首页 > 最新文献

Nature Structural & Molecular Biology最新文献

英文 中文
Returning home: building a scientific future in Chile 回国:在智利建设科学的未来
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-15 DOI: 10.1038/s41594-025-01648-9
Hugo Sepulveda
Doing science in Latin America can be as exciting as it is challenging. Starting my laboratory for transcription and epigenetics in Chile after working in the USA has required deep conviction and constant effort. It is a long-term project aimed at creating new opportunities for the next generation of Chilean scientists, offering Latin American perspectives to contribute to science.
在拉丁美洲从事科学研究既令人兴奋又具有挑战性。在美国工作之后,在智利开始了我的转录和表观遗传学实验室,这需要坚定的信念和不断的努力。这是一个长期项目,旨在为下一代智利科学家创造新的机会,提供拉丁美洲为科学做出贡献的视角。
{"title":"Returning home: building a scientific future in Chile","authors":"Hugo Sepulveda","doi":"10.1038/s41594-025-01648-9","DOIUrl":"10.1038/s41594-025-01648-9","url":null,"abstract":"Doing science in Latin America can be as exciting as it is challenging. Starting my laboratory for transcription and epigenetics in Chile after working in the USA has required deep conviction and constant effort. It is a long-term project aimed at creating new opportunities for the next generation of Chilean scientists, offering Latin American perspectives to contribute to science.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 10","pages":"1846-1846"},"PeriodicalIF":10.1,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290299","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}
引用次数: 0
Voices of NSMB NSMB之声
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-15 DOI: 10.1038/s41594-025-01694-3
We are delighted to introduce additional content types at Nature Structural & Molecular Biology, which allow us to offer more discussion of societal and scientific issues, better represent the unique perspectives of our readers, showcase their stories, and amplify their voices.
我们很高兴在《自然-结构与分子生物学》上引入更多的内容类型,这使我们能够提供更多关于社会和科学问题的讨论,更好地代表我们读者的独特观点,展示他们的故事,放大他们的声音。
{"title":"Voices of NSMB","authors":"","doi":"10.1038/s41594-025-01694-3","DOIUrl":"10.1038/s41594-025-01694-3","url":null,"abstract":"We are delighted to introduce additional content types at Nature Structural & Molecular Biology, which allow us to offer more discussion of societal and scientific issues, better represent the unique perspectives of our readers, showcase their stories, and amplify their voices.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 10","pages":"1841-1841"},"PeriodicalIF":10.1,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01694-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290285","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}
引用次数: 0
Structure and activation mechanism of a Lamassu phage and plasmid defense system Lamassu噬菌体和质粒防御系统的结构和激活机制。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-14 DOI: 10.1038/s41594-025-01677-4
Yan Li, David W. Adams, Hon Wing Liu, Steven J. Shaw, Emiko Uchikawa, Milena Jaskólska, Sandrine Stutzmann, Laurie Righi, Mark D. Szczelkun, Melanie Blokesch, Stephan Gruber
Lamassu is a diverse family of defense systems that protect bacteria, including seventh-pandemic strains of Vibrio cholerae, against both plasmids and phage infection. During phage infection, Lamassu targets essential cellular processes, thereby halting phage propagation by terminating the infected host. The mechanisms by which Lamassu effectors are activated when needed and otherwise suppressed are unknown. Here we present structures of a Lamassu defense system from Salmonella enterica. We show that an oligomerization domain of the nuclease effector subunit, LmuA, is sequestered by two tightly folded SMC-like LmuB protomers and LmuC. Upon activation, liberated LmuA assembles into homotetramers, in which two of four nuclease domains are brought into proximity to create an active site capable of cleaving DNA. We propose that tetramer formation is likely a one-way switch that establishes a threshold to limit potential spontaneous activation and cell death. Our findings reveal a mechanism of cellular defense, involving liberation and oligomerization of immune effectors, and shed light on how Lamassu systems balance potent immune responses with self-preservation. Li et al. show that a Lamassu defense system protects bacteria from phage infection by activating a lethal tetrameric DNA-cutting enzyme. In the absence of phages, a protein clamp holds the enzyme as an inactive monomer, preventing self-damage.
