Seed germination and post-germination growth are strictly regulated by phytohormones. In Arabidopsis thaliana, jasmonate (JA) and auxin suppress these processes by boosting abscisic acid (ABA) signaling. However, whether...Seed germination and post-germination growth are strictly regulated by phytohormones. In Arabidopsis thaliana, jasmonate (JA) and auxin suppress these processes by boosting abscisic acid (ABA) signaling. However, whether there exists a transcriptional switch orchestrating the intricate interplay among these hormones and the underlying molecular mechanisms remain elusive. Herein, we demonstrated that endogenous JA signaling, involving the CORONATINE INSENSITIVE1 (COI1)-JASMONATE ZIM-DOMAIN (JAZ) module and the downstream MYC2, MYC3, and MYC4 transcription factors, potentiates auxin-induced ABA responses. MYC2, MYC3, and MYC4 interact with AUXIN RESPONSE FACTOR10 (ARF10) and ARF16. Consistently, MYC2 and ARF16 synergistically augment ABA signaling-delayed seed germination. Furthermore, MYC2 and MYC4 form a protein complex with ABSCISIC ACID INSENSITIVE5 (ABI5), a master activator of ABA signaling. Genetic analyses suggested that MYC2 positively facilitates ABA responses largely through ABI5. Notably, MYC2 collaborates with ARF16 to enhance the transcriptional activity and protein abundance of ABI5. Intriguingly, MYC2, ARF16, and ABI5 assemble into a ternary complex. Simultaneously disrupting MYC, ARF10/ARF16, and ABI5 renders the seed germination process insensitive to combined JA, auxin, and ABA. Collectively, our findings unveil the MYC-ARF10/ARF16-ABI5 module as a pivotal molecular switch that integrates JA, auxin, and ABA signaling pathways, thereby enabling plants to mount adaptive responses to challenging environmental conditions.
Each of the 4 different cytokinin (CK) base forms, trans-zeatin (tZ), isopentenyladenine (iP), dihydrozeatin (DHZ), and cis-zeatin (cZ) has distinct chemical metabolism and affinity to the CK Histidine Kinase (CHK) recep...Each of the 4 different cytokinin (CK) base forms, trans-zeatin (tZ), isopentenyladenine (iP), dihydrozeatin (DHZ), and cis-zeatin (cZ) has distinct chemical metabolism and affinity to the CK Histidine Kinase (CHK) receptors. However, it remains unclear how the specific biochemical features of each form, such as receptor specificity or metabolic differences, drive distinct tissue-specific physiological output in response to application of these CK bases. Here, we show that CK receptor preference and metabolic persistence together shape isoform-specific CK signaling strength, including tissue-dependent hormone responses in Arabidopsis leaf versus root assays. Physiological, genetic, and multi-omics integration was used to show that tZ and iP anti-senescence activity is matched by DHZ through a distinct receptor metabolic mechanism. DHZ requires Arabidopsis Histidine Kinase 3 (AHK3) signaling to be fully effective in a leaf dark-induced senescence (DIS) assay and where it overcomes its lower receptor affinity through higher metabolic persistence, accumulating at levels ∼2.5-fold above tZ and iP early in a senescence time course. Together, these findings provide a framework for integration of receptor preference and metabolic stability to determine CK isoform activity.
