A workforce of physicists working on the intersection of principle and experiment are shedding new gentle on the “teamwork” of molecular motors — known as RNA polymerases (RNAPs) — that mediate DNA transcription. Throughout transcription, step one in gene expression, RNAPs “learn” DNA sequences and assemble messenger RNA (mRNA), which in flip serves because the template for the proteins obligatory for all times.
The workforce — comprising lead writer Purba Chatterjee , a latest Illinois Physics Ph.D. graduate, now a postdoctoral researcher at College of Pennsylvania; Illinois Physics Emeritus Analysis Professor Nigel Goldenfeld, now the Chancellor’s Distinguished Professor of Physics at College of California San Diego; and Illinois Physics Professor Sangjin Kim — introduces a brand new theoretical mannequin elucidating how the mechanism of supercoiling in DNA underlies the collective dynamics of RNAPs which might be concurrently translocating on the DNA for transcription. The RNAPs dynamics swap from cooperative to antagonistic mode, in response to the cell’s wants.
These findings had been revealed on November 16, 2021,within the article “DNA Supercoiling Drives a Transition between Collective Modes of Gene Synthesis,” within the journal Bodily Overview Letters.
Throughout transcription, DNA supercoiling happens when torsional stress is launched by the unzipping of a portion of the helix into two strands, certainly one of which can be transcribed. The researchers’ work revealed for the primary time two important components in modeling transcription underneath torsion: first, transcription elements which might be well-known to have an effect on the speed at which RNAP provoke transcription can even management the propagation of DNA supercoils, and second, the variety of RNAPs current impacts the torsional stress skilled by particular person RNAPs.
Goldenfeld explains, “Supercoiling is one thing acquainted to anybody who has wrestled with a backyard hose or, in instances previous, a phone wire. Semi-rigid tubes or, on this case, helices are tough to fold they usually bend into localized tangles — loops that may appear like determine eights or worse. Biology battles with the identical geometrical points on the DNA molecular stage inside residing cells.”
As soon as an RNAP initiates transcription, it translocates alongside the strand, assembling a complementary strand of mRNA. Further RNAPs are recruited, every RNAP initiating mRNA synthesis alongside the identical phase of DNA. The speed of the next RNAP initiations is usually managed by transcription issue, a protein that binds to the DNA website on the location the place RNAP initiates transcription.
Earlier experimental and theoretical research have predicted that the velocity at which RNAPs translocate alongside the DNA throughout transcription will increase with the variety of RNAPs actively transcribing the identical sequence, however in 2019, Kim, et al. noticed for the primary time that the velocity of RNAP translocation stays excessive so long as RNAPs provoke transcription at a price above a sure threshold, whatever the complete quantity. Surprisingly, they discovered that the variety of RNAPs affected the velocity as soon as the promoter is turned off — that’s when RNAPs cease initiating transcription. Within the present work, the workforce describes how supercoiling underlies these collective results.
The scientists modelled the organic system by which a number of RNAPs are transcribing the identical phase of DNA, with RNAP translocation velocity topic to torques generated by DNA supercoiling.
Chatterjee explains, “Our mannequin introduces two vital elements that haven’t been thought of earlier than for DNA supercoiling. First, the variety of RNAPs is vital. The extra RNAPs there are, the tougher it’s for particular person RNAPs to twist the DNA. It’s because the mass of every RNAP in addition to the mass of the mRNA being synthesized by every RNAP provides to the resistance of DNA to twisting. That is just like the real-life statement {that a} thick, heavy rubber band is tougher to twist than a skinny, gentle one.
“Second, the binding and unbinding of transcription elements on the promoter — the entry level for RNAPs — can be vital. Transcription elements not solely forestall loading of RNAPs by blocking their website of entry to the DNA, however, being cumbersome molecules, in addition they forestall the relief of DNA supercoils. Think about holding an overtwisted rubber band at each ends. While you let one finish go, it instantly unfurls to scale back the stress. Equally when transcription issue unbinds, the DNA supercoils that had been constrained between the transcription issue and the closest RNAP to the promoter diffuse, and the DNA phase returns to its relaxed state. This leisure assists the final loaded RNAP in its ahead movement.”
With these two novel concerns, the researchers discovered that DNA supercoiling produced by RNAP movement can drive the 2 contrasting modes of RNAP group dynamics. Cooperative dynamics emerge underneath situations favorable to transcription, when the promoter sequence initially of the DNA phase is “turned on.” On this mode, the mechanics of supercoiling diffusion facilitate faster transcription throughout the complete system, as a result of every RNAP cancels its nearest neighbor’s DNA supercoils successfully, resulting in optimum excessive speeds for every.
Kim provides, “Notably, the mechanics of supercoiling diffusion permit for the cancellation of supercoils for all RNAP densities, and therefore the cooperative dynamics might be noticed so long as the RNAP densities are over a sure threshold.”
Chatterjee explains, “Regardless of the associated fee related to having many RNAPs on the gene, the collective mode enhances transcription velocity. That is contingent on steady loading of RNAPs, that means there’s an lively promoter that’s loading RNAPs onto the gene uninterrupted. The continual loading of RNAPs takes place when the cell desires to make as many transcripts as potential. The cooperation between RNAPs throughout their translocation helps to perform the cell’s want.”
A swap to antagonistic dynamics, alternatively, slows translocation for all lively RNAPs — now, the a number of RNAPs transcribing a gene collectively truly impair one another’s movement and transcription is quickly shut down altogether.
Kim provides, “Whereas, within the cooperative mode, having a neighbor results in higher cancellation of supercoils and helps to scale back the torsional stress on an RNAP such that it could possibly transfer on the optimum velocity, within the antagonistic mode, having a neighbor is devastating. On this collective mode, the presence of a number of RNAPs ends in larger torsional stress and larger discount in velocity. This antagonistic mode takes place when the promoter is turned off — the entry is blocked by a transcription issue — in response to a sign to cease making transcripts.”
Chatterjee sums up, “Our theoretical mannequin helps Sangjin’s experimental statement and explains the discovering from the bodily perspective of DNA supercoiling.”
Goldenfeld provides, “Our modeling and Sangjin’s ingenious experiments reveal how the molecular machines often known as RNA polymerase primarily talk and work cooperatively within the processes that in the end result in the manufacture of proteins. This thrilling undertaking wouldn’t have been potential with out deep collaboration between theoretical modeling and experiment, and reveals how collective phenomena, already properly understood in statistical and condensed matter physics, additionally underpin probably the most basic facets of organic gene expression.”
Kim seems to be ahead to persevering with this line of analysis within the laboratory.
“There are a selection of thrilling future experiments to do,” she says. “We need to experimentally validate the 2 novel options launched within the mannequin by visualizing DNA supercoiling and measuring the DNA resisting torques instantly. Particularly, we need to check the impact of transcription elements on transcription effectivity by the blocking of DNA supercoil diffusion and measure the impact of the presence of a number of RNAPs on the restoring torque skilled by a person RNAP.”
This work was supported by the Nationwide Science Basis, the Nationwide Institutes of Well being, the Searle Students Program, and a Drickamer Analysis Fellowship of the College of Illinois Urbana-Champaign’s Division of Physics. The conclusions introduced are these of the researchers and never essentially these of the funding companies.
