The Plant Cell最新文献

Focus on Translational Research from Arabidopsis to Crop Plants and Beyond. 从拟南芥到农作物及其他植物的转化研究

The Plant Cell Pub Date : 2025-05-15 DOI: 10.1093/plcell/koaf119

Adrienne H K Roeder,Cristiana T Argueso,Mary Williams,Gabriela Auge,Xin Li,Lucia Strader,Cristobal Uauy,Shuang Wu

引用次数: 0

LIPID DROPLET PROTEIN OF SEEDS is involved in the control of lipid droplet size in Arabidopsis seeds and seedlings. 种子脂滴蛋白参与控制拟南芥种子和幼苗的脂滴大小。

The Plant Cell Pub Date : 2025-05-15 DOI: 10.1093/plcell/koaf121

Nathan M Doner,Alyssa C Clews,Nicolas Esnay,Payton S Whitehead,You Wang,Trevor B Romsdahl,Damien Seay,Philipp W Niemeyer,Martin Bonin,Yang Xu,Oliver Valerius,Gerhard H Braus,Till Ischebeck,Kent D Chapman,John M Dyer,Robert T Mullen

{"title":"LIPID DROPLET PROTEIN OF SEEDS is involved in the control of lipid droplet size in Arabidopsis seeds and seedlings.","authors":"Nathan M Doner,Alyssa C Clews,Nicolas Esnay,Payton S Whitehead,You Wang,Trevor B Romsdahl,Damien Seay,Philipp W Niemeyer,Martin Bonin,Yang Xu,Oliver Valerius,Gerhard H Braus,Till Ischebeck,Kent D Chapman,John M Dyer,Robert T Mullen","doi":"10.1093/plcell/koaf121","DOIUrl":"https://doi.org/10.1093/plcell/koaf121","url":null,"abstract":"In oilseeds, energy-rich carbon is stored as triacylglycerols in organelles called lipid droplets (LDs). While several of the major biogenetic proteins involved in LD formation have been identified, the full repertoire of LD proteins and their functional roles remains incomplete. Here, we show that the low-abundance, seed-specific LD protein LIPID DROPLET PROTEIN OF SEEDS (LDPS) contains an amphipathic α-helix and proline hairpin motif that serves as an LD-targeting signal and a separate region that binds to the LD protein OLEOSIN 1 (OLEO1). Loss of LDPS function results in smaller LDs and less seed oil in comparison to wild type, while over-expression of LDPS results in an increase in LD size and seed oil content. Loss of LDPS function also results in an inability of LDs to undergo fusion during post-germinative seedling growth. Analysis of oleo1 and ldps single and double mutant seeds and freeze-thaw treatment of seeds revealed that OLEO1 suppresses the ability of LDPS to promote larger LDs. Collectively, our results identify LDPS as an important player in LD biology that functions together with OLEO1 to determine LD size in Arabidopsis (Arabidopsis thaliana) seeds and seedlings through a process that involves LD-LD fusion.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A magic pocket: An all-in-one CRISPR toolbox for plants. 一个神奇的口袋：一个用于植物的多功能CRISPR工具箱。

The Plant Cell Pub Date : 2025-05-14 DOI: 10.1093/plcell/koaf120

Andrea Gomez-Felipe

引用次数: 0

NUE regulons conserved model-to-crop enhance machine learning predictions of nitrogen use efficiency. NUE规则保守的模型-作物增强了氮利用效率的机器学习预测。

The Plant Cell Pub Date : 2025-05-14 DOI: 10.1093/plcell/koaf093

Ji Huang,Chia-Yi Cheng,Matthew D Brooks,Tim L Jeffers,Nathan M Doner,Hung-Jui Shih,Samantha Frangos,Manpreet Singh Katari,Gloria M Coruzzi

