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Zinc sensing in nodules regulates symbiotic nitrogen fixation 结核中的锌感应调节共生固氮作用
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-12 DOI: 10.1038/s41477-024-01758-0
Lijin Qiao, Takuya Suzaki, Pengbo Liang
Plants constantly adjust their gene expression and metabolism to thrive in diverse environments. In legume root nodules, the surprising role of zinc as an intracellular messenger links environmental changes to transcriptional control.
植物不断调整自己的基因表达和新陈代谢,以便在不同的环境中茁壮成长。在豆科植物的根瘤中,锌作为细胞内信使的惊人作用将环境变化与转录控制联系在一起。
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引用次数: 0
Guidelines for naming and studying plasma membrane domains in plants 植物质膜结构域命名和研究指南
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-12 DOI: 10.1038/s41477-024-01742-8
Yvon Jaillais, Emmanuelle Bayer, Dominique C. Bergmann, Miguel A. Botella, Yohann Boutté, Tolga O. Bozkurt, Marie-Cecile Caillaud, Véronique Germain, Guido Grossmann, Ingo Heilmann, Piers A. Hemsley, Charlotte Kirchhelle, Alexandre Martinière, Yansong Miao, Sebastien Mongrand, Sabine Müller, Lise C. Noack, Yoshihisa Oda, Thomas Ott, Xue Pan, Roman Pleskot, Martin Potocky, Stéphanie Robert, Clara Sanchez Rodriguez, Françoise Simon-Plas, Eugenia Russinova, Daniel Van Damme, Jaimie M. Van Norman, Dolf Weijers, Shaul Yalovsky, Zhenbiao Yang, Enric Zelazny, Julien Gronnier
Biological membranes play a crucial role in actively hosting, modulating and coordinating a wide range of molecular events essential for cellular function. Membranes are organized into diverse domains giving rise to dynamic molecular patchworks. However, the very definition of membrane domains has been the subject of continuous debate. For example, in the plant field, membrane domains are often referred to as nanodomains, nanoclusters, microdomains, lipid rafts, membrane rafts, signalling platforms, foci or liquid-ordered membranes without any clear rationale. In the context of plant–microbe interactions, microdomains have sometimes been used to refer to the large area at the plant–microbe interface. Some of these terms have partially overlapping meanings at best, but they are often used interchangeably in the literature. This situation generates much confusion and limits conceptual progress. There is thus an urgent need for us as a scientific community to resolve these semantic and conceptual controversies by defining an unambiguous nomenclature of membrane domains. In this Review, experts in the field get together to provide explicit definitions of plasma membrane domains in plant systems and experimental guidelines for their study. We propose that plasma membrane domains should not be considered on the basis of their size alone but rather according to the biological system being considered, such as the local membrane environment or the entire cell. This Review aims to define an updated nomenclature for plasma membrane domains in plants. The authors are experts in this field who unite here in an effort to eliminate the ambiguities and confusion that have persisted until now.
生物膜在积极容纳、调节和协调对细胞功能至关重要的各种分子事件方面发挥着至关重要的作用。膜由不同的膜域组成,形成动态的分子拼接。然而,膜域的定义一直是争论不休的话题。例如,在植物领域,膜域通常被称为纳米域、纳米簇、微域、脂质筏、膜筏、信号平台、病灶或液序膜,但没有明确的理论依据。在植物-微生物相互作用的背景下,微域有时被用来指植物-微生物界面的大面积区域。其中一些术语的含义充其量只是部分重叠,但在文献中却经常被交替使用。这种情况造成了很多混淆,限制了概念上的进步。因此,作为科学界,我们迫切需要通过定义一个明确的膜域术语来解决这些语义和概念上的争议。在这篇综述中,该领域的专家们汇聚一堂,为植物系统中的质膜结构域提供了明确的定义以及研究它们的实验指南。我们建议,质膜结构域不应仅根据其大小来考虑,而应根据所考虑的生物系统,如局部膜环境或整个细胞来考虑。
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引用次数: 0
Where chloroplasts and ER meet 叶绿体和 ER 的交汇处
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-12 DOI: 10.1038/s41477-024-01776-y
Raphael Trösch
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引用次数: 0
Author Correction: Split complementation of base editors to minimize off-target edits 作者更正:对碱基编辑器进行分割补充,以尽量减少脱靶编辑。
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-05 DOI: 10.1038/s41477-024-01777-x
Xiangyu Xiong, Kehui Liu, Zhenxiang Li, Fan-Nv Xia, Xue-Ming Ruan, Xionglei He, Jian-Feng Li
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引用次数: 0
Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes 利用无参考基因组的 Hi-C 数据对单体型解析组装进行染色体级支架构建
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-05 DOI: 10.1038/s41477-024-01755-3
Xiaofei Zeng, Zili Yi, Xingtan Zhang, Yuhui Du, Yu Li, Zhiqing Zhou, Sijie Chen, Huijie Zhao, Sai Yang, Yibin Wang, Guoan Chen
Scaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As sequencing technologies and assembly algorithms advance, constructing haplotype-resolved genomes is increasingly preferred because haplotypes can provide additional genetic information on allelic and non-allelic variations. ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unravelling of haplotype-resolved genomes. Here we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. In addition, we provide new insights into the challenges in allele-aware scaffolding by conducting comprehensive analyses on various adverse factors. Finally, with the help of HapHiC, we constructed the haplotype-resolved allotriploid genome for Miscanthus × giganteus, an important lignocellulosic bioenergy crop. This study uncovers key challenges in allele-aware genome scaffolding with Hi-C data. A reference-independent Hi-C scaffolder showing superior performance was developed to construct the haplotype-resolved genome of triploid Miscanthus × giganteus.
