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Grassland degradation alters plant and soil biodiversity–multifunctionality relationships 草地退化改变了植物和土壤生物多样性-多功能关系
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-11-10 DOI: 10.1038/s41477-025-02147-x
Xiaoxia Gao, Dianye Zhang, Yunfeng Peng, Josep Peñuelas, Yann Hautier, Michel Loreau, Yaping Niu, Shiting Yao, Zan Wu, Qinlu Li, Lina Zhou, Yang Liu, Xuning Liu, Bin Wei, Shuqi Qin, Yutong Song, Luyao Kang, Lin Jiang, Shaopeng Wang, Yuanhe Yang
Biodiversity is known to promote ecosystem multifunctionality (EMF), but how grassland degradation influences the relationship between biodiversity and EMF remains unclear. Here, using paired observations at 44 sites (a total of 792 sampling quadrats) along a 2,600 km transect, we test how moderate grassland degradation influences 20 surrogates of ecosystem functions, EMF, plant richness, soil bacterial, fungal and protist richness, and biodiversity–EMF relationships in Tibetan alpine grasslands. Our results reveal significant declines in individual ecosystem functions and EMF with moderate grassland degradation. By contrast, both plant richness and integrated soil biodiversity exhibit significant increases. The structural equation models analyses show that following degradation, the effect of soil biodiversity on EMF strengthens, whereas that of plant richness weakens. These findings offer large-scale empirical evidence that moderate grassland degradation can amplify both soil biodiversity and its functional importance, emphasizing the key role of below-ground biodiversity in supporting ecosystem functioning in degraded grasslands. This study reports that grassland degradation reduces ecosystem functionality while promoting soil biodiversity, highlighting the role of this diversity in sustaining degraded grasslands.
生物多样性促进生态系统多功能性,但草地退化如何影响生物多样性与生态系统多功能性之间的关系尚不清楚。结果表明,在中度草地退化过程中,个体生态系统功能和EMF显著下降。相比之下,植物丰富度和土壤综合生物多样性均显著增加。结构方程模型分析表明,退化后土壤生物多样性对EMF的影响增强,而植物丰富度对EMF的影响减弱。这些发现提供了大规模的经验证据,表明中度草地退化可以放大土壤生物多样性及其功能重要性,强调了退化草地中地下生物多样性在支持生态系统功能方面的关键作用。本研究报道,草地退化降低了生态系统功能,同时促进了土壤生物多样性,强调了这种多样性在维持退化草地中的作用。
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引用次数: 0
Engineering RLP receptors from the C side 从C侧工程RLP受体
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-11-10 DOI: 10.1038/s41477-025-02164-w
Guillaume Tena
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引用次数: 0
Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana CDCA7的主要等位基因影响拟南芥的CG甲基化
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-11-07 DOI: 10.1038/s41477-025-02148-w
Pierre Bourguet, Zdravko J. Lorković, Darya Kripkiy Casado, Valentin Bapteste, Chung Hyun Cho, Anna A. Igolkina, Cheng-Ruei Lee, Magnus Nordborg, Frédéric Berger, Eriko Sasaki
DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements in eukaryotes. Numerous examples of cis elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans regulators of mCG leading to adaptation. Here, a genome-wide association study identifies CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 (CDCA7) as a major trans determinant of mCG in natural populations of Arabidopsis thaliana. CDCA7 or its paralogue physically binds the chromatin remodeller DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. Epigenomic analysis shows that while CDCA7 proteins control all DDM1-dependent processes, their predominant function is the maintenance of mCG. We identify a 26-bp promoter indel modulating CDCA7 expression in natural populations and determining the degree of mCG and transposable element silencing. The geographic distribution of CDCA7 alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Our findings establish CDCA7 proteins as dedicated regulators of mCG and imply that DDM1 relies on alternative partners to regulate other chromatin features. Broadly, they illustrate how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation. This genome-wide association study identifies CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 (CDCA7) as a regulator of DNA methylation in natural Arabidopsis thaliana populations. CDCA7 binds the chromatin remodeller DDM1 and modulates the control of CG methylation.