{"title":"NUE regulons conserved model-to-crop enhance machine learning predictions of nitrogen use efficiency.","authors":"Ji Huang,Chia-Yi Cheng,Matthew D Brooks,Tim L Jeffers,Nathan M Doner,Hung-Jui Shih,Samantha Frangos,Manpreet Singh Katari,Gloria M Coruzzi","doi":"10.1093/plcell/koaf093","DOIUrl":"https://doi.org/10.1093/plcell/koaf093","url":null,"abstract":"Systems biology aims to uncover gene regulatory networks (GRNs) for agricultural traits, but validating them in crops is challenging. We addressed this challenge by learning and validating model-to-crop GRN regulons governing nitrogen use efficiency (NUE). First, a fine-scale time-course nitrogen (N) response transcriptome analysis revealed a conserved temporal N response cascade in maize (Zea mays) and Arabidopsis (Arabidopsis thaliana). This data was used to infer time-based causal transcription factor (TF) target edges in N-regulated GRNs (N-GRNs). By validating 23 maize TFs in a cell-based TF-perturbation assay (TARGET), precision/recall analysis enabled us to prune high-confidence edges between ∼200 TFs/700 maize target genes. We next learned gene-to-NUE trait scores using XGBoost machine learning models trained on conserved N-responsive genes across maize and Arabidopsis accessions. By integrating NUE gene scores within our N-GRN, we ranked maize TFs based on a cumulative NUE regulon score. Regulons for top-ranked TFs were validated using the cell-based TARGET assay in maize (e.g. ZmMYB34/R3→24 targets) and the Arabidopsis ZmMYB34/R3 ortholog (e.g. AtDIV1→23 targets). The genes in this NUE regulon significantly enhanced the ability of XGBoost models to predict NUE traits in both maize and Arabidopsis. Thus, our pipeline for identifying NUE regulons that combines GRN inference, machine learning, and orthologous network regulons offers a strategic framework for crop trait improvement.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PROTEIN PHOSPHATASE2A B'η drives spliceosome subunit dephosphorylation to mediate alternative splicing following heat stress. 蛋白PHOSPHATASE2A B'η驱动剪接体亚基去磷酸化介导热应激后的选择性剪接。

The Plant Cell Pub Date : 2025-05-13 DOI: 10.1093/plcell/koaf117

Seung Hee Jo,Hyun Ji Park,Haemyeong Jung,Ga Seul Lee,Jeong Hee Moon,Hyun-Soon Kim,Hyo-Jun Lee,Choonkyun Jung,Hye Sun Cho

{"title":"PROTEIN PHOSPHATASE2A B'η drives spliceosome subunit dephosphorylation to mediate alternative splicing following heat stress.","authors":"Seung Hee Jo,Hyun Ji Park,Haemyeong Jung,Ga Seul Lee,Jeong Hee Moon,Hyun-Soon Kim,Hyo-Jun Lee,Choonkyun Jung,Hye Sun Cho","doi":"10.1093/plcell/koaf117","DOIUrl":"https://doi.org/10.1093/plcell/koaf117","url":null,"abstract":"Dephosphorylation of spliceosome components is an essential regulatory step for intron removal from pre-mRNA, thereby controlling gene expression. However, the specific phosphatase responsible for this dephosphorylation step has not been identified. Here, we show that Arabidopsis thaliana (Arabidopsis) PROTEIN PHOSPHATASE 2A B'η (PP2A B'η), a B subunit of PP2A, interacts with the splicing factors PRP18a, PRP16, and RH2 and facilitates their dephosphorylation by recognizing substrates through a conserved binding motif. This dephosphorylation is crucial for proper splicing of retained introns in heat stress-responsive genes, which is mediated by the PP2A interactor PRE-MRNA PROCESSING FACTOR 18a (PRP18a). Genetic inactivation of PP2A B'η abolished thermotolerance during seed germination and resulted in widespread intron retention in heat stress-responsive genes. Conversely, overexpression of PP2A B'η conferred enhanced thermotolerance, accompanied by the efficient removal of retained introns under heat stress. We demonstrate that a B regulatory subunit of PP2A plays a central role in dephosphorylating spliceosome components, regulating alternative splicing, facilitating acclimation to heat stress, and targeting specific spliceosome subunits that activate pre-mRNA splicing.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops 抗性觉醒：DNA、RNA和蛋白质水平的多样性为从拟南芥到农作物的植物免疫受体工程提供了信息

