Nature structural & molecular biology最新文献

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Botulinum neurotoxins exploit host digestive proteases to boost their oral toxicity via activating OrfXs/P47 肉毒杆菌神经毒素利用宿主消化蛋白酶,通过激活OrfXs/P47增强其口服毒性
Nature structural & molecular biology Pub Date : 2025-01-21 DOI: 10.1038/s41594-024-01479-0
Linfeng Gao, Maria Barbara Nowakowska, Katja Selby, Adina Przykopanski, Baohua Chen, Maren Krüger, François Paul Douillard, Kwok-ho Lam, Peng Chen, Ting Huang, Nigel Peter Minton, Martin Bernhard Dorner, Brigitte Gertrud Dorner, Andreas Rummel, Miia Lindström, Rongsheng Jin
{"title":"Botulinum neurotoxins exploit host digestive proteases to boost their oral toxicity via activating OrfXs/P47","authors":"Linfeng Gao, Maria Barbara Nowakowska, Katja Selby, Adina Przykopanski, Baohua Chen, Maren Krüger, François Paul Douillard, Kwok-ho Lam, Peng Chen, Ting Huang, Nigel Peter Minton, Martin Bernhard Dorner, Brigitte Gertrud Dorner, Andreas Rummel, Miia Lindström, Rongsheng Jin","doi":"10.1038/s41594-024-01479-0","DOIUrl":"https://doi.org/10.1038/s41594-024-01479-0","url":null,"abstract":"<p>Botulinum neurotoxins (BoNTs) rank among the most potent toxins and many of them are produced by bacteria carrying the <i>orfX</i> gene cluster that also encodes four nontoxic proteins (OrfX1, OrfX2, OrfX3 and P47). The <i>orfX</i> gene cluster is also found in the genomes of many non-BoNT-producing bacteria, often alongside genes encoding oral insecticidal toxins. However, the functions of these OrfXs and P47 remain elusive. Here, we demonstrate that the combined action of all four components (OrfXs and P47) drastically boosts the oral toxicity of BoNT in mice, following proteolytic activation by digestive proteases that oral toxins regularly confront. In particular, OrfX2 adopts a self-inhibiting state, engaging with BoNT through another clostridial protein, nontoxic non-hemagglutinin (NTNH), only after proteolytic activation. Cryo-electron microscopy studies unveil that two molecules of protease-activated OrfX2 simultaneously associate with NTNH, a binding mode crucial for boosting BoNT oral toxicity. Collectively, these studies offer novel insights into the physiological functions and regulatory mechanisms of OrfXs and P47 of BoNTs, shedding light on the pathogenesis of other bacterial toxins associated with homologous OrfXs and P47.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fascin structural plasticity mediates flexible actin bundle construction 筋膜蛋白结构可塑性介导柔性肌动蛋白束的构建
Nature structural & molecular biology Pub Date : 2025-01-20 DOI: 10.1038/s41594-024-01477-2
Rui Gong, Matthew J. Reynolds, Keith R. Carney, Keith Hamilton, Tamara C. Bidone, Gregory M. Alushin
{"title":"Fascin structural plasticity mediates flexible actin bundle construction","authors":"Rui Gong, Matthew J. Reynolds, Keith R. Carney, Keith Hamilton, Tamara C. Bidone, Gregory M. Alushin","doi":"10.1038/s41594-024-01477-2","DOIUrl":"https://doi.org/10.1038/s41594-024-01477-2","url":null,"abstract":"<p>Fascin cross-links actin filaments (F-actin) into bundles that support tubular membrane protrusions including filopodia and stereocilia. Fascin dysregulation drives aberrant cell migration during metastasis, and fascin inhibitors are under development as cancer therapeutics. Here, we use cryo-EM, cryo-electron tomography coupled with custom denoising and computational modeling to probe human fascin-1’s F-actin cross-linking mechanisms across spatial scales. Our fascin cross-bridge structure reveals an asymmetric F-actin binding conformation that is allosterically blocked by the inhibitor G2. Reconstructions of seven-filament hexagonal bundle elements, variability analysis and simulations show how structural plasticity enables fascin to bridge varied interfilament orientations, accommodating mismatches between F-actin’s helical symmetry and bundle hexagonal packing. Tomography of many-filament bundles and modeling uncover geometric rules underlying emergent fascin binding patterns, as well as the accumulation of unfavorable cross-links that limit bundle size. Collectively, this work shows how fascin harnesses fine-tuned nanoscale structural dynamics to build and regulate micron-scale F-actin bundles.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structures of aberrant spliceosome intermediates on their way to disassembly 异常剪接体中间体在解体途中的结构
