Molecular Plant最新文献

{"title":"Omics-assisted genetic dissection and coordinated improvement of apple flesh color, flavor, and fruit size.","authors":"Nan Wang, Wenjun Liu, Xuelian Han, Zhiqiang Li, Xin Jing, Zongying Zhang, Hongcheng Fang, Shuhui Zhang, Haifeng Xu, Qi Zou, Lei Yu, Tongyao Xu, Tong Wang, Ran Chen, Jiahao Zhao, Lingyu Meng, Zijing Chen, Shujing Wu, Dagang Hu, Zhiquan Mao, Chengzhi Jiao, Wei Xu, Zhangjun Fei, Yuanming Zhang, Jie Luo, Xuesen Chen","doi":"10.1016/j.molp.2026.05.021","DOIUrl":"10.1016/j.molp.2026.05.021","url":null,"abstract":"<p><p>Breeding red-fleshed apples with enhanced health benefits is a primary objective of modern apple improvement, yet high acidity and small fruit size limit their commercial potential. Resolving trade-offs among flesh color, flavor, and appearance and dissecting their underlying genetic relationships remain major challenges. In this study, using the red-fleshed 'CSR6R6' (Malus sieversii) and the cultivated 'Royal Gala' (M. domestica) as parents, we developed an F₁ population comprising 140 individuals and performed integrative large-scale multi-omics analyses, identifying 13,331,096 SNPs and 2,134 metabolites. Red flesh correlated positively with malic acid but negatively with fruit weight. A major QTL linked to red flesh was mapped, and six genes regulating anthocyanin and proanthocyanidin biosynthesis were functionally validated, including MdUGT89A2.1, MdUGT89A2.2, MdALMT4, MdALMT4-like, MdTT1, and MdLAR1. Notably, MdALMT4 and MdALMT4-like encode malate transporters that coordinate malate accumulation and anthocyanin biosynthesis, suggesting a genetic link between acidity and pigmentation. Integrative multi-omics analysis revealed a large-scale regulatory network, revealing gene-metabolite-phenotype interactions and accurately predicting pathways involving the anthocyanin regulator MdTT1 and the fruit shape gene MdMADS13. Leveraging this network, we identified opposing effects of red-flesh QTL haplotypes across traits, defining the genetic basis of phenotypic antagonism, and resolved 11 positive and 13 negative haplotypes affecting red flesh, malic acid, and fruit weight. Pseudo-backcrossing further demonstrated that aggregating positive haplotypes substantially mitigates trade-offs among flesh color, flavor, and appearance, enabling their concurrent improvement. These findings will advance omics-assisted apple breeding, offering potential strategies for genetic improvement of other perennial fruit trees.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1678-1694"},"PeriodicalIF":32.7,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148150395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Getting heated: Temperature signaling from the cell membrane to the nucleus.","authors":"Wei Zeng, Philip A Wigge","doi":"10.1016/j.molp.2026.06.002","DOIUrl":"10.1016/j.molp.2026.06.002","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1556-1558"},"PeriodicalIF":32.7,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148205600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abiotic stress sensing in plants: Biochemical and biophysical basis.","authors":"Qingya Lv, Jiawei Li, Changyun Liu, Kenz R Samraoui, Stephanie Hutin, Xu Li, Faming Dong, Haiyan Xiong, Yidan Ouyang, Honghong Hu, Yibo Li, Jo Hepworth, Jae-Hoon Jung, Xiangsong Chen, Chloe Zubieta, Lizhong Xiong, Yang Zhao, María José Clemente-Moreno, Xiaofeng Fang, Emily Flashman, Jörg Kudla, Xuelei Lai","doi":"10.1016/j.molp.2026.05.007","DOIUrl":"10.1016/j.molp.2026.05.007","url":null,"abstract":"<p><p>Plants cannot relocate when environmental conditions become unfavorable and therefore rely on sophisticated mechanisms to perceive, interpret, and respond to stresses. Stress sensing constitutes the first and often most decisive step in adaptation, because it determines how efficiently downstream signaling and protective responses are initiated. This review focuses on the biochemical and biophysical basis of abiotic-stress sensing, highlighting the fundamental molecular logic by which physical and chemical environmental changes are encoded, perceived, and converted into biological signals. We discuss representative sensing mechanisms associated with temperature stress, drought, salt and alkali stress, flooding, and soil compaction, and examine general messengers, including Ca²⁺ and reactive oxygen species, as central integrators across diverse abiotic stresses. Finally, we identify major outstanding questions, including the identity of the primary stress-associated cues, the spatial organization of sensing, and the perception of combined stresses, and highlight emerging approaches, including AI-driven biomolecular modeling, single-cell techniques, synthetic biology, and genome editing, as powerful tools to advance the mechanistic understanding of plant stress sensing.