Lamassu是一个多样化的防御系统家族,可以保护细菌,包括第七次大流行的霍乱弧菌菌株,免受质粒和噬菌体感染。在噬菌体感染期间,Lamassu靶向基本的细胞过程,从而通过终止被感染的宿主来阻止噬菌体的繁殖。Lamassu效应在需要时被激活或被抑制的机制尚不清楚。在这里,我们提出了肠道沙门氏菌Lamassu防御系统的结构。我们发现,核酸酶效应亚基LmuA的寡聚化结构域被两个紧密折叠的smc样LmuB原体和LmuC隔离。激活后,释放的LmuA组装成同型四聚体,其中四个核酸酶结构域中的两个被拉近,从而产生能够切割DNA的活性位点。我们认为,四聚体的形成可能是一种单向开关,它建立了一个阈值,以限制潜在的自发激活和细胞死亡。我们的发现揭示了细胞防御机制,涉及免疫效应物的解放和寡聚化,并阐明了Lamassu系统如何平衡有效的免疫反应和自我保护。
{"title":"Structure and activation mechanism of a Lamassu phage and plasmid defense system","authors":"Yan Li, David W. Adams, Hon Wing Liu, Steven J. Shaw, Emiko Uchikawa, Milena Jaskólska, Sandrine Stutzmann, Laurie Righi, Mark D. Szczelkun, Melanie Blokesch, Stephan Gruber","doi":"10.1038/s41594-025-01677-4","DOIUrl":"10.1038/s41594-025-01677-4","url":null,"abstract":"Lamassu is a diverse family of defense systems that protect bacteria, including seventh-pandemic strains of Vibrio cholerae, against both plasmids and phage infection. During phage infection, Lamassu targets essential cellular processes, thereby halting phage propagation by terminating the infected host. The mechanisms by which Lamassu effectors are activated when needed and otherwise suppressed are unknown. Here we present structures of a Lamassu defense system from Salmonella enterica. We show that an oligomerization domain of the nuclease effector subunit, LmuA, is sequestered by two tightly folded SMC-like LmuB protomers and LmuC. Upon activation, liberated LmuA assembles into homotetramers, in which two of four nuclease domains are brought into proximity to create an active site capable of cleaving DNA. We propose that tetramer formation is likely a one-way switch that establishes a threshold to limit potential spontaneous activation and cell death. Our findings reveal a mechanism of cellular defense, involving liberation and oligomerization of immune effectors, and shed light on how Lamassu systems balance potent immune responses with self-preservation. Li et al. show that a Lamassu defense system protects bacteria from phage infection by activating a lethal tetrameric DNA-cutting enzyme. In the absence of phages, a protein clamp holds the enzyme as an inactive monomer, preventing self-damage.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 12","pages":"2503-2516"},"PeriodicalIF":10.1,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145292993","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}
引用次数: 0
Author Correction: Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries 作者更正:Atg8将Atg1招募到吞噬体中协调自噬机制。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-13 DOI: 10.1038/s41594-025-01700-8
Jing-Zhen Song, Hui Li, Haiyan Yang, Rui Liu, Wenting Zhang, Tianlong He, Meng-Xi Xie, Chen Chen, Li Cui, Shian Wu, Yueguang Rong, Li-Feng Pan, Jing Zhu, Qingqiu Gong, Juan Wang, Zhao Qin, Zhiping Xie
{"title":"Author Correction: Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries","authors":"Jing-Zhen Song, Hui Li, Haiyan Yang, Rui Liu, Wenting Zhang, Tianlong He, Meng-Xi Xie, Chen Chen, Li Cui, Shian Wu, Yueguang Rong, Li-Feng Pan, Jing Zhu, Qingqiu Gong, Juan Wang, Zhao Qin, Zhiping Xie","doi":"10.1038/s41594-025-01700-8","DOIUrl":"10.1038/s41594-025-01700-8","url":null,"abstract":"","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 11","pages":"2371-2371"},"PeriodicalIF":10.1,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01700-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145286551","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}
引用次数: 0
Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses 结构系统发育揭示了革兰氏阳性细菌及其病毒通信系统的进化多样化。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-10 DOI: 10.1038/s41594-025-01649-8
David Moi, Charles Bernard, Martin Steinegger, Yannis Nevers, Mauricio Langleib, Christophe Dessimoz
