Qin Feng, Zhengyin Xu, Hui Tao, Wei Li, Zeyun Hao, Xiaoman You, Maria Bellizzi, Yuese Ning, Guo-Liang Wang
RNase P primarily functions in the 5' maturation of tRNAs. However, several protein subunits of the ribonucleoprotein complex perform non-canonical functions in animals, and recent studies suggest similar functions in plant immunity against viral and fungal pathogens. In rice (Oryza sativa), RNase P subunit 30 (OsRpp30) positively regulates immunity and interacts with the histone deacetylase OsHDT701, a known negative regulator of defense against Magnaporthe oryzae. However, the mechanisms controlling OsRpp30 protein turnover remain unclear. In this study, we identified OsHAG704, a histone acetyltransferase, that acetylates and stabilizes OsRpp30, although OsHAG704-mediated acetylation was not required for OsRpp30 stabilization. Overexpression of OsHAG704 enhanced hydrogen peroxide (H₂O₂) accumulation and conferred increased resistance to M. oryzae. Additionally, we identified OsBPM2, a BTB/POZ-domain containing E3 ubiquitin ligase, which also interacts with OsRpp30 and promotes its stability, leading to similar enhancements in H₂O₂ levels and disease resistance. Although OsHAG704 did not physically interact with OsBPM2, both proteins competitively bound to OsRpp30, resulting in mutual interference between their respective regulatory pathways. Together, our findings identify two distinct positive regulators of OsRpp30 stability and immunity, highlighting a coordinated mechanism involving HAT- and E3 ligase-mediated stabilization in rice defense against M. oryzae.
{"title":"Dual regulation of RNase P subunit Rpp30 by an acetyltransferase and E3 ligase in rice immunity","authors":"Qin Feng, Zhengyin Xu, Hui Tao, Wei Li, Zeyun Hao, Xiaoman You, Maria Bellizzi, Yuese Ning, Guo-Liang Wang","doi":"10.1093/plphys/kiag157","DOIUrl":"https://doi.org/10.1093/plphys/kiag157","url":null,"abstract":"RNase P primarily functions in the 5' maturation of tRNAs. However, several protein subunits of the ribonucleoprotein complex perform non-canonical functions in animals, and recent studies suggest similar functions in plant immunity against viral and fungal pathogens. In rice (Oryza sativa), RNase P subunit 30 (OsRpp30) positively regulates immunity and interacts with the histone deacetylase OsHDT701, a known negative regulator of defense against Magnaporthe oryzae. However, the mechanisms controlling OsRpp30 protein turnover remain unclear. In this study, we identified OsHAG704, a histone acetyltransferase, that acetylates and stabilizes OsRpp30, although OsHAG704-mediated acetylation was not required for OsRpp30 stabilization. Overexpression of OsHAG704 enhanced hydrogen peroxide (H₂O₂) accumulation and conferred increased resistance to M. oryzae. Additionally, we identified OsBPM2, a BTB/POZ-domain containing E3 ubiquitin ligase, which also interacts with OsRpp30 and promotes its stability, leading to similar enhancements in H₂O₂ levels and disease resistance. Although OsHAG704 did not physically interact with OsBPM2, both proteins competitively bound to OsRpp30, resulting in mutual interference between their respective regulatory pathways. Together, our findings identify two distinct positive regulators of OsRpp30 stability and immunity, highlighting a coordinated mechanism involving HAT- and E3 ligase-mediated stabilization in rice defense against M. oryzae.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"93 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147502293","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":"How Tomato Leaves Stay Green: The Role of SlGRAS17 and its partners.","authors":"Deeksha Singh","doi":"10.1093/plphys/kiag155","DOIUrl":"https://doi.org/10.1093/plphys/kiag155","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"57 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147483611","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":"Dose makes the defense: hormone thresholds reprogram nematode immunity in rice.","authors":"Marcella Teixeira","doi":"10.1093/plphys/kiag149","DOIUrl":"https://doi.org/10.1093/plphys/kiag149","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"16 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147483605","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}
