Plant Physiology最新文献

A point mutation in PsbW disrupts thylakoid membrane organization and causes aberrant starch granule formation PsbW的一个点突变破坏了类囊体膜组织并导致异常淀粉颗粒的形成

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-29 DOI: 10.1093/plphys/kiaf206

Theresa E Ilse, Hongyuan Zhang, Arvid Heutinck, Chun Liu, Simona Eicke, Mayank Sharma, Barbara Pfister, Diana Santelia, Samuel C Zeeman

{"title":"A point mutation in PsbW disrupts thylakoid membrane organization and causes aberrant starch granule formation","authors":"Theresa E Ilse, Hongyuan Zhang, Arvid Heutinck, Chun Liu, Simona Eicke, Mayank Sharma, Barbara Pfister, Diana Santelia, Samuel C Zeeman","doi":"10.1093/plphys/kiaf206","DOIUrl":"https://doi.org/10.1093/plphys/kiaf206","url":null,"abstract":"Chloroplast thylakoid membranes are the sites of the light reactions of photosynthesis. They are also thought to influence starch granule biogenesis via the thylakoid anchored protein MAR-BINDING FILAMENT-LIKE PROTEIN 1 (MFP1), but mechanistic understanding is scarce. Here we report an Arabidopsis mutant affected in PsbW, an integral thylakoid membrane protein associated with photosynthetic complexes of PSII. This mutant (psbw-2) was identified in a large-scale mutant screen designed to find proteins that regulate starch granule shape and size because it produces an excessive number of small, irregularly shaped starch granules. The mutation in psbw-2 causes a glycine-to-arginine substitution in PsbW’s transmembrane helix. The resulting PsbWG107R protein remains membrane-associated but has lost its ability to stabilize PSII supercomplexes. In addition, the transgenic expression of this mutated version results in abnormal thylakoid membranes that have drastically enlarged luminal spaces and no longer form distinct grana stacks, leading to reduced plant growth and impaired photosynthesis. These effects increase with PsbWG107R expression levels but are not observed in the psbw knockout mutant, suggesting that PsbWG107R has acquired an aberrant function. We analyzed psbw-2 mutants also lacking either MFP1 or STARCH SYNTHASE 4, a key factor involved in granule initiation and growth. These data suggest that thylakoid distortion is caused by the membrane insertion of PsbWG107R, which in turn affects the initiation and growth of starch granules. Our results reaffirm the link between thylakoid membrane system and starch formation and highlight the importance of proper thylakoid architecture for plant fitness.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"1 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144165279","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}

引用次数: 0

High-light-inducible proteins control associations between chlorophyll synthase and the Photosystem II biogenesis factor Ycf39 高光诱导蛋白控制叶绿素合酶和光系统II生物发生因子Ycf39之间的关联

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-25 DOI: 10.1093/plphys/kiaf213

Anna Wysocka, Natalia Kulik, Mahendra K Shukla, Monika Opatíková, Roman Kouřil, Philip J Jackson, Amanda A Brindley, Jan Janouškovec, Éva Kiss, Andrew Hitchcock, Josef Komenda, C Neil Hunter, Roman Sobotka

{"title":"High-light-inducible proteins control associations between chlorophyll synthase and the Photosystem II biogenesis factor Ycf39","authors":"Anna Wysocka, Natalia Kulik, Mahendra K Shukla, Monika Opatíková, Roman Kouřil, Philip J Jackson, Amanda A Brindley, Jan Janouškovec, Éva Kiss, Andrew Hitchcock, Josef Komenda, C Neil Hunter, Roman Sobotka","doi":"10.1093/plphys/kiaf213","DOIUrl":"https://doi.org/10.1093/plphys/kiaf213","url":null,"abstract":"The biogenesis of Photosystem II is a complicated process requiring numerous auxiliary factors to assist in all steps of its assembly. The cyanobacterial protein Ycf39 forms a stress-induced complex with two small chlorophyll-binding, High-light-inducible proteins C and D (HliC and HliD), and has been reported to participate in the insertion of chlorophyll molecules into the central D1 subunit of Photosystem II. However, how this process is organized remains unknown. Here, we show that Ycf39 and both HliC and HliD can form distinct complexes with chlorophyll synthase (ChlG) in the model cyanobacterium Synechocystis sp. PCC 6803. We isolated and characterized ChlG complexes from various strains grown under different conditions and provide a mechanistic view of the docking of Ycf39 to ChlG via HliD and the structural role of HliC. In the absence of stress, chlorophyll is produced by the ChlG-HliD2-ChlG complex, which is stabilized by chlorophyll and zeaxanthin molecules bound to the HliD homodimer. The switch to high light leads to stress pressure and greatly elevated synthesis of HliC, resulting in the replacement of HliD homodimers with HliC-HliD heterodimers. Unlike HliD, HliC cannot interact directly with ChlG or Ycf39. Therefore, the original ChlG-HliD2-ChlG complex is converted into a ChlG-HliD-HliC hetero-trimer that presumably binds transiently to Ycf39 and the nascent D1 polypeptide. We speculate that this molecular machinery promotes the delivery of chlorophyll to D1 upon high-light-induced chlorophyll deficiency. The HliD homodimers formed under standard, non-stress growth conditions and attached to ChlG could serve as an emergency chlorophyll reserve.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"139 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136754","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}

