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Two-layer quality control protects Arabidopsis from transcriptional errors under heat stress. 两层质量控制保护拟南芥免受热胁迫下转录错误的影响。
Pub Date : 2025-11-03 DOI: 10.1093/plcell/koaf264
Yu-Hung Hung
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引用次数: 0
How tomatoes balance defense: Orchestration of gray mold immunity by the SlMYC2-SlLBD40/42-SlBPM4 module. 番茄如何平衡防御:通过SlMYC2-SlLBD40/42-SlBPM4模块协调灰霉病免疫。
Pub Date : 2025-11-03 DOI: 10.1093/plcell/koaf261
Jiajun Wang,Yueyao Wang
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引用次数: 0
Duplicated genes find their space: Spatial transcriptomics illuminates evolutionary fates. 重复的基因找到了它们的空间:空间转录组学阐明了进化的命运。
Pub Date : 2025-11-01 DOI: 10.1093/plcell/koaf265
Min-Yao Jhu,Fabian van Beveren,Bruno Guillotin
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引用次数: 0
Transcription fidelity and control of alternative splicing contribute to heat stress survival in Arabidopsis. 转录保真度和选择性剪接控制有助于拟南芥热胁迫存活。
Pub Date : 2025-10-28 DOI: 10.1093/plcell/koaf256
Henrik Mihály Szaker,Radhika Verma,István Szádeczky-Kardoss,Nóra Gál,Syed Hussam Abbas,Éva Darkó,Aladár Pettkó-Szandtner,Dániel Silhavy,Tibor Csorba
Transcriptional quality control is essential to maintain the integrity of genetic information. Although well characterized in yeast and metazoans, the regulation of transcriptional fidelity in plants remains elusive. We explored transcriptional fidelity and alternative splicing control in Arabidopsis thaliana using genetic, molecular biology, and deep sequencing tools. Using circle-sequencing assays, we analyzed the error landscape of the transcriptome at single-nucleotide depth under ambient and heat-stress conditions in wild-type and different quality control mutant plants. We found that the frequency of nucleotide misincorporations and insertions is significantly elevated under heat stress, and that nucleotide imbalance also leads to error-prone transcription. We demonstrate that the RNA polymerase II-associated elongation cofactor TFIIS is a fidelity factor for both transcription and alternative splicing, as its absence reduces the accuracy of both processes. Moreover, we found that the nonsense-mediated mRNA decay (NMD) cytoplasmic surveillance system is also required for heat-stress tolerance: NMD degrades transcripts containing premature termination codons, generated by 1-2 nucleotide indels of erroneous transcription and by alternative splicing during heat stress. In conclusion, the interplay between these RNA surveillance systems safeguards the correct genetic information flow and is critical for developmental regulation and heat-stress adaptation in plants.
转录质量控制对维持遗传信息的完整性至关重要。虽然在酵母和后生动物中有很好的特征,但在植物中转录保真度的调节仍然难以捉摸。我们利用遗传、分子生物学和深度测序工具探索拟南芥的转录保真度和选择性剪接控制。利用环测序技术,我们分析了野生型和不同质量控制突变体植物在环境和热胁迫条件下单核苷酸深度转录组的错误景观。我们发现,在热胁迫下,核苷酸错配和插入的频率显著升高,核苷酸不平衡也导致转录容易出错。我们证明,RNA聚合酶ii相关的延伸辅助因子TFIIS是转录和选择性剪接的保真度因子,因为它的缺失降低了这两个过程的准确性。此外,我们发现无义介导的mRNA衰变(NMD)细胞质监测系统也是耐热性所必需的:NMD降解含有过早终止密码子的转录本,这些转录本是由1-2个核苷酸错误转录索引和热胁迫下的选择性剪接产生的。总之,这些RNA监视系统之间的相互作用保障了正确的遗传信息流,对植物的发育调节和热胁迫适应至关重要。
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引用次数: 0
Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella. 绿藻Auxenochlorella的靶向遗传操作和酵母样进化基因组学。
Pub Date : 2025-10-27 DOI: 10.1093/plcell/koaf259
Rory J Craig,Marco A Dueñas,Dimitrios J Camacho,Sean D Gallaher,Maria Clara Avendaño-Monsalve,Yang-Tsung Lin,Crysten E Blaby-Haas,Jeffrey L Moseley,Sabeeha S Merchant