The Plant Cell Pub Date : 2025-05-09 DOI: 10.1093/plcell/koaf109

Chandler A Sutherland, Danielle M Stevens, Kyungyong Seong, Wei Wei, Ksenia V Krasileva

{"title":"The Resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops","authors":"Chandler A Sutherland, Danielle M Stevens, Kyungyong Seong, Wei Wei, Ksenia V Krasileva","doi":"10.1093/plcell/koaf109","DOIUrl":"https://doi.org/10.1093/plcell/koaf109","url":null,"abstract":"Plants rely on germline-encoded, innate immune receptors to sense pathogens and initiate the defense response. The exponential increase in quality and quantity of genomes, RNA-seq datasets, and protein structures has underscored the incredible biodiversity of plant immunity. Arabidopsis continues to serve as a valuable model and the theoretical foundation of our understanding of wild plant diversity of immune receptors, while expansion of study into agricultural crops has also revealed distinct evolutionary trajectories and challenges. Here, we provide the classical context for study of both intracellular nucleotide-binding, leucine-rich repeat receptors (NLRs) and surface-localized pattern recognition receptors (PRRs) at the levels of DNA sequences, transcriptional regulation, and protein structures. We then examine how recent technology has shaped our understanding of immune receptor evolution and informed our ability to efficiently engineer resistance. We summarize current literature and provide an outlook on how researchers take inspiration from natural diversity in bioengineering efforts for disease resistance from Arabidopsis and other model systems to crops.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143930851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants. 翻译中的迷失：我们从拟南芥的特性中学到的东西，不能从拟南芥转化为其他植物。

The Plant Cell Pub Date : 2025-05-09 DOI: 10.1093/plcell/koaf036

Adrienne H K Roeder,Andrew Bent,John T Lovell,John K McKay,Armando Bravo,Karina Medina-Jimenez,Kevin W Morimoto,Siobhán M Brady,Lei Hua,Julian M Hibberd,Silin Zhong,Francesca Cardinale,Ivan Visentin,Claudio Lovisolo,Matthew A Hannah,Alex A R Webb

{"title":"Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants.","authors":"Adrienne H K Roeder,Andrew Bent,John T Lovell,John K McKay,Armando Bravo,Karina Medina-Jimenez,Kevin W Morimoto,Siobhán M Brady,Lei Hua,Julian M Hibberd,Silin Zhong,Francesca Cardinale,Ivan Visentin,Claudio Lovisolo,Matthew A Hannah,Alex A R Webb","doi":"10.1093/plcell/koaf036","DOIUrl":"https://doi.org/10.1093/plcell/koaf036","url":null,"abstract":"Research in Arabidopsis thaliana has a powerful influence on our understanding of gene functions and pathways. However, not everything translates from Arabidopsis to crops and other plants. Here, a group of experts consider instances where translation has been lost and why such translation is not possible or is challenging. First, despite great efforts, floral dip transformation has not succeeded in other species outside Brassicaceae. Second, due to gene duplications and losses throughout evolution, it can be complex to establish which genes are orthologs of Arabidopsis genes. Third, during evolution Arabidopsis has lost arbuscular mycorrhizal symbiosis. Fourth, other plants have evolved specialized cell types that are not present in Arabidopsis. Fifth, similarly, C4 photosynthesis cannot be studied in Arabidopsis, which is a C3 plant. Sixth, many other plant species have larger genomes, which has given rise to innovations in transcriptional regulation that are not present in Arabidopsis. Seventh, phenotypes such as acclimation to water stress can be challenging to translate due to different measurement strategies. And eighth, while the circadian oscillator is conserved, there are important nuances in the roles of circadian regulators in crop plants. A key theme emerging across these vignettes is that even when translation is lost, insights can still be gained through comparison with Arabidopsis.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"129 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143992089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Magnaporthe oryzae effector Pwl2 alters HIPP43 localization to suppress host immunity. Magnaporthe oryzae效应物Pwl2改变hip43的定位以抑制宿主免疫。

