Nature structural & molecular biology最新文献

{"title":"Structural insights into RNA-guided RNA editing by the Cas13b–ADAR2 complex","authors":"Junichiro Ishikawa, Kazuki Kato, Soumya Kannan, Sae Okazaki, Soh Ishiguro, Keitaro Yamashita, Nozomu Yachie, Tomohiro Nishizawa, Feng Zhang, Hiroshi Nishimasu","doi":"10.1038/s41594-025-01529-1","DOIUrl":"https://doi.org/10.1038/s41594-025-01529-1","url":null,"abstract":"<p>Cas13 is an RNA-guided RNA endonuclease derived from the type VI CRISPR–Cas system, which has been used in numerous RNA-targeting technologies, such as RNA knockdown, detection and editing. The catalytically inactive <i>Prevotella</i> sp. Cas13b (dPspCas13b) fused to the human adenosine deaminase acting on RNA 2 (ADAR2) deaminase domain can edit adenosine in target transcripts to inosine, in an RNA-editing technology called REPAIR (RNA editing for programmable A-to-I replacement), which has potential for gene therapy. Here we report the cryo-electron microscopy structures of the PspCas13b–guide RNA binary complex, the PspCas13b–guide RNA–target RNA ternary complex and the dPspCas13b–ADAR2–guide RNA–target RNA complex. These structures provide mechanistic insights into RNA cleavage and editing. We applied our structural insights to engineer a compact and efficient dPspCas13b–ADAR2 complex (REPAIR-mini). Overall, our findings advance the understanding of CRISPR–Cas13 effector nucleases and could enable the development of improved RNA-targeting technologies.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143819221","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}

{"title":"A transcription coupling model for how enhancers communicate with their target genes","authors":"Elisabeth Altendorfer, Stefan Mundlos, Andreas Mayer","doi":"10.1038/s41594-025-01523-7","DOIUrl":"https://doi.org/10.1038/s41594-025-01523-7","url":null,"abstract":"<p>How enhancers communicate with their target genes to influence transcription is an unresolved question of fundamental importance. Current models of the mechanism of enhancer–target gene or enhancer–promoter (E–P) communication are transcription-factor-centric and underappreciate major findings, including that enhancers are themselves transcribed by RNA polymerase II, which correlates with enhancer activity. In this Perspective, we posit that enhancer transcription and its products, enhancer RNAs, are elementary components of enhancer–gene communication. Specifically, we discuss the possibility that transcription at enhancers and at their cognate genes are linked and that this coupling is at the basis of how enhancers communicate with their targets. This model of transcriptional coupling between enhancers and their target genes is supported by growing experimental evidence and represents a synthesis of recent key discoveries.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143819220","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}

{"title":"NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome","authors":"Connor Arkinson, Ken C. Dong, Christine L. Gee, Shawn M. Costello, Aimee Chi Soe, Greg L. Hura, Susan Marqusee, Andreas Martin","doi":"10.1038/s41594-025-01527-3","DOIUrl":"https://doi.org/10.1038/s41594-025-01527-3","url":null,"abstract":"<p>The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor NUB1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system with human components and revealed that NUB1 uses the intrinsic instability of FAT10 to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin-independent and p97-independent manner. Using hydrogen–deuterium exchange, structural modeling and site-directed mutagenesis, we identified the formation of an intricate complex with FAT10 that activates NUB1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic NUB1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These findings identified a previously unknown mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143819279","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}

{"title":"Transcription stress causes an inflammatory response via release of IL-1α","authors":"Thomas D. J. Walker, Jessica P. Morris, Leonie Unterholzner","doi":"10.1038/s41594-025-01525-5","DOIUrl":"https://doi.org/10.1038/s41594-025-01525-5","url":null,"abstract":"DNA damage can be sensed as a danger signal by the innate immune system. Bournique et al. show that the transcription stress caused by DNA lesions can also initiate inflammation by causing the direct release of cytokine IL-1α, which then drives NF-κB activation in neighboring cells.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143819361","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}