Recent advances in artificial-intelligence-based protein structure modeling have yielded remarkable progress in predicting protein structures. Because structures are constrained by their biological function, their geometry tends to evolve more slowly than the underlying amino acids sequences. This feature of structures could in principle be used to reconstruct phylogenetic trees over longer evolutionary timescales than sequence-based approaches; however, until now, a reliable structure-based tree-building method has been elusive. Here, we introduce a rigorous framework for empirical tree accuracy evaluation and tested multiple approaches using sequence and structure information. The best results were obtained by inferring trees from sequences aligned using a local structural alphabet—an approach robust to conformational changes that confound traditional structural distance measures. We illustrate the power of structure-informed phylogenetics by deciphering the evolutionary diversification of a particularly challenging family: the fast-evolving RRNPPA quorum-sensing receptors. We were able to propose a more parsimonious evolutionary history for this critical protein family that enables gram-positive bacteria, plasmids and bacteriophages to communicate and coordinate key behaviors. The advent of high-accuracy structural phylogenetics enables a myriad of applications across biology, such as uncovering deeper evolutionary relationships, elucidating unknown protein functions or refining the design of bioengineered molecules. Using a new method called FoldTree, the authors compare proteins on the basis of their shape to construct more accurate family trees over long evolutionary timescales and capture distant relationships where sequence information becomes less reliable.
近年来,基于人工智能的蛋白质结构建模在预测蛋白质结构方面取得了显著进展。由于结构受其生物功能的限制,它们的几何结构往往比底层氨基酸序列进化得更慢。与基于序列的方法相比,这种结构特征原则上可用于在更长的进化时间尺度上重建系统发育树;然而,到目前为止,一种可靠的基于结构的树构建方法一直难以捉摸。在这里,我们引入了一个严格的经验树精度评估框架,并使用序列和结构信息测试了多种方法。通过使用局部结构字母表从序列中推断树获得了最好的结果,这是一种对构象变化具有鲁棒性的方法,这种方法混淆了传统的结构距离测量。我们通过破译一个特别具有挑战性的家族的进化多样化来说明结构信息系统发育的力量:快速进化的RRNPPA群体感应受体。我们能够为这个关键蛋白家族提出一个更简洁的进化史,使革兰氏阳性细菌、质粒和噬菌体能够交流和协调关键行为。高精度结构系统发育的出现使生物学领域的无数应用成为可能,例如揭示更深层次的进化关系,阐明未知的蛋白质功能或改进生物工程分子的设计。
{"title":"Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses","authors":"David Moi, Charles Bernard, Martin Steinegger, Yannis Nevers, Mauricio Langleib, Christophe Dessimoz","doi":"10.1038/s41594-025-01649-8","DOIUrl":"10.1038/s41594-025-01649-8","url":null,"abstract":"Recent advances in artificial-intelligence-based protein structure modeling have yielded remarkable progress in predicting protein structures. Because structures are constrained by their biological function, their geometry tends to evolve more slowly than the underlying amino acids sequences. This feature of structures could in principle be used to reconstruct phylogenetic trees over longer evolutionary timescales than sequence-based approaches; however, until now, a reliable structure-based tree-building method has been elusive. Here, we introduce a rigorous framework for empirical tree accuracy evaluation and tested multiple approaches using sequence and structure information. The best results were obtained by inferring trees from sequences aligned using a local structural alphabet—an approach robust to conformational changes that confound traditional structural distance measures. We illustrate the power of structure-informed phylogenetics by deciphering the evolutionary diversification of a particularly challenging family: the fast-evolving RRNPPA quorum-sensing receptors. We were able to propose a more parsimonious evolutionary history for this critical protein family that enables gram-positive bacteria, plasmids and bacteriophages to communicate and coordinate key behaviors. The advent of high-accuracy structural phylogenetics enables a myriad of applications across biology, such as uncovering deeper evolutionary relationships, elucidating unknown protein functions or refining the design of bioengineered molecules. Using a new method called FoldTree, the authors compare proteins on the basis of their shape to construct more accurate family trees over long evolutionary timescales and capture distant relationships where sequence information becomes less reliable.