Auxenochlorella spp. are diploid oleaginous green algae whose streamlined genomes can be readily manipulated by homologous recombination, making them highly amenable to discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity and aneuploidy; however, studies of these forces have largely focused on yeasts. Here, we present a telomere-to-telomere phased diploid genome assembly of Auxenochlorella UTEX 250-A (haploid length 22 Mb) and introduce a genetic toolkit for site-specific manipulation of the nuclear genome in multiple strains, featuring several selectable markers, inducible promoters, and fluorescent reporters for protein localization. UTEX 250-A is an allodiploid hybrid of Auxenochlorella protothecoides and Auxenochlorella symbiontica, two species differentiated by extensive chromosomal rearrangements. UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic. Loss-of-heterozygosity events are pervasive across Auxenochlorella and can evolve rapidly in the laboratory. High-quality structural annotation yielded ∼7,500 genes per haplotype. Auxenochlorella have experienced gene family loss and reduction, including core photosynthesis genes, and exhibit periodic adenine and cytosine methylation at promoters and gene bodies, respectively. Approximately 10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, which may participate in a regulatory mechanism. We demonstrate the utility of Auxenochlorella for fundamental research by knockout of a chlorophyll biosynthesis enzyme, and confirm one trisomy by allele-specific transformation. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy and provide a foundation for use of Auxenochlorella as a reference organism.
Auxenochlorella spp.是二倍体产油绿藻,其流线型基因组可以很容易地通过同源重组进行操作,使其高度适合于发现研究和生物工程。营养二倍体生物经历特殊的进化现象,包括异源二倍体杂交、有丝分裂重组、杂合性丧失和非整倍体;然而,对这些力量的研究主要集中在酵母上。在这里,我们展示了一个端粒到端粒的Auxenochlorella UTEX 250-A(单倍体长度为22 Mb)的二倍体基因组组装,并介绍了一个遗传工具包,用于在多个菌株中对核基因组进行位点特异性操作,该工具包具有几个可选择的标记,诱导启动子和荧光报告蛋白定位。UTEX 250-A是原coides Auxenochlorella和共生Auxenochlorella的异源二倍体杂交种,这两个物种通过广泛的染色体重排而分化。UTEX 250-A单倍型是每个亲本物种在有丝分裂重组后的马赛克,两条染色体是三体的。杂合性缺失事件在Auxenochlorella中普遍存在,并且在实验室中可以快速进化。高质量的结构注释得到每个单倍型约7500个基因。Auxenochlorella经历了基因家族的丢失和减少,包括核心光合作用基因,并在启动子和基因体上分别表现出周期性的腺嘌呤和胞嘧啶甲基化。大约10%的基因,特别是涉及DNA修复和性别的基因,重叠反义长链非编码rna,这可能参与调控机制。我们通过敲除叶绿素生物合成酶证明了Auxenochlorella在基础研究中的效用,并通过等位基因特异性转化证实了一个三体。这些结果表明了与营养二倍体相关的几种进化力的普遍性,并为利用Auxenochlorella作为参考生物提供了基础。
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引用次数: 0
MPK3- and MPK6-mediated phosphorylation of STOP1 triggers its nuclear stabilization to modulate hypoxia responses in Arabidopsis. MPK3-和mpk6介导的STOP1磷酸化触发其核稳定,调节拟南芥的缺氧反应。
Pub Date : 2025-10-24 DOI: 10.1093/plcell/koaf257
Jian-Hong Wang,Ying Zhou,Guo-Zhen Su,Qi-Qi Song,Gao-Fan Lin,Ying Xing,Qin-Fang Chen,Lu-Jun Yu,Shi-Hao Su,Ruo-Han Xie,Shi Xiao
In plants, responses to hypoxia include activation of fermentation pathways, cytosolic acidification, and other metabolic shifts. In Arabidopsis (Arabidopsis thaliana), the transcription factor SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) contributes to regulating cellular responses to low-oxygen stress; however, the underlying mechanism remains largely unknown. Here, we showed that transgenic lines overexpressing STOP1 exhibited improved tolerance of hypoxia and submergence, whereas knockout of STOP1 reduced