Journal of Integrative Plant Biology最新文献

{"title":"Global profiling of lysine-malonylated proteins in rice elucidates the immune-regulatory mechanisms of malonylation under herbivore or viral stresses.","authors":"Shuai Li, Xinyang Tan, Lei Yang, Xiaolong Deng, Miaomiao Li, Lang Qin, Liangxuan Qi, Jing Li, Guanghua Luo, Meng Yuan, Yang Sun, Chunqing Zhao, Kun Zhang, Jichao Fang, Zhen He, Rui Ji","doi":"10.1111/jipb.70050","DOIUrl":"https://doi.org/10.1111/jipb.70050","url":null,"abstract":"<p><p>Lysine malonylation (K_mal), an evolutionarily conserved post-translational modification, serves as a critical regulator of cellular processes including transcriptional control, metabolic coordination, and enzyme activation. While K_mal sites have been mapped in rice (Oryza sativa L.) seeds, their dynamic regulation in rice responses to biotic stresses remains poorly characterized. Here, we reported a global profiling of lysine-malonylated proteins in rice leaf sheaths, and the changes in these proteins under herbivore (Nilaparvata lugens/Chilo suppressalis) or viral (rice stripe virus/rice black-streaked dwarf virus) stresses. Using affinity enrichment and proteomics, we identified 3,113 K_mal sites across 1,324 proteins in wild-type rice leaf sheaths, these data demonstrated that lysine-malonylated proteins are involved in diverse biological processes. K_mal levels were significantly upregulated following herbivore infestation or viral infection, with two herbivores inducing more pronounced changes than viruses infection, revealing stress-specific malonylation landscapes. K_mal preferentially targeted highly expressed proteins in energy metabolism (e.g., glycolysis and the tricarboxylic acid cycle) and photosynthesis, exhibiting an inverse correlation between hypermalonylation and protein abundance. Cleavage under targets and tagmentation analyses revealed K_mal-mediated chromatin remodeling through promoter occupancy at defense-related genes. In addition, the histone deacetylases OsHDA702-704, OsHDA711-713 were functionally characterized as key regulators mediating the erasure of specific malonylation marks in rice plants, with OsHDA711 knockout lines exhibiting enhanced resistance against both herbivore and virus infection. Our work establishes K_mal as a regulator in rice biotic immunity, uncovering novel insights into K_mal-mediated plant defense responses against herbivorous pests and viral pathogens. These findings identify potential genetic targets for developing rice varieties with broad-spectrum immunity to biotic stresses, enhancing crop resilience.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306600","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":"Modulating the strigolactone pathway to optimize tomato shoot branching for vertical farming.","authors":"Jiwoo Lee, Myeong-Gyun Seo, Yoonseo Lim, Seungpyo Hong, Jeong-Tak An, Ho-Young Jeong, Chanhui Lee, Soon Ju Park, Giha Song, Choon-Tak Kwon","doi":"10.1111/jipb.70059","DOIUrl":"https://doi.org/10.1111/jipb.70059","url":null,"abstract":"<p><p>Optimizing plant architecture for specific cultivation methods is essential for enhancing fruit productivity. Unlike indeterminate growth plants, the total productivity of determinate growth plants relies on cumulative fruit production and synchronized fruit ripening from both main and axillary shoots. Here, we focused on SlD14 and SlMAX1, two key genes involved in the regulation of strigolactone (SL) signaling and biosynthesis, with the goal of maximizing yield and synchronizing fruit ripening by fine-tuning axillary shoot growth. Using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology, we found that the sld14, slmax1, and sld14 slmax1 mutant plants exhibited reduced plant height and increased axillary shoot proliferation compared to wild-type plants. However, these mutants showed reduced yield and delayed ripening, likely due to a source-sink imbalance caused by excessive axillary shoot development. A weak sld14 allele displayed a milder phenotype, maintaining total fruit yield and harvest index despite smaller individual fruit size. These findings indicate that allelic variation in SL-related genes can influence plant architecture and yield components. Our results suggest that weak or partial alleles may serve as promising targets for tailoring tomato architecture to space-limited cultivation systems.