Alternative polyadenylation (APA) serves as a critical co-transcriptional regulatory mechanism that shapes mRNA fate and protein function. POLY(A) POLYMERASE 1 (PAPS1) contributes to poly(A) tail synthesis; however, its...Alternative polyadenylation (APA) serves as a critical co-transcriptional regulatory mechanism that shapes mRNA fate and protein function. POLY(A) POLYMERASE 1 (PAPS1) contributes to poly(A) tail synthesis; however, its relationship to poly(A) site choice is less well characterized. Here, we profiled PAPS1-associated poly(A) site usage across Arabidopsis (Arabidopsis thaliana) tissues using UMI-quantified poly(A) tag sequencing (qPAT-seq). Across tissues, paps1-4 showed tissue-dependent shifts in poly(A) site usage, with pronounced effects in pollen. In the paps1-4 mutant, polyadenylated transcripts were biased toward longer isoforms with significantly longer 3' UTRs, and poly(A) signal usage was altered in distinct ways: a U-to-A shift immediately downstream of poly(A) sites occurred in leaves and flower buds, whereas pollen showed more complex motif combinations with reduced usage of canonical cis-elements. In pollen, DE-APAGs included multiple genes previously linked to a pollen developmental regulatory module involving AT-RICH INTERACTING DOMAIN-CONTAINING PROTEIN 1 (ARID1), RETINOBLASTOMA RELATED 1 (RBR1), and DUO POLLEN1 (DUO1), showing coordinated changes in APA and expression. Flowering-time-related terms were also enriched among genes with significantly altered APA in paps1-4, including regulators connected to FLOWERING LOCUS C (FLC) and photoperiod responses, and these changes were more consistent with poly(A) site selection differences than with widespread poly(A) tail length changes. Notably, multiple poly(A) factors in pollen switched between single- and multi-poly(A) site usage patterns in paps1-4, representing a major component of PAPS1-associated regulation. Together, these findings reveal tissue-specific APA alterations associated with PAPS1 and highlight pollen and flowering pathways as key contexts of its regulatory influence.
Kakei Y, Okumura M, Yamazaki C
… +14 more, Kimura A, Ishiyama N, Kashima H, Kawashima R, Sato A, Hoson T, Soga K, Fujioka S, Mori H, Kamiyoshihara Y, Yamagami A, Nakano T, Asami T, Shimada Y
To achieve self-standability, the apical region of the stem must remain extensible and bendable, whereas the basal region must form a rigid supporting tissue. However, the mechanisms regulating stem growth along the apic...To achieve self-standability, the apical region of the stem must remain extensible and bendable, whereas the basal region must form a rigid supporting tissue. However, the mechanisms regulating stem growth along the apical-basal axis remain poorly understood. Here, we show that brassinosteroid (BR) biosynthesis and signaling are elevated in the apical, actively elongating regions of Arabidopsis and mung bean stems. Exogenous brassinolide promoted stem elongation, concomitant with increased cell wall extensibility, but impaired stem self-standability. In contrast, BR deficiency reduced the elongation/bendable zone and inhibited gravitropic curvature. Through spatiotemporal transcriptome analysis along the apical-basal axis of Arabidopsis inflorescence stems, combined with analysis of BR-responsive genes in the BR-dependent transition zone, we identified a set of genes, termed BR Down-regulated in Stem (BRDS) genes. BRDS gene expression was repressed by BR and predominantly expressed in the non-elongating region, indicating that BR plays a central role in spatial gene expression along the apical-basal axis. These genes were enriched for functions related to secondary cell wall formation, suggesting that BR differentially regulates primary and secondary cell wall formation. While auxin governs growth direction along the abaxial-adaxial axis of the stem, BR defines the spatial domains of elongation along the apical-basal axis of the stem. The synergistic action of these hormones determines both the direction and spatial domain of gravitropic bending, thereby enabling stem elongation, gravitropism, and standability in three-dimensional space.
Enhancing cotton fiber quality is essential for improving textile production. The transition from fiber elongation to secondary cell wall (SCW) synthesis is a critical developmental phase that determines both fiber lengt...Enhancing cotton fiber quality is essential for improving textile production. The transition from fiber elongation to secondary cell wall (SCW) synthesis is a critical developmental phase that determines both fiber length and strength. Although MYB transcription factors regulate the process, their precise functions remain incompletely characterized. In this study, we employed genome-wide identification and expression screening, together with candidate gene association analysis, to identify GhMYS1. This gene, selected from 186 cotton 1R-MYB transcription factors, is specifically expressed during the fiber elongation stage (5-15 days post-anthesis (DPA)). CRISPR/Cas9-mediated knockout of GhMYS1 significantly reduced fiber length, increased cell wall thickness, and raised the micronaire value compared to the control. Concurrently, expression of SCW synthesis-related genes GhCESA4, GhCESA8, and GhCOBRA4D was markedly up-regulated, accompanied by a pronounced increase in cellulose content. Yeast one-hybrid (Y1H), electrophoretic mobility shift (EMSA), and luciferase (LUC) assays demonstrated that GhHOX3 binds to the L1-box motif in the GhMYS1 promoter and activates its transcription in fibers and trichomes. The nuclear-localized GhMYS1 protein contains a C-terminal EAR motif with transcriptional repression activity. Through its N-terminal MYB domain, GhMYS1 binds directly to the promoters of GhCESA4 and GhCESA8, repressing their transcription and thereby delaying the onset of SCW deposition to facilitate fiber elongation. We propose a GhHOX3-GhMYS1-GhCESA4/8 regulatory module that governs the transition from fiber elongation to SCW synthesis. This study provides valuable genetic resources for molecular design breeding of cotton fiber quality and offers insights into the function of 1R-MYB transcription factors in fiber development.
