Transposable elements (TEs) are essential constituents of plant genomes, promoting environmental adaptation and modulating gene expression through novel insertions. Although their activities can also trigger deleterious mutations, host mechanisms have evolved to repress them. Similarly, TEs have developed strategies to counteract silencing for their propagation. Here, the LTR retrotransposon Copia2 was identified as an active TE in japonica rice, with variations in 5-base-pair repeats within its 5′-LTR influencing promoter activity. The expression of Copia2 could be activated by drought conditions, with CG-1 motifs on LTR acting as cis-acting elements recognized by calmodulin-binding transcription activators. Under drought stress, the interaction of drought-induced proteins SCT1 and SCT2 with calmodulin OsCML4 and OsCML31 further activates Copia2 expression, enhancing its sensitivity to Ca²⁺ signaling. Additionally, decreased DNA methylation of Copia2 under drought conditions, regulated by Ca²⁺ signaling, facilitates the binding of SCT1 and SCT2 to the LTR. In summary, the drought-induced activity of Copia2 is regulated by the synergy of SCT1/SCT2 and DNA methylation mediated through Ca²⁺ signaling, potentially contributing to its recent activity in rice.

Waterlogging stress is a major abiotic stress that severely limits plant growth and development. However, little is known about the effects of waterlogging stress on the growth and development of gymnosperms. In this study, we demonstrated that the TgRAV1–TgWRKY74–TgACS13 module regulates ethylene-enhanced root vitality during waterlogging stress in the gymnosperm Torreya grandis. Root vitality, the physiological status of root tissues, reflects their metabolic activity and cell viability of roots. Waterlogging stress induces ethylene accumulation in T. grandis roots, thereby enhancing root vitality. The ethylene biosynthesis gene TgACS13 positively regulates root vitality under waterlogging stress by increasing ethylene levels. The transcription factors TgWRKY74 and TgRAV1 directly regulate TgACS13 expression by binding to its promoter. Furthermore, waterlogging stress activates TgWRKY74 to promote TgACS13 transcription and alleviates the inhibitory effect of TgRAV1 on its expression, resulting in ethylene-enhanced root vitality during waterlogging stress. In addition, TgRAV1 interacts with TgWRKY74 both in vivo and in vitro, reducing the transcriptional activity of TgWRKY74 by inhibiting its DNA-binding ability without affecting the transcriptional activity of TgRAV1. Therefore, the TgRAV1–TgWRKY74 module finely tunes TgACS13 expression to regulate ethylene accumulation through multiple mechanisms, thereby maintaining the vitality of T. grandis roots exposed to waterlogging stress.

Seed weight is a pivotal yield-determining trait in crops, and yet, the genetic and molecular mechanisms underlying its regulation in polyploid species remain underexplored. In a previous study, we identified cqSW.A03-2, a QTL that regulates thousand seed weight (TSW) in rapeseed (Brassica napus). Here, we identify BnaA3.AHK2, encoding a histidine kinase, as the causal gene of cqSW.A03-2. BnaA3.AHK2 enhances TSW through maternal control of seed coat cell expansion without significantly compromising other yield-related traits. Protein sequence divergence between parental haplotypes caused functional differentiation, with only the ZY50 allele showing functional kinase activity and rescuing developmental defects in Arabidopsis cytokinin receptor mutants. Strikingly, BnaA3.AHK2 seems to be a cytokinin-independent operator, contrasting with the canonical cytokinin signaling pathway. Transcriptome and protein interaction analyses reveal a signaling module where BnaA3.AHK2 engages BnaAHP–BnaARR phosphorelay components to regulate downstream targets. Notably, the favorable cqSW.A03-2 haplotype has been historically selected in modern breeding, and its introgression into elite hybrids boosted TSW by 3.6%–9.1%, demonstrating its breeding value. Our findings unveil a non-canonical signaling pathway for seed size regulation, providing a strategic genetic target to break yield trade-offs in polyploid crops.