Nature structural & molecular biology Pub Date : 2025-01-20 DOI: 10.1038/s41594-024-01480-7
Komal Soni, Attila Horvath, Olexandr Dybkov, Merlin Schwan, Sasanan Trakansuebkul, Dirk Flemming, Klemens Wild, Henning Urlaub, Tamás Fischer, Irmgard Sinning
{"title":"Structures of aberrant spliceosome intermediates on their way to disassembly","authors":"Komal Soni, Attila Horvath, Olexandr Dybkov, Merlin Schwan, Sasanan Trakansuebkul, Dirk Flemming, Klemens Wild, Henning Urlaub, Tamás Fischer, Irmgard Sinning","doi":"10.1038/s41594-024-01480-7","DOIUrl":"https://doi.org/10.1038/s41594-024-01480-7","url":null,"abstract":"<p>Intron removal during pre-mRNA splicing is of extraordinary complexity and its disruption causes a vast number of genetic diseases in humans. While key steps of the canonical spliceosome cycle have been revealed by combined structure–function analyses, structural information on an aberrant spliceosome committed to premature disassembly is not available. Here, we report two cryo-electron microscopy structures of post-B<sup>act</sup> spliceosome intermediates from <i>Schizosaccharomyces</i> <i>pombe</i> primed for disassembly. We identify the DEAH-box helicase–G-patch protein pair (Gih35–Gpl1, homologous to human DHX35–GPATCH1) and show how it maintains catalytic dormancy. In both structures, Gpl1 recognizes a remodeled active site introduced by an overstabilization of the U5 loop I interaction with the 5′ exon leading to a single-nucleotide insertion at the 5′ splice site. Remodeling is communicated to the spliceosome surface and the Ntr1 complex that mediates disassembly is recruited. Our data pave the way for a targeted analysis of splicing quality control.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The structure and function of the ghrelin receptor coding for drug actions 编码药物作用的胃饥饿素受体的结构和功能
Nature structural & molecular biology Pub Date : 2025-01-20 DOI: 10.1038/s41594-024-01481-6
Yuki Shiimura, Dohyun Im, Ryosuke Tany, Hidetsugu Asada, Ryoji Kise, Eon Kurumiya, Hideko Wakasugi-Masuho, Satoshi Yasuda, Kazuma Matsui, Jun-ichi Kishikawa, Takayuki Kato, Takeshi Murata, Masayasu Kojima, So Iwata, Ikuo Masuho
{"title":"The structure and function of the ghrelin receptor coding for drug actions","authors":"Yuki Shiimura, Dohyun Im, Ryosuke Tany, Hidetsugu Asada, Ryoji Kise, Eon Kurumiya, Hideko Wakasugi-Masuho, Satoshi Yasuda, Kazuma Matsui, Jun-ichi Kishikawa, Takayuki Kato, Takeshi Murata, Masayasu Kojima, So Iwata, Ikuo Masuho","doi":"10.1038/s41594-024-01481-6","DOIUrl":"https://doi.org/10.1038/s41594-024-01481-6","url":null,"abstract":"<p>Drugs targeting the ghrelin receptor hold therapeutic potential in anorexia, obesity and diabetes. However, developing effective drugs is challenging. To tackle this common issue across a broad drug target, this study aims to understand how anamorelin, the only approved drug targeting the ghrelin receptor, operates compared to other synthetic drugs. Our research elucidated the receptor’s structure with anamorelin and miniG<sub>q</sub>, unveiling anamorelin’s superagonistic activity. We demonstrated that ligands with distinct chemical structures uniquely bind to the receptor, resulting in diverse conformations and biasing signal transduction. Moreover, our study showcased the utility of structural information in effectively identifying natural genetic variations altering drug action and causing severe functional deficiencies, offering a basis for selecting the right medication on the basis of the individual’s genomic sequence. Thus, by building on structural analysis, this study enhances the foundational framework for selecting therapeutic agents targeting the ghrelin receptor, by effectively leveraging signaling bias and genetic variations.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular architecture of human LYCHOS involved in lysosomal cholesterol signaling 人LYCHOS参与溶酶体胆固醇信号传导的分子结构