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1571-1606"},"PeriodicalIF":32.7,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147949010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heat shock-induced zinc efflux repurposes Arabidopsis E3 ligase EMR as a molecular chaperone.","authors":"Ho Byoung Chae, Su Bin Bae, Joung Hun Park, Seol Ki Paeng, Seong Dong Wi, Meiai Zhao, Min Gab Kim, Woe-Yeon Kim, Sang Yeol Lee","doi":"10.1016/j.molp.2026.05.024","DOIUrl":"10.1016/j.molp.2026.05.024","url":null,"abstract":"<p><p>EMR, an endoplasmic reticulum (ER)-associated degradation-mediating RING-finger E3 ligase initially identified as an ER-resident protein, was unexpectedly detected in the cytoplasm under ER stress conditions. This unanticipated subcellular distribution prompted us to explore the uncharacterized functions of cytoplasmic EMR. Using an integrated approach that combines bioinformatics, biochemical, and physiological analyses, we show that EMR also acts as a specific heat-responsive regulator. Heat exposure causes Zn²⁺ to dissociate from the RING-finger domain of EMR, triggering a conformational change from monomeric to oligomeric form driven by increased hydrophobicity. This structural reorganization, mediated by Zn²⁺ coordination, transforms EMR's function from an E3 ligase to a molecular chaperone. Importantly, this functional switch contributes significantly to plant thermotolerance, as EMR's chaperone activity effectively prevents heat-induced protein unfolding and aggregation of vital cellular proteins. Consequently, transgenic Arabidopsis lines overexpressing EMR in an EMR-null-mutant (emr) background, 35S:EMR, showed significantly improved thermotolerance compared to wild-type and emr plants. The critical role of EMR's chaperone activity in conferring heat-stress resistance was further substantiated by the observation that 35S:EMR(C/S) plants, in which EMR(C/S) primarily retains chaperone function, exhibited heat-stress tolerance comparable to that of 35S:EMR plants. Proteomic profiling after heat shock identified candidate client substrates of EMR's chaperone activity, which are mainly involved in critical cellular processes such as protein translation and energy metabolism, highlighting EMR's broad cytoprotective role. Taken together, these results demonstrate that the bifunctional properties of EMR are essential for environmental-stress recognition and adaptive signaling, thereby driving thermotolerance in plants.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1695-1710"},"PeriodicalIF":32.7,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148150453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural snapshots of plant-specific KCS6-CER2 complex reveal the elongation mechanism of very-long-chain fatty acids.","authors":"Yang Wang, Haiyan Wang, Xianpeng Yang, Yujiao Qin, Rangwei Xu, Ting Liu, Chunmei Shi, Hongyan Zhang, Linlin Zhong, Xiaolu Qu, Feng Zhu, Xiuxin Deng, Youwei Xu, Qianmin Wang, Yunjiang Cheng","doi":"10.1016/j.molp.2026.07.007","DOIUrl":"10.1016/j.molp.2026.07.007","url":null,"abstract":"<p><p>Very-long-chain fatty acids (VLCFAs) are essential building blocks for sphingolipids, phospholipids, triacylglycerols, suberin, and cuticular waxes, all of which play crucial roles in plant development and environmental adaptation. The elongation of VLCFAs is governed by plant-specific β-ketoacyl-CoA synthases (KCSs) and ECERIFERUM2 (CER2) family proteins. However, the structural catalytic mechanisms underlying VLCFA elongation remain poorly understood. Here, we present structural snapshots of the KCS6-CER2 complex from the evolutionarily representative vascular plant Selaginella moellendorffii in multiple elongation reaction states. These structures delineate how the acyl chain of the substrate C22:0 acyl-CoA (behenoyl-CoA), the two-carbon donor malonyl-CoA, and the product C24:0 β-ketoacyl-CoA (3-oxo-lignoceroyl-CoA) sequentially engage the substrate binding channel of the KCS6-CER2 complex on the cytosolic side of the endoplasmic reticulum membrane. We further identify a previously unrecognized side channel that accommodates an additional acyl-CoA molecule, indicating an unexpected structural feature for VLCFA biosynthesis. In addition, structural and biochemical analyses of the KCS6-CER2 complex reveal that CER2 acts as a structural cofactor, extending the hydrophobic substrate binding channel of KCS6. Together, these findings uncover the molecular mechanism by which KCS6 and CER2 collaborate to drive chain-length-specific VLCFA elongation and provide a structural framework for understanding and engineering VLCFA elongation across the plant kingdom.