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

A review of changes at the phenotypic, physiological, biochemical, and molecular levels of plants due to high temperatures DOI

Que Wang,

Yaqiong Wu, Wenlong Wu

et al.

Planta, Journal Year: 2024, Volume and Issue: 259(3)

Published: Feb. 3, 2024

Language: Английский

Citations

18
Heavy metal stress and mitogen activated kinase transcription factors in plants: Exploring heavy metal‐ROS influences on plant signalling pathways DOI
Lee‐Ann Niekerk, Arun Gokul, Gerhard Basson

et al.

Plant Cell & Environment, Journal Year: 2024, Volume and Issue: 47(8), P. 2793 - 2810

Published: April 23, 2024

Due to their stationary nature, plants are exposed a diverse range of biotic and abiotic stresses, which heavy metal (HM) stress poses one the most detrimental targeting plant processes. HMs instigate overproduction reactive oxygen species (ROS), mitigate adverse effects ROS, induce multiple defence mechanisms. Besides negative implications these molecules play multitude signalling roles in plants, acting as central player complex network cells. One ROS-associated mechanisms is mitogen-activated protein kinase (MAPK) cascade, pathway transduces extracellular stimuli into intracellular responses. Plant MAPKs have been implicated involved response, phytohormone regulation, cell cycle cues. However, influence various on MAPK activation has not well documented. In this review, we address summarise several aspects related HM-induced ROS signalling. Additionally, touch how signals activate cascade downstream transcription factors that responses HMs. Moreover, propose workflow could characterise genes associated with during HM

Language: Английский

Citations

18
The complex transcriptional regulation of heat stress response in maize DOI Creative Commons

Mingxiu Ruan,

Heng Zhao,

Yujing Wen

et al.

Stress Biology, Journal Year: 2024, Volume and Issue: 4(1)

Published: April 26, 2024

As one of the most important food and feed crops worldwide, maize suffers much more tremendous damages under heat stress compared to other plants, which seriously inhibits plant growth reduces productivity. To mitigate heat-induced adapt high temperature environment, plants have evolved a series molecular mechanisms sense, respond temperatures stress. In this review, we summarized recent advances in regulations underlying sensing, response memory maize, especially focusing on several pathways signals complex transcriptional regulation ZmHSFs (Heat Shock Factors) response. addition, highlighted interactions between epigenetic factors coordinately regulating memory. Finally, laid out strategies systematically elucidate regulatory network response, discussed approaches for breeding future heat-tolerance maize.

Language: Английский

Citations

9
Exploring the interplay between angiosperm chlorophyll metabolism and environmental factors DOI Creative Commons

Shunyuan Yong,

Qian Chen, Fan Xu

et al.

Planta, Journal Year: 2024, Volume and Issue: 260(1)

Published: June 11, 2024

Abstract Main conclusion In this review, we summarize how chlorophyll metabolism in angiosperm is affected by the environmental factors: light, temperature, metal ions, water, oxygen, and altitude. The significance of (Chl) plant leaf morphogenesis photosynthesis cannot be overstated. Over time, researchers have made significant advancements comprehending biosynthetic pathway Chl angiosperms, along with pivotal enzymes genes involved process, particularly those related to heme synthesis light-responsive mechanisms. Various factors influence stability content angiosperms modulating metabolic pathways. Understanding interplay between plants has been a prominent research topic. This review mainly focuses on provides an overview regulatory mechanisms governing metabolism, impact such as ions (iron magnesium), altitude metabolism. these effects crucial for preserving homeostasis

Language: Английский

Citations

4
Plant Thermosensors DOI
Jorge J. Casal, Germán Murcia, Luciana Bianchimano

et al.

Annual Review of Genetics, Journal Year: 2024, Volume and Issue: 58(1), P. 135 - 158

Published: July 10, 2024

Plants are exposed to temperature conditions that fluctuate over different time scales, including those inherent global warming. In the face of these variations, plants sense adjust their functions and minimize negative consequences. Transcriptome responses underlie changes in growth, development, biochemistry (thermomorphogenesis acclimation extreme temperatures). We only beginning understand sensation by plants. Multiple thermosensors convey complementary information a given signaling network control gene expression. Temperature-induced protein or transcript structure and/or dynamics biomolecular condensates core sensing mechanisms known thermosensors, but impinges on activities via additional indirect pathways. The diversity plant anticipates many new eventually novel will be uncovered soon.

