The Plant Journal最新文献

{"title":"Fishing for a reelGene: evaluating gene models with evolution and machine learning","authors":"Aimee J. Schulz,&nbsp;Jingjing Zhai,&nbsp;Taylor AuBuchon-Elder,&nbsp;Carson M. Andorf,&nbsp;Mohamed Z. El-Walid,&nbsp;Taylor H. Ferebee,&nbsp;Elizabeth H. Gilmore,&nbsp;Matthew B. Hufford,&nbsp;Lynn C. Johnson,&nbsp;Elizabeth A. Kellogg,&nbsp;Thuy La,&nbsp;Evan Long,&nbsp;Zachary R. Miller,&nbsp;John L. Portwood II,&nbsp;M. Cinta Romay,&nbsp;Arun S. Seetharam,&nbsp;Michelle C. Stitzer,&nbsp;Margaret R. Woodhouse,&nbsp;Travis Wrightsman,&nbsp;Edward S. Buckler,&nbsp;Brandon Monier,&nbsp;Sheng-Kai Hsu","doi":"10.1111/tpj.70483","DOIUrl":"https://doi.org/10.1111/tpj.70483","url":null,"abstract":"<div>\u0000 \u0000 <p>Assembled genomes and their associated annotations have transformed our study of gene function. However, each new annotated assembly generates new gene models. Inconsistencies between annotations likely arise from biological and technical causes, including pseudogene misclassification, transposon activity, and intron retention from sequencing of unspliced transcripts. To evaluate gene model predictions, we developed reelGene, a pipeline of machine learning models focused on (1) transcription boundaries, (2) mRNA integrity, and (3) protein structure. The first two models leverage sequence characteristics and evolutionary conservation across related taxa to learn the grammar of conserved transcription boundaries and mRNA sequences, while the third uses the conserved evolutionary grammar of protein sequences to predict whether a gene can produce a protein. Evaluating 1.8 million transcript models in <i>Zea mays ssp. mays</i> (maize), reelGene classified 28% as incorrectly annotated or non-functional. We find that reelGene classifies 92.2% of genes in the maize proteome and 99.2% of genes within the maize classical gene list as functional. reelGene also provides a way to further investigate genome biology– for instance, reelGene indicates that 10.3% of dispensable genes in B73 are functional, and within retained duplicate genes, reelGene identifies a 30% bias toward the retention of the M1 subgenome when one copy is functional and the other is non-functional. As an annotation-evaluating tool, reelGene is directly applicable to species of the Andropogoneae tribe, including other important crops like sorghum and miscanthus. As a community resource, reelGene has been integrated onto MaizeGDB both as a browser track and as an individual Shiny App, allowing researchers to evaluate gene model accuracy and further investigate genome biology.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145110925","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":"Bimodal retrograde signaling disrupts a suppressor network and activates a key transcriptional activator to direct stress responses","authors":"Liping Zeng,&nbsp;Jingzhe Guo,&nbsp;Carlos Rodriguez,&nbsp;Maria Fernanda Gomez-Mendez,&nbsp;Yaqi Wang,&nbsp;Wilhelmina van de Ven,&nbsp;Malathy Palayam,&nbsp;Jose Pruneda-Paz,&nbsp;Nitzan Shabek,&nbsp;Katayoon Dehesh","doi":"10.1111/tpj.70478","DOIUrl":"https://doi.org/10.1111/tpj.70478","url":null,"abstract":"<div>\u0000 \u0000 <p>Plastid-to-nucleus communication, crucial for regulating stress-responsive gene expression, has long intrigued researchers. This study reveals how the plastidial metabolite 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate (MEcPP) orchestrates transcriptional reprogramming by modulating the rapid stress response element (RSRE), a conserved regulatory hub in the plant general stress response network. Yeast one-hybrid assays identified HAT1, a class II HD-Zip protein, as a negative regulator of RSRE. Genetic analyses, including HAT1 overexpression and knockdowns, confirmed its role in suppressing RSRE activity. Interaction assays uncovered a suppression network involving HAT1, the co-repressor TOPLESS (TPL), and the nuclear importin IMPα-9. Furthermore, HAT1 interacts with calmodulin-binding transcription activator 3 (CAMTA3), a calcium/calmodulin-binding transcription factor known to activate RSRE. AlphaFold modeling provided insights into the architecture of the HAT1-RSRE complex and HAT-CAMTA3 interaction, supported by conserved domains across plant species. Under stress condition, MEcPP accumulation promotes the 26S proteasomal degradation of TPL and IMPα-9 while reduces auxin-dependent HAT1 expression. Additionally, MEcPP enhances Ca²⁺ influx, activating CAMTA3 and enabling it to bind RSRE, thereby initiating the transcription of stress response genes. This dual mechanism—dismantling suppressors (HAT1, TPL, and IMPα-9) and activating CAMTA3—underscores MEcPP's central role in plastid-to-nucleus signaling. These findings emphasize MEcPP's pivotal function in dynamically regulating gene expression to maintain cellular homeostasis under environmental stress.