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290445","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":"Multi-omics analyses shed lights on the evolution and fruit development of Chinese raspberries (Rubus spp.).","authors":"Ticao Zhang, Dengli Luo, Guodong Li, Huanchong Wang, Qiang Cao, Rengang Zhang, Yuran Li, Yingan Zhu, Chunhua Ma, Aaron Liston, Hang Sun, Qin Qiao","doi":"10.1111/jipb.70052","DOIUrl":"https://doi.org/10.1111/jipb.70052","url":null,"abstract":"<p><p>Rubus (raspberries and blackberries) is a large genus of over 700 species well known for its taxonomic challenges. Many of its species hold significant economic value as important edible and medicinal plants. Here, near-complete genomes for four wild diploid raspberry species were assembled, including R. ellipticus, R. niveus, as well as the highly heterozygous diploid red raspberry (R. idaeus), and its closely related species R. sachalinensis. Pan-genome analysis of Rubus identified 10,243 core gene families (64% of total), and highlights expansions of flavonoid/terpenoid pathways in Rubus, correlating with fruit bioactive compound diversity. Our discovery of shared ancestral components between R. idaeus and R. sachalinensis subgenomes provides evidence for their homoploid hybrid origin. The centromere sequence characteristics could serve as markers for subgenome assignment in R. idaeus and R. sachalinensis. Moreover, population genomic studies of 125 accessions from ca. 80 species uncovered widespread genetic introgression, particularly in red raspberries, with centromeric haplotype signatures tracing ancestral contributions to cultivated varieties. By integrating metabolome and transcriptome data, we explore the fruit quality regulatory network of Chinese raspberries. We identified a glutathione S-transferase gene that may inhibit the successful transport of anthocyanins into the vacuole and appears to be a limiting factor for the anthocyanin pigmentation in R. ellipticus fruits. In summary, this research sheds new light on the genetic intricacies of raspberry species and their cultivars, and provides a robust foundation for horticultural improvement and genomic selection in raspberry breeding.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290498","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":"CPOP1 is a key enzyme required for nodule microenvironment control and successful symbiotic nitrogen fixation in Lotus japonicus.","authors":"Yu-Fang Tian, Yu Luo, Qi-Min Li, Zhi-Qin Zhang, Ya-Long Guo, Wei-Cai Yang","doi":"10.1111/jipb.70037","DOIUrl":"https://doi.org/10.1111/jipb.70037","url":null,"abstract":"<p><p>Symbiotic nitrogen fixation in legumes requires the exquisite regulation of the environment within the infected region of the nodule. The microaerobic environment critical for nitrogenase activity is maintained through the physical oxygen diffusion barrier of the cortex and locally the oxygen-binding protein leghemoglobin (Lb). Leghemoglobin binds and releases oxygen with heme moiety to maintain oxygen gradients inside the infected cell (IC) during nitrogen fixation. Heme binds to diverse proteins and plays critical roles in different redox reactions. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation are not clear. Here, we identified coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme biosynthesis in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The IC-specific expression of CPOP1 was directed by the -881 to -740 bp promoter region. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild-type. Intriguingly, bacteria proliferation is inhibited due to the down-regulation of cell division-related gene expression upon CPOP1 knockout. Our data showed that CPOP1 is essential for the microaerobic environment control of ICs and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290462","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":"Assembly mechanism of PSII-LHCII array from higher plants.","authors":"Jianghao Wu, Cang Wu, Shuaijiabin Chen, Chao Huang, Quan Wen, Weijun Lin, Chao Wang, Dexian Han, Dandan Lu, Xiumei Xu, Jun Gao, Sen-Fang Sui, Lixin Zhang","doi":"10.1111/jipb.70045","DOIUrl":"https://doi.org/10.1111/jipb.70045","url":null,"abstract":"<p><p>Photosystem II (PSII) comprises reaction centers and light-harvesting complexes of the major and minor antennas, forming diverse supercomplexes with varying antenna sizes and are organized as PSII arrays in grana thylakoids to respond to fluctuating light. However, the assembly mechanism of PSII arrays, excitation energy transfer and its regulation mechanisms in vascular plants remain poorly understood. Here, we report the cryo-electron microscopy structures of a 1.4-MDa PSII-LHCII (light-harvesting complex II) dimer and a 2.8-MDa tetramer, and present an initial model of hexamer from Arabidopsis. Structural and genetic analyses reveals that the tetramer is formed by two C₂S₂M₂ dimers arranged side by side through interactions between CP26/PsbZ and moderate (M)-LHCII within PSII arrays in the grana thylakoid. Furthermore, conformational changes of M-LHCII and CP24 facilitate the assembly transition from dimer to tetramer/hexamer. Chlorophyll rearrangement, supported by computational calculations and spectral analysis, suggests enhanced energy transfer efficiency in the tetramer compared to the dimer. Therefore, our findings provide new insights into the dynamic assembly and excitation energy redistribution within PSII arrays in higher plants.