支架对于构建大多数染色体级基因组至关重要。高通量染色质构象捕获(Hi-C)技术因其便利性和成本效益已成为主要的支架策略。随着测序技术和组装算法的进步,构建单倍型解析基因组越来越受到青睐,因为单倍型可以提供等位基因和非等位基因变异的额外遗传信息。ALLHiC 就是为此目的而设计的一种广泛使用的等位基因感知支架工具。然而,它对染色体级参考基因组的依赖性和较高的染色体错配率仍然阻碍着单倍型解析基因组的解开。在这里,我们介绍一种独立于参考的等位基因感知脚手架工具 HapHiC,它在染色体分配、等位基因排序和定向方面都有卓越的表现。此外,我们还对各种不利因素进行了全面分析,从而对等位基因感知搭架的挑战提出了新的见解。最后,在 HapHiC 的帮助下,我们构建了重要木质纤维素生物能源作物 Miscanthus × giganteus 的单倍型解析异源三倍体基因组。
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引用次数: 0
Achieving de novo scaffolding of chromosome-level haplotypes using Hi-C data 利用 Hi-C 数据实现染色体级单倍型的从头构建。
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-05 DOI: 10.1038/s41477-024-01756-2
To overcome key challenges in scaffolding chromosome-level haplotypes with Hi-C data, we developed HapHiC, a Hi-C scaffolding tool that exhibits superior performance in handling haplotype-resolved assemblies without the need for reference genomes. We used HapHiC to construct the complex genome of triploid Miscanthus × giganteus.
为了克服利用 Hi-C 数据构建染色体级单倍型支架的关键挑战,我们开发了 HapHiC,这是一种 Hi-C 支架工具,在处理单倍型解析的装配时表现出卓越的性能,而无需参考基因组。我们利用 HapHiC 构建了三倍体 Miscanthus × giganteus 的复杂基因组。
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引用次数: 0
Multilayered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm 水稻胚乳中持久性和阶段特异性印迹基因的多层表观遗传控制
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-07-30 DOI: 10.1038/s41477-024-01754-4
Kaoru Tonosaki, Daichi Susaki, Hatsune Morinaka, Akemi Ono, Hiroki Nagata, Hiroyasu Furuumi, Ken-Ichi Nonomura, Yutaka Sato, Keiko Sugimoto, Luca Comai, Katsunori Hatakeyama, Taiji Kawakatsu, Tetsu Kinoshita
In angiosperms, epigenetic profiles for genomic imprinting are established before fertilization. However, the causal relationships between epigenetic modifications and imprinted expression are not fully understood. In this study, we classified ‘persistent’ and ‘stage-specific’ imprinted genes on the basis of time-course transcriptome analysis in rice (Oryza sativa) endosperm and compared them to epigenetic modifications at a single time point. While the levels of epigenetic modifications are relatively low in stage-specific imprinted genes, they are considerably higher in persistent imprinted genes. Overall trends revealed that the maternal alleles of maternally expressed imprinted genes are activated by DNA demethylation, while the maternal alleles of paternally expressed imprinted genes with gene body methylation (gbM) are silenced by DNA demethylation and H3K27me3 deposition, and these regions are associated with an enriched motif related to Tc/Mar-Stowaway. Our findings provide insight into the stability of genomic imprinting and the potential variations associated with endosperm development, different cell types and parental genotypes. Time-course analysis of rice imprinted genes revealed persistent and stage-specific imprinted genes. These two classes showed differences in the degree of epigenetic status and biased expression in a temporal and spatial manner in the endosperm.