The vegetative phase change (VPC) is precisely controlled by microRNA156 (miR156) in flowering plants. We previously showed that mature miR156 is mainly produced from MdMIR156a5 in apple (Malus domestica Borkh.) and that...The vegetative phase change (VPC) is precisely controlled by microRNA156 (miR156) in flowering plants. We previously showed that mature miR156 is mainly produced from MdMIR156a5 in apple (Malus domestica Borkh.) and that MdMIR156a5 expression and miR156 abundance were positively correlated with glutathione (GSH) contents during the VPC. In this study, we identified three transcription factor genes co-expressed with MdMIR156a5: the REVEILLE member MdRVE1-1, PHYTOCHROME-INTERACTING FACTOR 4 (MdPIF4), and BES1/BZR1 HOMOLOG 4 (MdBEH4). MdRVE1-1 activated MdMIR156a5 transcription by directly binding to its promoter, whereas MdBEH4 and MdPIF4 bound to the MdRVE1-1 promoter to indirectly promote MdMIR156a5 expression. MdBEH4 also directly induced MdPIF4 expression. Application of the brassinosteroid (BR) epibrassinolide or the GSH precursor 2-oxothiazolidine-4-carboxylate elevated BR and GSH contents, increased expression of MdBEH4, MdPIF4, MdRVE1-1, MdMIR156a5, and BR and GSH biosynthesis genes, and increased miR156 abundance, indicative of reciprocal promotion of GSH and BR biosynthesis and MdMIR156a5 expression. Overexpression of MdMIR156a6 in apple plants resulted in higher BR and GSH contents, higher expression of MdBEH4, MdPIF4, MdRVE1-1, MdMIR156a5, and BR and GSH biosynthesis genes, and higher miR156 abundance, defining a GSH-BR-miR156 positive feedback loop that becomes gradually attenuated during the VPC. These results establish that the MdBEH4-MdPIF4-MdRVE1-1-MdMIR156a5 module regulates miR156 abundance by integrating GSH and BR signaling pathways during the VPC in apple.
Plants respond to environmental cues, such as light and temperature, which regulate their growth and development. In the model plant Arabidopsis (Arabidopsis thaliana), PHYTOCHROME-INTERACTING FACTORS (PIFs) are central...Plants respond to environmental cues, such as light and temperature, which regulate their growth and development. In the model plant Arabidopsis (Arabidopsis thaliana), PHYTOCHROME-INTERACTING FACTORS (PIFs) are central regulators of both shade-avoidance and thermomorphogenesis. However, their functional roles in crop species are less well known. Here, we generated a tomato (Solanum lycopersicum) mutant lacking all eight known PIF genes (slpifo), to investigate their roles under controlled and field conditions. We showed that SlPIFs are essential for shade responses, while thermomorphogenesis-induced elongation is largely independent of SlPIFs, revealing species-specific differences in regulatory mechanisms. Under low-red to far-red light (low R/FR), slpifo plants failed to exhibit characteristic wild-type responses, including shoot elongation, expansion and thinning of leaf blades, and depletion of leaf chlorophyll. We further identified redundant roles for SlPIF1a, SlPIF4, and SlPIF8a in regulating stem elongation and chlorophyll depletion in response to low R/FR. In addition, slpifo plants exhibited reduced overall growth, fruit size, fruit number, and seed dormancy under field conditions, highlighting broader roles for SlPIFs beyond neighbor detection. These findings provide insights into how PIFs orchestrate organ-specific developmental plasticity in tomato, offering avenues to optimize light responsiveness for crop improvement.