Leaf morphology varies substantially across plant species. In soybeans, the regulation of compound leaf development remains poorly characterized, despite its critical role in plant architecture. Some soybean cultivars have compound leaves with up to five leaflets, while most are trifoliolate. Using genetic mapping, we identified a gene behind the leaflet number variation as LF1, an AP2/ERF transcription factor. High expression levels of LF1 were further observed in leaf primordium initiation sites, leaf primordia, and leaflet initiation domains. Transgenic overexpression of LF1 increased leaflet number. Further investigation revealed that LF1 regulates leaflet development through negative autoregulation via GCC-box cis-element binding. In addition to the role of LF1, the CRISPR-edited mutant of TEOSINTE-BRANCHED1/CYCLOIDEA/PCF3 (GmTCP3) displayed serrated blade margins in juvenile leaves and increased compound leaflet numbers. Protein interaction assays confirmed LF1 binding affinity for GmTCP3. Furthermore, we demonstrate that LF1 induces the expression of GmLFY, a key regulator of leaflet development. Altogether, our findings establish LF1 as a central regulator of soybean leaflet morphogenesis and reveal its mechanistic interactions with GmTCP3 and LEAFY (GmLFY), offering novel mechanistic insights into the genetic control of compound leaf development.

Mitogen-activated protein kinase (MAPK) cascades play vital roles in regulating plant growth, development, and stress responses. Nevertheless, the complete MAPK cascade that regulates the flowering time of Arabidopsis thaliana has not been established. A MAPK module comprising MAPKKK18, MAPKK3, and MAPK1/2/7/14 accelerates flowering in Arabidopsis. Through direct interaction, MAPK1/2/7/14 phosphorylates the S²⁴ residue of NF-YB2. Phosphorylated NF-YB2 enhances the stability of the heterotrimeric CO ~ NF-YB2 ~ NF-YC3/C9 complex and the expression of FT. Accumulation of NF-YB2 significantly promotes flowering, whereas the role of NF-YB2^S24A in this process is less pronounced. Compared with the transgenic plants overexpressing MAPKKK18 in the wild-type (WT) background, the nf-yb2 plants overexpressing MAPKKK18 bolt considerably later. Taken together, the MAPKKK18-mediated signaling cascade exerts tight control over the flowering time of Arabidopsis by modulating the phosphorylation status of NF-YB2, unveiling a flexible regulatory pathway to fine-tune plant development.

The conversion of starch into sugar during postharvest banana (Musa acuminata, AAA group) ripening significantly influences fruit quality. Ethylene response factors (ERFs) regulate fruit ripening through ethylene signaling, while redox modifications affect their activity by post-translational changes. This study identifies MaERF95L, an EDLL-domain ERF in banana, as a central regulator of starch-to-sugar metabolism during postharvest ripening. Using electrophoretic mobility shift and dual-luciferase reporter assays, we demonstrate that MaERF95L directly binds to and activates the expression of six genes related to starch degradation and sucrose synthesis (MaGWD1, MaAMY3, MaBAM1, MaHK5, MaPGI1, and MaUPG3). MaERF95L overexpression accelerates starch degradation and sugar accumulation in both banana and tomato fruits during ripening. Notably, methionine (Met, M)-based oxidation modifications (e.g., Met-16 and Met-77) suppress MaERF95L's transcriptional regulatory function. Simulating oxidation by Met→glutamine (Gln, Q) substitutions (MaERF95L^M16Q/M77Q) alters its subcellular localization and also impairs its DNA-binding and transcriptional activation capabilities. In contrast, blocking oxidation by Met→Valine (Val, V) substitutions (MaERF95L^M16V/M77V) maintains its transcriptional activation activity. Furthermore, transient overexpression of MaERF95L^M16Q/M77Q in bananas reduced MaERF95L's activation of genes related to starch degradation and sucrose synthesis, and starch-to-sugar conversion. However, the overexpression of MaERF95L^M16V/M77V showed no effect on MaERF95L's activation function. These findings reveal a Met oxidation-sensitive regulatory mechanism connecting reactive oxygen species signaling to carbohydrate metabolism, providing molecular insights into quality formation regulation during ripening and potential strategies for reducing postharvest losses in climacteric fruits.

Endoplasmic reticulum-associated degradation (ERAD) is an important mechanism for degrading misfolded proteins, and is mediated by different complexes containing several conserved ER-localized ubiquitin ligases, such as Hrd1, Doa10, and gp78. Recent studies have shown that the ERAD machinery is conserved in eukaryotes. However, it remains unknown whether plants have gp78 homologs. We report a functional study of Arabidopsis homologs of gp78 and their involvement in ERAD. T-DNA insertion mutations in Arabidopsis gp78 genes, AtGP78A and AtGP78B, increased degradation of mutated brassinosteroid (BR) receptors, bri1-5 and bri1-9, leading to lower activation of the signaling protein BES1, and thereby enhancing the dwarf phenotypes of bri1-5/9. This is different from the effects of knockout in known ERAD components, which suppress the dwarf phenotypes of bri1-5/9. AtGP78s interacted with and affected the stability of AtOS9, but not other components in the AtHRD1 complex. AtOS9 accumulated in atgp78a-1 atgp78b bri1-5/9, and knockout of AtOS9 rescued the enhanced-dwarf phenotypes of atgp78a-1 atgp78b bri1-5/9. We determined that AtGP78s were involved in plant ERAD by modulating the stability of AtOS9. Taken together, our results not only reveal AtGP78s as new ERAD components but also reveal a relationship between AtGP78s and the AtHRD1 complex in plants.