在被子植物中,基因组印记的表观遗传图谱在受精前就已建立。然而,表观遗传修饰与印记表达之间的因果关系尚未完全明了。在这项研究中,我们根据对水稻(Oryza sativa)胚乳的时程转录组分析,对 "持久性 "和 "阶段特异性 "印记基因进行了分类,并将它们与单个时间点的表观遗传修饰进行了比较。阶段特异性印记基因的表观遗传修饰水平相对较低,而持久性印记基因的表观遗传修饰水平则要高得多。总体趋势显示,母系表达的印记基因的母系等位基因被DNA去甲基化激活,而具有基因体甲基化(gbM)的父系表达的印记基因的母系等位基因则被DNA去甲基化和H3K27me3沉积沉默,这些区域与Tc/Mar-Stowaway相关的富集基序有关。我们的发现有助于深入了解基因组印记的稳定性以及与胚乳发育、不同细胞类型和亲本基因型相关的潜在变化。
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引用次数: 0
Enhancers associated with unstable RNAs are rare in plants 植物中与不稳定 RNA 相关的增强子很少见
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-07-30 DOI: 10.1038/s41477-024-01741-9
Bayley R. McDonald, Colette L. Picard, Ian M. Brabb, Marina I. Savenkova, Robert J. Schmitz, Steven E. Jacobsen, Sascha H. Duttke
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many ‘distal’ elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans. Unstable transcripts like enhancer RNAs are common in vertebrates. McDonald et al. show that such unstable transcripts are rare in plants and that promoters can function as potent enhancers, suggesting diverse cis-regulatory mechanisms in eukaryotes.
在脊椎动物中,不稳定转录本已成为活性增强子的标记,并被证明与许多细胞过程和医学疾病有关。然而,它们在植物中的普遍性和作用在很大程度上尚未被探索。在这里,我们利用带帽小(cs)RNA 测序技术全面捕获了各种作物和其他植物中所有活跃的启动(新生)转录本。我们发现,与脊椎动物不同,不稳定的转录本在植物中很少见,即使存在,也往往源自启动子。此外,植物中的许多 "远端 "元件能启动组织特异性的稳定转录本,而且很可能是尚未注释的基因或非编码 RNA 的真正启动子,这就提醒我们不要使用参考基因组注释来推断推定的增强子位点。为了研究增强子的功能,我们整合了自转录活性调控区(STARR)测序的数据。我们发现,注释的启动子和其他启动稳定转录本的区域,而那些以不稳定或双向不稳定转录本为标志的区域,在这种检测中表现出更强的增强子活性。我们的发现强调了启动子和增强子之间的模糊界限,并表明真核生物(包括人类)中的顺式调控元件可以包含多种结构和机制。
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引用次数: 0
The dramatic effects of well-intentioned but ill-designed management strategies in plant biological invasions 用心良苦但设计不当的管理策略对植物生物入侵的巨大影响
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-07-26 DOI: 10.1038/s41477-024-01747-3
Sergi Munné-Bosch, Jessyca Adelle Silva Santos
Plant invasions are becomingly increasingly common with global climate change. As a significant threat to biodiversity, appropriate management of invasive species is critical for the protection of native flora. However, many of the management strategies aimed at combating the impacts of invasive species only end up exacerbating them.
随着全球气候变化,植物入侵越来越普遍。作为对生物多样性的一个重大威胁,适当管理入侵物种对保护本地植物至关重要。然而,许多旨在消除入侵物种影响的管理策略最终只会加剧入侵物种的影响。
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引用次数: 0
Arabidopsis floral buds are locked through stress-induced sepal tip curving 拟南芥花芽通过胁迫诱导的萼片尖端弯曲来锁定
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-07-26 DOI: 10.1038/s41477-024-01760-6
Duy-Chi Trinh, Isaty Melogno, Marjolaine Martin, Christophe Trehin, Richard S. Smith, Olivier Hamant
In most plant species, sepals—the outermost floral organs—provide a protective shield for reproductive organs. How the floral bud becomes sealed is unknown. In Arabidopsis, we identified a small region at the sepal tip that is markedly curved inward early on and remains curved even after anthesis. Through modelling and quantitative growth analysis, we find that this hook emerges from growth arrest at the tip at a stage when cortical microtubules align with growth-derived tensile stress. Depolymerizing microtubules specifically at young sepal tips hindered hook formation and resulted in open floral buds. Mutants with defective growth pattern at the tip failed to curve inwards, whereas mutants with enhanced alignment of cortical microtubules at the tip exhibited a stronger hook. We propose that floral buds are locked due to a stress-derived growth arrest event curving the sepal tip and forming a rigid hook early on during flower development. Floral buds are closed structures that protect reproductive organs. Here the authors find that differential growth prescribes transverse tensile stress and growth arrest at the sepal tip, which in turn curve it and form a rigid hook to seal the floral bud.
在大多数植物物种中,萼片--最外层的花器官--为生殖器官提供保护罩。花蕾是如何密封的尚不清楚。在拟南芥中,我们在萼片顶端发现了一个小区域,该区域早期明显向内弯曲,甚至在花后仍保持弯曲。通过建模和定量生长分析,我们发现在皮层微管与生长产生的拉应力相一致的阶段,顶端的生长停滞会产生这种钩。对幼嫩萼片顶端的微管进行特异性解聚会阻碍花钩的形成,并导致花蕾开放。顶端生长模式有缺陷的突变体不能向内弯曲,而顶端皮层微管排列增强的突变体则表现出更强的钩。我们认为,花蕾的锁定是由于在花发育的早期,萼片顶端弯曲并形成一个坚硬的钩子这一应力导致的生长停滞事件。
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引用次数: 0
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Nature Plants
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