin He, Sankar Adhya, and Heon M. Lim

 PNAS March 5, 2019 116 (10) 4440-4445

 GENETICS

 Significance

Transcription termination by RNA polymerase in prokaryotes is well understood in contrast to similar mechanisms in higher organisms. Despite the in vitro occurrence of two types of demonstrable transcription termination events in prokaryotes at the end of transcription units, they are obscured in vivo in two ways: suppression of termination by traversing of the RNA polymerase through the termination sites when coupled to translation, or by further processing of the actual terminated RNA 3′ ends by RNases, as in eukaryotes.

Abstract

Two kinds of signal-dependent transcription termination and RNA release mechanisms have been established in prokaryotes in vitro by: (i) binding of Rho to cytidine-rich nascent RNA [Rho-dependent termination (RDT)], and (ii) the formation of a hairpin structure in the nascent RNA, ending predominantly with uridine residues [Rho-independent termination (RIT)]. As shown here, the two signals act independently of each other and can be regulated (suppressed) by translation–transcription coupling in vivo. When not suppressed, both RIT- and RDT-mediated transcription termination do occur, but ribonucleolytic processing generates defined new 3′ ends in the terminated RNA molecules. The actual termination events at the end of transcription units are masked by generation of new processed 3′ RNA ends; thus the in vivo 3′ ends do not define termination sites. We predict generation of 3′ ends of mRNA by processing is a common phenomenon in prokaryotes as is the case in eukaryotes.

See: https://www.pnas.org/content/116/10/4440

Figure 1: (A) Schematic representation of the gal operon and the neighboring gpmA gene. Signals for the two tandem transcription terminations downstream of galM were shown. The RIT signal (the terminator hairpin) is presented as a cyan hairpin structure, and the RDT signal (C-rich region) is depicted as an orange line. Numbers indicate nucleotide position from the gal transcription initiation site, +1. E probe, which hybridizes to the first 500 nucleotides of galE, was used as the probe in Northern analyses throughout this study. (B) RNA sequences from the stop codon of galM to the start codon of gpmA. The terminator hairpin sequences are presented in cyan. The stem sequences are underlined. The C-rich region sequence is shown in orange. Numbers: 4285, the third nucleotide of the galM stop codon; 4313, the 3′ end of mM1 galmRNA; 4393, the 3′ end of the C-rich region; and 4487, the first nucleotide of the gpmA start codon.