{"title":"Insights into reproduction-regulating NOD-like receptors","authors":"Inga V. Hochheiser, Matthias Geyer","doi":"10.1038/s41594-024-01383-7","DOIUrl":"10.1038/s41594-024-01383-7","url":null,"abstract":"An understudied subset of NOD-like receptors are involved in the reproductive system, and their dysfunction can cause infertility. The recently obtained structures of the core subcortical maternal complex assembled around one of them, NLRP5, provide important insight into this building block of early embryo cytoplasmic lattices.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"31 11","pages":"1641-1643"},"PeriodicalIF":12.5,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325384","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":"Cryo-EM structure of the human subcortical maternal complex and the associated discovery of infertility-associated variants","authors":"Pengliang Chi, Guojin Ou, Sibei Liu, Qianhong Ma, Yuechao Lu, Jinhong Li, Jialu Li, Qianqian Qi, Zhuo Han, Zihan Zhang, Qingting Liu, Li Guo, Jing Chen, Xiang Wang, Wei Huang, Lei Li, Dong Deng","doi":"10.1038/s41594-024-01396-2","DOIUrl":"10.1038/s41594-024-01396-2","url":null,"abstract":"The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluating the pathogenicity of a missense variant in the SCMC is limited by the lack of information on its structure, although we recently solved the structure of the mouse SCMC and proposed that reproductive disorders caused by pathogenic variants are related to the destabilization of the SCMC core complex. Here we report the cryogenic electron microscopy structure of the human SCMC and uncover that the pyrin domain of NLRP5 is essential for the stability of SCMC. By combining prediction of SCMC stability and in vitro reconstitution, we provide a method for identifying deleterious variants, and we successfully identify a new pathogenic variant of TLE6 (p.A396T). Thus, on the basis of the structure of the human SCMC, we offer a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated variants. On the basis of the assembly mechanism and structures of the human subcortical maternal complex, the authors provide a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated SCMC variants.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"31 11","pages":"1798-1807"},"PeriodicalIF":12.5,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142384213","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":"Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies","authors":"Benedikt Junglas, David Kartte, Mirka Kutzner, Nadja Hellmann, Ilona Ritter, Dirk Schneider, Carsten Sachse","doi":"10.1038/s41594-024-01399-z","DOIUrl":"10.1038/s41594-024-01399-z","url":null,"abstract":"Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting complexes required for transport III superfamily, it is still unknown how Vipp1 remodels membranes. Here, we present cryo-electron microscopy structures of Synechocystis Vipp1 interacting with membranes: seven structures of helical and stacked-ring assemblies at 5–7-Å resolution engulfing membranes and three carpet structures covering lipid vesicles at ~20-Å resolution using subtomogram averaging. By analyzing ten structures of N-terminally truncated Vipp1, we show that helix α0 is essential for membrane tubulation and forms the membrane-anchoring domain of Vipp1. Lastly, using a conformation-restrained Vipp1 mutant, we reduced the structural plasticity of Vipp1 and determined two structures of Vipp1 at 3.0-Å resolution, resolving the molecular details of membrane-anchoring and intersubunit contacts of helix α0. Our data reveal membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion. The authors present structures of endosomal sorting complexes required for transport III family member vesicle-inducing protein in plastids 1, ranging from helical assemblies and stacked rings to flat carpets, providing insights into transitions dependent on membrane tubulation and curvature needed for forming different architectures involved in membrane remodeling.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 3","pages":"555-570"},"PeriodicalIF":12.5,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41594-024-01399-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142384214","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}
Zuhui Wang, Bo Wang, Di Niu, Chao Yin, Ying Bi, Claudia Cattoglio, Kyle M. Loh, Luke D. Lavis, Hao Ge, Wulan Deng
{"title":"Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells","authors":"Zuhui Wang, Bo Wang, Di Niu, Chao Yin, Ying Bi, Claudia Cattoglio, Kyle M. Loh, Luke D. Lavis, Hao Ge, Wulan Deng","doi":"10.1038/s41594-024-01385-5","DOIUrl":"10.1038/s41594-024-01385-5","url":null,"abstract":"Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable ‘confined target search’ mechanism. PTFs such as FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-PTF MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domains, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested that transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation. Live-cell single-molecule imaging of pioneer transcription factors revealed a ‘confined target search’ mechanism where they alternate between fast free diffusion in the nucleus and slower confined diffusion within compacted chromatin domains, leading to efficient pioneering on closed targets.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 1","pages":"125-136"},"PeriodicalIF":12.5,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374126","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}
Richard D. Schargel, M. Zuhaib Qayyum, Ajay Singh Tanwar, Ravi C. Kalathur, Elizabeth H. Kellogg