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290413","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":"GI as a dynamic integrator: Synchronizing photoperiod and temperature signals to control flowering time in Arabidopsis.","authors":"Gyeongik Ahn, Song Yi Jeong, Woe-Yeon Kim","doi":"10.1111/jipb.70051","DOIUrl":"https://doi.org/10.1111/jipb.70051","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290493","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":"Polar-localized EXO70G1 regulates root development in Arabidopsis thaliana.","authors":"Juan Li, Zhendong Liu, Lixue Gong, Shuju Zhao, Qing Lu, Shan Gao, Su Jiang, Xiaonan Liu, Long Ma, Guangyou Duan, Dayong Cui, Shipeng Li","doi":"10.1111/jipb.70053","DOIUrl":"https://doi.org/10.1111/jipb.70053","url":null,"abstract":"<p><p>Cellular asymmetry, which represents a fundamental characteristic of cell polarity, is prominently illustrated by the apical-basal localization of PIN-FORMED (PIN) auxin efflux carriers in Arabidopsis thaliana. Although the maintenance of PIN polarity at the plasma membrane (PM) relies on endomembrane trafficking, the pivotal factors responsible for recruiting PIN proteins to the PM remain largely unknown. In this study, we discover that EXO70G1 displays a polarized distribution at the PM in root cells. Acting as a putative subunit of the exocyst complex, which mediates the tethering of exocytic vesicles to the PM, EXO70G1 exhibits continuous recycling foci at the PM, and its dynamic behavior is akin to that of SEC6 and SEC8. Disruption of EXO70G1 and its homolog EXO70G2 in Arabidopsis reduces auxin accumulation and primary root length. Importantly, the recycling of PIN2 from the brefeldin A (BFA) compartment to the PM is compromised, and the abundance of PIN2 at the PM is reduced in the exo70G1 exo70G2 backgrounds. Interestingly, live-cell imaging reveals that the polarity of EXO70G1 is established during cytokinesis, prior to that of PIN2, and is maintained throughout the subsequent phases of cell elongation and differentiation. When the lipid raft was disturbed, the accumulation of EXO70G1 at the PM decreased. Our findings highlight the crucial role of EXO70G1 in root development by providing positional cues that facilitate the recycling efficiency of PIN2 to the PM.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290443","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":"Methylation of isopentenyl pyrophosphate by C-methyltransferase and optimizing irregular β-elemene yield using UniKP, an enzyme kinetic parameter prediction tool.","authors":"Tangli Li, Ming Wang, Huilin Ren, Han Yu, Xiaozhou Luo, Lifei Lv, Huanan Jin, Xiaopu Yin, Rong Chen","doi":"10.1111/jipb.70048","DOIUrl":"https://doi.org/10.1111/jipb.70048","url":null,"abstract":"<p><p>Although terpenoids display chemical and structural diversities as well as important biological activities, they are biosynthesized through polymerization of C5 isoprene units according to the \"biogenetic isoprene rule.\" However, recent observations have identified irregular terpenes, such as C11, C12, C16, and C17, in some microbial species. These irregular terpenes have garnered research interest due to the \"Magic Methyl Effect.\" These compounds are biosynthesized from the methyl modification of terpene skeletons at a detectable level in Escherichia coli. To explore key factors in the biosynthesis of irregular terpenes, we conducted a screening of C-methyltransferases by UniKP, synthesized methyl-isopentenyl pyrophosphate as a precursor building unit, and polymerized it with C5 isoprene units to generate methyl β-elemene via farnesyl pyrophosphate synthase and germacrene A synthase. Finally, the yield of methyl β-elemene reached 6.98 mg/L, representing a 2.46-fold increase, with a ratio of methylated to native β-elemene increasing by 0.21 through the introduction S-adenosyl-L-homocysteine hydrolase and the optimization of germacrene A synthase. These findings not only expand the chemical diversity of terpenoids but also highlight the evolutionary plasticity of terpene synthases in generating structural novelty.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278578","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":"Correction to \"The involvement of wheat U-box E3 ubiquitin ligase TaPUB1 in salt stress tolerance\".","authors":"","doi":"10.1111/jipb.70034","DOIUrl":"https://doi.org/10.1111/jipb.70034","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278521","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":"Issue information page","authors":"","doi":"10.1111/jipb.13702","DOIUrl":"https://doi.org/10.1111/jipb.13702","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 10","pages":"2527-2528"},"PeriodicalIF":9.3,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13702","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145228199","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}