Nature structural & molecular biology Pub Date : 2025-01-17 DOI: 10.1038/s41594-024-01474-5
Qi Xiong, Zhini Zhu, Tingting Li, Xiaotian Li, Zixuan Zhou, Yulin Chao, Chuanhui Yang, Suihan Feng, Qianhui Qu, Dianfan Li
{"title":"Molecular architecture of human LYCHOS involved in lysosomal cholesterol signaling","authors":"Qi Xiong, Zhini Zhu, Tingting Li, Xiaotian Li, Zixuan Zhou, Yulin Chao, Chuanhui Yang, Suihan Feng, Qianhui Qu, Dianfan Li","doi":"10.1038/s41594-024-01474-5","DOIUrl":"https://doi.org/10.1038/s41594-024-01474-5","url":null,"abstract":"<p>Lysosomal membrane protein LYCHOS (lysosomal cholesterol signaling) translates cholesterol abundance to mammalian target of rapamycin activation. Here we report the 2.11-Å structure of human LYCHOS, revealing a unique fusion architecture comprising a G-protein-coupled receptor (GPCR)-like domain and a transporter domain that mediates homodimer assembly. The NhaA-fold transporter harbors a previously uncharacterized intramembrane Na<sup>+</sup> pocket. The GPCR-like domain is stabilized, by analogy to canonical GPCRs, in an inactive state through ‘tethered antagonism’ by a lumenal loop and strong interactions at the cytosol side preventing the hallmark swing of the sixth transmembrane helix seen in active GPCRs. A cholesterol molecule and an associated docosahexaenoic acid (DHA)-phospholipid are entrapped between the transporter and GPCR-like domains, with the DHA-phospholipid occupying a pocket previously implicated in cholesterol sensing, indicating inter-domain coupling via dynamic lipid–protein interactions. Our work provides a high-resolution framework for functional investigations of the understudied LYCHOS protein.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ERK–USP9X-coupled regulation of thymidine kinase 1 promotes both its enzyme activity-dependent and its enzyme activity-independent functions for tumor growth erk - usp9x偶联调节胸苷激酶1促进其对肿瘤生长的酶活性依赖性和酶活性非依赖性功能
Nature structural & molecular biology Pub Date : 2025-01-17 DOI: 10.1038/s41594-024-01473-6
Jingjing Tao, Zheng Wang, Rongkai Shi, Liming Lin, Min Li, Ying Meng, Shudi Luo, Xiaoming Jiang, Zhanpeng Guo, Yongfeng Shang, Zhimin Lu
{"title":"ERK–USP9X-coupled regulation of thymidine kinase 1 promotes both its enzyme activity-dependent and its enzyme activity-independent functions for tumor growth","authors":"Jingjing Tao, Zheng Wang, Rongkai Shi, Liming Lin, Min Li, Ying Meng, Shudi Luo, Xiaoming Jiang, Zhanpeng Guo, Yongfeng Shang, Zhimin Lu","doi":"10.1038/s41594-024-01473-6","DOIUrl":"https://doi.org/10.1038/s41594-024-01473-6","url":null,"abstract":"<p>Thymidine kinase 1 (TK1), a crucial enzyme in DNA synthesis, is highly expressed in various cancers. However, the mechanisms underlying its elevated expression and the implications for tumor metabolism remain unclear. Here we demonstrate that activation of growth factor receptors enhances TK1 expression. Treatment with epidermal growth factor or insulin-like growth factor 1 induces the binding of ERK1/2 to TK1 and subsequent TK1 S13/231 phosphorylation by ERK1/2. This modification recruits ubiquitin carboxyl-terminal hydrolase 9X to deubiquitylate TK1, preventing its proteasomal degradation. Stabilized TK1 not only enhances its enzyme activity-dependent deoxythymidine monophosphate production for DNA synthesis but also promotes glycolysis independently of its enzymatic activity by upregulating phosphofructokinase/fructose bisphosphatase type 3 expression. This dual role of TK1 drives the proliferation of human hepatocellular carcinoma cells and liver tumor growth in mice. Our findings reveal a crucial mechanism by which growth factors promote tumor development through TK1-mediated DNA synthesis and glycolysis and highlight TK1 as a potential molecular target for cancer treatment.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"118 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS 低温电镜显示胆固醇在溶酶体gpcr样蛋白LYCHOS中的结合