{"title":"Bacterial clippases shift ubiquitin","authors":"Irene Serrano","doi":"10.1038/s41594-025-01545-1","DOIUrl":"https://doi.org/10.1038/s41594-025-01545-1","url":null,"abstract":"<p>Ubiquitination, a crucial post-translational modification in eukaryotic cells, has a pivotal role in the regulation of protein function, by either inducing protein degradation or altering protein activity. This system is subject to stringent regulation and is essential for maintaining cellular homeostasis and immune responses, particularly in identifying and eliminating pathogenic threats. However, intracellular bacteria have evolved sophisticated strategies to subvert the host defense mechanism, including the secretion of deubiquitinase (DUB) effectors that remove ubiquitin marks, thereby interfering with immune signaling and promoting bacterial fitness.</p><p>Hermanns et al. identify a family of bacterial DUBs structurally related to eukaryotic Josephin-type DUBs, which exhibit a unique irreversible deubiquitination mechanism. Conventional deubiquitinases and these ubiquitin C-terminal clippases (UCCs) differ in that the former cleave ubiquitin after the C-terminal diGly motif, whereas the latter cleave before this motif, leaving a residual fragment that marks the substrate as irreversibly deubiquitinated. The researchers performed a detailed structural analysis of the substrate-bound clippases and conventional DUBs to determine the observed cleavage shift, which was found to be attributable to distinct ubiquitin orientations. Structural analysis further revealed that UCCs possess a distinctive catalytic architecture that favors irreversible cleavage over the reversible hydrolysis exhibited by Josephin DUBs. This difference is primarily driven by evolutionary shifts in the catalytic pocket, in which the repositioning of key residues enforces a cleavage mechanism that leaves a residual fragment of ubiquitin attached to the substrate, effectively blocking re-ubiquitination.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"108 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143814053","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}

{"title":"Timing of complex I activity and lifespan control","authors":"Melina Casadio","doi":"10.1038/s41594-025-01541-5","DOIUrl":"https://doi.org/10.1038/s41594-025-01541-5","url":null,"abstract":"<p>The electron transport chain (ETC) is composed of several complexes, including complex I (CI), and is the base of oxidative phosphorylation in mitochondria. CI subunit genes are associated with diseases and CI impairments have been linked to longer and shorter lifespans in model organisms. Stefanatos et al. show that CI dysfunction differentially affects the lifespan of <i>Drosophila</i> depending on the timing of dysfunction.</p><p>The researchers generated inducible CI subunit depletion <i>Drosophila</i> models; CI defects during development shortened lifespan, whereas CI dysfunction in adult flies did not. Flies with impaired CI function from development showed increased sensitivity to stress, such as starvation. RNA-sequencing analyses in flies with perturbed CI activity during development revealed a signature of dysregulated energy metabolism and translation. Metabolomic and proteomic analyses suggested that changes to metabolic pathways in tissues such as the fat body are associated with reduced lifespan in flies with developmental CI disruption.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143814054","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}

{"title":"Accessible technology for diploid high-order 3D human genome analysis","authors":"","doi":"10.1038/s41594-025-01519-3","DOIUrl":"https://doi.org/10.1038/s41594-025-01519-3","url":null,"abstract":"We developed a method that improves the detection of haplotype-assigned chromatin interactions in humans by over tenfold, using far less data than traditional methods. This advance enabled an almost complete diploid 3D genome map, making high-order phased chromatin interaction studies more accessible to researchers.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"118 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143814055","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}