Language: Английский

Citations

4
Morphological, Physiological, and Molecular Responses to Heat Stress in Brassicaceae DOI Creative Commons
Iram Batool, Ahsan Ayyaz,

Tongjun Qin

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(2), P. 152 - 152

Published: Jan. 7, 2025

Food security is threatened by global warming, which also affects agricultural output. Various components of cells perceive elevated temperatures. Different signaling pathways in plants distinguish between the two types temperature increases, mild warm temperatures and extremely hot Given rising temperatures, heat stress has become a major abiotic challenge, affecting growth development various crops significantly reducing productivity. Brassica napus, second-largest source vegetable oil worldwide, faces drastic reductions seed yield quality under stress. This review summarizes recent research on genetic physiological impact Brassicaceae family, as well model Arabidopsis rice. Several studies show that extreme fluctuations during crucial stages negatively affect plants, leading to impaired reduced production. The discusses mechanisms adaptation key regulatory genes involved. It explores emerging understanding epigenetic modifications While such are limited B. contrasting trends gene expression have been observed across different species cultivars, suggesting these play complex role tolerance. Key knowledge gaps identified regarding napus. In-depth still needed. profound response tissue-specific models advancing our thermo-tolerance regulation napus supporting future breeding efforts for heat-tolerant crops.

Language: Английский

Citations

0
The Arabidopsis demethylase REF6 physically interacts with phyB to promote hypocotyl elongation under red light DOI Creative Commons
Yan Yan,

Jiaping Zhu,

Qi Qiu

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(11)

Published: March 10, 2025

The plant photoreceptor phytochrome B (phyB) mediates the responses of plants to red (R) light. Trimethylation histone H3 at Lys27 (H3K27me3) plays a crucial role in governing gene expression and controlling response environmental changes. However, how dynamic H3K27me3 R light is poorly understood. Here, we report that RELATIVE OF EARLY FLOWERING 6 (REF6), an demethylase, promotes hypocotyl elongation under Arabidopsis . Upon exposure light, REF6 preferentially interacts with active Pfr form phyB. Consequently, phyB enhances accumulation its binding ability, which are necessary for inducing cell-elongation-related genes from open chromatin, ensuring normal growth prolonged exposure. Moreover, acts together phyB-PIF4 module mediate regulation growth. These findings provide insights into understanding phytochromes, epigenetic factors, transcription factors coordinately control changing environment.

Language: Английский

Citations

0
Phenotypic Plasticity and Stability in Plants: Genetic Mechanisms, Environmental Adaptation, Evolutionary Implications, and Future Directions DOI

Peigang Li,

Zhenghong An,

Nan Xu

et al.

Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

ABSTRACT The phenotypic display, survival, and reproduction of organisms depend on genotype–environment interactions that drive development, evolution, diversity. Biological systems exhibit two basic but paradoxical features contribute to developmental robustness: plasticity stability. However, the understanding these concepts remains ambiguous. morphology structure plant reproductive organs—flowers fruits—exhibit substantial stability display a certain level under environmental changes, thus representing promising for study how jointly govern development evolution. Beyond genes underlying organ formation, may maintain induce plasticity. Variations in relevant can repatterning, thereby altering or light temperature fluctuations, which often affects fitness. regulation robustness vegetative organs involves transcriptional post‐transcriptional regulation, epigenetics, phase separation; however, mechanisms flowering plants remain poorly investigated. Moreover, specifically determine have rarely been cloned. This review clarifies attributes further proposes potential avenues paradigm investigate elucidate adapt thrive diverse environments, is crucial design genetically modified crops.

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.

Oecologia, Journal Year: 2025, Volume and Issue: 207(6)

Published: May 15, 2025

Language: Английский

Citations

0
How Rice Responds to Temperature Changes and Defeats Heat Stress DOI Creative Commons
Yufeng Xing, Hongyu Lu,

Xinxing Zhu

et al.

Rice, Journal Year: 2024, Volume and Issue: 17(1)

Published: Nov. 29, 2024

With the intensification of greenhouse effect, a series natural phenomena, such as global warming, are gradually recognized; when ambient temperature increases to extent that it causes heat stress in plants, agricultural production will inevitably be affected. Therefore, several issues associated with crops urgently need solved. Rice is one momentous food for humans, widely planted tropical and subtropical monsoon regions. It prone high summer, leading decrease yield quality. Understanding how rice can tolerate through genetic effects particularly vital. This article reviews respond rising by integrating molecular regulatory pathways introduce its physiological mechanisms tolerance from perspective biology. In addition, genome selection engineering were emphasized provide theoretical basis sustainability stability crop yield-quality structures under temperatures point view breeding.

Language: Английский

Citations

3