Bosseno M, Demba A, Horta Araújo N
… +10 more, Colinet D, Israel A, Pacoud M, Maucourt M, El Fazaa Y, Jacob D, Lepetit M, Rolin D, Brouquisse R, Boscari A
Plant Physiol
· 2026 Jul · PMID 42302289
·
Full text
Nitrate reductase (NR) is a key enzyme in nitrate assimilation, yet its function within nodules remains poorly understood. In Medicago truncatula, 3 NR genes, MtNR1, MtNR2, and MtNR3, exhibit distinct evolutionary origin...Nitrate reductase (NR) is a key enzyme in nitrate assimilation, yet its function within nodules remains poorly understood. In Medicago truncatula, 3 NR genes, MtNR1, MtNR2, and MtNR3, exhibit distinct evolutionary origins and regulatory features. Phylogenetic analyses indicate that NR3-type genes, originated from a duplication of NR1 within the inverted repeat-lacking clade (IRLC) legumes, have lost the conserved phosphorylation sites critical for post-translational regulation. To assess the functional significance of these isoforms, we characterized single and double nr mutants obtained through Tnt1 transposon insertion under nitrate nutrition and during symbiosis. MtNR1 is the primary contributor to total NR activity, with nr1 and nr2 mutants retaining around 10% and 30% of wild-type levels, respectively. The nr1/nr2 double mutant shows an almost complete loss of NR activity and fails to survive under nitrate supply, demonstrating the essential and non-redundant roles of both isoforms. Under symbiotic conditions, single mutants displayed normal nodulation, whereas nodule development was nearly abolished in the double mutant despite continued MtNR3 expression. In addition to its role in nitrogen assimilation, single nr mutants showed increased sensitivity to hypoxic stress and impaired recovery of nitrogen fixation, revealing a role for NR in nodule energy metabolism through the phytoglobin-NO respiration pathway. We propose that the combined loss of NR1 and NR2 disrupts NO cycling linked to mitochondrial electron transport, thereby compromising the energy balance required for symbiosis under microoxic conditions. This work provides a framework to investigate NR diversification in legumes and opens perspectives for improving nitrogen fixation under environmental constraints.
Rice responds to salt stress by modulating a vast array of genes integrated into a sophisticated regulatory network. This complexity makes it challenging to identify the key genes and the specific alleles that confer tol...Rice responds to salt stress by modulating a vast array of genes integrated into a sophisticated regulatory network. This complexity makes it challenging to identify the key genes and the specific alleles that confer tolerance. We used time-course expression analysis to profile gene and miRNA expression associated with salt tolerance in Pokkali, a salt-tolerant rice variety. We established a framework for studying transcription factor-target(mRNA/miRNA) interactions using gene co-expression and machine-learning models. Moreover, we developed a hypergeometric distribution-based method to elucidate the interactions of salt stress-related miRNA-targets. Using these approaches, we established co-expression (GCN) and gene regulatory networks (GRN) based on co-expression and TF/miRNA-target interactions. Hub genes with high connectivity in our networks were enriched for previously reported salt tolerance genes, a finding largely supported by subsequent haplotype analysis of 374 rice accessions. Finally, we functionally validated three crucial hub genes, OsCAF1B, OsADR3 and Ospdr9, by demonstrating their roles in salt tolerance using their knockout mutants. The crucial genes, haplotypes and networks for salt tolerance identified in this study (resource available at https://cbi.njau.edu.cn/RiceSALTnet) provide a foundation for breeding rice cultivars with enhanced salt tolerance.
