Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF

Watson, George D.; Chan, Elliot W.; Leake, Mark C.; Noy, Agnes

doi:10.1016/j.csbj.2022.09.020

Cited by 12 publications

(14 citation statements)

References 80 publications

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“…DNA molecules were implicitly solvated using a generalised Born model, salt concentration 0.2M with GBneck2 corrections, mbondi3 Born radii set and no cutoff for better reproduction of molecular surfaces, salt bridges and solvation forces. Langevin dynamics was employed using similar temperature regulation as above with collision frequency 0.01 ps to reduce solvent viscosity 81 . The BSC1 forcefield was used to represent the DNA molecule 70 .…”

Section: Discussionmentioning

confidence: 99%

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Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA

Shepherd,

Guilbaud,

Zhou

et al. 2024

Preprint

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Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.

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Section: Discussionmentioning

confidence: 99%

“…molecular surfaces, salt bridges and solvation forces. Langevin dynamics was employed using similar temperature regulation as above with collision frequency 0.01 ps to reduce solvent viscosity 81 . The BSC1 forcefield was used to represent the DNA molecule 70 .…”

Section: Determination Of Bubbles In Silicomentioning

confidence: 99%

Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA

Shepherd,

Guilbaud,

Zhou

et al. 2024

Preprint

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“…In support of this hypothesis, inhibition of negative DNA supercoiling by the DNA gyrase inhibitor novobiocin decreases the ability of datA to repress replication initiation in vivo . IHF preferentially binds to curved DNA rather than to straight-shaped DNA ( Watson et al, 2022 ). (3) Transcription of datA , i.e., the minimal region of datA required for full DDAH activity is located at the intergenic region downstream of the tRNA-Gly ( glyV-X-Y ) operon and queG gene ( Figure 2 ; Kitagawa et al, 1996 ; Kasho and Katayama, 2013 ), which enables a hypothesis that datA -IHF binding/dissociation is regulated by transcription of the datA locus.…”

Section: Introductionmentioning

confidence: 99%

Read-through transcription of tRNA underlies the cell cycle-dependent dissociation of IHF from the DnaA-inactivating sequence datA

Kasho,

Sakai,

Ito

et al. 2024

Front. Microbiol.

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Timely initiation of chromosomal protect DNA replication in Escherichia coli is achieved by cell cycle-coordinated regulation of the replication origin, oriC, and the replication initiator, ATP-DnaA. Cellular levels of ATP-DnaA increase and peak at the time for initiation at oriC, after which hydrolysis of DnaA-bound ATP causes those to fall, yielding initiation-inactive ADP-DnaA. This hydrolysis is facilitated by the chromosomal locus datA located downstream of the tRNA-Gly (glyV-X-Y) operon, which possesses a cluster of DnaA-binding sequences and a single binding site (IBS) for the DNA bending protein IHF (integration host factor). While IHF binding activates the datA function and is regulated to occur specifically at post-initiation time, the underlying regulatory mechanisms remain obscure. Here, we demonstrate that datA-IHF binding at pre-initiation time is down-regulated depending on the read-through transcription of datA IBS initiated at the glyV-X-Y promoter. During the cell cycle, the level of read-through transcription, but not promoter activity, fluctuated in a manner inversely related to datA-IHF binding. Transcription from the glyV-X-Y promoter was predominantly interrupted at datA IBS by IHF binding. The terminator/attenuator sequence of the glyV-X-Y operon, as well as DnaA binding within datA overall, contributed to attenuation of transcription upstream of datA IBS, preserving the timely fluctuation of read-through transcription. These findings provide a mechanistic insight of tRNA transcription-dependent datA-IHF regulation, in which an unidentified factor is additionally required for the timely datA-IHF dissociation, and support the significance of datA for controlling the cell cycle progression as a connecting hub of tRNA production and replication initiation.

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“…To this end, we built linear DNA molecules of 300 bp with a randomly generated sequence containing an AT percentage of 49% and different values of σ. The DNA molecules were modeled using Amber18 [25], BSC1 force field [26] and the implicit generalized Born model with GBneck2 corrections [27,28] at a salt concentration of 0.2 M following our latest protocols [29,30]. After minimization and thermalization, we performed an equilibration step of 40 ns with restraints on the canonical bp hydrogen bonds to avoid the premature disruption of the double helix, allowing re-distribution of twist and writhe [30].…”

mentioning

confidence: 99%

“…The DNA molecules were modeled using Amber18 [25], BSC1 force field [26] and the implicit generalized Born model with GBneck2 corrections [27,28] at a salt concentration of 0.2 M following our latest protocols [29,30]. After minimization and thermalization, we performed an equilibration step of 40 ns with restraints on the canonical bp hydrogen bonds to avoid the premature disruption of the double helix, allowing re-distribution of twist and writhe [30]. Then, the systems were modeled under a series of restraints in order to maintain the torsional stress and to apply a constant pulling force (see Supplementary Material and Figure S1).…”

mentioning

confidence: 99%

Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA

Burman

Noy

2023

Preprint

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Although the response of DNA to physiological torsion and tension is well characterized, the detailed structures are not known yet. By using molecular dynamics simulations on linear DNA with 300 bp, we provide, for the first time, the conformational phase diagram at atomic resolution. Our simulations reveal a novel state in negative supercoiling, where denaturation bubbles form in AT-rich regions independently of the underlying DNA topology, focusing at the tip of plectonemes only when tension is applied. We propose these sequence-dependent bubbles could position plectonemes in longer DNA.

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Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF

Cited by 12 publications

References 80 publications

Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA

Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA

Read-through transcription of tRNA underlies the cell cycle-dependent dissociation of IHF from the DnaA-inactivating sequence datA

Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA

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