Termination factor

Termination is part of the process of transcribing RNA. In eukaryotes, a termination factor is required to release the newly made (nascent) RNA from the transcription complex. Prokaryote mRNAs often do not require a termination factor: an inverted repeat followed by a string of Us (uracils) in the mRNA template strand forms a stem-loop structure which destabilizes binding by the RNA polymerase and causes Rho-independent transcription termination. Termination is part of the process of transcribing RNA. In eukaryotes, a termination factor is required to release the newly made (nascent) RNA from the transcription complex. Prokaryote mRNAs often do not require a termination factor: an inverted repeat followed by a string of Us (uracils) in the mRNA template strand forms a stem-loop structure which destabilizes binding by the RNA polymerase and causes Rho-independent transcription termination. The most extensively studied transcriptional termination factor is the Rho protein of E. coli. The Rho protein recognizes a cytosine-rich region of the elongating mRNA, but the exact features of the recognized sequences remain unknown. Rho forms a ring-shaped hexamer and advances along the mRNA, hydrolyzing ATP, toward RNA polymerase (5' to 3' with respect to the mRNA). When the Rho protein reaches the RNA polymerase complex, transcription is terminated by dissociation of the RNA polymerase from the DNA. The structure, as well as the activity, of the Rho protein is similar to that of the F1 subunit of ATP synthase, supporting the theory that the two share an evolutionary link. The antibiotic bicyclomycin works by inhibiting Rho. Mechanisms that regulate the transcript termination in E.coli Rho-Independent termination is the most effective terminator that occurs in E.coli. Rho appears at Characteristic Sequences that have two features, U residues and rich region of GC. It starts its function by binding to a sequence called a rut site in the RNA.  After that it translocate through the RNA to catch up with the RNA polymerase.  When the RNA polymerase reach the rich GC region of the gene being transcribed, the transcribed RNA binds to itself which forming a stem-loop. This stem- loop interact with the RNA polymerase resulting in pausing the transcription. After stalling the transcript the base-paring between the U residues in RNA and the A nucleotides in the template DNA causes an unstable complementary that make the enzyme to fall off and release the new RNA transcription. Rho-Dependent termination is depending on how fast Rho can moves during the transcription to catch up with the RNA polymerase to activate the termination process. Along with Rho movement there is a transcription stop point in the DNA that help Rho to catch up with the polymerase. To initiate, Rho bind to a specific sequence in the RNA and climbing up toward RNA polymerase. After catching up with polymerase Rho tears RNA and the template DNA strand apart, so the RNA released and the transcription stopped. Rho Translocation In order to work efficiently and accurately Rho factor needs a movement pathway. Tethered tracking is thought to be the main pathway for Rho factor translocation through the RNA. During the translocation, this mechanism ensures that the subset of subunits remain sequentially cross-linked to each other by the RNA chain running between the PBS sites. The process of transcriptional termination is less well understood in eukaryotes, which have extensive post-transcriptional RNA processing. Each of the three types of eukaryotic RNA polymerase has a different termination system. Eukaryotic termination factors bind to the termination signal region and disturb RNA polymerase II as it moves by, causing it to fall off the DNA strand within the next 300 base pairs. This 300 bp region is removed during processing, before poly(A)tailing (see Polyadenylation). F Transcription termination factor Rho: a hub linking diverse physiological processes in bacteria