Fructan stores constitute the most important reserve carbohydrate pools of cool season (C3) grasses, but it is largely unknown how the variation of atmospheric CO2 concentration ([CO2]) between past and projected future...Fructan stores constitute the most important reserve carbohydrate pools of cool season (C3) grasses, but it is largely unknown how the variation of atmospheric CO2 concentration ([CO2]) between past and projected future levels affects their function in source (photosynthesis) - sink (growth and respiration) relationships. This study addressed this question with perennial ryegrass (Lolium perenne L.) grown at [CO2] of 200, 400 or 800 μmol mol-1 with growth-limiting nitrogen fertilization. Sixty-six days-old vegetative stands were labelled with 13CO2/12CO2 mixtures for 7 days and the 13C-tracer dynamics in whole-shoot sucrose, fructans, glucose and fructose pools evaluated with a four-pool compartmental model of central carbohydrate metabolism. Increasing [CO2] from 200 to 800 μmol mol-1 increased shoot mass 1.6-fold and fructan concentration from 35% to 50% of dry weight, while decreasing the nitrogen nutrition status of stands. Conversely, [CO2] had no effect on the half-lives of water-soluble carbohydrate pools (fructans, ∼7.7 days; sucrose, glucose and fructose, 2.3-4.5 hours). Carbon cycling through the fructan pool was enhanced by [CO2], increasing the mean residence time of carbon in the carbohydrate system from 9 to 14 days between 200 and 800 μmol mol-1 [CO2]. Sucrose resynthesis from breakdown products of fructans (fructose) was extensive and corresponded to 65% and 113% of concurrent sucrose neo-synthesis (or sucrose consumption in growth and respiration) at 200 and 800 μmol mol-1 [CO2], respectively. These results imply a strong constitutive buffering of sucrose availability in the source-sink system of perennial ryegrass (and likely most other C3 grasses) by fructan metabolism.
Plastid stromules are frequently observed under stress, yet their function remains enigmatic. In the current study, we tested two alternative hypotheses: stromules might channel metabolic flux from plastids to peroxisome...Plastid stromules are frequently observed under stress, yet their function remains enigmatic. In the current study, we tested two alternative hypotheses: stromules might channel metabolic flux from plastids to peroxisomes during jasmonate biosynthesis, or they might serve as conduits for plastid-nucleus retrograde signaling. We used Nicotiana tabacum BY-2 cells to investigate stromulation in non-photosynthetic plastids. Fluorescent markers for stroma, plastid outer membrane, peroxisomes, and the OPDA exporter were combined with confocal visualization and AI-based quantification of stromule frequency and length. Exogenous methyl jasmonate (MeJA) and salicylic acid (SA) each triggered a rapid (∼60 min) ∼3-fold increase in stromule frequency. This increase primarily resulted from more initiation events, rather than elongation. Disrupting microtubules with oryzalin stopped MeJA from causing stromule formation, while actin depolymerization had no effect. Inhibition of jasmonate biosynthesis with phenidone prevented SA-triggered stromule formation. Induction of genes for jasmonate biosynthesis (AOC) and response (JAZ1, JAZ3) by MeJA was amplified when stromulation was suppressed by oryzalin, suggesting that stromules act as modulators of jasmonate-dependent gene expression. The GFP-fusion of the OPDA exporter JASSY showed a significant preference for stromules, and over 80% of them associated with peroxisomes. Stromule frequency was highest during the cell-expansion phase. We discuss our findings in the context of a role for stromules in stress-dependent retrograde signaling from plastids to the nucleus.
Fusarium head blight (FHB), one of the most devastating diseases affecting wheat, is primarily caused by Fusarium graminearum. The TaHRC gene (also designated Fhb1), encoding a histidine-rich calcium-binding protein, exi...Fusarium head blight (FHB), one of the most devastating diseases affecting wheat, is primarily caused by Fusarium graminearum. The TaHRC gene (also designated Fhb1), encoding a histidine-rich calcium-binding protein, exists as two allelic variants, TaHRC-R (resistant) and TaHRC-S (susceptible), which are widely present in wheat cultivars. However, the role of TaHRC in FHB resistance remains controversial. In this study, we demonstrated that TaHRC physically interacts with Fg34, a secreted effector protein of F. graminearum. This interaction induced a translocation of TaHRC-R from the nucleus to the cytoplasmic membrane, thereby enhancing FHB resistance. In contrast, TaHRC-S retained nuclear localization and conferred susceptibility. In this study, we demonstrate that TaHRC physically interacts with Fg34, a secreted effector protein of F. graminearum. This interaction triggers the translocation of TaHRC-R from the nucleus to the plasma membrane, thereby enhancing resistance to FHB. In contrast, TaHRC-S remains localized in the nucleus and confers susceptibility. Notably, this is the first report of a direct physical interaction between TaHRC and a Fusarium-derived effector. The TaHRC-R/Fg34 complex elevates intracellular Ca2+ levels, activating calcium signaling pathways that reinforce FHB resistance. Furthermore, Fg34 also binds to TaCBL4, forming a ternary complex with TaCIPK5 that enhances TaCIPK5 kinase activity, leading to increased phosphorylation of TaRBOHB. Collectively, these findings elucidate a novel calcium-signal-dependent mechanism potentially mediated by TaHRC underlying Fusarium head blight resistance in wheat. These discoveries deepen the understanding of the molecular mechanisms of Fusarium head blight resistance and provide a theoretical foundation for developing breeding strategies for durable disease resistance.