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111384","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":"LpSAPK9 phosphorylates and activates LpABF2/LpABF3 to transactivate expression of chlorophyll catabolic genes and promote leaf senescence in perennial ryegrass","authors":"Yuwei Yang,&nbsp;Jing Xing,&nbsp;Huanhuan Hao,&nbsp;Hao Guan,&nbsp;Huadong Yang,&nbsp;Tingchao Yin,&nbsp;Yingjun Chi,&nbsp;Bin Xu,&nbsp;Jing Zhang","doi":"10.1111/tpj.70477","DOIUrl":"10.1111/tpj.70477","url":null,"abstract":"<div>\u0000 \u0000 <p>Leaf senescence is an active and tightly controlled process that is particularly important for perennial plants to survive over hostile environmental conditions. The phytohormone ABA plays a vital regulatory role in leaf senescence, and the subclass III SnRK2 family genes, such as SnRK2.2/2.3/2.6, are known as key components in ABA signaling. Yet, the functional roles and molecular mechanisms of subclass I SnRK2s in ABA-mediated leaf senescence remain less well understood. In this study, we characterized one subclass I SnRK2 kinase, LpSAPK9, in perennial ryegrass (<i>Lolium perenne</i>). LpSAPK9 was localized in both the chloroplast and the nucleus, and its gene expression was positively correlated with the process of leaf senescence. Overexpressing <i>LpSAPK9</i> accelerated developmental and drought/osmotic-induced leaf senescence. The interactive proteins of LpSAPK9, including LpABF2 and LpABF3, were identified using yeast two-hybrid (Y2H) library screening and confirmed by firefly luciferase complementation assay (LCA), bimolecular fluorescence complementation (BiFC), and co-immunoprecipitation (Co-IP) assays. Combining Y1H, <i>in planta</i> transactivation assay, and CUT&amp;Tag-qPCR, we identified that LpABF2 and LpABF3 directly bound promoters of four chlorophyll catabolic genes (<i>LpSGR</i>, <i>LpNYC1</i>, <i>LpNOL</i>, and <i>LpPPH</i>) to activate their transcription. By phosphorylating the S89 and T130 amino acid residues in LpABF2 and the S122 in LpABF3, LpSAPK9 enhances the transcription activities of LpABF2/3 to promote chlorophyll degradation and leaf senescence. Interestingly, <i>LpSAPK9</i> overexpression not only accelerated these senescence processes but also reduced leaf ABA content and down-regulated ABA biosynthetic genes. Collectively, our results reveal that the LpSAPK9-LpABF2/LpABF3 module coordinately regulates the expression of chlorophyll catabolic genes to control leaf senescence in perennial ryegrass.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084494","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":"Plastoquinone redox status influences carboxysome integrity via a RpaA- and reactive oxygen species-dependent regulatory network","authors":"María Santos-Merino,&nbsp;Lauri Nikkanen,&nbsp;Emmanuel J. Kokarakis,&nbsp;Yagut Allahverdiyeva,&nbsp;Daniel C. Ducat","doi":"10.1111/tpj.70480","DOIUrl":"10.1111/tpj.70480","url":null,"abstract":"<p>Carboxysomes are bacterial microcompartments that encapsulate Rubisco and are a core component of the cyanobacterial carbon concentration mechanism (CCM). While carboxysome number, size, and spatial organization vary in different environmental conditions (CO₂, light availability, redox state, temperature, and light quality), the molecular mechanisms underlying this potentially adaptive process remain elusive. Herein, we observe that mutants of the circadian rhythm/metabolism factor, Regulator of Phycobilisome Association A (RpaA), exhibit a striking breakdown of carboxysomes under certain environmental conditions. We find that conditions leading to overreduction of the plastoquinone (PQ) pool (mixotrophic growth, high irradiance, or chemical inhibition of electron transfer from PQ to the cytochrome <i>b</i>_<i>6</i><i>f</i> complex) are accompanied by an elevated generation of reactive oxygen species (ROS) and correlate with the loss of carboxysome integrity. Carboxysome breakdown is reversed by environmental conditions or chemical inhibitors that prevent PQ overreduction and accompanying ROS generation. Taken together, our data support a novel link between the redox status of the PQ pool and carboxysome integrity. Our results have implications for the fundamental understanding of cyanobacterial energy-balancing pathways and may indicate new research directions for understanding how the carboxysome is remodeled in response to changing environments.