Multi-exponential DNA Residence Behaviors of Transcription Factors Under The Discrete Affinity Model DOI Creative Commons
Zafer Koşar, Aykut Erbaş

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 23, 2023

The transcription process is regulated by temporal interactions of factors with DNA. In the last decade, computational and experimental studies revealed residence times on DNA correlate transcriptional output. Biochemical suggest that factor bindings exhibit bi-exponential dynamics, often explained binary affinity model composed nonspecific specific protein-DNA interactions. Recently, were shown to display a power law in vivo implicating effective controlling dissociation kinetics are rather more complex than suggested. One contribution can cause such continuous residence-time distributions could be higher-order complexes or protein coacervates. Here, using molecular dynamics simulations coarse-grained polymer for bacterial chromosomes interacting homodimeric at physiologically relevant concentrations, we demonstrate time dimeric proteins follow multi-exponential pattern even when single interaction describes between protein. Our reveal this emergent behavior due formation DNA-protein clusters various sizes wide range concentrations affinities. These findings add another layer regulation and, consequently, gene expression connecting affinities, clusters, factors.

Language: Английский

Multiple Omics Analyses Reveal Activation of Nitrogen Metabolism and Flavonoid Glycosylation in Toxicodendron vernicifluum Under High Temperature DOI Creative Commons
Guoqing Bai,

Ruiwen Ding,

Qi Su

et al.

Biology, Journal Year: 2024, Volume and Issue: 13(11), P. 876 - 876

Published: Oct. 28, 2024

Lacquer trees (

Language: Английский

Citations

0
Native Australian seedlings exhibit novel strategies to acclimate to repeated heatwave events DOI Creative Commons
Philippa R. Alvarez, Rosalie J. Harris, Alicia M. Cook

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 19, 2024

Abstract 1. Heatwaves are becoming more intense and frequent. Plant photosystem thermal thresholds can vary with species, but also shift in response to environmental triggers. Both upper lower acclimate repeated heatwaves through ecological stress memory, where prior exposure primes them for subsequent events. The extent which acclimation heat events varies among origin and/or species is unknown. Different strategies might reflect biome of origin, or may be species-specific. 2. For 12 from two contrasting biomes – extreme desert benign coastal temperate we investigated responses simulated heatwaves, via shifts critical temperatures II, the difference between these thresholds, tolerance breadth (TTB). 3. Biome had no effect on tolerance. Observed differences following suggested possible acclimatory strategies. In some cases, increased during first heatwave, at cost reduced second a sprinter strategy. Other acclimated heatwave further indicative marathoner 4. Synthesis: These among-species could suggest distinct vulnerabilities resilience repeat events, having limited capacity tolerate consecutive possibly as too great, other advantage helping survive future stress, least short-term.

Language: Английский

Citations

0
Multi-exponential DNA Residence Behaviors of Transcription Factors Under The Discrete Affinity Model DOI Creative Commons
Zafer Koşar, Aykut Erbaş

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 23, 2023

The transcription process is regulated by temporal interactions of factors with DNA. In the last decade, computational and experimental studies revealed residence times on DNA correlate transcriptional output. Biochemical suggest that factor bindings exhibit bi-exponential dynamics, often explained binary affinity model composed nonspecific specific protein-DNA interactions. Recently, were shown to display a power law in vivo implicating effective controlling dissociation kinetics are rather more complex than suggested. One contribution can cause such continuous residence-time distributions could be higher-order complexes or protein coacervates. Here, using molecular dynamics simulations coarse-grained polymer for bacterial chromosomes interacting homodimeric at physiologically relevant concentrations, we demonstrate time dimeric proteins follow multi-exponential pattern even when single interaction describes between protein. Our reveal this emergent behavior due formation DNA-protein clusters various sizes wide range concentrations affinities. These findings add another layer regulation and, consequently, gene expression connecting affinities, clusters, factors.

Language: Английский

Citations

0