Focus on DnaJ protein research from Arabidopsis to crop improvement

Reframing Pathogenesis-Related proteins: from plant immune drivers to stress resilience integration nodes.

Plants are constantly exposed to biotic and abiotic stresses, but the molecular mechanisms integrating these signals remain underexplored. Traditionally viewed as defense proteins against pathogen infection, pathogenesis-related (PR) proteins comprise 19 diverse families encompassing defense-related enzymes (glucanases, chitinases, nucleases, proteases), antimicrobial peptides, enzyme inhibitors and reactive oxygen species (ROS)-generating proteins. While their significance during biotic stresses is well-documented, research has started to emerge on their dynamic regulation and functional roles in abiotic stresses, e.g. salinity, drought, heavy metal exposure, temperature and flooding. By synthesizing recent insights and critical knowledge gaps, we propose that PR proteins are global plant stress integration nodes, linking responses to abiotic and biotic stresses. We distill the core molecular principles and regulatory mechanisms underpinning the abiotic regulation of PR genes and proteins, implicating the central importance of plant hormone and ROS signaling pathways. We also critically examine the functional diversity and versatility of PR proteins, as they orchestrate cell wall remodeling, membrane stabilization, ion homeostasis, proteolytic balance and ROS metabolism in stress resilience pathways. Overall, a detailed understanding of the abiotic regulation and function of PR proteins offers rich insights into how plants coordinate survival under environmental challenge and has significant implications for developing stress-resilient crops.

Smart Scaffolds: How WD40 Proteins Integrate Plant Development, Metabolism, and Stress Adaptation.

WD40 repeat proteins are evolutionarily conserved molecular scaffolding that function as key regulators of plant growth, development, and stress resilience. These proteins, highlighted by tandem WD (Trp-Asp) motifs forming a stable β-propeller structure, serve as versatile platforms for protein-protein and protein-DNA interactions, facilitating the assembly of multiprotein complexes and the integration of environmental and hormonal signals into specific physiological responses. In plants, WD40 proteins orchestrate essential functions such as anthocyanin biosynthesis, blooming timing, embryogenesis, gametogenesis, and fruit development, often through regulatory modules like the MYB-bHLH-WD40 (MBW) complex. In addition to development, they serve as crucial centers for adaptation to abiotic and biotic stress by regulating phytohormonal interactions, maintaining reactive oxygen species balance, and facilitating ubiquitin-mediated protein degradation, especially via SCF E3 ligase complexes. These roles relate significant hormone pathways, such as abscisic acid, auxin, gibberellin, ethylene, and brassinosteroids, to environmental interactions. Recent progress in CRISPR-based functional genomics, interactome mapping, and high-resolution structural modeling is revealing the plasticity and evolutionary conservation of WD40 scaffolds. This review 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.

Histone acetyltransferases as integrative epigenetic regulators of plant abiotic stress responses

Cold stress tolerance in pepper: role of transcription factors in molecular signaling and adaptive responses

Pepper (Capsicum annum L.) is an important horticultural commodity known for its nutritional and medicinal properties. However, cold stress severely hinders its growth, development, and productivity, posing a major challenge to stable production in many cultivation regions. Cold stress disrupts membrane integrity and impairs photosynthesis, cellular homeostasis, and osmotic balance, while also promoting excessive accumulation of reactive oxygen species (ROS), leading to oxidative damage and metabolic imbalance. To mitigate these adverse effects, pepper plants initiate complex molecular signal transduction pathways, which are controlled by transcription factors (TFs) that regulate the expression of stress-responsive genes. Major TF families involved in cold stress responses include MYB, WRKY, Cys2/His2-type zinc finger protein (C2H2), NAC, Phytochrome-Interacting Factor (PIF), C-repeat Binding Factor/Dehydration-Responsive Element Binding protein (CBF/DREB), and bHLH. These genes are responsible mainly for perceiving and transmitting cold signals in pepper via abscisic acid (ABA)-mediated and ABA-independent pathways, calcium–mitogen-activated protein kinase (MAPK) cascades, ROS signaling, and hormone regulation. Functional investigations have revealed that multiple TFs, such as CaNAC064, SNF1-Related Protein Kinase 2.4 (CaSnRK2.4), CaNAC035, CaCBF1B, CaWRKY40, and CaMYB80, are essential positive regulators of cold tolerance, resulting in improved scavenging of ROS, osmotic balance, and membrane integrity. Recent advances in genomics and transgenic strategies, such as CRISPR/Cas-based genome editing, has further elucidated these TF-mediated regulatory pathways, providing potential approaches for developing cold-tolerant pepper cultivars. By elucidating the molecular mechanisms underlying cold stress responses, it offers key perspectives for the breeding of climate-tolerant pepper varieties to ensure sustainable agricultural production.