Seed storage proteins (SSPs) are stored in protein storage vacuoles (PSVs) within plant endosperm cells. In rice, glutelins undergo post-Golgi trafficking via dense vesicles (DVs) to protein body II (PBII). Phosphatidylinositol 3-phosphate (PI3P) regulates endosomal, autophagic, and vacuolar trafficking, yet its role in glutelin transport remains unclear. Here, we characterized the glutelin precursor accumulation14 (gpa14) mutant, which exhibits over-accumulation of 57-kDa glutelin precursors and floury, shrunken endosperm. Map-based cloning identified a single adenine insertion in Vacuolar Protein Sorting 34 (OsVPS34), resulting in a putative truncated protein lacking the PI3Ka and PI3_PI4_kinase domains. OsVPS34 encodes phosphatidylinositol 3-kinase (PI3K), which interacts with other subunits of the PI3K complex to regulate the production of PI3P. PI3P was enriched in the trans-Golgi network (TGN) and pre-vacuolar compartment (PVC), co-localized with Rab5a and GPA5, and was detected in DVs and PBIIs. In gpa14, PI3P levels were reduced, leading to mis-localization and decreased membrane association of Rab5a and GPA5, key regulators of glutelin trafficking. Our findings demonstrate that OsVPS34 is essential for synthesis of PI3P, which plays a crucial role in recruiting GPA5 and Rab5a to DVs for glutelin post-Golgi trafficking in rice endosperm.
种子储存蛋白（ssp）储存在植物胚乳细胞内的蛋白质储存液泡（psv）中。在水稻中，谷蛋白通过密集囊泡（DVs）转运至蛋白体II （PBII）。磷脂酰肌醇3-磷酸（PI3P）调节内体、自噬和空泡运输，但其在谷蛋白运输中的作用尚不清楚。在这里，我们描述了谷蛋白前体积累14 （gpa14）突变体，它表现出57 kda谷蛋白前体的过度积累和面粉状、萎缩的胚乳。基于图谱的克隆在液泡蛋白分类34 （Vacuolar Protein Sorting 34, OsVPS34）中发现了一个单腺嘌呤插入，导致推测的截断蛋白缺乏PI3Ka和PI3_PI4_kinase结构域。OsVPS34编码磷脂酰肌醇3-激酶（PI3K），其与PI3K复合物的其他亚基相互作用以调节PI3P的产生。PI3P富集于反式高尔基网络（TGN）和前液泡室（PVC）中，与Rab5a和GPA5共定位，并在DVs和PBIIs中检测到。在gpa14中，PI3P水平降低，导致谷蛋白运输的关键调节因子Rab5a和GPA5的错定位和膜关联减少。我们的研究结果表明OsVPS34对PI3P的合成至关重要，而PI3P在水稻胚乳中将GPA5和Rab5a募集到谷蛋白后高尔基转运的DVs中起着关键作用。
{"title":"OsVPS34-generated PI3P recruits GPA5/Rab5a to regulate post-Golgi glutelin trafficking in rice endosperm.","authors":"Shanbin Xu,Mingqing Ma,Huanhuan Zhao,Aoni Zhou,Zi Li,Bo Li,Yuzhe He,Guiping Zhang,Hongping Cai,Chuanwei Gu,Ting Yu,Xue Yang,Lei Zhou,Yu Zhang,Erchao Duan,Xuan Teng,Xi Liu,Shijia Liu,Yunlu Tian,Ling Jiang,Yulong Ren,Yihua Wang,Hui Dong,Jianmin Wan","doi":"10.1093/plphys/kiag154","DOIUrl":"https://doi.org/10.1093/plphys/kiag154","url":null,"abstract":"Seed storage proteins (SSPs) are stored in protein storage vacuoles (PSVs) within plant endosperm cells. In rice, glutelins undergo post-Golgi trafficking via dense vesicles (DVs) to protein body II (PBII). Phosphatidylinositol 3-phosphate (PI3P) regulates endosomal, autophagic, and vacuolar trafficking, yet its role in glutelin transport remains unclear. Here, we characterized the glutelin precursor accumulation14 (gpa14) mutant, which exhibits over-accumulation of 57-kDa glutelin precursors and floury, shrunken endosperm. Map-based cloning identified a single adenine insertion in Vacuolar Protein Sorting 34 (OsVPS34), resulting in a putative truncated protein lacking the PI3Ka and PI3_PI4_kinase domains. OsVPS34 encodes phosphatidylinositol 3-kinase (PI3K), which interacts with other subunits of the PI3K complex to regulate the production of PI3P. PI3P was enriched in the trans-Golgi network (TGN) and pre-vacuolar compartment (PVC), co-localized with Rab5a and GPA5, and was detected in DVs and PBIIs. In gpa14, PI3P levels were reduced, leading to mis-localization and decreased membrane association of Rab5a and GPA5, key regulators of glutelin trafficking. Our findings demonstrate that OsVPS34 is essential for synthesis of PI3P, which plays a crucial role in recruiting GPA5 and Rab5a to DVs for glutelin post-Golgi trafficking in rice endosperm.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"69 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147478951","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}
