Aug 2026· Plant physiology and biochemistry : PPB· Vol 238, pp.
111660
· 0 citations· 95 references
Medicine
TL;DR
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.
Abstract
Transcriptional regulation is the cornerstone of plant developmental plasticity and environmental resilience. Central to these processes are the B-Box (BBX) proteins, a family of zinc-finger transcription factors that have emerged as pivotal signaling hubs. While their roles were initially defined through light signaling and photoperiodic flowering in Arabidopsis, recent advances have repositioned BBX proteins as integrative nodes across a vast array of physiological processes, including seed germination, thermomorphogenesis, shade avoidance and senescence, as well as responses to both abiotic and biotic stresses. The remarkable functional diversity of BBX proteins emerges from a highly orchestrated, hierarchical regulatory landscape. 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. We propose that understanding BBX function requires a shift from identifying isolated target genes to decoding the combinatorial logic of their interactions. Deciphering this interactome under fluctuating environments not only deepens our knowledge of the molecular mechanisms regulating plant plasticity but also identifies highly promising targets for the precision breeding of climate-resilient crops.
The DNA-binding with one finger (Dof) family comprises plant-specific transcription factors that serve as key hubs regulating plant growth, development, stress responses, and metabolism. Advances in multi-species genome sequencing have deepened our understanding of the structure and function of this family. This review systematically describes the conserved structural features of Dof proteins and their expansion patterns during plant evolution. It further focuses on the molecular mechanisms and regulatory networks underlying organ development, growth coordination, stress responses, and metabolic regulation. Comprehensive analysis reveals that the Dof family exhibits conserved core functions across evolution, along with pronounced species specificity. In terms of regulatory mechanisms, Dof proteins integrate external signals and internal transduction pathways to coordinate growth, development, and stress defense. They achieve this through multiple modes, including transcriptional regulation of target genes and protein–protein interactions. This review highlights the pivotal roles of the Dof family across diverse developmental stages and physiological processes. It thus provides a theoretical foundation for dissecting its biological mechanisms and advancing molecular breeding in crops.
Liang Yang, Xiang-Kai Guo, Kaitong Wang et al.· Horticulture Research· 0 citations
A review of WD40 repeat proteins strengthens current findings relating their structural properties, molecular mechanisms, and functional diversity, underscoring their potential as targets for developing stress-resilient, high-yield crops in a changing climate.
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.
Xinpei Han, Guodong Chen, Jun Peng et al.· Cells· 0 citations
Chromatin remodeling plays a central role in regulating plant development and physiology by shaping the gene expression patterns that drive biological processes. Among epigenetic modifications, histone acetylation is particularly relevant as it alters chromatin structure and influences transcriptional activity. MYST-type histone acetyltransferases (HAT) are evolutionarily conserved components of the Nucleosome Acetyltransferase of histone H4 (NuA4) complex, a key regulator that acetylates histones H4, H2A, and the histone variant H2A.Z. Growing evidence supports the presence of a canonical NuA4-C in plants, similar to that described in yeast. In this review, we summarize recent studies that have begun to uncover its broad role in plant biology, highlighting its involvement in diverse processes such as the skoto- to photomorphogenesis switch, chloroplast development, shade avoidance responses, thermomorphogenesis, the vegetative-to-reproductive transition, plant growth, reproduction and hormonal signalling. In addition, we discuss recent advances in understanding the crosstalk of NuA4-C-mediated H4ac and H2A.Z deposition with other chromatin remodeling complexes in plants. Although significant progress has been made, a full understanding of the complex functions remains unavailable. Current evidence indicates that NuA4-C in yeast and TIP60 in humans are central regulators of transcription, acting not only through histone acetylation but also by influencing transcription elongation and RNA splicing, although direct evidence for similar functions in plant NuA4-C still remains limited. This regulatory role might be critical for integrating developmental programs with environmental signalling pathways. While initial insights into the recruitment of NuA4-C to target genes have emerged, further research is needed to clarify how its activity is controlled and modulated in different biological contexts.
María Guillem-Bernal, J. Barrero-Gil, J. A. Jarillo et al.· Journal of Experimental Bota...· 0 citations
Signalling pathways have originated and diversified extensively during evolution. Using AUXIN RESPONSE FACTORs (ARFs) as a model, we examine how a plant signalling system evolved through the co-option of pre-existing transcriptional regulators, a principle well established in evolutionary biology in organisms, such as animals. ARFs are an ancient family of DNA-binding proteins that predate the canonical nuclear auxin pathway and likely acted as auxin-independent transcriptional repressors. The emergence of auxin signalling involved coupling this ancestral transcriptional module to a regulatory system based on a series of co-repressors regulated through F-box-mediated degradation, thereby conferring signal responsiveness without altering core ARF biochemical properties. Molecular diversification and innovation - through gene duplication, acquisition of transcriptional activation, and changes in interaction partners - expanded the developmental outputs controlled by auxin while preserving the underlying regulatory logic. Beyond their role as auxin effectors, ARFs function as integrative hubs that coordinate multiple developmental and environmental inputs. Using this family as an example, we illustrate how signalling pathways are built by rewiring existing regulatory frameworks, providing general principles for understanding the evolution and function of plant signalling networks.
Melissa Dipp-Álvarez, J. Hernández-García· New Phytologist· 0 citations
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