Nature structural & molecular biology Pub Date : 2025-01-17 DOI: 10.1038/s41594-024-01470-9
Jie Zhao, Qingya Shen, Xihao Yong, Xin Li, Xiaowen Tian, Suyue Sun, Zheng Xu, Xiaoyu Zhang, Lu Zhang, Hao Yang, Zhenhua Shao, Haoxing Xu, Yiyang Jiang, Yan Zhang, Wei Yan
{"title":"Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS","authors":"Jie Zhao, Qingya Shen, Xihao Yong, Xin Li, Xiaowen Tian, Suyue Sun, Zheng Xu, Xiaoyu Zhang, Lu Zhang, Hao Yang, Zhenhua Shao, Haoxing Xu, Yiyang Jiang, Yan Zhang, Wei Yan","doi":"10.1038/s41594-024-01470-9","DOIUrl":"https://doi.org/10.1038/s41594-024-01470-9","url":null,"abstract":"<p>Cholesterol plays a pivotal role in modulating the activity of mechanistic target of rapamycin complex 1 (mTOR1), thereby regulating cell growth and metabolic homeostasis. LYCHOS, a lysosome-localized G-protein-coupled receptor-like protein, emerges as a cholesterol sensor and is capable of transducing the cholesterol signal to affect the mTORC1 function. However, the precise mechanism by which LYCHOS recognizes cholesterol remains unknown. Here, using cryo-electron microscopy, we determined the three-dimensional structural architecture of LYCHOS in complex with cholesterol molecules, revealing a unique arrangement of two sequential structural domains. Through a comprehensive analysis of this structure, we elucidated the specific structural features of these two domains and their collaborative role in the process of cholesterol recognition by LYCHOS.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Maternal ELL3 loss-of-function leads to oocyte aneuploidy and early miscarriage 母体 ELL3 功能缺失导致卵母细胞非整倍体和早期流产
Nature structural & molecular biology Pub Date : 2025-01-16 DOI: 10.1038/s41594-024-01471-8
Shiqi Zhu, Peng Xie, Yi Yang, Yan Wang, Chuanxin Zhang, Yu Zhang, Shuhan Si, Jin Zhang, Jingjing He, Hao Si, Ke Fang, Binbin Ma, Xu Jiang, Lindi Huang, Jiamin Li, Tian Min, Beihong Zheng, Lincui Da, Dianliang Lin, Kun Gao, Yuanyuan Li, Mingtao Huang, Fengchang Qiao, Haiqin Huo, Haoyang Feng, Han Zhao, Zijiang Chen, Zhengfeng Xu, Jing Xie, Hua Cao, Jin Liu, Xuebiao Yao, Wei Xie, Yan Sun, Keliang Wu, Bo Xiong, Ping Hu, Zhuojuan Luo, Chengqi Lin
{"title":"Maternal ELL3 loss-of-function leads to oocyte aneuploidy and early miscarriage","authors":"Shiqi Zhu, Peng Xie, Yi Yang, Yan Wang, Chuanxin Zhang, Yu Zhang, Shuhan Si, Jin Zhang, Jingjing He, Hao Si, Ke Fang, Binbin Ma, Xu Jiang, Lindi Huang, Jiamin Li, Tian Min, Beihong Zheng, Lincui Da, Dianliang Lin, Kun Gao, Yuanyuan Li, Mingtao Huang, Fengchang Qiao, Haiqin Huo, Haoyang Feng, Han Zhao, Zijiang Chen, Zhengfeng Xu, Jing Xie, Hua Cao, Jin Liu, Xuebiao Yao, Wei Xie, Yan Sun, Keliang Wu, Bo Xiong, Ping Hu, Zhuojuan Luo, Chengqi Lin","doi":"10.1038/s41594-024-01471-8","DOIUrl":"https://doi.org/10.1038/s41594-024-01471-8","url":null,"abstract":"<p>Up to an estimated 10% of women experience miscarriage in their lifetimes. Embryonic aneuploidy is a leading cause for miscarriage, infertility and congenital defects. Here we identify variants of <i>ELL3</i>, a gene encoding a transcription elongation factor, in couples who experienced consecutive early miscarriages due to embryonic aneuploidy. Maternal ELL3 knockout leads to mouse oocyte aneuploidy, subfertility and miscellaneous embryonic defects. Mechanistically, we find that ELL3 localizes to the spindle during meiosis, and that ELL3 depletion in both mouse and human oocytes increases the incidence of meiotic spindle abnormality. ELL3 coordinates with TPX2 to ensure the proper function of the microtubule motor KIF11. Live imaging analysis shows that ELL3 is paramount for promoting spindle assembly and driving chromosome movement. Together, our findings implicate maternal ELL3 deficiency in causing oocyte aneuploidy and early miscarriage.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142986739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The translational landscape of HIV-1 infected cells reveals key gene regulatory principles HIV-1感染细胞的翻译景观揭示了关键的基因调控原理