Yuxuan Lou,Tianhao Wu,Fan Xia,Anwen Zhao,Xiangfeng Wang
Artificial intelligence (AI) is poised to reshape the research paradigm of the life sciences by rapidly advancing the adoption of protein language models and their derivative tools. These technologies are increasingly being applied to protein structure prediction, function analysis, and protein design throughout the life sciences, and have only recently begun to gain attention within the plant science community. Moreover, while the era of AI-driven bio-breeding is on the horizon, it remains largely in the proof-of-concept stage. Therefore, there is a pressing need not only to outline the fundamental principles, models, and tools in this rapidly evolving field, but also to explore their potential applications in plant research and crop breeding. This review begins by introducing general principles and widely used models for protein understanding and generation, supported by illustrative case studies that highlight how these tools are advancing fundamental plant research. For instance, the analyses of two maize (Zea mays) genes demonstrate how a structure-aware interpretation of the relationships between mutations and protein function enables more precise hypothesis generation and facilitates experimental validation. Subsequently, the review presents generic AI-enabled protein engineering strategies and pipelines, including rational, semi-rational, refactoring, and de novo design, tailored to diverse protein engineering objectives. These approaches aim to create artificial variants and synthetic proteins with improved or novel functions to foster innovation in crop breeding. Finally, the significant challenges of applying protein design in plants are discussed, particularly in light of the limited availability of experimentally resolved protein structures and the inherent complexity of plant biological systems.
{"title":"AI-enabled protein design facilitates future plant research and crop breeding.","authors":"Yuxuan Lou,Tianhao Wu,Fan Xia,Anwen Zhao,Xiangfeng Wang","doi":"10.1093/plphys/kiag147","DOIUrl":"https://doi.org/10.1093/plphys/kiag147","url":null,"abstract":"Artificial intelligence (AI) is poised to reshape the research paradigm of the life sciences by rapidly advancing the adoption of protein language models and their derivative tools. These technologies are increasingly being applied to protein structure prediction, function analysis, and protein design throughout the life sciences, and have only recently begun to gain attention within the plant science community. Moreover, while the era of AI-driven bio-breeding is on the horizon, it remains largely in the proof-of-concept stage. Therefore, there is a pressing need not only to outline the fundamental principles, models, and tools in this rapidly evolving field, but also to explore their potential applications in plant research and crop breeding. This review begins by introducing general principles and widely used models for protein understanding and generation, supported by illustrative case studies that highlight how these tools are advancing fundamental plant research. For instance, the analyses of two maize (Zea mays) genes demonstrate how a structure-aware interpretation of the relationships between mutations and protein function enables more precise hypothesis generation and facilitates experimental validation. Subsequently, the review presents generic AI-enabled protein engineering strategies and pipelines, including rational, semi-rational, refactoring, and de novo design, tailored to diverse protein engineering objectives. These approaches aim to create artificial variants and synthetic proteins with improved or novel functions to foster innovation in crop breeding. Finally, the significant challenges of applying protein design in plants are discussed, particularly in light of the limited availability of experimentally resolved protein structures and the inherent complexity of plant biological systems.