Journal of Integrative Plant Biology最新文献

{"title":"Histone deacetylase MiHDA3 enhances mango fruit resistance to Colletotrichum gloeosporioides by deacetylating MiCAT1.","authors":"Yue Xiang, Donald J Huber, Lisha Zhu, Xuewu Duan, Xiangbin Xu, Yueming Jiang, Guoxiang Jiang, Zhengke Zhang","doi":"10.1111/jipb.70023","DOIUrl":"10.1111/jipb.70023","url":null,"abstract":"<p><p>The anthracnose caused by Colletotrichum gloeosporioides poses a significant threat to the global mango (Mangifera indica L.) fruit industry. Although histone deacetylases (HDACs) are well recognized to be involved in plant immunity, the role of HDAC-mediated nonhistone deacetylation in the fruit immune response remains elusive. In the present study, MiHDA3, an HDAC from the RPD3/HDA1 subfamily, was identified as a candidate for regulating mango resistance based on the greatest induction of MiHDA3 in response to infection of C. gloeosporioides among the 19 tested HDAC genes. Transient overexpression of MiHDA3 in mango fruit strengthened the disease resistance by enhancing the activities of defense-related enzymes (phenylalanine ammonia-lyase (PAL) and β-1,3-glucanase (GLU)) and upregulating the expression levels of MiPAL and MiGLU. These increases occurred concomitantly with increased accumulation of local H₂O₂, a critical signaling molecule. The opposite effects on resistance and H₂O₂ production were observed in MiHDA3-silenced mango fruit. Physiological assays revealed that exogenous H₂O₂ treatment suppressed anthracnose development in mango fruit after inoculation with C. gloeosporioides, whereas treatment with diphenylene iodonium, an inhibitor of endogenous H₂O₂ generation, exacerbated disease symptoms. Furthermore, the mango catalase 1 (MiCAT1), a redox homeostasis-related protein, was confirmed to negatively regulate the resistance of mango fruit to C. gloeosporioides by catalyzing the decomposition of H₂O₂. Mechanistic investigations revealed that MiHDA3-mediated deacetylation of MiCAT1 at lysine residues K227 and K233 reduced the enzymatic activity and protein stability of MiCAT1, contributing to enhanced resistance in mango fruit. Collectively, these findings highlight that the functional interplay between HDACs and catalases can modulate the immune response in post-harvest fruits, and reveal a novel mechanism by which HDACs enhance mango disease resistance through the deacetylation of nonhistone proteins and the regulation of their biochemical functions.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870559","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":"MdGRF10 phosphorylation stabilizes MdASMT1 for melatonin-mediated salt tolerance in apple.","authors":"Zehui Hu, Tianci Yan, Tong Zhang, Silong Dong, Yixue Bai, Handong Song, Chanyu Wang, Xin Liu, Ruoxue Li, Hongpeng Zhao, Bingcan Lv, Yan Guo, Jin Kong","doi":"10.1111/jipb.70021","DOIUrl":"10.1111/jipb.70021","url":null,"abstract":"<p><p>Salt stress, especially the increasing secondary salt stress, severely compromises apple production worldwide. Mitigation of oxidative damage caused by salt stress is critical for salt tolerance in apple plants. However, it remains unclear how the salt signal triggers the excessive reactive oxygen species (ROS) mitigation system in apple. In this study, we identified a salt-induced gene MdGRF10 (encoding a 14-3-3 protein), whose overexpression conferred transgenic apple plants reduced oxidative damage and enhanced salt tolerance. Furthermore, a salt-activated receptor-like cytoplasmic kinase MdPBL34 was found to interact with and phosphorylate the C-terminal of MdGRF10. This phosphorylation promoted the interaction between MdGRF10 and a melatonin rate-limiting synthetase MdASMT1 (N-acetylserotonin methyltransferase). Its overexpression or knockdown by CRISPR/Cas9 in transgenic apple plants demonstrated that MdASMT1 is critical in melatonin-mediated ROS scavenging for salt tolerance. Their interaction stabilizes MdASMT1 by decreasing its ubiquitin-mediated degradation for increased melatonin level, decreased oxidative damage and therefore promoted salt tolerance. Our findings revealed that 14-3-3 protein could integrate the salt signal in a phosphorylation-dependent manner. Moreover, MdPBL34 was also identified for the first time to be involved in salt signaling. Our research uncovered a novel MdPBL34-MdGRF10-MdASMT1 regulatory module in response to salt stress in apple, which will contribute to the molecular breeding of melatonin-enriched salt-tolerant apple trees.