scholarly journals DNA Supercoiling Drives a Transition between Collective Modes of Gene Synthesis

2021 ◽  
Author(s):  
Purba Chatterjee ◽  
Nigel Goldenfeld ◽  
Sangjin Kim
Keyword(s):  
Deterministic Model ◽  
Molecular Machines ◽  
Dna Supercoiling ◽  
Quantitative Agreement ◽  
Gene Synthesis ◽  
Torsional Stress ◽  
Mrna Synthesis ◽  
Long Distance ◽  
Multiple Copies ◽  
Physical Barriers

Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in long-distance antagonistic interactions that drastically reduce the speed of RNAPs and cause a quick arrest of mRNA synthesis. The mechanism underlying this transition between cooperative and antagonistic dynamics remains poorly understood. In this Letter, we introduce a continuum deterministic model for the translocation of RNAPs, where the speed of an RNAP is coupled to the local DNA supercoiling as well as the density of RNAPs on the gene. We assume that torsional stress experienced by individual RNAPs is exacerbated by high RNAP density on the gene and that transcription factors act as physical barriers to the diffusion of DNA supercoils. We show that this minimal model exhibits two transcription modes mediated by the torsional stress: a fluid mode when the promoter is active and a torsionally stressed mode when the promoter is repressed, in quantitative agreement with experimentally observed dynamics of co-transcribing RNAPs. Our work provides an important step towards understanding the collective dynamics of molecular machines involved in gene expression.

scholarly journals Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

Cell ◽  
2019 ◽  
Vol 179 (1) ◽  
pp. 106-119.e16 ◽  
Author(s):  
Sangjin Kim ◽  
Bruno Beltran ◽  
Irnov Irnov ◽  
Christine Jacobs-Wagner
Keyword(s):  
Rna Polymerase ◽  
Dna Supercoiling ◽  
Long Distance

Experimental Investigation on Stochastic Crack Growth Model of GH4133B at Fatigue-Creep

2009 ◽  
Author(s):  
Dianyin Hu ◽  
Rongqiao Wang
Keyword(s):  
Experimental Data ◽  
High Temperature ◽  
Crack Growth ◽  
Room Temperature ◽  
Deterministic Model ◽  
Hold Time ◽  
Testing Machine ◽  
Crack Size ◽  
Long Distance ◽  
Crack Growth Model

Experiments on the fatigue crack growth have shown great dispersancy. Study on stochastic crack growth of material at room temperature has been widely performed. However, probabilistic model for crack growth at fatigue-creep has been little investigated due to the complexity of the deterministic model for crack growth at fatigue-creep as well as the time-consuming and the difficulty of the experiments. Traditional crack measurement such as direct current and alternating current electrical potential technique, compliance method is limited for circuit interference at large crack, especially when the temperature is higher than 500°C. Experimental system to achieve real-time FCCG detection at high temperature is established by introducing a long-distance microscope with high magnification and resolution from distances of 15cm to 35cm. The experimental setup consists of a dynamic testing machine, a machine controller, a temperature controlled box, a long-distance microscope and a high temperature furnace from room temperature to 1000°C. Then the fatigue-creep crack growth (FCCG) rate tests on thirty compact tension (CT) specimens made of GH4133B material at 600°C are carried out. The reason for choosing the GH4133B Ni-based superalloy is owing to its popularity in use for the turbine disc of the aero-engine. The tests are conducted on a 100KN capacity servo-hydraulic closed-loop machine employed trapezoidal load with hold time at upon peak load. Based on the crack growth models used for room temperature, the deterministic model for FCCG rate considering the parameters including temperature, hold time is established through comparison of the analytical results with the experimental data. Then the stochastic FCCG model for GH4133B is proposed and the probability of random to reach a specified crack size can be obtained as well as the distribution function of crack size at the service time. Through comparison between the analytical and experimental results, it’s found that the probabilistic FCCG model can fit the experimental data well. Once the stochastic FCCG model is established, it can be used for the probabilistic damage tolerance design of the turbine components made of GH4133B material.

scholarly journals BZIP Transcription Factors Modulate DNA Supercoiling Transitions

2019 ◽  
Author(s):  
Johanna Hörberg ◽  
Anna Reymer
Keyword(s):  
Transcription Factors ◽  
Conformational Changes ◽  
Molecular Motors ◽  
Specific Binding ◽  
Dna Supercoiling ◽  
Bzip Transcription Factor ◽  
Specific Response ◽  
Torsional Stress ◽  
Nucleosome Remodeling ◽  
The Impact

