Question

Describe the allosteric and torpedo models for transcriptional termination of RNA polymerase II. Which model is more similar to \(\rho\)-dependent termination in bacteria and which model is more similar to \(\rho\)-independent termination?

Short answer

The allosteric model involves RNA Polymerase II changing its conformation after transcribing the polyadenylation signal, which leads to termination, while the torpedo model involves termination through the activity of an exonuclease. The \(\rho\)-dependent termination process is more similar to the torpedo model, while the \(\rho\)-independent termination process is more similar to the allosteric model.

Step-by-step solution

Describe the Allosteric Model

In the allosteric model, the RNA Polymerase II changes its conformational structure as it transcribes the polyadenylation signal, leading to a reduction of processivity and ultimately ending the process of transcription.

Describe the Torpedo Model

The torpedo model proposes that an exonuclease (usually Rat1 in yeast and Xrn2 in other eukaryotes) degrades the transcript from the 5’ end once Poly(A) signal has been transcribed. This exonuclease can catch up to and dislodge the elongating polymerase if it slows down, promoting termination.

Compare with \(\rho\)-Dependent Termination

The \(\rho\)-dependent termination is more similar to the torpedo model. In \(\rho\)-dependent termination, a \(\rho\) protein in prokaryotes attaches to the RNA and moves towards the RNA polymerase, causing it to detach from the DNA and RNA, leading to termination in a manner reminiscent of the torpedo model.

Compare with \(\rho\)-Independent Termination

The \(\rho\)-independent termination process can be related to the allosteric model since it involves a change in the RNA structure (formation of stem-loop structure) to cause termination, just like conformational change in the allosteric model.