引用次数: 0

Many transcription factor families have evolutionarily conserved binding motifs in plants 许多转录因子家族在植物中具有进化上保守的结合基序

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-23 DOI: 10.1093/plphys/kiaf205

Sanja Zenker, Donat Wulf, Anja Meierhenrich, Prisca Viehöver, Sarah Becker, Marion Eisenhut, Ralf Stracke, Bernd Weisshaar, Andrea Bräutigam

{"title":"Many transcription factor families have evolutionarily conserved binding motifs in plants","authors":"Sanja Zenker, Donat Wulf, Anja Meierhenrich, Prisca Viehöver, Sarah Becker, Marion Eisenhut, Ralf Stracke, Bernd Weisshaar, Andrea Bräutigam","doi":"10.1093/plphys/kiaf205","DOIUrl":"https://doi.org/10.1093/plphys/kiaf205","url":null,"abstract":"Transcription factors control gene expression during development and in response to a broad range of internal and external stimuli. They regulate promoter activity by directly binding cis-regulatory elements in DNA. The angiosperm Arabidopsis (Arabidopsis thaliana) contains more than 1,500 annotated transcription factors, each containing a DNA-binding domain that is used to define transcription factor families. Analyzing the binding motifs of 686 and the binding sites of 335 Arabidopsis transcription factors, as well as motifs of 92 transcription factors from other plants, we identified a constrained vocabulary of 74 conserved motifs spanning 50 families in plants. Among 21 transcription factor families, we found one core motif for all analyzed members and between 2% and 72% overlapping binding sites. Five families show conservation of the motif along phylogenetic clades. Five families, including the C2H2 zinc finger family, show high diversity among motifs in plants, suggesting potential for the neofunctionalization of duplicated transcription factors based on the motif recognized. We tested whether conserved motifs remained conserved since at least 450 million years ago by determining the binding motifs of 17 transcription factors from 11 families in Marchantia (Marchantia polymorpha) using amplified DNA affinity purification sequencing. We detected nearly identical binding motifs as predicted from the angiosperm data. Our findings show a large repertoire of overlapping binding sites within a transcription factor family and species and a high degree of binding motif conservation for at least 450 million years, indicating more potential for evolution in cis- rather than trans-regulatory elements.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"16 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144130208","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}

引用次数: 0

"Seeds tyranny: No flowers for old plants". “种子暴政：老植物不开花”。

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-23 DOI: 10.1093/plphys/kiaf201

María Flores-Tornero

引用次数: 0

GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence GRANA：一个基于人工智能的工具，用于使用混合智能加速叶绿体颗粒纳米形态分析

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-23 DOI: 10.1093/plphys/kiaf212

Alicja Bukat, Marek Bukowicki, Michał Bykowski, Karolina Kuczkowska, Szymon Nowakowski, Anna Śliwińska, Łucja Kowalewska

{"title":"GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence","authors":"Alicja Bukat, Marek Bukowicki, Michał Bykowski, Karolina Kuczkowska, Szymon Nowakowski, Anna Śliwińska, Łucja Kowalewska","doi":"10.1093/plphys/kiaf212","DOIUrl":"https://doi.org/10.1093/plphys/kiaf212","url":null,"abstract":"Grana are fundamental structural units of the intricate chloroplast membrane network. Investigating their nanomorphology is essential for understanding photosynthetic efficiency regulation. Here, we present GRANA (Graphical Recognition and Analysis of Nanostructural Assemblies), an AI-enhanced, user-friendly software tool that recognizes grana on thylakoid network electron micrographs and generates a complex set of their structural parameters. GRANA employs three artificial neural networks of different architectures and binds them in a one-click workflow. Its output is designed to facilitate hybrid intelligence analysis, securing fast and reliable results from large datasets. The GRANA tool is over 100 times faster compared with currently used manual approaches. As a proof of concept, we have successfully applied GRANA software to diverse grana structures across different land plant species grown under various conditions, demonstrating the wide range of potential applications for our software. GRANA tool supports large-scale analysis of grana nanomorphological features, facilitating advancements in photosynthesis-oriented studies.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"134 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144130207","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}