tolerance. STOP1 accumulated during hypoxia and was degraded during post-hypoxia reoxygenation via ubiquitination by PLANT U-BOX-TYPE UBIQUITIN LIGASE 24 (PUB24). Under hypoxia, MITOGEN-ACTIVATED PROTEIN KINASE 3 (MPK3) and MPK6 interacted with and phosphorylated STOP1 to compete with its PUB24-mediated ubiquitination, thus stabilizing STOP1 in the nucleus, where it activated the transcription of GLUTAMATE DEHYDROGENASE 1 (GDH1) and GDH2 for cellular homeostasis of acidic metabolism during hypoxia. Mutating three phosphorylated residues in STOP1 to alanine attenuated its nuclear accumulation and diminished STOP1-mediated hypoxia tolerance. Moreover, we identified the lipid phosphatidic acid as a critical modulator of the MPK3/6-STOP1 association. Overall, these findings uncover an antagonistic biochemical mechanism in which MPK3/6-dependent phosphorylation and PUB24-dependent ubiquitination of STOP1 modulate its nuclear accumulation to control hypoxia responses in Arabidopsis.
在植物中,对缺氧的反应包括发酵途径的激活、细胞质酸化和其他代谢变化。在拟南芥(Arabidopsis thaliana)中,转录因子SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1)参与调节细胞对低氧胁迫的反应;然而,潜在的机制在很大程度上仍然未知。在这里,我们发现过表达STOP1的转基因系对缺氧和浸泡的耐受性提高,而敲除STOP1则会降低耐受性。STOP1在缺氧过程中积累,并在缺氧后的再氧化过程中通过PLANT U-BOX-TYPE UBIQUITIN LIGASE 24 (PUB24)的泛素化降解。在缺氧条件下,丝裂原活化蛋白激酶3 (MPK3)和MPK6与STOP1相互作用并磷酸化STOP1,与其pub24介导的泛素化竞争,从而稳定STOP1在细胞核中的表达,并激活谷氨酸脱氢酶1 (GDH1)和GDH2的转录,以维持缺氧条件下细胞酸性代谢的稳态。将STOP1中的三个磷酸化残基突变为丙氨酸可减弱其核积累并降低STOP1介导的缺氧耐受性。此外,我们发现脂质磷脂酸是MPK3/6-STOP1关联的关键调节剂。总的来说,这些发现揭示了一个拮抗的生化机制,其中mpk3 /6依赖性磷酸化和pub24依赖性泛素化STOP1调节其核积累以控制拟南芥的缺氧反应。
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引用次数: 0
Fine-tuning of MYC2-mediated Botrytis defense response by the LBD40/42-CRL3BPM4 module in tomato. LBD40/42-CRL3BPM4模块对番茄myc2介导的葡萄孢菌防御反应的微调
Pub Date : 2025-10-24 DOI: 10.1093/plcell/koaf258
Jialong Zhang,Danhui Dong,Congyang Jia,Hongxin Li,Lun Liu,Jiayi Xu,Hao Cui,Na Zhang,Yang-Dong Guo
Gray mold caused by the fungal pathogen Botrytis cinerea is a major disease of vegetable and fruit crops. This study elucidates mechanism that fine-tunes B. cinerea resistance mediated by the transcription factor SlMYC2 in tomato (Solanum lycopersicum), characterized by a dynamic balance between "active braking" and "brake release". The Lateral Organ Boundaries Domain (LBD) transcription factor family members SlLBD40 and SlLBD42 repress transcription and form homodimers or heterodimers, with heterodimers demonstrating higher activity. SlLBD40 and SlLBD42 are transcriptionally up-regulated by SlMYC2, but SlLBD40 and SlLBD42 attenuate SlMYC2-orchestrated defenses against B. cinerea, thereby safeguarding the plant from immune over-activation. Moreover, the BTB/POZ-MATH (BPM) protein family member SlBPM4 targets and degrades SlLBD40 and SlLBD42, releasing the defense response and enhancing B. cinerea resistance. Genetic analyses demonstrated that SlLBD40 and SlLBD42 are epistatic to SlBPM4. Additionally, SlLBD40 and SlLBD42 play dual roles in fruit development and B. cinerea defense, and SlBPM4 functions as a protective factor under pathogen attack. Our study uncovered a MYC2-LBD40/42-CRL3BPM4 module in tomato that allocates growth and defense resources by finely regulating gene expression and balancing immune response activation levels. This module also provides potential targets for optimizing the balance between plant growth and defense through gene-editing technologies.