Nature structural & molecular biology Pub Date : 2025-01-15 DOI: 10.1038/s41594-024-01468-3
Anuja Kibe, Stefan Buck, Anne-Sophie Gribling-Burrer, Orian Gilmer, Patrick Bohn, Tatyana Koch, Chiara Noemi-Marie Mireisz, Andreas Schlosser, Florian Erhard, Redmond P. Smyth, Neva Caliskan
{"title":"The translational landscape of HIV-1 infected cells reveals key gene regulatory principles","authors":"Anuja Kibe, Stefan Buck, Anne-Sophie Gribling-Burrer, Orian Gilmer, Patrick Bohn, Tatyana Koch, Chiara Noemi-Marie Mireisz, Andreas Schlosser, Florian Erhard, Redmond P. Smyth, Neva Caliskan","doi":"10.1038/s41594-024-01468-3","DOIUrl":"https://doi.org/10.1038/s41594-024-01468-3","url":null,"abstract":"<p>Human immunodeficiency virus-1 (HIV-1) uses a number of strategies to modulate viral and host gene expression during its life cycle. To characterize the transcriptional and translational landscape of HIV-1 infected cells, we used a combination of ribosome profiling, disome sequencing and RNA sequencing. We show that HIV-1 messenger RNAs are efficiently translated at all stages of infection, despite evidence for a substantial decrease in the translational efficiency of host genes that are implicated in host cell translation. Our data identify upstream open reading frames in the HIV-1 5′-untranslated region as well as internal open reading frames in the <i>Vif</i> and <i>Pol</i> coding domains. We also observed ribosomal collisions in <i>Gag-Pol</i> upstream of the ribosome frameshift site that we attributed to an RNA structural fold using RNA structural probing and functional analysis. Antisense oligonucleotides designed to alter the base of this structure decreased frameshift efficiency. Overall, our data highlight the complexity of HIV-1 gene regulation and provide a key resource for decoding of host–pathogen interactions upon HIV-1 infection. Furthermore, we provide evidence for a RNA structural fold including the frameshift site that could serve as a target for antiviral therapy.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dynamic PRC1–CBX8 stabilizes a porous structure of chromatin condensates 动态PRC1-CBX8稳定了染色质凝聚物的多孔结构
Nature structural & molecular biology Pub Date : 2025-01-15 DOI: 10.1038/s41594-024-01457-6
Michael Uckelmann, Vita Levina, Cyntia Taveneau, Xiao Han Ng, Varun Pandey, Jasmine Martinez, Shweta Mendiratta, Justin Houx, Marion Boudes, Hari Venugopal, Sylvain Trépout, Alex J. Fulcher, Qi Zhang, Sarena Flanigan, Minrui Li, Emma Sierecki, Yann Gambin, Partha Pratim Das, Oliver Bell, Alex de Marco, Chen Davidovich
{"title":"Dynamic PRC1–CBX8 stabilizes a porous structure of chromatin condensates","authors":"Michael Uckelmann, Vita Levina, Cyntia Taveneau, Xiao Han Ng, Varun Pandey, Jasmine Martinez, Shweta Mendiratta, Justin Houx, Marion Boudes, Hari Venugopal, Sylvain Trépout, Alex J. Fulcher, Qi Zhang, Sarena Flanigan, Minrui Li, Emma Sierecki, Yann Gambin, Partha Pratim Das, Oliver Bell, Alex de Marco, Chen Davidovich","doi":"10.1038/s41594-024-01457-6","DOIUrl":"https://doi.org/10.1038/s41594-024-01457-6","url":null,"abstract":"<p>The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organization and dynamics of chromatin compacted by gene-repressing factors are unknown. Here, using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the polycomb repressive complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilized through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provide a mechanistic framework for dynamic and accessible PRC1–chromatin condensates.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"52 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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