Verticillium wilt (VW) severely limits cotton production, yet the molecular mechanisms underlying cotton immunity remain incompletely understood. Here, comparative transcriptomic analyses of resistant and susceptible cot...Verticillium wilt (VW) severely limits cotton production, yet the molecular mechanisms underlying cotton immunity remain incompletely understood. Here, comparative transcriptomic analyses of resistant and susceptible cotton germplasms identified the cold-regulated gene GhCOR27 as a positive regulator of VW resistance. GhCOR27 expression was consistently induced by Verticillium dahliae infection in both resistant and susceptible materials. Functional validation showed that silencing GhCOR27 enhanced susceptibility, whereas its overexpression in cotton and Arabidopsis markedly improved VW resistance. Through yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), luciferase complementation (LCI), co-immunoprecipitation (Co-IP) and GST pull-down, we further demonstrated that GhCOR27 directly interacts with the trihelix transcription factor GhASIL1. Silencing and overexpression in Arabidopsis revealed GhASIL1 acts as a negative regulator of VW resistance. Transcriptome profiling indicated that GhCOR27 and GhASIL1 coregulate the phenylpropanoid pathway, lignin accumulation, and ROS/NO signaling during defense. Mechanistically, DNA affinity purification sequencing (DAP-seq), yeast one-hybrid (Y1H), dual-luciferase (LUC) and electrophoretic mobility shift assay (EMSA) assays revealed that GhASIL1 directly binds the GT-box cis-element in the promoter of GhERF114, a defense-related transcription factor, and represses its expression. Importantly, GhCOR27 antagonizes GhASIL1-mediated repression of GhERF114 without binding to the GhERF114 promoter itself. Subsequently, GhERF114 activates the expression of the lignin biosynthetic gene GhHCT1, thereby promoting lignification and strengthening disease resistance. Together, we conclude that GhCOR27 confers VW resistance in cotton by relieving the GhASIL1-GhERF114-mediated repression of lignin accumulation, which provide a new insight into the molecular mechanisms of cotton defense against VW.
The C18OO fractionation during photosynthesis (Δ18OA), a powerful isotopic proxy, is strongly influenced by the 18O exchange between CO2 and leaf water. Δ18OA is believed to relate to physiological parameters such as the...The C18OO fractionation during photosynthesis (Δ18OA), a powerful isotopic proxy, is strongly influenced by the 18O exchange between CO2 and leaf water. Δ18OA is believed to relate to physiological parameters such as the evaporative 18O enrichment of leaf water (Δe), CO2 influx and efflux; however, the key mechanism remains unclear. Here, we investigated the response of Δ18OA to short-term changes in CO2 levels in three C3 species (Helianthus annuus, Vigna unguiculata and Triticum aestivum) and one C4 species (Cleistogenes squarrosa) grown under different levels of vapor pressure deficit (VPD) and nitrogen supply. We found a significant CO2 effect on Δ18OA for C. squarrosa, but not for the C3 species. Δ18OA was not significantly correlated with Δe in the C3 species, and Δ18OA of the C4 species was not sensitive to changes in Δe driven by VPD. The gross CO2 efflux and Δ18OA were significantly correlated for both C3 and C4 species (r2 = 0.92), demonstrating its role in regulating Δ18OA. We also found that the C3 species had significantly higher Δ18OA than the C4 species, due to the lower ratio of intercellular to atmospheric CO2 (Ci/Ca) in the latter. Δ18OA was significantly (r2 = 0.94) correlated with Ci/Ca, supported by a compiled literature dataset that included 31 species. Our study reveals the distinct difference in Δ18OA between C3 and C4 species and the remarkable relationship between Δ18OA and Ci/Ca, providing new insights into how Δ18OA can be used to infer carbon cycle processes from leaf to ecosystem scales.