ABSTRACTTorsional stress on DNA, introduced by molecular motors, constitutes an important regulatory mechanism of transcriptional control. Torsional stress can modulate specific binding of transcription factors to DNA and introduce local conformational changes that facilitate the opening of promoters and nucleosome remodeling. Using all-atom microsecond scale molecular dynamics simulations together with a torsional restraint that controls the total helical twist of a DNA fragment, we addressed the impact of torsional stress on DNA complexation with a human BZIP transcription factor, MafB. We gradually over- and underwind DNA alone and in complex with MafB by 5° per dinucleotide step, monitoring the evolution of the protein-DNA contacts at different degrees of torsional strain. Our computations show that MafB changes the DNA sequence-specific response to torsional stress. The dinucleotide steps that are susceptible to absorb most of the torsional stress become more torsionally rigid, as they are involved in the protein-DNA contacts. Also, the protein undergoes substantial conformational changes to follow the stress-induced DNA deformation, but mostly maintains the specific contacts with DNA. This results in a significant asymmetric increase of free energy of DNA twisting transitions, relative to free DNA, where overtwisting is more energetically unfavorable. Our data suggest that MafB could act as a torsional stress insulator, modulating the propagation of torsional stress along the chromatin fiber, which might promote cooperative binding of other transcription factors.

scholarly journals Will reconnecting ecosystems allow long-distance mammal migrations to resume? A case study of a zebra Equus burchelli migration in Botswana

Oryx ◽  
2011 ◽  
Vol 45 (2) ◽  
pp. 210-216 ◽  
Author(s):  
H.L.A. Bartlam-Brooks ◽  
M.C. Bonyongo ◽  
Stephen Harris
Keyword(s):  
Large Scale ◽  
Long Distance ◽  
North West ◽  
Ecosystem Connectivity ◽  
Ecosystem Fragmentation ◽  
Equus Burchelli ◽  
Future System ◽  
Physical Barriers ◽  
Migratory Routes

AbstractTerrestrial wildlife migrations, once common, are now rare because of ecosystem fragmentation and uncontrolled hunting. Botswana historically contained migratory populations of many species but habitat fragmentation, especially by fences, has decreased the number and size of many of these populations. During a study investigating herbivore movement patterns in north-west Botswana we recorded a long-distance zebra Equus burchelli antiquorum migration between the Okavango Delta and Makgadikgadi grasslands, a round-trip distance of 588 km; 55% of 11 animals collared in the south-eastern peripheral delta made this journey. This was unexpected as, between 1968 and 2004, the migration could not have followed its present course because of the bisection of the route by a veterinary cordon fence. As little evidence exists to suggest that large-scale movements by medium-sized herbivores can be restored, it is of significant interest that this migration was established to the present highly directed route within 4 years of the fence being removed. The success of wildlife corridors, currently being advocated as the best way to re-establish ecosystem connectivity, relies on animals utilizing novel areas by moving between the connected areas. Our findings suggest that medium-sized herbivores may be able to re-establish migrations relatively quickly once physical barriers have been removed and that the success of future system linkages could be increased by utilizing past migratory routes.

scholarly journals Satb1integrates DNA sequence,shape, motif densityand torsional stressto differentially bind targets in nucleosome-dense regions

2018 ◽  
Author(s):  
Rajarshi P. Ghosh ◽  
Quanming Shi ◽  
Linfeng Yang ◽  
Michael P. Reddick ◽  
Tatiana Nikitina ◽  
...  
Keyword(s):  
Single Molecule ◽  
Selection Criteria ◽  
Molecular Machines ◽  
Torsional Stress ◽  
Multiple Site ◽  
Dna Interactions ◽  
Binding Motifs ◽  
Site Selectivity ◽  
A Genome ◽  
Genomic Regions

AbstractSatb1 is a genome organizer that regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout the genome. We used live-cell single molecule imaging and deep sequencing to assess determinants of Satb1 binding-site selectivity. We found that Satb1 preferentially targets nucleosome-dense regions and can directly bind consensus motifs within nucleosomes. Some genomic regions harbor multiple regularly spaced Satb1 binding motifs (typical separation ∼1 turn of the DNA helix), characterized by highly cooperative binding. The Satb1 homeodomain is dispensable for high-affinity binding but is essential for specificity. Finally, Satb1⇔DNA interactions are mechanosensitive: increasing negative torsional stress in DNA enhances Satb1 binding and Satb1 stabilizes base unpairing regions (BURs) against melting by molecular machines. The ability of Satb1 to control diverse biological programs may reflect its ability to combinatorially use multiple site selection criteria.