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":32.7,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The SlbZIP30-SlbZIP51 module safeguards photosynthesis under chilling stress by coordinating nuclear transcriptional activation and chloroplast protein stabilization in tomato","authors":"Yingqi Hu, Tiantian Wang, Guanghong Zhang, Nana Ma, Chong Chen, Wei Lv, Chuanzhao Wu, Baozhen Jiao, Zeen Yao, Ke Bi, Minghui Zhang, Feng Xiong, Xiaocui Ma, Congming Lu, Qingwei Meng, Kunyang Zhuang","doi":"10.1016/j.molp.2026.07.001","DOIUrl":"https://doi.org/10.1016/j.molp.2026.07.001","url":null,"abstract":"Chilling stress severely restricts plant growth and productivity by impairing photosynthetic performance. However, the molecular mechanisms underlying chilling-induced photoinhibition and its mitigation remain incompletely understood. Here, we functionally characterized two basic leucine zipper (bZIP) transcription factors, SlbZIP30 and SlbZIP51, from tomato (<ce:italic>Solanum lycopersicum</ce:italic>), identifying them as important regulators involved in photosynthetic protection in response to chilling stress. SlbZIP30 localizes to both chloroplasts and the nucleus with distinct compartment-specific functions. In chloroplasts, SlbZIP30 interacts with and stabilizes triose phosphate isomerase 1 (SlTPI1) and light-harvesting complex protein SlLHCA1 to preserve photosynthetic machinery integrity. In the nucleus, chilling induces SlbZIP51 translocation from the cytoplasm, where it forms a heterodimer with SlbZIP30 and activates transcription of <ce:italic>SlCPN60α1</ce:italic>, <ce:italic>SlTPI2</ce:italic> and <ce:italic>SlRBCS1</ce:italic>, which encode chaperonin 60 subunit alpha 1, triose phosphate isomerase isoform, and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit 1, respectively. These proteins support carbon assimilation, sustaining photosynthetic capacity under chilling stress. Collectively, our findings uncover a photoprotective mechanism mediated by dual-localized SlbZIP30, which coordinates chloroplastic protein stabilization and nuclear transcriptional regulation to mitigate chilling-induced photodamage, providing a practical framework for engineering chilling-resilient crops.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"56 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148402002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Translation-dependent retrograde signaling coordinates high-light acclimation in plants","authors":"Marten Moore, Aaron B. Smith, Melanie Wegener, Pravin B. Khambalkar, Rebeccah Victoria Tyrrell, Brea Camille Watts, Samuel J. Nix, Hong Ting Tsang, Mohammad A. Farooq, Diep R. Ganguly, Robert T. Furbank, Maria Ermakova, Barry J. Pogson, Karl-Josef Dietz","doi":"10.1016/j.molp.2026.07.002","DOIUrl":"https://doi.org/10.1016/j.molp.2026.07.002","url":null,"abstract":"Canonical chloroplast retrograde signaling is typically defined as chloroplast-initiated signaling circuits that regulate nuclear transcription for acclimation. This study reveals that high light (HL) also initiates translation-dependent retrograde signaling pathways (TraDeRS), which bifurcate to increase translation of chloroplast-targeted proteins and nuclear transcription factors thereby enhancing photosynthesis and reducing photoinhibition. Reprogramming of translation within 10 min of HL predominates over transcriptional regulation, evidenced by global downregulation of translation based both on ribosomal footprints (RPF) and polysome profiles in <ce:italic>Arabidopsis</ce:italic>. RPF-seq reveal four distinct subsets of transcripts for ribosome-mediated regulation: two subsets showing changes in ribosomal association only, and two showing combined changes of ribosomal association and transcript abundance. The ‘increased translation’ subset is enriched for chloroplast-targeted photosynthetic proteins containing evolutionarily-conserved 5’-UTR mRNA motifs. The motifs bind and release an RNA-binding protein, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), in a HL and co-factor dependent manner. The motifs were sufficient to increase reporter gene translation and Rieske protein expression in vitro and in <ce:italic>Setaria viridis</ce:italic>. This light intensity-dependant, redox-regulated switch responds to pharmacological treatments that perturb photosynthesis and retrograde signaling, but not a generic abiotic stress, namely heat. It promotes the translation of photosynthesis proteins and HL-responsive transcription factors, such as Stress-associated proteins (SAPs), creating a rapidly responsive feed-forward loop to amplify known retrograde transcriptional responses, thereby reducing photoinhibition. The functional conservation of the GAPDH-motif interaction in <ce:italic>Setaria viridis</ce:italic> foreshadows new strategies for improving photosynthesis and expands our understanding of translational control mechanisms in response to chloroplast communication.