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 12","pages":"2492-2502"},"PeriodicalIF":10.1,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01649-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145275379","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}
引用次数: 0
Nuclear pore passage of the HIV capsid is driven by its unusual surface amino acid composition HIV衣壳的核孔通过是由其不寻常的表面氨基酸组成驱动的。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-09 DOI: 10.1038/s41594-025-01684-5
Liran Fu, Shiya Cheng, Dietmar Riedel, Leonie Kopecny, Melina Schuh, Dirk Görlich
Nuclear transport receptors (NTRs) carry cargo across the permeability barrier of nuclear pore complexes (NPCs)—an FG phase condensed from disordered but cohesive FG-repeat domains. This phase repels inert macromolecules but allows NTR passage. When the human immunodeficiency virus (HIV) infects nondividing cells, its capsid is transported into nuclei not like a cargo but crosses NPCs like an NTR. Here we uncovered the molecular determinants of the capsid’s NTR behavior. The FG-binding pocket is insufficient. Hexameric and pentameric capsomers contribute. The highly exposed outer capsid surface is key. It lacks FG-repulsive charged residues (K, D and E) that are very abundant on other protein surfaces. FG-attractive residues dominate the capsid surface instead. Introducing FG-repulsive amino acids impedes FG phase partitioning, NPC targeting and NPC passage of assembled capsids. Capsids are, thus, made soluble in the FG phase by a myriad of transient FG-attractive interactions originating from individual surface side chains. We propose that CPSF6 releases the capsid from NPCs by masking its FG-attractive surface and switching the capsid to an FG-repulsive species. Fu et al. uncover the features that allow the HIV capsid to cross the permeability barrier of nuclear pores in an importin-independent manner, explaining how the viral genome can reach the nuclear compartment when infecting nondividing cells.
核转运受体(NTRs)携带货物穿过核孔复合物(npc)的渗透性屏障-一种由无序但有凝聚力的FG重复结构域凝聚而成的FG相。该相排斥惰性大分子,但允许NTR通过。当人类免疫缺陷病毒(HIV)感染非分裂细胞时,它的衣壳不像货物一样被运送到细胞核中,而是像NTR一样穿过npc。在这里,我们揭示了衣壳的NTR行为的分子决定因素。绑扎袋不够。六聚体和五聚体起作用。高度暴露的外衣壳表面是关键。它缺乏在其他蛋白质表面非常丰富的fg排斥带电残基(K, D和E)。而fg吸引残基则主导衣壳表面。引入FG排斥氨基酸阻碍了FG相分配、NPC靶向和组装衣壳的NPC通过。因此,衣壳通过源自单个表面侧链的无数瞬时FG吸引相互作用在FG相中溶解。我们建议CPSF6通过掩盖其fg吸引表面并将衣壳转换为fg排斥物种来释放npc的衣壳。
{"title":"Nuclear pore passage of the HIV capsid is driven by its unusual surface amino acid composition","authors":"Liran Fu, Shiya Cheng, Dietmar Riedel, Leonie Kopecny, Melina Schuh, Dirk Görlich","doi":"10.1038/s41594-025-01684-5","DOIUrl":"10.1038/s41594-025-01684-5","url":null,"abstract":"Nuclear transport receptors (NTRs) carry cargo across the permeability barrier of nuclear pore complexes (NPCs)—an FG phase condensed from disordered but cohesive FG-repeat domains. This phase repels inert macromolecules but allows NTR passage. When the human immunodeficiency virus (HIV) infects nondividing cells, its capsid is transported into nuclei not like a cargo but crosses NPCs like an NTR. Here we uncovered the molecular determinants of the capsid’s NTR behavior. The FG-binding pocket is insufficient. Hexameric and pentameric capsomers contribute. The highly exposed outer capsid surface is key. It lacks FG-repulsive charged residues (K, D and E) that are very abundant on other protein surfaces. FG-attractive residues dominate