{"title":"Structure of Fanzor2 reveals insights into the evolution of the TnpB superfamily","authors":"Richard D. Schargel, M. Zuhaib Qayyum, Ajay Singh Tanwar, Ravi C. Kalathur, Elizabeth H. Kellogg","doi":"10.1038/s41594-024-01394-4","DOIUrl":"10.1038/s41594-024-01394-4","url":null,"abstract":"RNA-guided endonucleases, once thought to be exclusive to prokaryotes, have been recently identified in eukaryotes and are called Fanzors. They are classified into two clades, Fanzor1 and Fanzor2. Here we present the cryo-electron microscopy structure of Acanthamoeba polyphaga mimivirus Fanzor2, revealing its ωRNA architecture, active site and features involved in transposon-adjacent motif recognition. A comparison to Fanzor1 and TnpB structures highlights divergent evolutionary paths, advancing our understanding of RNA-guided endonucleases. This study presents the cryo-electron microscopy structure of Fanzor2, showcasing its unique structural elements and nucleic acid interaction sites. A comparison to TnpB-related RNA-guided endonucleases highlights divergent evolutionary paths.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 2","pages":"243-246"},"PeriodicalIF":12.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41594-024-01394-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142360099","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}
Svetlana Farberov, Omer Ziv, Jian You Lau, Rotem Ben-Tov Perry, Yoav Lubelsky, Eric Miska, Grzegorz Kudla, Igor Ulitsky
{"title":"Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity","authors":"Svetlana Farberov, Omer Ziv, Jian You Lau, Rotem Ben-Tov Perry, Yoav Lubelsky, Eric Miska, Grzegorz Kudla, Igor Ulitsky","doi":"10.1038/s41594-024-01393-5","DOIUrl":"10.1038/s41594-024-01393-5","url":null,"abstract":"Long noncoding RNAs (lncRNAs) are increasingly appreciated for their important functions in mammalian cells. However, how their functional capacities are encoded in their sequences and manifested in their structures remains largely unknown. Some lncRNAs bind to and modulate the availability of RNA-binding proteins, but the structural principles that underlie this mode of regulation are unknown. The NORAD lncRNA is a known decoy for Pumilio proteins, which modulate the translation and stability of hundreds of messenger RNAs and, consequently, a regulator of genomic stability and aging. Here we probed the RNA structure and long-range RNA–RNA interactions formed by human NORAD inside cells under different stressful conditions. We discovered a highly modular structure consisting of well-defined domains that contribute independently to NORAD function. Following arsenite stress, most structural domains undergo relaxation and form interactions with other RNAs that are targeted to stress granules. We further revealed a unique structural organization that spatially clusters the multiple Pumilio binding sites along NORAD and consequently contributes to the derepression of Pumilio targets. We then applied these structural principles to design an effective artificial decoy for the let-7 microRNA. Our work demonstrates how the sequence of a lncRNA spatially clusters its function into separated domains and how structural principles can be employed for the rational design of lncRNAs with desired activities. Here the authors experimentally describe the secondary structure of the NORAD long noncoding RNA in human cells. NORAD’s modular structure and specific structural elements allow it to efficiently antagonize the Pumilio RNA-binding proteins.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 2","pages":"287-299"},"PeriodicalIF":12.5,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321494","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}
Ireneusz Górniak, Zachery Stephens, Satchal K. Erramilli, Tomasz Gawda, Anthony A. Kossiakoff, Jochen Zimmer
{"title":"Structural insights into translocation and tailored synthesis of hyaluronan","authors":"Ireneusz Górniak, Zachery Stephens, Satchal K. Erramilli, Tomasz Gawda, Anthony A. Kossiakoff, Jochen Zimmer","doi":"10.1038/s41594-024-01389-1","DOIUrl":"10.1038/s41594-024-01389-1","url":null,"abstract":"Hyaluronan (HA) is an essential component of the vertebrate extracellular matrix. It is a heteropolysaccharide of N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) reaching several megadaltons in healthy tissues. HA is synthesized and translocated in a coupled reaction by HA synthase (HAS). Here, structural snapshots of HAS provide insights into HA biosynthesis, from substrate recognition to HA elongation and translocation. We monitor the extension of a GlcNAc primer with GlcA, reveal the coordination of the uridine diphosphate product by a conserved gating loop and capture the opening of a translocation channel to coordinate a translocating HA polymer. Furthermore, we identify channel-lining residues that modulate HA product lengths. Integrating structural and biochemical analyses suggests an avenue for polysaccharide engineering based on finely tuned enzymatic activity and HA coordination. Hyaluronan (HA) is an essential glycosaminoglycan. Here, the authors provide mechanistic insights into how HA synthase synthesizes HA and creates a membrane-spanning secretion channel, as well as how channel-lining residues modulate the HA length distribution.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 1","pages":"161-171"},"PeriodicalIF":12.5,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41594-024-01389-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142317257","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}
Kei Saotome, Luke L. McGoldrick, Jo-Hao Ho, Trudy F. Ramlall, Sweta Shah, Michael J. Moore, Jee Hae Kim, Raymond Leidich, William C. Olson, Matthew C. Franklin