Jasmonate ZIM-domain protein 2 orchestrates ABA/JA signaling and flavonoid biosynthesis to suppress cold tolerance in grapevine.

Low temperature is a significant abiotic stressor that severely constrains grape cultivation and productivity. Jasmonate ZIM-domain (JAZ) proteins, which function as critical transcriptional repressors in the jasmonic acid signaling pathway, play essential roles in plant stress adaptation. Nevertheless, their specific functions and regulatory mechanisms in grape cold tolerance remain unclear. This work investigated the role and regulatory network of a cold-inducible VvJAZ2 gene by integrating physiological, molecular, and transcriptomic approaches. Functional analyses revealed that overexpression of VvJAZ2 compromised cold tolerance in Arabidopsis and grape calli, manifested as aggravated oxidative damage and compromised antioxidant capacity. Furthermore, transgenic materials exhibited decreased endogenous ABA and JA levels, reduced flavonoid accumulation, and downregulation of the ICE-CBF-COR regulatory module. Consistently, transcriptomic profiling further indicated that VvJAZ2 functions as a negative regulator by coordinating the suppression of ABA/JA signaling cascades, MAPK pathway activity, and flavonoid biosynthetic processes. Mechanistically, the transcription factor VvMSA (Abscisic acid-stress-ripening protein) was identified as an upstream activator that directly binds to the VvJAZ2 promoter and induces its expression under normal conditions; however, this activation is markedly attenuated during cold stress. Moreover, VvJAZ2 physically interacts with VvUGT74F5 (UDP-glycosyltransferase 74F5) implicated in flavonoid modification. Collectively, these findings suggest that VvJAZ2 may function as a potential regulatory node, and support a working model of a dynamic "transcription-protein interaction" module to coordinate hormone signaling and metabolic reprogramming under cold stress. This study provides novel insights into the molecular basis of cold adaptation in grapevine and identifies potential genetic targets for improving cold resilience in viticulture.

ROS-Centered Transcriptomic Regulatory Networks Linking Salinity Stress, Antioxidant Defense and Processability Traits in Salicornia spp.

Salinity stress affects not only the survival and productivity of halophytic plants, but also the composition, structure and processability of their biomass. In Salicornia spp., salt-induced regulation of ion transport, osmotic adjustment, reactive oxygen species signaling, antioxidant defense, and cell wall remodeling can directly influence residual salinity, water retention, texture, extractability, drying behavior, and oxidative stability of plant biomass. However, most existing transcriptomic studies of Salicornia and related halophytes have focused mainly on salt tolerance mechanisms, whereas the connection between stress-regulated molecular networks and processing-related biomass traits remains insufficiently systematized. This review addresses this gap by proposing a mechanistic framework that links salinity perception, ROS-mediated signaling, ABA and MAPK pathways, antioxidant gene families, transcription factor networks and processing-oriented quality traits. Special attention is given to enzymatic antioxidant systems, including SOD, CAT, APX, POD and components of the ascorbate-glutathione cycle, as well as to non-enzymatic defense mechanisms involving ascorbate, glutathione, phenolic compounds, carotenoids, proline and glycine betaine. The review also discusses the regulatory roles of WRKY, DREB/CBF, NAC, bZIP and MYB transcription factor families as molecular control points connecting salinity stress responses with downstream metabolic and structural traits. Network-based approaches, including WGCNA, pathway signatures and transcript panels, are considered more informative than single-gene markers for predicting complex quality traits in Salicornia biomass. In addition, recent genomic and computational strategies, including CRISPR/Cas-mediated functional validation, GWAS, genomic selection, multi-omics integration and AI-assisted modeling, are discussed as emerging tools for candidate-gene prioritization and predictive assessment of stress-dependent biomass quality. Overall, this review shifts the interpretation of Salicornia transcriptomics from a descriptive salt-tolerance model toward a mechanistic and application-oriented framework for improving halophytic raw materials for food, feed and bioprocessing applications.