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"12 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147478478","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":"Perks of being a wallflower: A high-quality wallflower reference genome reveals its chromosome evolution and flower color variation.","authors":"William J W Thomas","doi":"10.1093/plphys/kiag150","DOIUrl":"https://doi.org/10.1093/plphys/kiag150","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"10 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147478903","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}
Xian Duo Zhang,Jianbo Song,Xinyu Wu,Yuxiang Han,Bing Geng,Jie Hou,Liping Wang,Zhi Min Yang,Di Sun
RNA helicases are a large family of ATPases that participate in RNA structure remodeling and ribonucleoprotein rearrangement to regulate plant growth, development, and responses to environmental stress. Here, we observed that the expression of Arabidopsis (Arabidopsis thaliana) DDX6-like RNA helicase genes RH6, RH8, and RH12 was down-regulated by salt stress. Loss-of-function mutants showed enhanced salt-stress tolerance, manifested as precocious seed germination, accelerated growth, less oxidative stress, and reduced Na+ accumulation compared with wild-type plants. Conversely, overexpression of RH6 led to salt hypersensitivity. Transcriptome analysis further revealed that DDX6-like RNA helicases destabilize the transcripts of numerous salt stress responsive genes. A modified 5'-RNA ligase mediated rapid amplification of cDNA ends (5'-RLM-RACE) assay indicated that this destabilization can likely be attributed to enhanced decapping activity under NaCl treatment. Lack of DDX6-like RNA helicases attenuated P-body formation under saline conditions. We conclude that DDX6-like RNA helicases negatively regulate the salt-stress response by modulating 5'-3' decay of salt-related mRNA transcripts.
{"title":"DDX6-like RNA helicases compromise salt-stress tolerance by facilitating mRNA decapping activity in Arabidopsis.","authors":"Xian Duo Zhang,Jianbo Song,Xinyu Wu,Yuxiang Han,Bing Geng,Jie Hou,Liping Wang,Zhi Min Yang,Di Sun","doi":"10.1093/plphys/kiag134","DOIUrl":"https://doi.org/10.1093/plphys/kiag134","url":null,"abstract":"RNA helicases are a large family of ATPases that participate in RNA structure remodeling and ribonucleoprotein rearrangement to regulate plant growth, development, and responses to environmental stress. Here, we observed that the expression of Arabidopsis (Arabidopsis thaliana) DDX6-like RNA helicase genes RH6, RH8, and RH12 was down-regulated by salt stress. Loss-of-function mutants showed enhanced salt-stress tolerance, manifested as precocious seed germination, accelerated growth, less oxidative stress, and reduced Na+ accumulation compared with wild-type plants. Conversely, overexpression of RH6 led to salt hypersensitivity. Transcriptome analysis further revealed that DDX6-like RNA helicases destabilize the transcripts of numerous salt stress responsive genes. A modified 5'-RNA ligase mediated rapid amplification of cDNA ends (5'-RLM-RACE) assay indicated that this destabilization can likely be attributed to enhanced decapping activity under NaCl treatment. Lack of DDX6-like RNA helicases attenuated P-body formation under saline conditions. We conclude that DDX6-like RNA helicases negatively regulate the salt-stress response by modulating 5'-3' decay of salt-related mRNA transcripts.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"4 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471753","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}
Xuening Kang,Ming Kan,Shixin Guan,Rujie Xin,Wenhui Song,Siyang Duan,Xiaoqing Zhou,Xiaomei Sun,Panpan Yang