灰霉病是由灰霉病菌灰霉病引起的蔬菜和水果作物的主要病害。本研究阐明了转录因子SlMYC2在番茄(Solanum lycopersicum)中介导的葡萄球菌(B. cinerea)抗性微调机制,其特点是“主动制动”和“制动释放”之间的动态平衡。侧器官边界域(LBD)转录因子家族成员SlLBD40和SlLBD42抑制转录并形成同型二聚体或异源二聚体,其中异源二聚体表现出更高的活性。SlLBD40和SlLBD42被SlMYC2转录上调,但SlLBD40和SlLBD42减弱SlMYC2对灰葡萄球菌的防御,从而保护植物免受免疫过度激活。此外,BTB/POZ-MATH (BPM)蛋白家族成员SlBPM4靶向并降解SlLBD40和SlLBD42,释放防御反应,增强灰绿杆菌的抗性。遗传分析表明SlLBD40和SlLBD42对SlBPM4具有上位性。SlLBD40和SlLBD42在果实发育和防御中起双重作用,SlBPM4在病原菌攻击下起保护作用。我们的研究发现了番茄中MYC2-LBD40/42-CRL3BPM4模块,该模块通过精细调节基因表达和平衡免疫反应激活水平来分配生长和防御资源。该模块还为通过基因编辑技术优化植物生长和防御之间的平衡提供了潜在的目标。
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引用次数: 0
"Two scoops, please!": twin cryo-EM structures of an Arabidopsis thaliana DNA methyltransferase. “请给我两勺!”拟南芥DNA甲基转移酶的双低温电镜结构。
Pub Date : 2025-10-23 DOI: 10.1093/plcell/koaf255
Jan Hübbers
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引用次数: 0
Rational design of induced regeneration via somatic embryogenesis in the absence of exogenous phytohormones 无外源植物激素诱导体细胞胚胎再生的合理设计
Pub Date : 2025-10-19 DOI: 10.1093/plcell/koaf252
Jana Wittmer, Menno Pijnenburg, Tristan Wijsman, Sieme Pelzer, Kelvin Adema, Merijn Kerstens, An-Nikol Kutevska, Joke Fierens, Hugo Hofhuis, Robert Sevenier, Bjorn Kloosterman, Michiel de Both, Wouter Kohlen, Harm Nijveen, Ben Scheres, Renze Heidstra
Plants have a remarkable regenerative capacity, but this varies widely among species and tissue types. Important crop cultivars show regenerative recalcitrance, which is a major obstacle for the application of modern plant propagation and breeding techniques. Regeneration generally involves empirically determined tissue culture methods that are based on the principle of inducing totipotency. Cells are first persuaded to change fate towards root stem cell-like identity and then are reprogrammed to acquire shoot fate. Alternatively, pluri- or totipotent cells can lead to the formation of a complete plantlet through somatic embryogenesis. We applied our knowledge of root stem cell niche biology to directly use the implicated stem cell factors, including RETINOBLASTOMA (RBR), SCARECROW (SCR), SHORT ROOT (SHR) and members of the AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) and WUSCHEL-related homeobox (WOX) gene families, as a tool to induce regeneration in a way similar to the principle of induced pluripotent stem cells in the animal field. We show that stem cell factors synergistically induce regeneration involving the somatic embryogenesis pathway and can break recalcitrance in Arabidopsis (Arabidopsis thaliana) and pepper (Capsicum annuum).