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870560","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 miR172a-ERF416/413 module regulates soybean seed traits.","authors":"Meng Jin, Jia-Qi Han, Lu-Yao Zhang, Zhi-Hao Jiang, Yue Liu, Jun-Jie Wei, Ling-Yi Zheng, Shang-Shang Xiong, Yang Hu, Tong Cheng, Xiao-Hua Bian, Chun-Mei Wu, Wei Wei, Yi-Hua Huang, Cui-Cui Yin, Feng Gao, Wei Li, Ying-Dong Bi, Yong-Cai Lai, Bin Zhou, De-Yue Yu, Shou-Yi Chen, Jian-Jun Tao, Wan-Ke Zhang, Jin-Song Zhang","doi":"10.1111/jipb.70015","DOIUrl":"https://doi.org/10.1111/jipb.70015","url":null,"abstract":"<p><p>Soybean (Glycine max) provides vegetable oils and proteins for human consumption. Its production depends on seeds and other production-related agronomic traits. How the seed traits are regulated in soybean remains largely unclear. In this study, we identified a miR172a-ERF416/413 module for the regulation of seed traits. The miR172a can cleave the targets ERF416 and ERF413 to affect the downstream gene expression for the reduction of soybean seed size and weight. Both the MIR172a-overexpressing transgenic soybean plants and the erf416/413 mutants produced smaller seeds than the control. Consistently, the ERF416-overexpressing transgenic soybean plants generated larger seeds. ERF416 and ERF413 were directly targeted to the promoter of GmKIX8-1 and GmSWEET10a to regulate their gene expression for seed size/weight control. Interestingly, the erf416/413 mutants showed higher seed yield per plant and higher total seed fatty acid (FA) content, whereas the MIR172a-transgenic soybean had lower total seed FA content compared with the control cultivar, suggesting that miR172a and ERF416/413 may function in FA accumulation through different pathways. Haplotypes of the ERF416 promoter region were further analyzed and Hap1 was correlated with higher gene expression and higher seed weight, while Hap3 was correlated with higher total seed lipid content. Our study revealed a new module for seed trait control. Manipulation of such alleles should facilitate breeding for high-oil and high-yield soybean cultivars.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843886","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":"Clonal longevity and the enigmatic flowering of woody bamboos are associated with rates of protein evolution.","authors":"Xin Wang, Zhi-Hua Zeng, Peng-Fei Ma, Yun-Long Liu, Hua-Ying Sun, Hong Wang, Hong Ma, De-Zhu Li, Wei Zhou","doi":"10.1111/jipb.70019","DOIUrl":"https://doi.org/10.1111/jipb.70019","url":null,"abstract":"<p><p>Rates of protein evolution (d_N/d_S) vary widely across the tree of life. In plants, both life-history traits and GC-biased gene conversion (gBGC) are thought to contribute to this variation, although disentangling their individual contributions remains a challenge. Using information on variation in life-history traits and molecular data in 148 species from Poaceae subfamilies Bambusoideae (mostly woody) and Pooideae (exclusively herbaceous), we investigated the relative importance of modes of reproduction and the non-selective forces of gBGC on protein evolutionary rates between the two subfamilies. Elevated rates of protein evolution associated with relaxed purifying selection were more evident in woody bamboos than in Pooideae and were better explained by reproductive modes than by traits that are likely proxies of effective population size. Although gBGC slightly reduced protein evolutionary rates in both subfamilies, its contribution had only a limited effect on molecular divergence between the groups. Forward simulations generally supported our empirical results on the influence of reproductive mode on selection and gBGC. Our findings from two sister lineages of the grass family provide evidence for association between protein evolution and life-history traits governing reproductive mode and enhance understanding of molecular evolution in plants with contrasting reproductive strategies.