Nanobiology of RNA polymerase: biological consequence of inhomogeneity in reactant

Single-molecule evidence for a chemical ratchet in binding between the cam repressor and its operator

The affinity for regulator-operator binding on DNA sometimes depends on the length of the DNA harboring the operator, which is known as the antenna effect. One-dimensional diffusion along DNA has been suggested to be the cause, but this may contradict the binding affinity independent of the reaction pathways, which is derived from the detailed balance of the reaction at equilibrium. Recently, the chemical ratchet was proposed to solve this contradiction by suggesting a stationary state containing microscopic non-equilibrium. In a single-molecule observation, P. putida CamR molecules associate with their operator via one-dimensional diffusion along the DNA, while they mostly dissociated from the operator without the diffusion. Consistently, the observed overall association rate was dependent on the DNA length, while the overall dissociation rate was not, leading to an antenna effect. E. coli RNA polymerase did not show this behavior, and thus it is a specific property of a protein. The bipartite interaction domains containing the helix-turn-helix motif are speculated to be one of the possible causes. The biological significance of the chemical ratchet and a model for its microscopic mechanism are also discussed.

Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics

The review is devoted to a new and rapidly developing area related to the application of ideas and methods of nonlinear mathematics and theoretical physics to study the internal dynamics of DNA and, in particular, the behavior of the open states of DNA. There are two main competing approaches to this research. The first approach is based on the molecular dynamics method, which takes into account the motions of all structural elements of the DNA molecule and all interactions between them. The second approach is based on prior selection of the main (dominant) motions and their mathematical description using a small number of model equations. This review describes the results of the study of the open states of DNA performed within the framework of the second approach using the McLaughlin-Scott equation. We present the results obtained both in the case of homogeneous sequences: poly (A), poly (T), poly (G) and poly (C), and in the inhomogeneous case when the McLaughlin-Scott equation has been used for studying the dynamics of open states activated in the promoters A1, A2 and A3 of the bacteriophage T7 genome, in the genes IFNA17, ADRB2, NOS1 and IL-5, in the pBR322 and pTTQ18 plasmids. Particular attention is paid to the results concerning the effect of various external fields on the behavior of open states. In the concluding part of the review, new possibilities and prospects for the development of the considered approach and especially of the McLaughlin-Scott equation are discussed.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12551-021-00801-0.

Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach

The time spent by a single RNA polymerase (RNAP) at specific locations along the DNA, termed "residence time," reports on the initiation, elongation, and termination stages of transcription. At the single-molecule level, this information can be obtained from dual ultrastable optical trapping experiments, revealing a transcriptional elongation of RNAP interspersed with residence times of variable duration. Successfully discriminating between long and short residence times was used by previous approaches to learn about RNAP's transcription elongation dynamics. Here, we propose an approach based on the Bayesian sticky hidden Markov model that treats all residence times for an Escherichia coli RNAP on an equal footing without a priori discriminating between long and short residence times. Furthermore, our method has two additional advantages: we provide full distributions around key point statistics and directly treat the sequence dependence of RNAP's elongation rate. By applying our approach to experimental data, we find assigned relative probabilities on long versus short residence times, force-dependent average residence time transcription elongation dynamics, ∼10% drop in the average backtracking durations in the presence of GreB, and ∼20% drop in the average residence time as a function of applied force in the presence of RNaseA.

RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions

The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate equations are commonly used to describe reactions involved in transcription, but they tend to be used unaware of the timescales of relevant physical processes. In this review, we discuss the limitation of rate equation for describing three-dimensional diffusion and one-dimensional diffusion along DNA. We then introduce the chemical ratchet mechanism recently proposed for explaining the antenna effect, an enhancement of the binding affinity to a specific site on longer DNA, which deviates from a thermodynamic rule. We show that chemical ratchet cannot be described with a single set of rate equations but alternative sets of rate equations that temporally switch no faster than the binding reaction.

Gre factors prevent thermal and mechanical stresses induced by terahertz irradiation during transcription

During transcription in cells, the transcription complex consisting of RNA polymerase, DNA and nascent RNA is exposed to fluctuating temperature and pressure. However, little is known about the mechanism of transcriptional homeostasis under fluctuating physical parameters. In this study, we generated these fluctuating parameters using pulsed local heating and acoustic waves in the reaction system of transcription by Escherichia coli RNA polymerase, using a terahertz free-electron laser. We demonstrated that transcription processes, including abortive initiation and elongation pausing, and the fidelity of elongation are significantly affected by the laser-based local perturbations. We also found that all these functional alternations in the transcription process are almost completely mitigated by the presence of Gre proteins. It is well known that Gre proteins enhance RNA cleavage of polymerase by binding to the pore structure termed secondary channel. Recently, the chaperone activities have also been proposed for Gre proteins, yet the details directly associated with transcription are largely unknown. Our finding indicates that Gre proteins are necessary for maintaining transcriptional homeostasis under thermal and mechanical stresses.

Dependence of DNA length on binding affinity between TrpR and trpO of DNA

We scrutinize the length dependency of the binding affinity of bacterial repressor TrpR protein to trpO (specific site) on DNA. A footprinting experiment shows that the longer the DNA length, the larger the affinity of TrpR to the specific site on DNA. This effect termed “antenna effect” might be interpreted as follows: longer DNA provides higher probability for TrpR to access to the specific site aided by one-dimensional diffusion along the nonspecific sites of DNA. We show that, however, the antenna effect cannot be explained while detailed balance holds among three kinetic states, that is, free protein/DNA, nonspecific complexes, and specific complex. We propose a working hypothesis that slow degree(s) of freedom in the system switch(es) different potentials of mean force causing transitions among the three states. This results in a deviation from detailed balance on the switching timescale. We then derive a simple reaction diffusion/binding model that describes the antenna effect on TrpR binding to its target operator. Possible scenarios for such slow degree(s) of freedom in TrpR–DNA complex are addressed.

Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences

In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences, when enriched with thymine bases, contain the signal for inducing abortive transcription, whereas certain repetitive sequence elements embedded in promoter regions constitute the signal for inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we suggest that repetitive sequence elements within the promoter DNA modulate the nonlocal base pair stability of its double-stranded form. This stability profoundly influences the reaction coordinates of the productive initiation via pausing.

The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase

Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation.

The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase

RNA polymerase can cleave a phosphodiester bond at the 3' end of a nascent RNA in the presence of pyrophosphate producing NTP. Pyrophosphorolysis has been characterized during elongation steps of transcription where its rate is significantly slower than the forward rate of NMP addition. In contrast, we report here that pyrophosphorolysis can occur in a millisecond time scale during the transition of Escherichia coli RNA polymerase from initiation to elongation at the psbA2 promoter. This rapid pyrophosphorolysis occurs during productive RNA synthesis as opposed to abortive RNA synthesis. Dissociation of σ⁷⁰ or RNA extension beyond nine nucleotides dramatically reduces the rate of pyrophosphorolysis. We argue that the rapid pyrophosphorolysis allows iterative cycles of cleavage and re-synthesis of the 3' phosphodiester bond by the productive complexes in the early stage of transcription. This iterative process may provide an opportunity for the σ⁷⁰ to dissociate from the RNA exit channel of the enzyme, enabling RNA to extend through the channel.

Transcription pausing: biological significance of thermal fluctuations biased by repetitive genomic sequences

Transcription of DNA by RNA polymerase (RNAP) takes place in a cell environment dominated by thermal fluctuations. How are transcription reactions including initiation, elongation, and termination on genomic DNA so well-controlled during such fluctuations? A recent statistical mechanical approach using high-throughput sequencing data reveals that repetitive DNA sequence elements embedded into a genomic sequence provide the key mechanism to functionally bias the fluctuations of transcription elongation complexes. In particular, during elongation pausing, such repetitive sequence elements can increase the magnitude of one-dimensional diffusion of the RNAP enzyme on the DNA upstream of the pausing site, generating a large variation in the dwell times of RNAP pausing under the control of these genomic signals.

Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences

In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing. This effect stems from the increased microscopic heterogeneity of an elongation complex, and thus is entropy-dominated. This report shows a linkage between repetitive sequence elements encoded in the genome and regulation of RNAP pausing driven by thermal fluctuations.

Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications

Regulation of transcription elongation via pausing of RNA polymerase has multiple physiological roles. The pausing mechanism depends on the sequence heterogeneity of the DNA being transcribed, as well as on certain interactions of polymerase with specific DNA sequences. In order to describe the mechanism of regulation, we introduce the concept of heterogeneity into the previously proposed alternative models of elongation, power stroke and Brownian ratchet. We also discuss molecular origins and physiological significances of the heterogeneity.

Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis

In addition to RNA synthesis, multisubunit RNA polymerases (msRNAPs) support enzymatic reactions such as intrinsic transcript cleavage. msRNAP active sites from different species appear to exhibit differential intrinsic transcript cleavage efficiency and have likely evolved to allow fine-tuning of the transcription process. Here we show that a single amino-acid substitution in the trigger loop (TL) of Saccharomyces RNAP II, Rpb1 H1085Y, engenders a gain of intrinsic cleavage activity where the substituted tyrosine appears to participate in acid-base chemistry at alkaline pH for both intrinsic cleavage and nucleotidyl transfer. We extensively characterize this TL substitution for each of these reactions by examining the responses RNAP II enzymes to catalytic metals, altered pH, and factor inputs. We demonstrate that TFIIF stimulation of the first phosphodiester bond formation by RNAP II requires wild type TL function and that H1085Y substitution within the TL compromises or alters RNAP II responsiveness to both TFIIB and TFIIF. Finally, Mn(2+) stimulation of H1085Y RNAP II reveals possible allosteric effects of TFIIB on the active center and cooperation between TFIIB and TFIIF.

Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo

BACKGROUND

Transcription elongation is frequently interrupted by pausing signals in DNA, with downstream effects on gene expression. Transcription errors also induce prolonged pausing, which can lead to a destabilized genome by interfering with DNA replication. Mechanisms of pausing associated with translocation blocks and misincorporation have been characterized in vitro, but not in vivo.

RESULTS

We investigate the pausing pattern of RNA polymerase (RNAP) in Escherichia coli by a novel approach, combining native elongating transcript sequencing (NET-seq) with RNase footprinting of the transcripts (RNET-seq). We reveal that the G-dC base pair at the 5' end of the RNA-DNA hybrid interferes with RNAP translocation. The distance between the 5' G-dC base pair and the 3' end of RNA fluctuates over a three-nucleotide width. Thus, the G-dC base pair can induce pausing in post-translocated, pre-translocated, and backtracked states of RNAP. Additionally, a CpG sequence of the template DNA strand spanning the active site of RNAP inhibits elongation and induces G-to-A errors, which leads to backtracking of RNAP. Gre factors efficiently proofread the errors and rescue the backtracked complexes. We also find that pausing events are enriched in the 5' untranslated region and antisense transcription of mRNA genes and are reduced in rRNA genes.

CONCLUSIONS

In E. coli, robust transcriptional pausing involves RNAP interaction with G-dC at the upstream end of the RNA-DNA hybrid, which interferes with translocation. CpG DNA sequences induce transcriptional pausing and G-to-A errors.