TL;DR
Understanding how E3 ubiquitin ligases shape these processes provides a valuable perspective on plant biology while also opening new possibilities for improving crop performance in increasingly variable environments.
This review synthesizes recent progress in how BBX activity is modulated through chromatin remodeling, alternative splicing and E3-ligase-mediated protein stability, among other mechanisms, and proposes that understanding BBX function requires a shift from identifying isolated target genes to decoding the combinatorial logic of their interactions.
Regulatory mechanisms of several types of PTMs, including phosphorylation, ubiquitination, SUMOylation, acetylation, crotonylation, and S-acylation, in the cold stress signaling pathway are summarized.
Highlights What are the main findings? Plant bHLH factors regulate specialized metabolism through direct, cascade, or hybrid architectures centered on signal-responsive modules such as JA-JAZ-MYC. Cross-species comparison identifies six determinants of bHLH output: signal gating, pathway topology, promoter and partner logic, spatial competence, feedback regulation, and evidence context. What are the implications of the main findings? Effective metabolic engineering should match the intervention to the pathway bottleneck and combine transcription-factor tuning with tissue-specific control, precursor supply, transport, and storage capacity. This framework supports more precise improvement of crop defense, food quality, and medicinal-metabolite production while minimizing growth penalties and toxicity. Abstract Plant specialized metabolites connect genetic programs and environmental responses with ecologically and economically valuable natural products. Their accumulation is rarely constitutive, varying instead with tissue identity, developmental stage, stress exposure, hormone signaling, and cellular storage capacity. This review examines basic helix-loop-helix (bHLH) transcription factors as regulatory switch points in plant specialized metabolism, with emphasis on the jasmonate-JAZ-MYC module. In resting tissues, JAZ repressors constrain MYC/bHLH activity; after wounding, herbivory, pathogen challenge, or elicitation, jasmonoyl-isoleucine triggers COI1-dependent JAZ turnover, releasing MYC factors to bind E-box/G-box motifs, recruit coregulators such as MED25, and activate biosynthetic genes or downstream transcription-factor cascades. Plant lineages have repeatedly adapted this regulatory logic to control terpenoids, alkaloids, phenylpropanoids, flavonoids, glucosinolates, phytoalexins, and related metabolites. Comparative examples include Arabidopsis sesquiterpenes and glucosinolates, Taxus taxanes, Artemisia artemisinin, Catharanthus terpenoid indole alkaloids, Salvia phenolic acids and tanshinones, Ginkgo terpene trilactones, rice diterpenoid phytoalexins, and cotton gossypol. Across these systems, bHLH output depends on dimer choice, promoter grammar, chromatin accessibility, hormone crosstalk, partner transcription factors, and cell-type competence. Six shared principles emerge: signal gating, topology matched to pathway architecture, partner-dependent promoter decoding, spatial competence, feedback rheostats, and evidence-dependent transferability. We further discuss evidence standards, multi-omics-guided factor discovery, miRNA-mediated post-transcriptional control, and engineering strategies for crop defense, food quality, medicinal-metabolite production, and synthetic biology. Unlike pathway- or MYC2-centered surveys, this review organizes the literature within a direct–cascade–hybrid framework that integrates promoter grammar, spatial competence, storage anatomy, and an explicit evidence hierarchy.
Brassinosteroids (BRs) are essential steroid hormones that coordinate plant growth, development and adaptation to changing environments. Although BR signaling has long been viewed primarily as a phosphorylation-dependent pathway, increasing evidence shows that ubiquitination provides an additional regulatory layer that shapes the abundance, activity, subcellular distribution and turnover of key signaling components. Ubiquitin-mediated regulation operates at multiple points in the BR pathway, including receptor homeostasis at the plasma membrane, turnover of GSK3-like kinases, and stability control of the transcription factors BES1/BZR1. These processes determine not only the strength and duration of BR signaling but also its coordination with other hormonal and stress-response pathways. In this review, we discuss recent advances in ubiquitin-mediated regulation of BR signaling, focusing on receptor-level control, proteolytic regulation of core signaling components, and modulation of transcriptional outputs. We also highlight emerging links between ubiquitination, selective autophagy, deubiquitination and BR-associated stress responses and outline key questions concerning ubiquitin chain specificity, substrate recognition and conservation of these regulatory modules in crops. Defining how ubiquitination fine-tunes BR signaling will deepen our understanding of plant steroid hormone regulation and may provide new strategies for optimizing crop architecture, productivity, and stress resilience.
Although plants are exposed to many environmental stressors (heat, drought, salinity, and pathogen), they survive by rapidly reprogramming their gene expression. Recent findings show that many regulatory mechanisms are maintained within liquid-liquid phase separation (LLPS) formed biomolecular condensates, instead of maintaining these mechanisms within membrane-bound organelles. LLPS has been shown to exist in plant cells; however, the integration of LLPS with functional stress adaptations and gene regulations is still unclear from the studies that have been published thus far. In this review, we discuss recent research that demonstrates how these biomolecular condensates act as dynamic regulatory centers by linking environmental stress perception to transcriptional and post-transcriptional regulation of genes in plants. We describe the biophysical principles that govern the occurrence of LLPS in a plant cellular environment and provide an overview of how both abiotic (e.g., drought, heat) and biotic (i.e., pathogens) stressors initiate the LLPS and remodel nuclear and cytosolic condensate structures. The focus of this work will be on the effects of stress-induced changes (both qualitatively and quantitatively) in the condensate composition and material properties on transcription factor activity (either as an activator or repressor) and the organization of chromatin, RNA stability, and selective translation. We will also discuss post-translational modifications (PTMs) that modulate condensate dynamics and allow for reversibility. Collectively, these findings suggest that LLPS likely contributes significantly to gene regulation and stress adaptation in plants, although the degree of mechanistic validation varies among different condensate systems.
As sessile organisms, plants have evolved elaborate epigenetic regulatory networks to adapt to a wide range of abiotic stress. Chromatin remodelling is a core epigenetic regulatory mechanism that refers to the process by which chromatin remodelling complexes mediate dynamic changes in chromatin spatial conformation and DNA accessibility through nucleosome sliding, histone variant exchange, nucleosome eviction, or spacing adjustment. The flexible and reversible modifications of chromatin structure enable plants to rapidly respond to external stimuli, thereby safeguarding their survival and promoting adaptive plasticity. This review summarises the research progress on chromatin remodelling complexes and their regulatory mechanisms in plant environmental adaptation. Furthermore, we discuss the current challenges and future research directions in this field, including the need to decipher the recruitment specificity of chromatin remodellers, investigate their coordination networks under combined abiotic stresses, and translate mechanistic insights into epigenetic engineering for crop improvement. Collectively, this review aims to provide a comprehensive overview of chromatin remodelling-mediated stress adaptation and lay a foundation for developing stress-tolerant crop varieties via epigenetic engineering.
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