Rice is one of the most important food crops in the world and it is prone to attack by many diseases, such as the rice blast, sheath blight, bacterial leaf blight, and so on. These diseases represent the main constraints in rice production, threatening food security and safety. Here, new control strategies against these major rice diseases have been developed either by heterologous expression of a pathogen effector UvScd1 from false smut fungus Ustilaginoidea virens or by spraying the engineered biocontrol agent Bacillus subtilis secreting the effector UvScd1. Compared to the wild-type rice Zhonghua11 (ZH11), the rice line heterologously expressing UvScd1 showed lesion mimics and upregulated the expression of defense-related genes in leaves, including genes related to the JA and SA signaling pathways. As expected, the transgenic rice line showed broad-spectrum resistance to hemibiotrophic fungus Magnaporthe oryzae, necrotrophic fungus Rhizoctonia solani, and bacterium Xanthomonas oryzae pv. oryzae (Xoo), while there was no effect on yield-related agronomic traits compared with ZH11, suggesting that the effector UvScd1 confers both plant resistance via induction of ROS and defense-related genes, and maintains the balance between plant resistance and yield. In field experiments, comparable control efficiencies against these major rice diseases were achieved by spraying B. subtilis engineered to secrete UvScd1 and corresponding chemical pesticides, underscoring that use of biocontrol agents to secrete certain pathogen effector proteins is an effective strategy for the management of plant diseases. It is noteworthy that the application of B. subtilis engineered to secrete UvScd1 also achieved effective control for a variety of crop diseases, suggesting its excellent potential for use in practice.

After cellular damage caused by wounding or pathogens, Arabidopsis thaliana endogenous elicitor peptides (Peps) are released into the apoplast, enhancing innate immunity by directly binding to the membrane-localized leucine-rich repeat receptor kinase PEP RECEPTOR1 (PEPR1). Ligand binding induces PEPR1 heterodimerization with the co-receptor BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE1 (BAK1), followed by PEPR1 internalization, both essential for a subset of Pep1-induced responses. However, the role of BAK1 in Pep1-triggered PEPR1 endocytosis remains unclear. Here, we show that the ligand-induced PEPR1 endocytosis depends on its kinase activity and requires BAK1 C-terminal tail phosphorylation, which is equally indispensable for immune signaling and BAK1 internalization. Using a GFP insertional mutagenesis approach, we generated a partially functional GFP-tagged BAK1 to demonstrate that, following Pep1 elicitation, BAK1 and PEPR1 are endocytosed together with similar dynamics. Our findings identify the BAK1 function as a prerequisite for PEPR1 internalization.

Acid-producing fungal pathogens like Valsa mali enhance infectivity by secreting organic acids to acidify host environments, though the underlying cellular pH manipulation mechanisms remain unclear. Here, we identified VmAGP1 as a V. mali virulence factor whose knockout reduces virulence while heterologous expression in apples increases susceptibility. Using yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and co-immunoprecipitation (Co-IP) assays, we demonstrated that VmAGP1 interacts with apple receptor-like kinase MdLecRK2, which negatively regulates disease resistance. VmAGP1 promotes MdLecRK2 homo-dimerization, confirmed by luciferase complementation imaging (LCI) and Co-IP. Further studies reveal that MdLecRK2 interacts with and phosphorylates vacuolar H⁺-ATPase MdVHAc” 1, which also negatively regulates resistance. Flow cytometry shows that VmAGP1 expression lowers intracellular pH in apple protoplasts, further decreased by MdLecRK2/MdVHAc” 1 overexpression. We conclude that V. mali secretes VmAGP1 to induce MdLecRK2 homo-dimerization, triggering a phosphorylation cascade with MdVHAc” 1 that acidifies apple cells to facilitate infection. This study reveals a novel pH manipulation strategy in V. mali pathogenesis, identifying potential targets for controlling Apple Valsa canker.