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70480","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090863","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":"Genetic suppressors of the growth-immunity trade-off in the Arabidopsis salicylic acid-accumulating dmr6 dlo1 mutant","authors":"Tijmen van Butselaar,&nbsp;Tom Schermer,&nbsp;Frederike Bijlmer,&nbsp;Joyce Elberse,&nbsp;Chris van Schie,&nbsp;Guido Van den Ackerveken","doi":"10.1111/tpj.70467","DOIUrl":"10.1111/tpj.70467","url":null,"abstract":"<p>Plants actively suppress growth and development upon activation of immunity. In turn, when pathogen attack has subsided, immune responses are suppressed again. Phytohormones play an important role in regulating this balance and the growth–immunity trade-off in general. The trade-off is evident in the Arabidopsis <i>dmr6 dlo1</i> mutant, which accumulates the immune-activating phytohormone salicylic acid (SA) to high levels, resulting in high disease resistance but repression of growth. Little is known about the SA-induced growth trade-off mechanism. In this study, we performed a genetic suppressor screen on the <i>dmr6 dlo1</i> double mutant to select mutants with reduced growth repression and identify suppressors of the SA-mediated trade-off. We identified 7 independent <i>zund</i> (<i>giant</i>) mutants, with restored growth but retained resistance to downy mildew. Through bulked segregant analysis and whole-genome sequencing (BSA-seq), we identified three mutant alleles of <i>MED15a</i>, an <i>NPR1</i> allele, one <i>ICS1/SID2</i> allele, and a <i>PAD4</i> splice defect. Genetic complementation of mutants confirmed the roles of these genes in the SA-mediated growth–immunity trade-off. We discuss their application in tweaking SA signaling to optimize the balance between growth and immunity that is important when deploying immunity traits in breeding.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70467","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090852","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":"Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)","authors":"Kevin Karbstein,&nbsp;Nancy Choudhary,&nbsp;Ting Xie,&nbsp;Salvatore Tomasello,&nbsp;Natascha D. Wagner,&nbsp;Birthe H. Barke,&nbsp;Claudia Paetzold,&nbsp;John P. Bradican,&nbsp;Michaela Preick,&nbsp;Axel Himmelbach,&nbsp;Nils Stein,&nbsp;Argyris Papantonis,&nbsp;Iker Irisarri,&nbsp;Jan de Vries,&nbsp;Boas Pucker,&nbsp;Elvira Hörandl","doi":"10.1111/tpj.70390","DOIUrl":"10.1111/tpj.70390","url":null,"abstract":"<p>Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus <i>Ranunculus</i> (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species <i>R. cassubicifolius</i> (<i>R. auricomus</i> species complex) and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., <i>infA</i>, <i>ycf15</i>, or <i>rps</i>) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35 482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70390","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090807","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":"A SlEIN2-centered epigenetic network equilibrates fruit ripening and innate immunity in tomato","authors":"Wei Huang,&nbsp;Yan Xu,&nbsp;Yali Song,&nbsp;Hongli Wang,&nbsp;Xiayi Chen,&nbsp;Jingmin Kang,&nbsp;Xuemei Ni,&nbsp;Huan Liu,&nbsp;Sibo Wang","doi":"10.1111/tpj.70484","DOIUrl":"10.1111/tpj.70484","url":null,"abstract":"<div>\u0000 \u0000 <p>Ethylene and DNA/RNA methylation serve as essential factors in controlling fruit ripening. In tomato, the mRNA N6-methyladenosine (m⁶A) demethylase SlALKBH2 regulates mRNA stability of the DNA 5-methylcytosine demethylase gene <i>SlDML2</i> via modulating m⁶A modifications. However, the interplay between ethylene and these epigenetic marks remains unclear. Here, we show that <i>SlDML2</i> expression is significantly inhibited in <i>slein2</i> fruits, but remains unchanged in the high-order <i>sleil</i> mutant (<i>sleil1 sleil2 sleil3</i>/<i>SlEIL3 sleil4</i> and <i>sleil1 sleil2</i>/<i>SlEIL2 sleil3 sleil4</i>) fruits, indicative of post-transcriptional regulation of <i>SlDML2</i> expression by SlEIN2, a core ethylene