DNA topoisomerases: harnessing and constraining energy to govern chromosome topology

2008 ◽  
Vol 41 (1) ◽  
pp. 41-101 ◽  
Author(s):  
Allyn J. Schoeffler ◽  
James M. Berger
Keyword(s):  
Nucleic Acid ◽  
Ground State ◽  
Molecular Machines ◽  
Dna Supercoiling ◽  
Dna Topoisomerases ◽  
Chromosome Topology ◽  
Biochemical Studies ◽  
Topological State ◽  
Dna Strand ◽  
And Control

AbstractDNA topoisomerases are a diverse set of essential enzymes responsible for maintaining chromosomes in an appropriate topological state. Although they vary considerably in structure and mechanism, the partnership between topoisomerases and DNA has engendered commonalities in how these enzymes engage nucleic acid substrates and control DNA strand manipulations. All topoisomerases can harness the free energy stored in supercoiled DNA to drive their reactions; some further use the energy of ATP to alter the topology of DNA away from an enzyme-free equilibrium ground state. In the cell, topoisomerases regulate DNA supercoiling and unlink tangled nucleic acid strands to actively maintain chromosomes in a topological state commensurate with particular replicative and transcriptional needs. To carry out these reactions, topoisomerases rely on dynamic macromolecular contacts that alternate between associated and dissociated states throughout the catalytic cycle. In this review, we describe how structural and biochemical studies have furthered our understanding of DNA topoisomerases, with an emphasis on how these complex molecular machines use interfacial interactions to harness and constrain the energy required to manage DNA topology.

scholarly journals Transcription elongation through lac repressor-mediated DNA loops

2021 ◽  
Author(s):  
Wenxuan Xu ◽  
Yan Yan ◽  
Irina Artsimovitch ◽  
Nicolas Sunday ◽  
David Dunlap ◽  
...  
Keyword(s):  
Dna Supercoiling ◽  
Pause Duration ◽  
Magnetic Tweezers ◽  
Lac Repressor ◽  
Long Distance ◽  
Dna Templates ◽  
Dna Loop ◽  
Tethered Particle Motion ◽  
Dna Template ◽  
Positive Supercoiling

AbstractDuring elongation, RNA polymerase (RNAP) must navigate through proteins that decorate genomic DNA. Several of these mediate long-distance interactions via structures, such as loops, that alter DNA topology and create torsional barriers. We used the tethered particle motion (TPM) technique and magnetic tweezers to monitor transcription of DNA templates in the presence of the lac repressor (LacI) protein which could bind at two sites, one proximal to, and one distal from, the promoter. The bivalent LacI tetramer binds recognition sites (operators) with up to nanomolar affinity depending on the sequence, and the concentration of LacI was adjusted to promote binding to either one or both operators, so as to produce unlooped or looped DNA. We observed that RNAP pausing before a LacI-securing loop was determined not by the affinity of LacI for the operator, but by the order in which the elongating RNAP encountered these operators. TPM experiments showed that, independent of affinity, LacI bound at the promoter-proximal operator became a stronger roadblock when securing a loop. In contrast, LacI bound to the distal operator was a weaker roadblock in a looped configuration suggesting that RNAP might more easily displace LacI obstacles within a torsion-constrained DNA loop. Since protein junctions can efficiently block the diffusion of DNA supercoiling, these data indicate that the positive supercoiling generated ahead of a transcribing RNAP may facilitate the dissociation of a roadblock. In support of this idea, magnetic tweezers measurements indicated that pauses are shorter when RNAP encounters obstacles on positively supercoiled than on relaxed DNA. Furthermore, at similar winding levels of the DNA template, RNAP pause duration decreased with tension. These findings are significant for our understanding of transcription within the crowded and tensed nucleoid.

Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling

2011 ◽  
Vol 39 (2) ◽  
pp. 611-616 ◽  
Author(s):  
Dagmar Klostermeier
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Molecular Machines ◽  
Dna Supercoiling ◽  
Single Molecule Fret ◽  
Gyrase A ◽  
Rna Unwinding

Many complex cellular processes in the cell are catalysed at the expense of ATP hydrolysis. The enzymes involved bind and hydrolyse ATP and couple ATP hydrolysis to the catalysed process via cycles of nucleotide-driven conformational changes. In this review, I illustrate how smFRET (single-molecule fluorescence resonance energy transfer) can define the underlying conformational changes that drive ATP-dependent molecular machines. The first example is a DEAD-box helicase that alternates between two different conformations in its catalytic cycle during RNA unwinding, and the second is DNA gyrase, a topoisomerase that undergoes a set of concerted conformational changes during negative supercoiling of DNA.

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