引用次数: 0

The transcription factor BnaA9.NST3 promotes flowering via the photoperiod pathway in Brassica napus L 转录因子BnaA9。NST3通过光周期途径促进甘蓝型油菜开花

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-23 DOI: 10.1093/plphys/kiaf214

Jia Wang, Shuyao Ran, Minmin Zhang, Xiaoke Ping, Chen Yan, Na Lin, Jiaming Song, Cunmin Qu, Jiana Li, Hao Wang, Liezhao Liu

{"title":"The transcription factor BnaA9.NST3 promotes flowering via the photoperiod pathway in Brassica napus L","authors":"Jia Wang, Shuyao Ran, Minmin Zhang, Xiaoke Ping, Chen Yan, Na Lin, Jiaming Song, Cunmin Qu, Jiana Li, Hao Wang, Liezhao Liu","doi":"10.1093/plphys/kiaf214","DOIUrl":"https://doi.org/10.1093/plphys/kiaf214","url":null,"abstract":"Flowering and secondary growth are two important biological processes in plant development, and there is a close association between flowering and xylem expansion in stem and root secondary growth. Here, we report the discovery of NAC secondary wall thickening promoting factor 3 (BnaA9.NST3), a key regulator of secondary cell wall formation in xylem fiber cells that affects B. napus (Brassica napus L.) flowering in a photoperiod pathway-dependent manner. We show that the subfunctionalized BnaA9.NST3 directly binds to the BnaC8.NF-YC9 and Bna.CO promoters to regulate their transcription. BnaC8.NF-YC9 interacts with Bna.CO, forming NF‒CO complexes that regulate Bna.FT transcription, thereby affecting flowering. Moreover, we found that florigen upregulated secondary cell wall biogenesis (SCWB)-related genes including BnaA9.NST3, accelerating SCWB in stems and promoting vascular maturation and adaptation of the shoot system to meet the plant’s mechanical support needs during the reproductive phase. Our results provide insights into the connection between flowering and secondary growth and suggest gene targets for cultivating B. napus lines that flower at the optimal time.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"8 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144130304","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}

引用次数: 0

Sizing up beauty: Mechanisms of petal size regulation in ornamental plants 评定美：观赏植物花瓣大小调节机制

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-22 DOI: 10.1093/plphys/kiaf198

Yunxiao Guan, Chui Eng Wong, Qiaoyu Zhang, Donghui Peng, Siren Lan, Fadi Chen, Zhong-Jian Liu, Hao Yu

引用次数: 0

The rice AT-rich pincer-like element family of conserved noncoding sequences regulates chromatin loop formation. 水稻富含at的钳状元件家族的保守非编码序列调控染色质环的形成。

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-22 DOI: 10.1093/plphys/kiaf211

Yonghan Xu,Dechuan Wu,Manman Zhao,Wei Tang,Xiang Cheng,Qunwen Hu,Zhiwei Liu,Jiangtao Gan,Jiahao Hua,Guoxing Zou,Ai Lu,Chen Yang,Yunxing Zheng,Wenjin Li,Jincai Li,Xiaobo Wang,Chuanxi Ma

{"title":"The rice AT-rich pincer-like element family of conserved noncoding sequences regulates chromatin loop formation.","authors":"Yonghan Xu,Dechuan Wu,Manman Zhao,Wei Tang,Xiang Cheng,Qunwen Hu,Zhiwei Liu,Jiangtao Gan,Jiahao Hua,Guoxing Zou,Ai Lu,Chen Yang,Yunxing Zheng,Wenjin Li,Jincai Li,Xiaobo Wang,Chuanxi Ma","doi":"10.1093/plphys/kiaf211","DOIUrl":"https://doi.org/10.1093/plphys/kiaf211","url":null,"abstract":"The comprehensive annotation of regulatory elements in linear genomes is needed to elucidate the molecular mechanisms underlying chromatin loop formation in plants. Here, we characterized a novel family of conserved noncoding sequences (CNSs) in the rice (Oryza sativa) genome. These sequences, known as AT-rich pincer-like elements (APEs), are composed of 13-bp repeat unit arrays in a reverse-forward configuration. Our findings revealed that there are 611 APE copies across the japonica genome. Deletion of single APEs disrupted the long-range chromatin loops anchoring target APE regions and moderately remodeled the profile of A/B compartments, topologically associating domains (TADs), and chromatin loops, thereby rewiring the expression of looped gene(s) including those controlling important agronomic traits. Thus, APEs function as hub motifs directly mediating chromatin looping and maintaining 3D genome integrity and stability at the levels of compartments, TADs, and loops. Moreover, neighboring genomic regions harboring numerous paired non-APE (NA) CNSs were more likely to interact with each other. This finding suggests that NA CNS pairs might play a helper role in determining loop frequency in a dose-dependent manner, likely by ensuring the pairing selectivity of anchor sites. Our study highlights the importance of APEs and NA CNSs in maintaining 3D genome structure, thereby providing the framework required to link many noncoding repetitive elements to their molecular functions in plants.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"10 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122309","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}