the capsid surface instead. Introducing FG-repulsive amino acids impedes FG phase partitioning, NPC targeting and NPC passage of assembled capsids. Capsids are, thus, made soluble in the FG phase by a myriad of transient FG-attractive interactions originating from individual surface side chains. We propose that CPSF6 releases the capsid from NPCs by masking its FG-attractive surface and switching the capsid to an FG-repulsive species. Fu et al. uncover the features that allow the HIV capsid to cross the permeability barrier of nuclear pores in an importin-independent manner, explaining how the viral genome can reach the nuclear compartment when infecting nondividing cells.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 12","pages":"2476-2491"},"PeriodicalIF":10.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01684-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145254766","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}
引用次数: 0
Returning home: a story of chromatin and community 回家:一个关于染色质和社区的故事。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-06 DOI: 10.1038/s41594-025-01645-y
Mayra Furlan-Magaril
Exile, discovery, and resilience have shaped my journey as a group leader in Mexico. From exploring chromatin architecture to building a lab and community, this is how science became my vocation and my home.
流亡、探索和坚韧塑造了我作为墨西哥小组组长的旅程。从探索染色质结构到建立实验室和社区,这就是科学如何成为我的职业和家。
{"title":"Returning home: a story of chromatin and community","authors":"Mayra Furlan-Magaril","doi":"10.1038/s41594-025-01645-y","DOIUrl":"10.1038/s41594-025-01645-y","url":null,"abstract":"Exile, discovery, and resilience have shaped my journey as a group leader in Mexico. From exploring chromatin architecture to building a lab and community, this is how science became my vocation and my home.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 10","pages":"1847-1847"},"PeriodicalIF":10.1,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145235642","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}
引用次数: 0
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus 报道型CRISPR筛选破译了Xist位点的顺式调控和跨式调控原理。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-06 DOI: 10.1038/s41594-025-01686-3
Till Schwämmle, Gemma Noviello, Eleni Kanata, Jonathan J. Froehlich, Melissa Bothe, Alexandra Martitz, Aybuge Altay, Jade Scouarnec, Vivi-Yun Feng, Heleen Mallie, Martin Vingron, Edda G. Schulz
Developmental genes are controlled by an ensemble of cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding how a cis-regulatory landscape integrates information from many dynamically expressed TFs has remained a challenge. Here we develop a combined CRISPR screening approach using endogenous RNA and RE reporters as readouts. Applied to the murine Xist locus, which is crucial for X-chromosome inactivation in females, this method allows us to comprehensively identify Xist-controlling TFs and map their TF–RE wiring. We find a group of transiently upregulated TFs, including ZIC3, that regulate proximal REs, driving the binary activation of Xist expression. These basal activators are more highly expressed in cells with two X chromosomes, potentially governing female-specific Xist upregulation. A second set of developmental TFs that include OTX2 is upregulated later during differentiation and targets distal REs. This regulatory axis is crucial to achieve high levels of Xist RNA, which is necessary for X-chromosome inactivation. OCT4 emerges as the strongest activator overall, regulating both proximal and distal elements. Our findings support a model for developmental gene regulation, in which factors targeting proximal REs drive binary on–off decisions, whereas factors interacting with distal REs control the transcription output. Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.
