Wood remains the world’s most abundant and renewable resource for timber and pulp and is an alternative to fossil fuels. Understanding the molecular regulation of wood formation can advance the engineering of wood for more efficient material and energy productions. We integrated a black cottonwood (Populus trichocarpa) wood-forming cell system with quantitative transcriptomics and chromatin binding assays to construct a transcriptional regulatory network (TRN) directed by a key transcription factor (TF), PtrSND1-B1 (secondary wall-associated NAC-domain protein). The network consists of four layers of TF–target gene interactions with quantitative regulatory effects, describing the specificity of how the regulation is transduced through these interactions to activate cell wall genes (effector genes) for wood formation. PtrSND1-B1 directs 57 TF–DNA interactions through 17 TFs transregulating 27 effector genes. Of the 57 interactions, 55 are novel. We tested 42 of these 57 interactions in 30 genotypes of transgenic P. trichocarpa and verified that ∼90% of the tested interactions function in vivo. The TRN reveals common transregulatory targets for distinct TFs, leading to the discovery of nine TF protein complexes (dimers and trimers) implicated in regulating the biosynthesis of specific types of lignin. Our work suggests that wood formation may involve regulatory homeostasis determined by combinations of TF–DNA and TF–TF (protein–protein) regulations.

Sustained drought tolerance in plants relies on transcriptional memory through successive stress cycles, yet the chromatin-based mechanisms underlying this memory remain unclear. Previously, we revealed that PtrMYB161 overexpression in Populus trichocarpa results in phenotypes characteristic of drought tolerance. Here, we confirm that such transgenesis instills an epigenetic path to gene transregulation for drought tolerance. PtrMYB161 binds directly to the MYB-core motif in the promoter of PtrNAC120, a drought response/tolerance gene, to recruit the histone acetyltransferase (HAT) dimer GENERAL CONTROL NON-DEREPRESSIBLE5-1–ALTERATION/DEFICIENCY IN ACTIVATION2b-3 (PtrGCN5-1–PtrADA2b-3), forming the ternary protein complex (PtrMYB161–PtrGCN5-1–PtrADA2b-3). This ternary system enables enhanced acetylation of nucleosome histone 3 lysine-9, -14, and -27 (H3K9, H3K14, and H3K27) for enriched RNA Pol II occupancy in the PtrNAC120 promoter to elevate its expression for drought tolerance. Unlike PtrAREB1-2, an important drought-inducible transcription factor that can also mediate PtrNAC120 transactivation for tolerance, PtrMYB161 expression remains unaffected by drought. However, under drought conditions, induced PtrAREB1-2 could form HAT ternary complex, PtrAREB1-2–PtrGCN5-1–PtrADA2b-3, and bind to PtrAREB1-binding sites (ABREs) in the PtrNAC120 promoter for PtrNAC120's enhanced H3K acetylation, RNA Pol II occupancy, and transactivation for drought tolerance. PtrMYB161–PtrGCN5-1–PtrADA2b-3-mediated PtrNAC120 transactivation was induced following severe, prolonged drought stress (below 40% relative soil water content) and PtrAREB1-2-induced PtrNAC120 transactivation. Further loss- and gain-of-function transgenesis experiments in whole plants and stem differentiating xylem protoplasts suggest that, under stress, the PtrAREB1-2 regulatory system activates an ancillary regulation mediated by PtrMYB161. Our findings propose coordinated epigenetic regulations mediated by HAT complexes to jointly sustain drought tolerance in Populus.

Lonicera caerulea is a wild fruit species with high edible and medicinal value. However, the molecular regulation and metabolic mechanisms of L. caerulea under salt stress are still unclear. Salt stress causes damage to the cell membrane of L. caerulea and induces changes in malondialdehyde content, relative electrolyte leakage, leaves’ stomatal opening, and the water loss rate. It also increases the activity of antioxidant enzymes and the content of soluble sugars. A comprehensive transcriptomic and metabolomic analysis of L. caerulea exposed to salt stress at four different (treatment) time intervals yielded a total of 99,574 unigenes and 1375 metabolites. Among these, 4081, 4042, and 4403 differentially expressed genes (DEGs) were identified in 12 transcriptomes, while 776, 832, and 793 differentially accumulated metabolites (DAMs) were detected in 12 metabolomes. The DEGs play important roles in several signaling pathways, including MAPK signaling, fatty acid metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction. KEGG pathway enrichment analysis revealed that these DEGs and DAMs are associated with flavonoid and lipid biosynthesis pathways. The combined transcriptomic and metabolomic analyses suggest that flavonoid and fatty acid compounds may be involved in regulating plant responses to salt stress. These findings will lay the foundation for the selection of L. caerulea germplasm resources and the expansion of its cultivation area. These research findings will lay the foundation for the cultivation of salt-tolerant new varieties of L. caerulea and their planting in saline–alkali soils.

Background/Objectives: bHLH transcription factors regulate key plant processes including development, stress adaptation, and metabolism. In Kandelia obovata, a mangrove species well known for its high tolerance to harsh environments, the bHLH gene family has not been systematically investigated. Here, this study aims to perform genome-wide identification and expression profiling of KobHLH genes under normal and saline conditions. Methods: bHLH members were identified by homology searches (HMMER and BLASTp) against the K. obovata protein dataset and verified with SMART-based domain analysis. Subsequent analyses covered physicochemical features, conserved motif composition, and phylogenetic relationships. Transcript abundance was quantified via RNA-seq in various organs (roots, stems, leaves, flowers, and fruits) as well as under saline conditions. Differentially expressed transcripts were selected for co-expression network construction. Results: Phylogenetic analysis of the 118 identified KobHLH loci assigned them into 18 distinct clades. Organ-preferential expression patterns were observed, leading to their classification into three putative functional categories. Upon salinity exposure (10–30‰), 61 of the 118 KobHLH genes exhibited differential expression, grouped into ten significant clusters. A co-expression network comprising 20 hub genes and 198 edges was constructed. Conclusions: This study provides the first genome-wide characterization of the bHLH family in K. obovata, revealing its evolutionary divergence and identifying 61 salt-responsive candidates, notably KobHLH108 and KobHLH5 associated with secondary metabolism, for further functional validation. The findings provide a foundation for future functional studies on stress adaptation mechanisms in this ecologically valuable mangrove species.