DNA-Dependent Synthesis of RNA:- Specific Sequences Signal Termination of RNA Synthesis
RNA synthesis is processive necessarily so, because if an RNA polymerase released an RNA transcript prematurely, it could not resume synthesis of the same RNA but instead would have to start over. However, an encounter with certain DNA sequences results in a pause in RNA synthesis, and at some of these sequences transcription is terminated. The process of termination is not yet well understood in eukaryotes, so our focus is again on bacteria. E. coli has at least two classes of termination signals: one class relies on a protein factor called ρ (rho) and the other is ρ-independent.
Most ρ-independent terminators have two distinguishing features. The first is a region that produces an RNA transcript with self-complementary sequences, permitting the formation of a hairpin structure centered 15 to 20 nucleotides before the projected end of the RNA strand. The second feature is a highly conserved string of three A residues in the template strand that are transcribed into U residues near the 3 end of the hairpin. When a polymerase ar rives at a termination site with this structure, it pauses (Fig. 1). Formation of the hairpin structure in the RNA disrupts several A=U base pairs in the RNA-DNA hybrid segment and may disrupt important interactions between RNA and the RNA polymerase, facilitating dis sociation of the transcript. The ρ-dependent terminators lack the sequence of repeated A residues in the template strand but usually include a CA-rich sequence called a rut (rho utilization) element. The protein associates with the RNA at specific binding sites and migrates in the 5→3 direction until it reaches the transcription complex that is paused at a termination site. Here it contributes to release of the RNA transcript. The protein has an ATP-depend ent RNA-DNA helicase activity that promotes translocation of the protein along the RNA, and ATP is hydrolyzed by ρ protein during the termination process. The detailed mechanism by which the protein promotes the release of the RNA transcript is not known.
FIGURE 1 Model for -independent termination of transcription in E. coli. RNA polymerase pauses at a variety of DNA sequences, some of which are terminators. One of two outcomes is then possible: the polymerase bypasses the site and continues on its way, or the com plex undergoes a conformational change (isomerization). In the latter case, intramolecular pairing of complementary sequences in the newly formed RNA transcript may form a hairpin that disrupts the RNA-DNA hybrid and/or the interactions between the RNA and the polymerase, resulting in isomerization. An A=U hybrid region at the 3 end of the new transcript is relatively unstable, and the RNA dissociates completely, leading to termination and dissociation of the RNA molecule. This is the usual outcome at terminators. At other pause sites, the complex may escape after the isomerization step to continue RNA synthesis.
