In prokaryotes, transcriptional termination is the process by which RNA polymerase stops transcribing a DNA template into RNA. There are two main mechanisms of transcriptional termination in prokaryotes: Rho-dependent termination and Rho-independent termination.

1) Rho-Dependent Termination

Rho-dependent termination involves the protein factor Rho, which is a hexameric ATP-dependent RNA helicase. The termination process begins when the RNA polymerase transcribes a specific sequence called the Rho utilization (rut) site. As the RNA transcript elongates, Rho binds to the rut site and travels along the RNA transcript in the 5’ to 3’ direction using energy from ATP hydrolysis. When the RNA polymerase encounters a pause site, it allows Rho to catch up to it. Rho then destabilizes the RNA-DNA hybrid, leading to the release of the RNA transcript and dissociation of the RNA polymerase from the DNA template.

2) Rho-Independent Termination

Rho-independent termination, also known as intrinsic termination, relies on specific sequences within the RNA transcript and does not require additional protein factors. This mechanism typically involves the formation of a hairpin structure in the nascent RNA transcript, followed by a stretch of uracil-rich sequence. As the hairpin forms, it causes the RNA polymerase to pause and eventually dissociate from the DNA template, releasing the completed RNA transcript.

Comparison of Mechanisms

Rho-dependent termination requires the Rho protein and a rut site, while Rho-independent termination relies on specific sequences within the RNA transcript. Rho-independent termination is often facilitated by a GC-rich region followed by a stretch of uracil residues, which destabilizes the RNA-DNA hybrid and leads to termination.

In summary, transcriptional termination in prokaryotes involves two main mechanisms: Rho-dependent termination, which requires the Rho protein and ATP hydrolysis, and Rho-independent termination, which relies on specific sequences within the RNA transcript to induce termination.

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