DNA甲基化是影响真核生物基因表达和抑制转座因子的关键表观遗传标记。许多被DNA甲基化靶向的顺式元件,特别是在CG位点(mCG),已经报道在动物和植物中处于选择压力下。相比之下,对mCG导致适应的反调节因子的了解有限。在这里,一项全基因组关联研究发现,细胞分裂周期相关蛋白7 (CDCA7)是拟南芥自然种群中mCG的主要反式决定因素。CDCA7或其旁代物物理结合染色质重塑剂DNA甲基化1的减少(DDM1),从而促进甲基转移酶进入DNA。表观基因组学分析表明,虽然CDCA7蛋白控制所有ddm1依赖性过程,但其主要功能是维持mCG。我们发现了一个26 bp的启动子,可以调节CDCA7在自然群体中的表达,并确定mCG和转座因子沉默的程度。CDCA7等位基因的地理分布表明,新的等位基因已经反复扩展到新的生态位,表明在当地适应中具有潜在的作用。我们的研究结果证实了CDCA7蛋白是mCG的专门调节剂,并暗示DDM1依赖于替代伙伴来调节其他染色质特征。总的来说,它们说明了通过表观遗传机制的转录调节,全球DNA甲基化水平的变化如何促进局部适应的能力。
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引用次数: 0
The Arabidopsis thaliana nuclear pore complex structure reveals conserved and distinct features 拟南芥核孔复合体结构具有保守而独特的特点
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-11-06 DOI: 10.1038/s41477-025-02139-x
Despite the extensive use of Arabidopsis thaliana as a model system, parts of its biology remain unknown, including the architecture of its largest cellular protein assembly, the nuclear pore complex (NPC). Using cryo-electron tomography, we have obtained the three-dimensional architecture of the A. thaliana NPC, which suggests it has both conserved and distinct features.
尽管拟南芥被广泛用作模型系统,但其部分生物学特性仍然未知,包括其最大的细胞蛋白质组装体核孔复合物(NPC)的结构。利用低温电子断层成像技术,我们获得了拟南蝽鼻咽癌的三维结构,这表明它既保守又具有鲜明的特征。
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引用次数: 0
Author Correction: Reverse engineering of the pattern recognition receptor FLS2 reveals key design principles of broader recognition spectra against evading flg22 epitopes 作者更正:模式识别受体FLS2的逆向工程揭示了针对flg22表位的更广泛识别光谱的关键设计原则
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-11-06 DOI: 10.1038/s41477-025-02166-8
Songyuan Zhang, Songyuan Liu, Hung-Fei Lai, Kyle W. Bender, Gijeong Kim, Amedeo Caflisch, Cyril Zipfel
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引用次数: 0
A modular high-throughput approach for advancing synthetic biology in the chloroplast of Chlamydomonas 推进衣藻叶绿体合成生物学的模块化高通量方法
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-11-03 DOI: 10.1038/s41477-025-02126-2
René M. Inckemann, Tanguy Chotel, Michael Burgis, Cedric K. Brinkmann, Laura Andreas, Jessica Baumann, Priyati Sharma, Melanie Klose, James Barrett, Fabian Ries, Nicole Paczia, Timo Glatter, Luke C. M. Mackinder, Felix Willmund, Tobias J. Erb
Chloroplast synthetic biology holds promise for advancing photosynthetic organisms through improving the function of plastids. However, chloroplast engineering efforts face limitations due to the scarcity of genetic tools and the low throughput of plant-based systems. To address these challenges, we here established Chlamydomonas reinhardtii as a prototyping chassis for chloroplast synthetic biology. To that end, we developed an automation workflow that enables the generation, handling and analysis of thousands of transplastomic strains in parallel. Furthermore, we expanded the repertoire of effective selection markers and reporter genes, and we characterized over 140 regulatory parts, including native and synthetic promoters, 5′ and 3′ untranslated regions, and intercistronic expression elements. We integrated the system with existing molecular cloning standards and demonstrated several applications, including a library-based approach to develop synthetic promoter designs in plastids. Finally, we provide a proof of concept for prototyping metabolic pathways in plastids by introducing a chloroplast-based synthetic photorespiration pathway, resulting in a threefold increase in biomass production. Overall, our study advances current chloroplast engineering efforts by providing a high-throughput platform and standardized genetic parts for the rapid prototyping and characterization of plastid manipulations with the prospect of high transferability between different chloroplasts, including those of higher plants and crops. This study reports a modular-cloning-based platform for high-throughput chloroplast engineering in Chlamydomonas reinhardtii that allows large-scale characterization of genetic parts and prototyping of new traits, as demonstrated for the photorespiration pathway.