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"6 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148401889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning uncovers conserved regulatory logic and element dosage underlying stable gene expression in grasses.","authors":"Jiacheng Li, Xinbing Xu, Chunjiao Xia, Yinmeng Liu, Luchang Ming, Wenhui Li, Yujian Yang, Weibo Xie","doi":"10.1016/j.molp.2026.05.017","DOIUrl":"10.1016/j.molp.2026.05.017","url":null,"abstract":"<p><p>Gene expression programs are widely conserved across grasses despite rapid evolutionary turnover of cis-regulatory element (CRE) sequences, yet the mechanisms that maintain expression stability remain unclear. In this study, we generated chromatin accessibility (CA) maps and matched transcriptomes for five orthologous tissues across five Poaceae species, and trained deep learning models to predict CA from DNA sequence. Models trained in one species accurately predicted CA in rice, with cross-species correlations frequently exceeding 0.70, indicating that the regulatory logic mapping sequence to CA remains conserved despite extensive non-coding divergence. We developed Basenji-HMM, which combines deep-learning-derived mutational effect profiles and a hidden Markov model to delineate high-impact candidate CREs (cCREs) at nucleotide resolution. Integrating Basenji-HMM with motif scanning and footprinting identified complementary cCRE classes and revealed strong positional and tissue-dependent regulatory architectures. Although only 27%-36% of rice cCREs have detectable sequence orthologs in other grasses, cCRE abundance around orthologous genes is conserved across species and aligns with conserved CA and expression. These results support a \"regulatory equivalence\" model, wherein compensatory CRE turnover may maintain element dosage under conserved regulatory logic, thereby preserving stable gene expression across grass species.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1473-1493"},"PeriodicalIF":32.7,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Age-dependent nuclear accumulation of the membrane-associated NAC transcription factor GER1 activates SA biosynthesis to promote leaf senescence in Arabidopsis.","authors":"Yi Wang, Yutao Wang, Fengying An, Yu Cao, Ping Chen, Xuanzhi Wang, Hongwei Guo, Genji Qin","doi":"10.1016/j.molp.2026.05.013","DOIUrl":"10.1016/j.molp.2026.05.013","url":null,"abstract":"<p><p>Leaf senescence is a programmed physiological process that enhances nutrient use efficiency, thereby promoting plant adaptation and crop productivity. However, the molecular mechanisms that govern the initiation and precisely control the progression of senescence remain poorly understood. Here, we identify GERAS1 (GER1), a membrane-associated NAC transcription factor that acts as an age-dependent integrator of the leaf senescence program. As leaves age, GER1 expression is induced, and its protein undergoes age-dependent translocation from the plasma membrane to the nucleus. The activation tagging mutant ger1-D exhibits early leaf senescence, while the disruption of GER1 and its three homologs in a quadruple ger1 ger2 ger3 ger4 mutant causes significantly delayed leaf senescence. We further show that the nucleus-localized GER1 directly binds and activates the promoter of the central senescence regulator ORE1. Moreover, GER1 and ORE1 form a transcriptional activation complex that directly upregulates SID2, which encodes a key salicylic acid (SA) biosynthetic enzyme. The accumulation of SA in turn promotes the expression of GER1, establishing a positive feedforward loop that drives leaf senescence. Taken together, these findings not only unveil that GER1 acts as a central spatiotemporal regulator of leaf senescence, but also uncover a straightforward membrane-to-nucleus signaling pathway that finely regulates leaf aging.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1452-1472"},"PeriodicalIF":32.7,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148005843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering plant phytoalexin biosynthetic pathways for broad-spectrum disease resistance.","authors":"Minghuan Bi, Yuexiao Li, Savithramma P Dinesh-Kumar, Yongliang Zhang","doi":"10.1016/j.molp.2026.05.011","DOIUrl":"10.1016/j.molp.2026.05.011","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1341-1344"},"PeriodicalIF":32.7,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147988362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}