Factor-independent termination of transcription

See also Structure of RNA Polymerase, Interactions with Promoters, Initiation and Elongation, Factor-Independent Termination of Transcription, Factor-Dependent Termination of Transcription... 

Figure 26.15 A model for factor-independent termination of transcription. 

See also trp Operon Regulation, Factor-Independent Termination of Transcription, Eukaryotic Termination of Transcription (from Chapter 28)... 

Termination of transcription in vitro is classified as to its dependence on the protein factor, rho (p). Rho-independent terminators have a characteristic structure, which features (a) A strong G-C rich stem and loop, (b) a sequence of 4-6 U residues in the RNA, which are transcribed from a corresponding stretch of As in the template. Rho-factor-depen-dent terminators are less well defined, as shown in Figure 10-8. 

Factor-dependent termination - Factor-dependent termination sites are less frequent than factor-independent termination sites, and the mechanism of factor-dependent termination is complex. The P protein, a hexamer composed of identical subunits, has been characterized as an RNA—DNA helicase (see here for more about helicases) and contains a nucleoside triphosphatase activity that is activated by binding to polynucleotides. Apparently P acts by binding to the nascent transcript at a specific site near the 3 end, when RNA polymerase has paused (Figure 26.16). Then P moves along the transcript toward the 3 end, with the helicase activity unwinding the 3 end of the transcript from the template (and/or the RNA polymerase molecule), thus causing it to be released. 

Prokaryotes use two means for terminating transcription, factor-independent and factor-dependent. Certain DNA sequences function as signals that tell the RNA polymerase to terminate transcription. The DNA of a terminator sequence encoded an inverted repeat and an adjacent stretch of uracils. Factor-dependent termination involves a terminator sequence as well as a factor or protein called rho. The mechanisms by which eukaryotes terminate transcription are poorly understood. Most eukaryotic genes are transcribed for upto several thousand base pairs beyond the actual end of the gene. The excess RNA is then cleaved from the transcript when the RNA is processed into its mature form. 

Termination sequences contain palindromes. The RNA transcript of the DNA palindrome forms a stable hairpin turn. Apparently, this structure causes the RNA polymerase to slow or stop and partially disrupts the RNA-DNA hybrid structure. In some termination sequences, referred to as p (rho)-independent termination sites, several (about six) uridine residues follow the hairpin structure. Because U-A base pair interactions are weak, the short U-A sequence promotes the dissociation of the newly synthesized RNA from the DNA strand. In p-dependent termination the p factor (an enzyme that catalyzes the ATP-dependent unwinding of RNA-DNA helices) promotes the dissociation of the RNA polymerase complex from the RNA-DNA hybrid, p binds to RNA and not to RNA polymerase. 

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 p (rho) and the other is p-independent. 

Peroxisome proliferator activated receptors (PPARs) are members of the nuclear hormone receptors superfamily of ligand-activated transcription factors that are related to retinoid, steroid and thyroid receptors. All members of this superfamily have a similar structure the amino-terminal region allows ligand-independent activation, confers con-... 

In the case of the ermK operon, the synthesis of mRNA required for ErmK is not previously achieved because of termination independent of the p factor, transcriptional attenuation, in the absence of the drag [175]. 

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