Why doesn't RNA polymerase just rotate?

Question

I read A little help understanding DNA supercoiling , Understanding DNA supercoiling , and Why does underwinding create topological strain of DNA? , but there's still something I don't get. Transcription creates positive supercoils ahead of the RNA polymerase and negative supercoils behind it, and according to my TA's, this causes enough mechanical strain to sometimes even stop transcription from occurring. Why doesn't the polymerase just rotate around the DNA to relieve the strain?

The video below is helpful to communicate what the question is asking. The model I was taught is that the polymerase proceeds on a linear path, not a helical path, and thus the transcription bubble forces positive supercoils ahead and negative behind. The video shows this with a pen in place of the polymerase and a shoelace in place of the DNA; displacement of the pen tightens coils downstream and loosens them upstream. The way this seems to depart from reality is the desk or backdrop in the video, which keeps the pen from spinning, and the air, which offers no friction or thermal energy. In real life, the polymerase isn't a pen and the DNA isn't sitting on a desk and the surrounding medium is aqueous and of course the whole thing is at a smaller physical scale such that heat is experienced differently. But why doesn't the pen (polymerase) just spin?

https://www.youtube.com/watch?v=J4YlcD59-yw

P.S. I also looked at Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?, but I'm not sure what to take from that thread. Some answers disagree and others only mention unwinding, which afaik is a much lesser source of strain compared to the lack of rotation.

Answer 1

Consider that:

• RNA polymerase (RNAP) is a large complex (~400 kDa in bacteria); inertia and drag would hinder its rotation.
• RNAP is attached to its RNA transcript, which becomes increasingly large as transcription proceeds thus increasing inertia and drag. Additionally, if RNAP were to begin to rotate around DNA, the transcript could begin to wrap around the DNA.
• The RNA transcript is often bound by proteins/ribonucleoproteins, including ribosomes in prokaryotes (which undergo cotranscriptional translation), further increasing the complex’s size and making it more difficult to rotate.

These ideas are discussed in the original paper which proposes the “twin transcriptional loop” or “twin supercoiled domain” model to explain the observation of transcriptionally coupled DNA supercoiling:

Liu LF, Wang JC. 1987. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84(20):7024–7027.

For this model to work, the torque required to supercoil DNA, which would cause rotation of the RNAP complex, must be overcome by the frictional torque opposing rotation of said complex. A mathematical treatment in this paper estimates that RNAP itself with a modestly sized transcript and a single ribosome bound would not be sufficient to introduce significant supercoiling in dilute aqueous solution.

However, they estimate that a larger transcript with 20 ribosomes attached would have sufficient frictional torque opposing RNAP rotation to cause some supercoiling of DNA. Furthermore, the authors recognize that this model in dilute aqueous solution is not representative of actual conditions within a cell, where the presence of other macromolecules could impede RNAP rotation much more significantly than water alone.

Additionally, RNAP itself, the RNA transcript or the proteins which bind it may be physically anchored to some cellular structure during transcription. For example:

• RNAP can be bound to DNA outside of the transcription bubble through some intermediary regulatory protein
• Ribosomes translating extracellular or membrane-bound proteins are attached to the cell membrane in prokaryotes.

Such physical anchoring of the transcription complex would certainly prevent its rotation around the DNA helix.

---

It is perhaps also important to point out that cells have topoisomerases which relieve the superhelical strain generated by transcription (among other processes). If the torque on RNAP caused by supercoiling is negated by these topoisomerases, there isn’t really another force which would cause RNAP to rotate. Nevertheless, supercoiling as a result of transcription does occur in vivo and has important implications on genomic structure and gene regulation. See the following paper for a review:

Ma J, Wang MD. 2016. DNA supercoiling during transcription. Biophys Rev 8(Suppl 1):75–87.