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833562","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":"Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales.","authors":"Ying-Ying Yang, Gregory W Stull, Xiao-Jian Qu, Min Deng, Lei Zhao, Yi Hu, Zhi-Heng Wang, Hong Ma, De-Zhu Li, Stephen A Smith, Ting-Shuang Yi","doi":"10.1111/jipb.70011","DOIUrl":"https://doi.org/10.1111/jipb.70011","url":null,"abstract":"<p><p>While many plant lineages display remarkable diversity in morphological form, our understanding of how phenotypic diversity, or disparity, arises in relation to genomic evolution over geologic scales remains poorly understood. Here, we investigated the relationship between phenotypic and genomic evolution in the Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. We examine newly generated transcriptomic and trait datasets representing most extant genera and a rich diversity of Cretaceous fossil representatives. Our phylogenomic analyses identify recurrent hotspots of gene duplication and genomic conflict across the order. Our phenotypic analyses showed that the morphospace occupied by Fagales was largely filled by the early Cenozoic, and rates of evolution were highest during the early radiation of the Fagales crown and its major families. These results suggest that Fagales conforms to an \"early-burst\" model of disparification, with morphospace being filled early in the order's diversification history, and that elevated levels of phenotypic evolution also often correspond to hotspots of gene duplication. Species diversification appears decoupled from patterns of both phenotypic and genomic evolution, highlighting the multidimensional nature of the evolution of plant diversity across geological timescales.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833565","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":"Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules","authors":"Lixiang Wang,&nbsp;Chunhai Mai,&nbsp;Suqin He,&nbsp;Bingjie Niu,&nbsp;Gaiya Jia,&nbsp;Tao Yang,&nbsp;Yiwei Xu,&nbsp;Meng Ren,&nbsp;Xiaorui Zhao,&nbsp;Xin Liu,&nbsp;Zhaosheng Kong","doi":"10.1111/jipb.70007","DOIUrl":"10.1111/jipb.70007","url":null,"abstract":"<p>Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil-borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three-dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high-resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high-throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive <i>cis</i>-interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase-accessible chromatin with high-throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation-related genes. Notably, novel TADs and long-range chromatin loops are detected in peanut nodules, including an H3K27me3 modification-mediated loop that may regulate the expression of <i>Nodule Inception</i>. Another altered chromatin loop highlights the nodule highly expressed <i>AhMsrA</i> gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 10","pages":"2624-2642"},"PeriodicalIF":9.3,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The bZIP3-AS1 complex promotes CONSTANS-induced FLOWERING LOCUS T activation in a daylength-dependent manner.","authors":"Wonbok Lee, Sun Ho Kim, Junsang Park, So Hee Yoon, Sung Won Cho, Nayoung Lee, Shogo Ito, Takato Imaizumi, Jong Chan Hong, Woo Sik Chung, Young Hun Song","doi":"10.1111/jipb.70014","DOIUrl":"10.1111/jipb.70014","url":null,"abstract":"<p><p>Plants monitor daylength to synchronize their flowering time with their surroundings and thus maximize reproductive fitness. In Arabidopsis (Arabidopsis thaliana), CONSTANS (CO) activates the expression of FLOWERING LOCUS T (FT); this activation is a crucial aspect of the daylength-dependent regulation of flowering time. Here, we demonstrate that the basic leucine zipper 3 (bZIP3) transcription factor is important for CO-induced FT expression under long photoperiod conditions in Arabidopsis. We isolated bZIP3 as a CO-interacting protein by yeast two-hybrid screening and verified bZIP3-CO complex formation in Arabidopsis through co-immunoprecipitation assays. The temporal and spatial expression patterns of bZIP3 are very similar to those of CO, and bZIP3 protein levels fluctuate throughout the day, with high abundance in the late afternoon. The bzip3 mutant displayed delayed flowering under long photoperiods, whereas bZIP3 overexpression accelerated flowering regardless of daylength. bZIP3 directly binds to the FT promoter region containing CO-responsive elements in vivo. FT messenger RNA (mRNA) levels in the bzip3 mutant and bZIP3 overexpression lines correlated with their flowering times and changed only during the daytime. bZIP3 overexpression resulted in significantly lower FT transcript levels in the co mutant background than in the wild type. Furthermore, bZIP3 forms a complex with ASYMMETRIC LEAVES1 (AS1), a CO partner that helps CO induce FT expression. The bzip3 as1 double mutant flowered later than the two single mutants under longer daylengths, and FT mRNA levels were much lower in the double mutant than in the bzip3 single mutant. Collectively, our findings uncover a new layer of photoperiod-dependent FT regulation in which bZIP3 facilitates CO to activate FT transcription by forming a complex with AS1.