{"title":"Structural insights into CXCR4 modulation and oligomerization","authors":"Kei Saotome, Luke L. McGoldrick, Jo-Hao Ho, Trudy F. Ramlall, Sweta Shah, Michael J. Moore, Jee Hae Kim, Raymond Leidich, William C. Olson, Matthew C. Franklin","doi":"10.1038/s41594-024-01397-1","DOIUrl":"10.1038/s41594-024-01397-1","url":null,"abstract":"Activation of the chemokine receptor CXCR4 by its chemokine ligand CXCL12 regulates diverse cellular processes. Previously reported crystal structures of CXCR4 revealed the architecture of an inactive, homodimeric receptor. However, many structural aspects of CXCR4 remain poorly understood. Here, we use cryo-electron microscopy to investigate various modes of human CXCR4 regulation. CXCL12 activates CXCR4 by inserting its N terminus deep into the CXCR4 orthosteric pocket. The binding of US Food and Drug Administration-approved antagonist AMD3100 is stabilized by electrostatic interactions with acidic residues in the seven-transmembrane-helix bundle. A potent antibody blocker, REGN7663, binds across the extracellular face of CXCR4 and inserts its complementarity-determining region H3 loop into the orthosteric pocket. Trimeric and tetrameric structures of CXCR4 reveal modes of G-protein-coupled receptor oligomerization. We show that CXCR4 adopts distinct subunit conformations in trimeric and tetrameric assemblies, highlighting how oligomerization could allosterically regulate chemokine receptor function. Here, cryo-electron microscopy structures reveal how the chemokine receptor CXCR4 oligomerizes and how it is regulated by its physiological ligand CXCL12, the small-molecule drug AMD3100 and the monoclonal antibody REGN7663.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 2","pages":"315-325"},"PeriodicalIF":12.5,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41594-024-01397-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276833","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}
You Yu, Juncheng Wang, Kaixian Liu, Zhi Zheng, Meret Arter, Corentin Claeys Bouuaert, Stephen Pu, Dinshaw J. Patel, Scott Keeney
{"title":"Cryo-EM structures of the Spo11 core complex bound to DNA","authors":"You Yu, Juncheng Wang, Kaixian Liu, Zhi Zheng, Meret Arter, Corentin Claeys Bouuaert, Stephen Pu, Dinshaw J. Patel, Scott Keeney","doi":"10.1038/s41594-024-01382-8","DOIUrl":"10.1038/s41594-024-01382-8","url":null,"abstract":"DNA double-strand breaks that initiate meiotic recombination are formed by the topoisomerase-relative enzyme Spo11, supported by conserved auxiliary factors. Because high-resolution structural data have not been available, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-electron microscopy structures at up to 3.3-Å resolution of DNA-bound core complexes of Saccharomyces cerevisiae Spo11 with Rec102, Rec104 and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3′-OH and first 5′ overhanging nucleotide, establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex. High-resolution structures of DNA-bound multiprotein Spo11 complexes, the DNA-cleaving ensembles that initiate meiotic recombination, elucidate the structural basis of its DNA-binding specificity and explain recombination initiation patterns in vivo.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 1","pages":"113-124"},"PeriodicalIF":12.5,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41594-024-01382-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276081","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}
Ying Zhang, Kaijing Chen, Seng Chuan Tang, Yichao Cai, Akiko Nambu, Yi Xiang See, Chaoyu Fu, Anandhkumar Raju, Benjamin Lebeau, Zixun Ling, Jia Jia Chan, Yvonne Tay, Marek Mutwil, Manikandan Lakshmanan, Greg Tucker-Kellogg, Wee Joo Chng, Daniel G. Tenen, Motomi Osato, Vinay Tergaonkar, Melissa Jane Fullwood
{"title":"Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth","authors":"Ying Zhang, Kaijing Chen, Seng Chuan Tang, Yichao Cai, Akiko Nambu, Yi Xiang See, Chaoyu Fu, Anandhkumar Raju, Benjamin Lebeau, Zixun Ling, Jia Jia Chan, Yvonne Tay, Marek Mutwil, Manikandan Lakshmanan, Greg Tucker-Kellogg, Wee Joo Chng, Daniel G. Tenen, Motomi Osato, Vinay Tergaonkar, Melissa Jane Fullwood","doi":"10.1038/s41594-024-01391-7","DOIUrl":"10.1038/s41594-024-01391-7","url":null,"abstract":"Human silencers have been shown to regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form ‘super-silencers’ and whether they are linked to cancer progression. Here, we show two silencer components of the FGF18 gene can cooperate through compensatory chromatin interactions to form a super-silencer. Double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes in cell identity. To perturb the super-silencers, we applied combinational treatment of an enhancer of zeste homolog 2 inhibitor GSK343, and a repressor element 1-silencing transcription factor inhibitor, X5050 (‘GR’). Interestingly, GR led to severe loss of topologically associated domains and loops, which were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GR synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects in vivo. Overall, our data demonstrated a super-silencer example and showed that GR can disrupt super-silencers, potentially leading to cancer ablation. Here, the authors unveiled a ‘super-silencer’ and its mechanisms of action. They revealed that a combined treatment of an enhancer of zeste homolog 2 inhibitor and a repressor element 1-silencing transcription factor inhibitor can disrupt super-silencers, potentially leading to cancer ablation.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 1","pages":"137-149"},"PeriodicalIF":12.5,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41594-024-01391-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276078","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}