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1. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases

   https://doi.org/10.1093/nar/gkab1252  

   Tripathi, Shubham ; Brahmachari, Sumitabha ; Onuchic, José N. ; Levine, Herbert ( December 2021 , Nucleic Acids Research)

   Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.

    

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2. An Accurate and Stable Filtered Explicit Scheme for Biopolymerization Processes in the Presence of Perturbations

   Davis, L. ( November 2021 , Applied and computational mathematics)

   The focus of this paper is the development, numerical simulation and parameter analysis of a model of the transcription of ribosomal RNA in highly transcribed genes. Inspired by the well-known classic Lighthill-Whitham-Richards (LWR) traffic flow model, a linear advection continuum model is used to describe the DNA transcription process. In this model, elongation velocity is assumed to be essentially constant as RNA polymerases move along the strand through different phases of gene transcription. One advantage of using the linear model is that it allows one to quantify how small perturbations in elongation velocity and inflow parameters affect important biology measures such as Average Transcription Time (ATT) for the gene. The ATT per polymerase is the amount of time an individual RNAP spends traveling through the DNA strand. The numerical treatment for model simulations includes introducing a low complexity and time accurate method by adding a simple linear time filter to the classic upwind scheme. This improved method is modular and requires a minimal modification of adding only one line of code resulting in increased accuracy without increased computational expense. In addition, it removes the overdamping of upwind. A stability condition for the new algorithm is derived, and numerical computations illustrate stability and convergence of the filtered scheme as well as improved ATT estimation. 

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3. Transcription factor regulation of RNA polymerase’s torque generation capacity

   https://doi.org/10.1073/pnas.1807031116  

   Ma, Jie ; Tan, Chuang ; Gao, Xiang ; Fulbright, Jr., Robert M. ; Roberts, Jeffrey W. ; Wang, Michelle D. ( February 2019 , Proceedings of the National Academy of Sciences)

   During transcription, RNA polymerase (RNAP) supercoils DNA as it translocates. The resulting torsional stress in DNA can accumulate and, in the absence of regulatory mechanisms, becomes a barrier to RNAP elongation, causing RNAP stalling, backtracking, and transcriptional arrest. Here we investigate whether and how a transcription factor may regulate both torque-inducedEscherichia coliRNAP stalling and the torque generation capacity of RNAP. Using a unique real-time angular optical trapping assay, we found that RNAP working against a resisting torque was highly prone to extensive backtracking. We then investigated transcription in the presence of GreB, a transcription factor known to rescue RNAP from the backtracked state. We found that GreB greatly suppressed RNAP backtracking and remarkably increased the torque that RNAP was able to generate by 65%, from 11.2 pN⋅nm to 18.5 pN·nm. Variance analysis of the real-time positional trajectories of RNAP after a stall revealed the kinetic parameters of backtracking and GreB rescue. These results demonstrate that backtracking is the primary mechanism by which torsional stress limits transcription and that the transcription factor GreB effectively enhances the torsional capacity of RNAP. These findings suggest a broader role for transcription factors in regulating RNAP functionality and elongation.

    

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4. The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in Acinetobacter baumannii: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication

   https://doi.org/10.1128/mBio.01127-19  

   Geisinger, Edward ; Vargas-Cuebas, Germán ; Mortman, Nadav J. ; Syal, Sapna ; Dai, Yunfei ; Wainwright, Elizabeth L. ; Lazinski, David ; Wood, Stephen ; Zhu, Zeyu ; Anthony, Jon ; et al ( June 2019 , mBio)

   Miller, Samuel I. (Ed.)

   ABSTRACT The emergence of fluoroquinolone resistance in nosocomial pathogens has restricted the clinical efficacy of this antibiotic class. In Acinetobacter baumannii , the majority of clinical isolates now show high-level resistance due to mutations in gyrA (DNA gyrase) and parC (topoisomerase IV [topo IV]). To investigate the molecular basis for fluoroquinolone resistance, an exhaustive mutation analysis was performed in both drug-sensitive and -resistant strains to identify loci that alter ciprofloxacin sensitivity. To this end, parallel fitness tests of over 60,000 unique insertion mutations were performed in strains with various alleles in genes encoding the drug targets. The spectra of mutations that altered drug sensitivity were found to be similar in the drug-sensitive and gyrA parC double-mutant backgrounds, having resistance alleles in both genes. In contrast, the introduction of a single gyrA resistance allele, resulting in preferential poisoning of topo IV by ciprofloxacin, led to extreme alterations in the insertion mutation fitness landscape. The distinguishing feature of preferential topo IV poisoning was enhanced induction of DNA synthesis in the region of two endogenous prophages, with DNA synthesis associated with excision and circularization of the phages. Induction of the selective DNA synthesis in the gyrA background was also linked to heightened prophage gene transcription and enhanced activation of the mutagenic SOS response relative to that observed in either the wild-type (WT) or gyrA parC double mutant. Therefore, the accumulation of mutations that result in the stepwise evolution of high ciprofloxacin resistance is tightly connected to modulation of the SOS response and endogenous prophage DNA synthesis. IMPORTANCE Fluoroquinolones have been extremely successful antibiotics due to their ability to target multiple bacterial enzymes critical to DNA replication, the topoisomerases DNA gyrase and topo IV. Unfortunately, mutations lowering drug affinity for both enzymes are now widespread, rendering these drugs ineffective for many pathogens. To undermine this form of resistance, we examined how bacteria with target alterations differentially cope with fluoroquinolone exposures. We studied this problem in the nosocomial pathogen A. baumannii , which causes drug-resistant life-threatening infections. Employing genome-wide approaches, we uncovered numerous pathways that could be exploited to raise fluoroquinolone sensitivity independently of target alteration. Remarkably, fluoroquinolone targeting of topo IV in specific mutants caused dramatic hyperinduction of prophage replication and enhanced the mutagenic DNA damage response, but these responses were muted in strains with DNA gyrase as the primary target. This work demonstrates that resistance evolution via target modification can profoundly modulate the antibiotic stress response, revealing potential resistance-associated liabilities. 

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5. Alternative transcription cycle for bacterial RNA polymerase

   https://doi.org/10.1038/s41467-019-14208-9  

   Harden, Timothy T. ; Herlambang, Karina S. ; Chamberlain, Mathew ; Lalanne, Jean-Benoît ; Wells, Christopher D. ; Li, Gene-Wei ; Landick, Robert ; Hochschild, Ann ; Kondev, Jane ; Gelles, Jeff ( January 2020 , Nature Communications)

   RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. Here we use single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remains bound to DNA and sometimes exhibits one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarts transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this secondary initiation in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.

    

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