signaling component acting upstream of the master transcription factors SlEILs. Interestingly, SlEIN2 preferentially regulates the asymmetric CHH methylation in promoters of several key ripening regulator genes. Mechanistically, SlEIN2 physically interacts with SlALKBH2, which promotes <i>SlDML2</i> expression in a SlEIN2-dependent manner. Furthermore, <i>SlAGO4A and SlAGO4B</i>, components of the RNA-directed DNA methylation pathway, were upregulated in <i>slein2</i> fruits. Silencing <i>SlAGO4A/B</i> in wild-type fruit caused precocious ripening with necrosis, indicative of hyperimmunity. Conversely, <i>SlAGO4A/B</i> silencing in <i>slein2</i> markedly delayed this hyperimmunity. Taken together, our study reveals that ethylene, beyond transcriptional regulation, employs an elaborate epigenetic machinery mediated by the SlAGO4A/B-SlEIN2-SlALKBH2 module to balance fruit ripening and innate immunity.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079219","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":"Riboflavin in phloem sap helps wild tomato combat whiteflies","authors":"Gwendolyn K. Kirschner","doi":"10.1111/tpj.70474","DOIUrl":"10.1111/tpj.70474","url":null,"abstract":"&lt;p&gt;The whitefly &lt;i&gt;Bemisia tabaci&lt;/i&gt; feeds on vegetable and ornamental crops including chilli, okra, potato, tobacco and tomato, causing global annual losses of up to billions of US dollars (Sani et al., &lt;span&gt;2020&lt;/span&gt;). As phloem-feeding insects, &lt;i&gt;B. tabaci&lt;/i&gt; feed on host plants by inserting their mouthpart, the stylet, directly into the phloem. During that process, they inject RNA and protein that suppress the plant immune system. Additionally, they can transfer viruses such as the tomato yellow leaf curl virus (Jones, &lt;span&gt;2003&lt;/span&gt;). Whitefly is a rapidly adapting pest that has evolved resistance to even the most potent chemical treatments (Barman et al., &lt;span&gt;2022&lt;/span&gt;). Sustainable whitefly management requires integrating multiple defence layers—including genetic resistance—into comprehensive integrated pest management strategies. Some wild relatives of cultivated tomato are resistant to whitefly damage. Identifying the mechanisms and genes underlying whitefly resistance in wild tomato can equip the vegetable breeding industry with genetic tools to introgress this trait into cultivated varieties.&lt;/p&gt;&lt;p&gt;Most of these resistance mechanisms in wild tomato are based on the production of specialised metabolites in glandular trichomes that are bioactive against &lt;i&gt;B. tabaci&lt;/i&gt; (Kortbeek et al., &lt;span&gt;2021&lt;/span&gt;). Lissy-Anne Denkers, first author of the highlighted publication, did a research internship in Petra Bleeker's lab at the University of Amsterdam, in which she worked on this resistance mechanism. This sparked her interest in tomato and the role of specialised metabolites in biotic interactions. She was fascinated by the tomato–whitefly interaction as a research system because it presents complex yet tangible questions that can be approached from multiple disciplines, including plant physiology, biochemistry, insect physiology and behaviour, ecotoxicology and broader ecology. Although the different tomato species with their large variation in appearance, chemistry and resistances were what captured her initial interest, she could not help but develop some secret appreciation for whiteflies, especially the clumsily walking first instar nymphs.&lt;/p&gt;&lt;p&gt;For her PhD project, Denkers analysed a defence mechanism that was independent of trichome repellents. The wild tomato accession &lt;i&gt;Solanum chmielewskii&lt;/i&gt; was found to be susceptible to adult whiteflies; however, the whiteflies deposited fewer eggs on its leaves, and the development of juvenile whitefly stages was hampered (de Almeida et al., &lt;span&gt;2023&lt;/span&gt;). The team hypothesised that this resistance in &lt;i&gt;S. chmielewskii&lt;/i&gt; might be due to something in the phloem that specifically targets young stages of whiteflies, the nymphs, which rely on constant feeding from the phloem (Denkers et al., &lt;span&gt;2025&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;Whiteflies deposit their eggs on host plant leaves, then the first instar nymph hatches and searches for a feeding site towards the leaf