叶绿体合成生物学有望通过改善质体的功能来促进光合生物的发展。然而,由于遗传工具的缺乏和基于植物的系统的低通量,叶绿体工程的努力面临限制。为了解决这些挑战,我们在这里建立了莱茵衣藻作为叶绿体合成生物学的原型底盘。为此,我们开发了一个自动化工作流程,可以并行生成、处理和分析数千个跨质体菌株。此外,我们扩展了有效选择标记和报告基因的曲目,并鉴定了超过140个调控部分,包括天然和合成启动子,5 ‘和3 ’非翻译区,以及顺子间表达元件。我们将该系统与现有的分子克隆标准集成,并演示了几种应用,包括基于文库的方法在质体中开发合成启动子设计。最后,我们通过引入基于叶绿体的合成光呼吸途径,为质体中代谢途径的原型化提供了概念证明,从而使生物质产量增加了三倍。总的来说,我们的研究通过提供高通量平台和标准化的遗传部分,为质体操作的快速原型和表征提供了一个高通量平台,从而推进了当前的叶绿体工程工作,并有望在不同叶绿体之间(包括高等植物和作物的叶绿体)实现高可转移性。
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引用次数: 0
Nitrate to spark parched plants. 硝酸盐可以点燃干燥的植物。
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-11-01 DOI: 10.1038/s41477-025-02150-2
Justine Broutin, Christian Meyer
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引用次数: 0
In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana 高等植物拟南芥核孔复合物的原位结构
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-31 DOI: 10.1038/s41477-025-02138-y
Ingrid Berenice Sanchez Carrillo, Patrick C. Hoffmann, Agnieszka Obarska-Kosinska, Victor Fourcassié, Martin Beck, Hugo Germain
The nucleus is enclosed by the nuclear envelope, which contains nuclear pore complexes (NPCs). While NPCs have been well studied in vertebrates, yeast and algae, in situ structural data for higher plants is lacking. Here we show that individual nucleoporins of Arabidopsis thaliana and humans exhibit high structural similarity. We report an in situ NPC structure of higher plants, derived from A. thaliana root protoplasts using cryo-electron tomography, subtomogram averaging and homology-based integrative modelling. We present the AtNPC model based on predictions of A. thaliana nucleoporins (NUPs), supported by mass spectrometry. Here the AtNPC scaffold contains one Y-complex ring at the cytosolic and two at the nuclear ring. The AtNPC contains prominent NUP155 connector elements that are conserved in human NPCs but not in Chlamydomonas reinhardtii NPCs. Our model suggests that the ELYS homologue HOS1 plays an important role in the head-to-tail connection of Y-complexes in AtNPCs. Using advanced imaging techniques and computer modelling, the authors were able to create a detailed structural model of a nuclear pore complex from a seed plant.