发育基因由一系列顺式作用调控元件(REs)控制,这些元件反过来对多个反式作用转录因子(TFs)作出反应。理解顺式监管环境如何整合来自许多动态表达的tf的信息仍然是一个挑战。在这里,我们开发了一种结合CRISPR筛选方法,使用内源性RNA和RE报告基因作为读数。将该方法应用于小鼠Xist位点,该位点对雌性x染色体失活至关重要,使我们能够全面鉴定控制Xist的tf并绘制其TF-RE接线。我们发现一组瞬时上调的tf,包括ZIC3,调节近端REs,驱动Xist表达的二元激活。这些基础激活因子在具有两条X染色体的细胞中表达更高,可能控制女性特异性的Xist上调。包括OTX2在内的第二组发育tf在分化后期被上调,并靶向远端res。这一调节轴对于实现高水平的Xist RNA至关重要,这是x染色体失活所必需的。总的来说,OCT4是最强的激活剂,调节近端和远端元件。我们的研究结果支持了一个发育基因调控模型,其中靶向近端REs的因子驱动二元开关决定,而与远端REs相互作用的因子控制转录输出。
{"title":"Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus","authors":"Till Schwämmle, Gemma Noviello, Eleni Kanata, Jonathan J. Froehlich, Melissa Bothe, Alexandra Martitz, Aybuge Altay, Jade Scouarnec, Vivi-Yun Feng, Heleen Mallie, Martin Vingron, Edda G. Schulz","doi":"10.1038/s41594-025-01686-3","DOIUrl":"10.1038/s41594-025-01686-3","url":null,"abstract":"Developmental genes are controlled by an ensemble of cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding how a cis-regulatory landscape integrates information from many dynamically expressed TFs has remained a challenge. Here we develop a combined CRISPR screening approach using endogenous RNA and RE reporters as readouts. Applied to the murine Xist locus, which is crucial for X-chromosome inactivation in females, this method allows us to comprehensively identify Xist-controlling TFs and map their TF–RE wiring. We find a group of transiently upregulated TFs, including ZIC3, that regulate proximal REs, driving the binary activation of Xist expression. These basal activators are more highly expressed in cells with two X chromosomes, potentially governing female-specific Xist upregulation. A second set of developmental TFs that include OTX2 is upregulated later during differentiation and targets distal REs. This regulatory axis is crucial to achieve high levels of Xist RNA, which is necessary for X-chromosome inactivation. OCT4 emerges as the strongest activator overall, regulating both proximal and distal elements. Our findings support a model for developmental gene regulation, in which factors targeting proximal REs drive binary on–off decisions, whereas factors interacting with distal REs control the transcription output. Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 12","pages":"2465-2475"},"PeriodicalIF":10.1,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01686-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145235665","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}
引用次数: 0
Molecular basis for the activation of outer dynein arms in cilia 纤毛外动力蛋白臂激活的分子基础。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-09-29 DOI: 10.1038/s41594-025-01680-9
Karim Housseini B. Issa, Muyang Ren, Bradley Burnet, Hao Lu, Charlotte Melia, Kate Heesom, Anthony J. Roberts, Sudipto Roy, Girish R. Mali
Multiciliogenesis requires large-scale biosynthesis of motility-powering axonemal inner and outer dynein arm motors (IDAs and ODAs) before their intraflagellar transport (IFT) into cilia. ODAs are inhibited by the packaging chaperone Shulin during ciliogenesis in Tetrahymena thermophila. How Shulin is released for ODAs to become active inside cilia remains unclear. Here we uncover a molecular mechanism for ODA activation. We establish interactions between DNAAF9 (human Shulin) and mammalian ODA subunits, IFT proteins and the ciliary small guanosine triphosphatase (GTPase) ARL3 using proteomics and in vitro reconstitutions. Mutagenesis combined with biochemical and structural studies reveal that DNAAF9 and Shulin preferentially bind active Arl3–GTP highlighting a cross-species conservation of this interaction. GTP-loaded Arl3 can access, bind and displace Shulin from the packaged ODA–Shulin complex. We propose that, once the inhibited ODA complex enters growing cilia, Arl3–GTP displaces Shulin (DNAAF9) and sequesters it away from ODAs, promoting activation of their motility specifically inside cilia. Issa et al. show that the ciliary small guanosine triphosphatase Arl3 displaces the inhibitory regulator Shulin/DNAAF9 from the outer dynein arm, leading to motor activation.