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833566","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":"Expanding functionalities of immune receptors through simultaneous transfer of sensor and helper NLRs.","authors":"Dongjiao Wang, Qibin Wu, Daowen Wang, Youxiong Que, Zheng Qing Fu","doi":"10.1111/jipb.70020","DOIUrl":"https://doi.org/10.1111/jipb.70020","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833564","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":"Genetic optimization of the source, sink and flow for increasing seed oil content in rapeseed.","authors":"Wenhao Shen, Liangqian Yu, Qian Qu, Xu Han, Wei Ma, Feng Zu, Liang Guo, Shan Tang","doi":"10.1111/jipb.70017","DOIUrl":"https://doi.org/10.1111/jipb.70017","url":null,"abstract":"<p><p>Rapeseed (Brassica napus) is one of the most important oilseed crops worldwide, with its seed oil content (SOC) and quality directly determining its economic value. To resolve the challenges of growing demand for vegetable oil and advancements in rapeseed production, substantial progress has been achieved in the genetic improvement of SOC. This review systemizes genetic optimization strategies across three hierarchical processes: source expansion via enhanced photosynthesis, optimized carbon allocation, and metabolic redirection of photoassimilates; sink enhancement through targeted elevation of fatty acid (FA) synthesis, triacylglycerol (TAG) assembly, and seed coat development coupled with suppression of lipolytic pathways; flow optimization by modifying carbon partitioning, sucrose phloem loading and channeling to developing seeds. We synthesize reported genetic determinants of these processes and underscore their potential for enhancing SOC. Furthermore, we postulate that synergistic integration of source-flow-sink coordination with push-pull-package-protect frameworks could maximize oil accumulation, thereby establishing a multi-tiered roadmap for transcending SOC ceilings in rapeseed.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820256","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":"Architecture of photosystem I-light-harvesting complex from the eukaryotic filamentous yellow-green alga Tribonema minus.","authors":"Ruiqi Shao, Yuqi Zou, Hui Shang, Yue Qiu, Zuxing Liang, Xiaodong Su, Shumeng Zhang, Mei Li, Xiaowei Pan","doi":"10.1111/jipb.70010","DOIUrl":"https://doi.org/10.1111/jipb.70010","url":null,"abstract":"<p><p>Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light absorption capacity of the core complex. Throughout the evolution of oxygenic photoautotrophs, the core subunits of PSI have remained highly conserved, while LHCIs exhibit significant variability, presumably to adapt to diverse environments. This study presents a 2.82 Å resolution structure of PSI from the filamentous yellow-green alga Tribonema minus (Tm), a member of the class Xanthophyceae that evolved from red algae through endosymbiosis and is considered a promising candidate for biofuel production due to its high biomass and lipid content. Our structure reveals a supramolecular organization consisting of 12 core subunits and 13 LHCIs, here referred to as Xanthophyceae light-harvesting complexes (XLHs), along with the arrangement of pigments within the TmPSI-XLH supercomplex. A structural comparison between TmPSI-XLH and PSI-LHCI from various red lineages highlights distinctive features of TmPSI-XLH, suggesting that it represents a unique intermediate state in the PSI assembly process during the evolutionary transition from red algae to diatoms. Our findings advance the understanding of the molecular mechanisms responsible for energy transfer in Xanthophyceae PSI-XLH and the evolutionary adaptation of red lineages.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144797749","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}