vasculature. There, ","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70474","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145068759","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":"RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana","authors":"Mitsuru Saraumi,&nbsp;Takahiro Tanaka,&nbsp;Daiki Koyama,&nbsp;Yoshitaka Nishi,&nbsp;Yoshihiro Takahashi,&nbsp;Hiroyasu Motose,&nbsp;Taku Takahashi","doi":"10.1111/tpj.70476","DOIUrl":"https://doi.org/10.1111/tpj.70476","url":null,"abstract":"<p>Thermospermine is involved in negative regulation of xylem differentiation by enhancing the translation of mRNAs of the <i>SAC51</i> gene family in Arabidopsis (<i>Arabidopsis thaliana</i>). These mRNAs contain conserved upstream open reading frames (uORFs) that interfere with the translation of the main ORF. To investigate the mechanism by which thermospermine acts in this process, we isolated mutants insensitive to thermospermine, named ‘<i>its</i>’. We show that the four genes responsible for these mutants, <i>its1</i> to <i>its4</i>, encode: (i) a homolog of SPOUT RNA methyltransferase, (ii) an rRNA pseudouridine synthase CBF5/NAP57, (iii) a putative spliceosome disassembly factor STIPL1/NTR1, and (iv) a plant-specific RNA-binding protein PHIP1. These four mutants were found to have much higher levels of thermospermine than the wild-type. While all these mutants except <i>its1</i> appear almost normal, they enhance the dwarf phenotype of a mutant of <i>ACL5,</i> which encodes thermospermine synthase, resulting in tiny plants resembling a double knockout of <i>ACL5</i> and <i>SACL3</i>, a member of the <i>SAC51</i> family. Reporter assays revealed that GUS activity from the CaMV 35S promoter-<i>SAC51</i> 5′-GUS fusion construct was significantly reduced in <i>its1</i> and <i>its4</i> or not affected in <i>its2</i> and <i>its3</i>, while it was slightly increased in <i>its1</i>, <i>its3</i>, and <i>its4</i>, or not changed in <i>its2</i> by thermospermine. These findings underscore the critical role of RNA processing and modification in the thermospermine-dependent translational regulation of uORF-containing transcripts.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70476","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145057814","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":"Whole-tissue 3D immunostaining of shoot apical meristems in rice at single-cell resolution","authors":"Yurika Morishita,&nbsp;Ryosuke Takata,&nbsp;Asuka Higo,&nbsp;Aya Yoshida,&nbsp;Hiroyuki Tsuji","doi":"10.1111/tpj.70470","DOIUrl":"https://doi.org/10.1111/tpj.70470","url":null,"abstract":"<div>\u0000 \u0000 <p>The shoot apical meristem (SAM) produces all above-ground organs of plants and is thus a central focus of plant developmental biology. Developmental processes in the SAM are regulated by various factors that control gene expression at the cellular level. Key among these are the chemical modifications of the N-terminal tails of histones, which are essential components of nucleosomes and chromatin that play crucial roles in these processes. While immunostaining is a valuable method for the spatial analysis of histone modifications, its application to the SAM has posed technical challenges. Here, we developed a three-dimensional immunostaining method for rice (<i>Oryza sativa</i>) SAMs at single-cell resolution using a permeabilization process with specific cell wall degrading enzymes, along with the iTOMEI clearing technique (Sakamoto et al. [2022] <i>Communications Biology</i>, 5, 12). We detected clear signals throughout the deeper tissue layers, allowing us to visualize histone modifications associated with both active and repressive chromatin states, as well as M phase–specific modifications localized on chromosomes. The repressive modifications H3K9me2 and H3K27me3 exhibited punctate patterns within the nuclei, whereas the modifications linked to transcriptional activity were more diffusely distributed. Double staining showed that H3K9me2 forms a peripheral layer around a central domain enriched in H3K4me1. A comparative analysis of SAMs during the vegetative and reproductive phases indicated that active modifications persisted across both phases, whereas repressive modifications increased during the reproductive phase. Our protocol facilitates the three-dimensional visualization of chromatin states in the SAM, offering a robust tool for exploring the spatial regulation of plant development at the single-cell level.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145057929","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}