细胞核被包膜包裹,包膜中含有核孔复合物。虽然npc已经在脊椎动物、酵母和藻类中得到了很好的研究,但缺乏高等植物的原位结构数据。本研究表明拟南芥和人类的核孔蛋白具有高度的结构相似性。本文利用低温电子断层扫描、亚层析成像平均和基于同源性的综合模型,报道了从拟南芥根原生质体中提取的高等植物原位NPC结构。我们提出了基于拟南芥核孔蛋白(NUPs)预测的AtNPC模型,并得到质谱分析的支持。在这里,AtNPC支架在细胞质上包含一个y复合物环,在核环上包含两个。AtNPC包含突出的NUP155连接器元件,该元件在人类npc中保守,但在莱茵原胞菌npc中不保守。我们的模型表明,ELYS同源物HOS1在atnpc中y复合物的头尾连接中起重要作用。
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引用次数: 0
Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape 静电变化使胞囊亚基通过蛋白质复合物逃逸而多样化
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-31 DOI: 10.1038/s41477-025-02135-1
Juan Carlos De la Concepcion, Héloïse Duverge, Yoonwoo Kim, Jose Julian, Haonan D. Xu, Matthew N. Watt, Sara Ait Ikene, Anita Bianchi, Nenad Grujic, Ranjith K. Papareddy, Irina Grishkovskaya, David Haselbach, David H. Murray, Marion Clavel, Nicholas A. T. Irwin, Yasin Dagdas
Protein neofunctionalization is a key driver of cellular complexity. However, subunits of multimeric protein complexes are often thought to be evolutionarily constrained, limiting their capacity for functional divergence. This presents a paradox in plants, where the Exo70 subunit of the exocyst—an octameric complex essential for exocytosis—has undergone striking expansion and diversification. Here we show that electrostatic changes in the N-terminal helix of Exo70 facilitated its physical and functional dissociation from the exocyst, relieving constraints imposed by complex integration. Using Marchantia polymorpha and Arabidopsis thaliana, we demonstrate that this ‘complex escape’ enables Exo70 paralogues to acquire distinct localizations, interactomes and functions independent of canonical exocytosis. Ancestral reconstructions across land plants reveal that this electrostatic shift predates the extensive radiation of the plant Exo70 protein family, with some lineages later reassociating with the complex. Our findings reveal a reversible mechanism that enabled Exo70 to circumvent the evolutionary and biophysical constraints imposed by complex integration and diversify—a mechanism that could represent a generalizable route to protein neofunctionalization and cellular innovation. The evolutionary diversification of an exocyst subunit was enabled by electrostatic shifts leading to its dissociation from the ancestral complex.
蛋白质的新功能化是细胞复杂性的关键驱动因素。然而,多聚体蛋白复合物的亚基通常被认为是进化受限的,限制了它们的功能分化能力。这在植物中提出了一个悖论,在植物中,胞囊的Exo70亚基-胞囊分泌所必需的八聚体复合体-经历了惊人的扩张和多样化。本研究表明,Exo70 n端螺旋的静电变化促进了其与囊泡的物理和功能分离,从而缓解了复杂整合所带来的限制。利用多形地豆和拟南芥,我们证明了这种“复杂逃逸”使Exo70亲本获得不同的定位、相互作用组和独立于典型胞吐作用的功能。陆地植物的祖先重建表明,这种静电转移早于植物Exo70蛋白家族的广泛辐射,一些谱系后来与该复合体重新关联。我们的研究结果揭示了一种可逆机制,使Exo70能够绕过复杂整合和多样性所施加的进化和生物物理限制,这一机制可能代表了蛋白质新功能化和细胞创新的一般途径。
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引用次数: 0
Discovery of a gene in a Mendelian locus controlling dichogamy 在孟德尔基因座中发现控制二婚的基因
IF 13.6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-31 DOI: 10.1038/s41477-025-02153-z
Dichogamy — the temporal separation of anther dehiscence and stigma receptivity — is ubiquitous in angiosperms. Using field investigations, Mendelian inheritance experiments, multi-omics analysis based on haplotype-resolved genomes and validation of gene function, we identify SMPED1 as a novel gene that controls the synchrony of sex organ behaviour in angiosperms.
在被子植物中,花药开裂和柱头接受性的时间分离是普遍存在的。通过实地调查、孟德尔遗传实验、基于单倍型解析基因组的多组学分析和基因功能验证,我们确定SMPED1是一个控制被子植物性器官行为同步的新基因。
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引用次数: 0
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Nature Plants
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