The Plant Cell Pub Date : 2025-05-09 DOI: 10.1093/plcell/koaf116

Vincent M Were,Xia Yan,Andrew J Foster,Jan Sklenar,Thorsten Langner,Amber Gentle,Neha Sahu,Adam Bentham,Rafał Zdrzałek,Lauren S Ryder,Davies K Kaimenyi,Diana Gómez De La Cruz,Yohan Petit-Houdenot,Alice Bisola Eseola,Matthew Smoker,Mark Jave Bautista,Weibin Ma,Jiorgos Kourelis,Dan Maclean,Mark J Banfield,Sophien Kamoun,Frank L H Menke,Matthew J Moscou,Nicholas J Talbot

{"title":"The Magnaporthe oryzae effector Pwl2 alters HIPP43 localization to suppress host immunity.","authors":"Vincent M Were,Xia Yan,Andrew J Foster,Jan Sklenar,Thorsten Langner,Amber Gentle,Neha Sahu,Adam Bentham,Rafał Zdrzałek,Lauren S Ryder,Davies K Kaimenyi,Diana Gómez De La Cruz,Yohan Petit-Houdenot,Alice Bisola Eseola,Matthew Smoker,Mark Jave Bautista,Weibin Ma,Jiorgos Kourelis,Dan Maclean,Mark J Banfield,Sophien Kamoun,Frank L H Menke,Matthew J Moscou,Nicholas J Talbot","doi":"10.1093/plcell/koaf116","DOIUrl":"https://doi.org/10.1093/plcell/koaf116","url":null,"abstract":"The rice blast fungus Magnaporthe oryzae secretes a battery of effector proteins to facilitate host infection. Among these effectors, Pathogenicity toward Weeping Lovegrass 2 (Pwl2) was originally identified as a host specificity determinant for the infection of weeping lovegrass (Eragrostis curvula) and is also recognized by the barley (Hordeum vulgare) Mla3 resistance protein. However, the biological activity of Pwl2 remains unknown. Here, we showed that the Pmk1 MAP kinase regulates PWL2 expression during the cell-to-cell movement of M. oryzae at plasmodesmata-containing pit fields. Consistent with this finding, we provided evidence that Pwl2 binds to the barley heavy metal-binding isoprenylated protein HIPP43, which results in HIPP43 displacement from plasmodesmata. Transgenic barley lines overexpressing PWL2 or HIPP43 exhibit attenuated immune responses and increased disease susceptibility. In contrast, a Pwl2SNDEYWY variant which does not interact with HIPP43 fails to alter the plasmodesmata localization of HIPP43. Targeted deletion of three PWL2 copies in M. oryzae resulted in a Δpwl2 mutant showing gain of virulence toward weeping lovegrass and barley Mla3 lines, but reduced blast disease severity on susceptible host plants. Taken together, our results provide evidence that Pwl2 is a virulence factor that suppresses host immunity by perturbing the plasmodesmatal deployment of HIPP43.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143926423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A BRASSINOSTEROID INSENSISTIVE 1 receptor kinase ortholog is required for sex determination in Ceratopteris richardii. 一种油菜素内酯不敏感1受体激酶同源基因是决定richardii蠓性别所必需的。