{"title":"Ion-conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic-resolution structures of open and closed states","authors":"Dmitrii Zabelskii, Sergey Bukhdruker, Siarhei Bukhalovich, Fedor Tsybrov, Gerrit H. U. Lamm, Roman Astashkin, Demid Doroginin, Grigory Matveev, Vsevolod Sudarev, Alexander Kuzmin, Egor Zinovev, Anastasiia Vlasova, Yury Ryzhykau, Nikolay Ilyinsky, Ivan Gushchin, Gleb Bourenkov, Alexey Alekseev, Adam Round, Josef Wachtveitl, Ernst Bamberg, Valentin Gordeliy","doi":"10.1038/s41594-025-01488-7","DOIUrl":"https://doi.org/10.1038/s41594-025-01488-7","url":null,"abstract":"<p>Channelrhodopsins (ChRs) have emerged as major optogenetics tools, particularly in neuroscience. Despite their importance, the molecular mechanism of ChR opening remains elusive. Moreover, all reported structures of ChRs correspond to either a closed or an early intermediate state and lack the necessary level of detail owing to the limited resolution. Here we present the structures of the closed and open states of a cation-conducting ChR, OLPVR1, from Organic Lake phycodnavirus, belonging to the family of viral ChRs solved at 1.1- and 1.3-Å resolution at physiologically relevant pH conditions (pH 8.0). OLPVR1 was expressed in <i>Escherichia coli</i> and crystallized using an <i>in meso</i> approach, and the structures were solved by X-ray crystallography. We also present the structure of the OLPVR1 protonated state at acidic pH (pH 2.5) at 1.4-Å resolution. Together, these three structures elucidate the molecular mechanisms of the channel’s opening and permeability in detail. Extensive functional studies support the proposed mechanisms. Channel opening is controlled by isomerization of the retinal cofactor, triggering protonation of proton acceptors and deprotonation of proton donors located in the three gates of the channel. The E51 residue in the core of the central gate (similar to E90 of ChR2 from <i>Chlamydomonas</i> <i>reinhardtii</i>) plays a key role in the opening of the channel. E51 flips out of the gate and towards the proton acceptor D200 (D253 in ChR2 in <i>C.</i> <i>reinhardtii</i>), establishing a hydrogen bond between them. Despite differences in subfamilies of ChRs, they share a common gate–cavity architecture, suggesting that they could have similar general gating mechanisms. These results enabled us to design viral rhodopsin with improved properties for optogenetic applications. The structural data and mechanisms might also be helpful for better understanding other ChRs and their engineering.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"96 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805681","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}

{"title":"Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213","authors":"Katerina Naydenova, Keith B. Boyle, Claudio Pathe, Prathyush Pothukuchi, Ana Crespillo-Casado, Felix Scharte, Pierre-Mehdi Hammoudi, Elsje G. Otten, Neal M. Alto, Felix Randow","doi":"10.1038/s41594-025-01530-8","DOIUrl":"https://doi.org/10.1038/s41594-025-01530-8","url":null,"abstract":"<p>Pathogens have evolved diverse strategies to counteract host immunity. Ubiquitylation of lipopolysaccharide (LPS) on cytosol-invading bacteria by the E3 ligase RNF213 creates ‘eat me’ signals for antibacterial autophagy, but whether and how cytosol-adapted bacteria avoid LPS ubiquitylation remains poorly understood. Here, we show that the enterobacterium <i>Shigella flexneri</i> actively antagonizes LPS ubiquitylation through IpaH1.4, a secreted effector protein with ubiquitin E3 ligase activity. IpaH1.4 binds to RNF213, ubiquitylates it and targets it for proteasomal degradation, thus counteracting host-protective LPS ubiquitylation. To understand how IpaH1.4 recognizes RNF213, we determined the cryogenic electron microscopy structure of the IpaH1.4–RNF213 complex. The specificity of the interaction is achieved through the leucine-rich repeat of IpaH1.4, which binds the RING domain of RNF213 by hijacking the conserved RING interface required for binding to ubiquitin-charged E2 enzymes. IpaH1.4 also targets other E3 ligases involved in inflammation and immunity through binding to the E2-interacting face of their RING domains, including the E3 ligase LUBAC that is required for the synthesis of M1-linked ubiquitin chains on cytosol-invading bacteria downstream of RNF213. We conclude that IpaH1.4 has evolved to antagonize multiple antibacterial and proinflammatory host E3 ligases.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805682","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}

{"title":"Finding and recycling stalled spliceosomes","authors":"Charles C. Query, Jadwiga Meissner, Maria M. Konarska","doi":"10.1038/s41594-025-01536-2","DOIUrl":"https://doi.org/10.1038/s41594-025-01536-2","url":null,"abstract":"Splicing of pre-mRNA requires both high fidelity and enormous sequence flexibility, inevitably resulting in aberrant, stalled complexes that must be discarded. A study now describes cryo-EM structures of stalled complexes poised for disassembly, determining aspects of aberrant complex recognition and splicing quality control.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797801","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}