植物具有显著的再生能力,但这在物种和组织类型之间差异很大。重要的作物品种表现出再生抗性,这是现代植物繁殖育种技术应用的主要障碍。再生通常涉及基于诱导全能性原则的经验确定的组织培养方法。细胞首先被说服改变命运向根干细胞样的身份,然后被重新编程以获得芽的命运。另外,多能或全能细胞可以通过体细胞胚胎形成一个完整的植株。我们运用我们的根干细胞生态位生物学知识,直接使用相关的干细胞因子,包括视网膜母细胞瘤(RBR), SCARECROW (SCR), SHORT root (SHR)和AINTEGUMENTA-LIKE/ overxx (AIL/PLT)和wuschelrelated homeobox (WOX)基因家族成员,以类似于动物领域诱导多能干细胞原理的方式诱导再生。我们发现,干细胞因子通过体细胞胚胎发生途径协同诱导了拟南芥(Arabidopsis thaliana)和辣椒(Capsicum annuum)的再生,并能打破抗性。
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引用次数: 0
Single-cell and spatial omics reveal progressive loss of xylem developmental complexity across seed plants 单细胞组学和空间组学揭示了种子植物木质部发育复杂性的逐渐丧失
Pub Date : 2025-10-19 DOI: 10.1093/plcell/koaf253
Peng Shuai, Jo-Wei Allison Hsieh, Chung-Ting Kao, Chen-Wei Hu, Ray Wang, Shang-Che Kuo, Ming-Ren Yen, Pin-Chien Liou, Yi-Chi Ho, Chia-Chen Chu, Shuotian Huang, Jiao Liu, Lixia Zhang, Chia-Chen Wu, Yi-Jyun Luo, Quanzi Li, Chuan-Chih Hsu, Chao-Li Huang, Jung-Chen Su, Mei-Chun Tseng, Ying-Lan Chen, Te-Lun Mai, Ying-Chung Jimmy Lin
Secondary growth is a key characteristic evolved from seed plants and generates secondary xylem—the most abundant tissue on Earth. Recent studies have uncovered xylem developmental lineages in eudicots and magnoliids of angiosperms. However, xylem development in gymnosperms, the other representative clade of seed plants, remained elusive. We performed single-cell transcriptomics for xylem cells of conifers (Cunninghamia lanceolata), the major clade in gymnosperms. Using Seurat and scVI-based cross-species integration, we reconstructed the xylem differentiation trajectories and revealed that the radial system is conserved across seed plants, while the axial system in C. lanceolata exhibits a composite lineage architecture resembling both eudicots and magnoliids. To validate these trajectories, we established a multi-modal spatial framework incorporating spatial transcriptomics, spatial proteomics, and spatial metabolomics. These three spatial layers provided orthogonal evidence confirming cell-type identities and trajectory inference. Additionally, we identified a xylem cell population unique to gymnosperms, suggesting a lineage-specific specialization. Together, our findings uncover a more complex ancestral xylem architecture in gymnosperms and propose a progressive simplification of axial developmental programs from gymnosperms to angiosperms, highlighting a trajectory of reductive evolution in seed plant vascular development.
次生生长是从种子植物进化而来的关键特征,并产生次生木质部——地球上最丰富的组织。近年来的研究揭示了被子植物的木质部发育谱系。然而,种子植物的另一个代表性分支裸子植物的木质部发育仍然难以捉摸。我们对裸子植物的主要分支针叶树(Cunninghamia lanceolata)的木质部细胞进行了单细胞转录组学研究。利用Seurat和基于scvi的跨种整合,我们重建了木质部分化轨迹,发现径向系统在种子植物中是保守的,而轴向系统则表现出类似于木质部和木质部的复合谱系结构。为了验证这些轨迹,我们建立了一个包含空间转录组学、空间蛋白质组学和空间代谢组学的多模态空间框架。这三个空间层提供了正交证据,证实了细胞类型的身份和轨迹推断。此外,我们还发现了裸子植物特有的木质部细胞群,表明存在谱系特异性特化。总之,我们的发现揭示了裸子植物中更复杂的原始木质部结构,并提出了从裸子植物到被子植物的轴向发育程序的逐步简化,突出了种子植物维管发育的还原进化轨迹。
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引用次数: 0
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The Plant Cell
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