Bacillus is a beneficial soil microorganism that enhances plant growth and stress resistance, yet its mechanism in boosting drought resistance remains unclear. This study explored its role in enhancing herbaceous peony (Paeonia lactiflora) drought resistance via gradient soil moisture treatments (T0: 75%±5%; T1: 55%±5%; T2: 35%±5%; T3: 15%±5%). Bacillus significantly improved P. lactiflora drought resistance, especially at T2 and T3 stages, alleviating drought damage by increasing photosynthetic efficiency, antioxidant enzyme activity, and osmolyte accumulation, with abscisic acid (ABA) as a core functional component. To clarify the molecular mechanisms underlying this improvement, we performed transcriptome sequencing of P. lactiflora at the T2 and T3 stages, as well as Weighted Gene Co-expression Network Analysis (WGCNA). We identified key modules linked to Bacillus action, with WRKY transcription factors as dominant hub genes. Among these, the P. lactiflora WRKY transcription factor 70 (PlWRKY70) showed high induction by Bacillus or drought and the highest module membership (kME) in the core module. Notably, Bacillus enhanced drought resistance in P. lactiflora by upregulating PlWRKY70. Overexpressing PlWRKY70 reduced hydrogen peroxide (H₂O₂), superoxide anion (O₂·⁻), and stomatal aperture, whereas silencing PlWRKY70 produced the opposite effect, and this upregulation by Bacillus further promoted reactive oxygen species (ROS) scavenging and stomatal closure. Overall, this study reveals the physiological and transcriptional changes of P. lactiflora during Bacillus-enhanced drought resistance, identifies multiple key candidate genes responsive to Bacillus, and provides theoretical support for the popularization and application of Bacillus-based biological agents.
{"title":"Transcriptome and functional analysis reveal the drought-alleviating ability of Bacillus on Paeonia lactiflora Pall.","authors":"Xuening Kang,Ming Kan,Shixin Guan,Rujie Xin,Wenhui Song,Siyang Duan,Xiaoqing Zhou,Xiaomei Sun,Panpan Yang","doi":"10.1093/plphys/kiag138","DOIUrl":"https://doi.org/10.1093/plphys/kiag138","url":null,"abstract":"Bacillus is a beneficial soil microorganism that enhances plant growth and stress resistance, yet its mechanism in boosting drought resistance remains unclear. This study explored its role in enhancing herbaceous peony (Paeonia lactiflora) drought resistance via gradient soil moisture treatments (T0: 75%±5%; T1: 55%±5%; T2: 35%±5%; T3: 15%±5%). Bacillus significantly improved P. lactiflora drought resistance, especially at T2 and T3 stages, alleviating drought damage by increasing photosynthetic efficiency, antioxidant enzyme activity, and osmolyte accumulation, with abscisic acid (ABA) as a core functional component. To clarify the molecular mechanisms underlying this improvement, we performed transcriptome sequencing of P. lactiflora at the T2 and T3 stages, as well as Weighted Gene Co-expression Network Analysis (WGCNA). We identified key modules linked to Bacillus action, with WRKY transcription factors as dominant hub genes. Among these, the P. lactiflora WRKY transcription factor 70 (PlWRKY70) showed high induction by Bacillus or drought and the highest module membership (kME) in the core module. Notably, Bacillus enhanced drought resistance in P. lactiflora by upregulating PlWRKY70. Overexpressing PlWRKY70 reduced hydrogen peroxide (H₂O₂), superoxide anion (O₂·⁻), and stomatal aperture, whereas silencing PlWRKY70 produced the opposite effect, and this upregulation by Bacillus further promoted reactive oxygen species (ROS) scavenging and stomatal closure. Overall, this study reveals the physiological and transcriptional changes of P. lactiflora during Bacillus-enhanced drought resistance, identifies multiple key candidate genes responsive to Bacillus, and provides theoretical support for the popularization and application of Bacillus-based biological agents.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"1 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471751","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}
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