引用次数: 0

Genome modification in plant mitochondria 植物线粒体的基因组修饰

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-22 DOI: 10.1093/plphys/kiaf197

Joachim Forner

{"title":"Genome modification in plant mitochondria","authors":"Joachim Forner","doi":"10.1093/plphys/kiaf197","DOIUrl":"https://doi.org/10.1093/plphys/kiaf197","url":null,"abstract":"Mitochondria are an indispensable component of every plant cell and are inextricably linked to many vital functions. One of their key characteristics is that they have their own genome. This genome, although greatly reduced, encodes several essential genes. While this has been known for decades, until recently it has not been possible to study the mitochondrial genome and its function in detail due to the lack of suitable tools for forward and reverse genetics. This is partly due to the low mutation rate in mitochondria and the lack of methods for direct transformation. A breakthrough came with the use of nuclear encoded transcription activator-like effector (TALE) nucleases (TALENs) for targeted mitochondrial mutagenesis. One of the first applications was to show unambiguously that certain ORFs were causal for cytoplasmic male sterility (CMS). This had previously been beyond our technical capabilities. TALENs are suitable for all plant species amenable to nuclear transformation because they are protein-only and can be imported post-transcriptionally into the mitochondria. Unfortunately, TALEN mutagenesis in plant mitochondria often seems to be associated with large genomic rearrangements. DNA base editors, the latest addition to the toolbox, bypass these side effects and merely introduce point mutations. They are based on TALEs and could only be developed after the discovery of a cytosine deaminase that acts on double-stranded DNA. The possibilities for targeted modification of the mitochondrial genome in plants are developing rapidly. This article aims to show where we stand in this development and what we can expect in the near future.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"57 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114076","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}

引用次数: 0

Three transcription factors form an activation–inhibition module to regulate anthocyanin accumulation in Asiatic hybrid lilies 三个转录因子组成一个激活-抑制模块来调控亚洲杂交百合花青素的积累

IF 7.4 1区生物学

Plant Physiology Pub Date : 2025-05-21 DOI: 10.1093/plphys/kiaf203

Mengmeng Bi, Leifeng Xu, Jiawen Wang, Xin Liu, Panpan Yang, Jingyi Bai, Yulin Luo, Chenlu Yang, Yue Yang, Jun Ming

{"title":"Three transcription factors form an activation–inhibition module to regulate anthocyanin accumulation in Asiatic hybrid lilies","authors":"Mengmeng Bi, Leifeng Xu, Jiawen Wang, Xin Liu, Panpan Yang, Jingyi Bai, Yulin Luo, Chenlu Yang, Yue Yang, Jun Ming","doi":"10.1093/plphys/kiaf203","DOIUrl":"https://doi.org/10.1093/plphys/kiaf203","url":null,"abstract":"Asiatic hybrid lilies (Lilium spp.) are favored by consumers for their vibrant colors and diverse anthocyanin pigmentations. Although the regulation of anthocyanin accumulation by transcription factors has been explored, the role of HD-Zip proteins with ethylene-responsive element binding factor associated amphiphilic repression (EAR) motifs in modulating anthocyanin levels through histone acetylation remains unclear. In this study, we identified Lhhomeobox-leucine zipper protein 4 (LhHB4) as a δ group member of the HD-Zip II family, acting as a repressor of anthocyanin accumulation in lilies. LhHB4 directly suppresses the expression of LhMYBSPLATTER by binding to its promoter. In addition, LhHB4 inhibits the gene expression of the anthocyanin activator LhWRKY44, which, in turn, activates LhMYBSPLATTER expression, forming a regulatory module involving LhHB4, LhWRKY44, and LhMYBSPLATTER. Moreover, LhHB4 interacts with the LhTOPLESS-RELATED protein (LhTPR3), a histone deacetylase corepressor, through the EAR motif to form a repressive complex. This interaction reduces histone H3 acetylation levels at the promoter regions of LhWRKY44 and LhMYBSPLATTER. The downregulation of LhWRKY44 and LhMYBSPLATTER results in reduced anthocyanin biosynthesis in lilies. Furthermore, LhHB4 and LhMYBSPLATTER establish a feedback loop that finely regulates flower coloration, with LhMYBSPLATTER inhibition by LhHB4 subsequently promoting LhHB4 expression. In conclusion, LhHB4, LhWRKY44, and LhMYBSPLATTER form an activation–inhibition module that controls anthocyanin accumulation through histone acetylation in Asiatic hybrid lilies.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"78 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114078","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}

引用次数: 0