The Plant Cell Pub Date : 2025-05-09 DOI: 10.1093/plcell/koaf058

Katelin M Burow,Xi Yang,Yun Zhou,Brian P Dilkes,Jennifer H Wisecaver

{"title":"A BRASSINOSTEROID INSENSISTIVE 1 receptor kinase ortholog is required for sex determination in Ceratopteris richardii.","authors":"Katelin M Burow,Xi Yang,Yun Zhou,Brian P Dilkes,Jennifer H Wisecaver","doi":"10.1093/plcell/koaf058","DOIUrl":"https://doi.org/10.1093/plcell/koaf058","url":null,"abstract":"Most ferns, unlike all seed plants, are homosporous and produce sexually undifferentiated spores. Sex ratio in many homosporous species is environmentally established by the secretion of antheridiogen from female/hermaphrodite gametophytes. Nearby undetermined gametophytes perceive antheridiogen, which induces male development. In the fern Ceratopteris richardii (Ceratopteris), hermaphroditic (her) mutants develop as hermaphrodites even in the presence of antheridiogen. Modern sequencing and genomic tools make the molecular identification of mutants in the 11-Gbp genome of this fern possible. We mapped 2 linked mutants, her7-14 and her7-19, to the same 16-Mbp interval on chromosome 29 of the Ceratopteris genome. An ortholog of the receptor kinase gene BRASSINOSTEROID INSENSITIVE 1 (BRI1) within this interval encoded a deletion mutation in her7-14 and a missense mutation in her7-19. Three other linked her mutants encoded missense mutations in the same gene, which we name HER7. Consistent with a function as a receptor kinase, HER7-GFP fusion protein localized to the plasma membrane and cytoplasm. Analysis of gene expression showed that brassinosteroid biosynthesis was upregulated in hermaphrodites compared with male gametophytes. Our work demonstrates that HER7 is required for sex determination in Ceratopteris and opens avenues for studying the evolution of antheridiogen systems.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143932521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neutral transcriptome rewiring promotes quantitative disease resistance evolvability at the species level. 中性转录组重接线促进物种水平上的定量抗病进化能力。

The Plant Cell Pub Date : 2025-05-09 DOI: 10.1093/plcell/koaf105

Florent Delplace,Mehdi Khafif,Remco Stam,Adelin Barbacci,Sylvain Raffaele

{"title":"Neutral transcriptome rewiring promotes quantitative disease resistance evolvability at the species level.","authors":"Florent Delplace,Mehdi Khafif,Remco Stam,Adelin Barbacci,Sylvain Raffaele","doi":"10.1093/plcell/koaf105","DOIUrl":"https://doi.org/10.1093/plcell/koaf105","url":null,"abstract":"Quantitative disease resistance (QDR) is an immune response limiting pathogen damage in plants. It involves transcriptomic reprogramming of numerous genes, each having a small contribution to plant immunity. Despite the broad-spectrum nature of QDR, the evolution of its underlying transcriptome reprogramming remains largely uncharacterized. Here, we analyzed global gene expression in response to the necrotrophic fungus Sclerotinia sclerotiorum in 23 Arabidopsis (Arabidopsis thaliana) accessions of diverse origin and contrasting QDR phenotypes. Over half of the species pan-transcriptome displayed local responses to S. sclerotiorum, with global reprogramming patterns incongruent with accession phylogeny. Due to frequent small-amplitude variations, only ∼11% of responsive genes were common across all accessions, defining a core transcriptome enriched in highly-responsive genes. Co-expression and correlation analyses showed that QDR phenotypes result from the integration of the expression of numerous genes. Promoter sequence comparisons revealed that variation in DNA-binding sites within cis-regulatory regions contributes to gene expression rewiring. Finally, transcriptome-phenotype maps revealed abundant neutral networks connecting diverse QDR transcriptomes with no loss of resistance, hallmarks of robust and evolvable traits. This navigability associated with regulatory variation in core genes highlights their role in QDR evolvability. This work provides insights into the evolution of complex immune responses, informing models for plant disease dynamics.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143926412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0