多纤毛发生需要在鞭毛内运输(IFT)进入纤毛之前,进行大规模的运动动力轴突内和外动力臂马达(ida和oda)的生物合成。在嗜热四膜虫纤毛发生过程中,ODAs受到包装伴侣舒林的抑制。鞘林是如何被释放,使oda在纤毛内变得活跃的,目前尚不清楚。在这里,我们揭示了ODA激活的分子机制。我们利用蛋白质组学和体外重组技术建立了DNAAF9(人鞘蛋白)与哺乳动物ODA亚基、IFT蛋白和纤毛小鸟苷三磷酸酶(GTPase) ARL3之间的相互作用。诱变结合生化和结构研究表明,DNAAF9和Shulin优先结合活性ar13 - gtp,表明这种相互作用具有跨物种保守性。装载gtp的Arl3可以从包装好的oda - sholin复合物中获取、结合和置换sholin。我们认为,一旦被抑制的ODA复合物进入生长中的纤毛,ar13 - gtp取代Shulin (DNAAF9)并将其从ODA中隔离出来,促进它们在纤毛内的运动激活。
{"title":"Molecular basis for the activation of outer dynein arms in cilia","authors":"Karim Housseini B. Issa, Muyang Ren, Bradley Burnet, Hao Lu, Charlotte Melia, Kate Heesom, Anthony J. Roberts, Sudipto Roy, Girish R. Mali","doi":"10.1038/s41594-025-01680-9","DOIUrl":"10.1038/s41594-025-01680-9","url":null,"abstract":"Multiciliogenesis requires large-scale biosynthesis of motility-powering axonemal inner and outer dynein arm motors (IDAs and ODAs) before their intraflagellar transport (IFT) into cilia. ODAs are inhibited by the packaging chaperone Shulin during ciliogenesis in Tetrahymena thermophila. How Shulin is released for ODAs to become active inside cilia remains unclear. Here we uncover a molecular mechanism for ODA activation. We establish interactions between DNAAF9 (human Shulin) and mammalian ODA subunits, IFT proteins and the ciliary small guanosine triphosphatase (GTPase) ARL3 using proteomics and in vitro reconstitutions. Mutagenesis combined with biochemical and structural studies reveal that DNAAF9 and Shulin preferentially bind active Arl3–GTP highlighting a cross-species conservation of this interaction. GTP-loaded Arl3 can access, bind and displace Shulin from the packaged ODA–Shulin complex. We propose that, once the inhibited ODA complex enters growing cilia, Arl3–GTP displaces Shulin (DNAAF9) and sequesters it away from ODAs, promoting activation of their motility specifically inside cilia. Issa et al. show that the ciliary small guanosine triphosphatase Arl3 displaces the inhibitory regulator Shulin/DNAAF9 from the outer dynein arm, leading to motor activation.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 12","pages":"2454-2464"},"PeriodicalIF":10.1,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01680-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145189271","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}
引用次数: 0
A guide to using small-molecule ferroptosis inhibitors 小分子铁下垂抑制剂的使用指南。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-09-26 DOI: 10.1038/s41594-025-01682-7
Derek A. Pratt, Scott J. Dixon
Inhibitors of ferroptosis are key tools for studies of cell death and may ultimately prove useful for the treatment of various diseases. In this Comment, we discuss major types of ferroptosis inhibitors and considerations for their use in mechanistic and preclinical studies.
铁下垂抑制剂是研究细胞死亡的关键工具,并可能最终证明对治疗各种疾病有用。在这篇评论中,我们讨论了主要类型的铁下垂抑制剂及其在机制和临床前研究中的应用。
{"title":"A guide to using small-molecule ferroptosis inhibitors","authors":"Derek A. Pratt, Scott J. Dixon","doi":"10.1038/s41594-025-01682-7","DOIUrl":"10.1038/s41594-025-01682-7","url":null,"abstract":"Inhibitors of ferroptosis are key tools for studies of cell death and may ultimately prove useful for the treatment of various diseases. In this Comment, we discuss major types of ferroptosis inhibitors and considerations for their use in mechanistic and preclinical studies.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 10","pages":"1848-1851"},"PeriodicalIF":10.1,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145153441","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}
引用次数: 0
期刊
Nature Structural & Molecular Biology
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1