Pub Date : 2026-01-13DOI: 10.1038/s41594-025-01708-0
Minji Kim, Ping Wang, Patricia A. Clow, Eli Chien, Xiaotao Wang, Jianhao Peng, Haoxi Chai, Xiyuan Liu, Byoungkoo Lee, Chew Yee Ngan, Olgica Milenkovic, Jeffrey H. Chuang, Chia-Lin Wei, Rafael Casellas, Albert W. Cheng, Yijun Ruan
Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely debated. Here we investigated the relationship between cohesin and RNA polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNA polymerase II and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific downregulated genes. By contrast, short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly constitutively expressed. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions in cohesin-depleted cells. Remarkably, RAD21 depletion appeared to upregulate genes that were involved in initiating DNA replication and disrupted DNA replication timing. Our results elucidate the multifaceted roles of cohesin in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes and maintaining timely DNA replication.
{"title":"Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription","authors":"Minji Kim, Ping Wang, Patricia A. Clow, Eli Chien, Xiaotao Wang, Jianhao Peng, Haoxi Chai, Xiyuan Liu, Byoungkoo Lee, Chew Yee Ngan, Olgica Milenkovic, Jeffrey H. Chuang, Chia-Lin Wei, Rafael Casellas, Albert W. Cheng, Yijun Ruan","doi":"10.1038/s41594-025-01708-0","DOIUrl":"https://doi.org/10.1038/s41594-025-01708-0","url":null,"abstract":"Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely debated. Here we investigated the relationship between cohesin and RNA polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNA polymerase II and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific downregulated genes. By contrast, short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly constitutively expressed. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions in cohesin-depleted cells. Remarkably, RAD21 depletion appeared to upregulate genes that were involved in initiating DNA replication and disrupted DNA replication timing. Our results elucidate the multifaceted roles of cohesin in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes and maintaining timely DNA replication.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145956332","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}
Pub Date : 2026-01-08DOI: 10.1038/s41594-025-01736-w
Bin Chen, Guangchao Sun, Jake A. Kloeber, Huaping Xiao, Yaobin Ouyang, Fei Zhao, Ya Li, Shilin Xu, Sonja Dragojevic, Zheming Wu, Shouhai Zhu, Yiqun Han, Ping Yin, Xinyi Tu, Hongran Qin, Xiang Zhou, Kuntian Luo, Kevin L. Peterson, Jinzhou Huang, Taro Hitosugi, Haiming Dai, Min Deng, Robert W. Mutter, Zhenkun Lou
Okazaki fragment maturation requires efficient removal of RNA primers to form a continuous lagging strand, yet how mismatched primers introduced by error-prone primase are corrected remains unresolved. Here, we show that physiological levels of reactive oxygen species (ROS) initiate a redox-dependent mechanism that drives ADAR1-mediated adenosine-to-inosine (A-to-I) editing. Oxidation triggers ADAR1 dimerization at replication forks, enhancing RNA editing of mismatched primers—particularly those caused by ATP misincorporation on d(T+C)-rich centromeric DNA. This A-to-I editing step facilitates more efficient RNA primer degradation by RNase H2, thereby ensuring proper Okazaki fragment maturation. Disruption of ADAR1 oxidation results in increased unligated Okazaki fragments, single-stranded gaps and double-strand breaks, most prominently at centromeres. These findings reveal a role for ROS in safeguarding lagging-strand synthesis by coupling ADAR1 oxidation-induced A-to-I RNA editing to replication fork stability.
Okazaki片段成熟需要有效地去除RNA引物以形成连续的滞后链，但如何纠正易出错引物引入的不匹配引物仍未解决。在这里，我们表明生理水平的活性氧（ROS）启动氧化还原依赖机制，驱动adar1介导的腺苷到肌苷（a -to-i）编辑。氧化触发复制叉上的ADAR1二聚化，增强错配引物的RNA编辑，特别是那些由富含d（T+C）的着丝粒DNA上ATP错误结合引起的引物。这一A-to-I编辑步骤有助于RNase H2更有效地降解RNA引物，从而确保适当的Okazaki片段成熟。ADAR1氧化的破坏导致未结扎的冈崎片段，单链间隙和双链断裂增加，最显著的是在着丝粒处。这些发现揭示了ROS通过将ADAR1氧化诱导的a -to- i RNA编辑与复制叉稳定性耦合，在保护滞后链合成方面的作用。
{"title":"Redox-driven ADAR1 activation promotes Okazaki fragment maturation and DNA replication integrity","authors":"Bin Chen, Guangchao Sun, Jake A. Kloeber, Huaping Xiao, Yaobin Ouyang, Fei Zhao, Ya Li, Shilin Xu, Sonja Dragojevic, Zheming Wu, Shouhai Zhu, Yiqun Han, Ping Yin, Xinyi Tu, Hongran Qin, Xiang Zhou, Kuntian Luo, Kevin L. Peterson, Jinzhou Huang, Taro Hitosugi, Haiming Dai, Min Deng, Robert W. Mutter, Zhenkun Lou","doi":"10.1038/s41594-025-01736-w","DOIUrl":"https://doi.org/10.1038/s41594-025-01736-w","url":null,"abstract":"Okazaki fragment maturation requires efficient removal of RNA primers to form a continuous lagging strand, yet how mismatched primers introduced by error-prone primase are corrected remains unresolved. Here, we show that physiological levels of reactive oxygen species (ROS) initiate a redox-dependent mechanism that drives ADAR1-mediated adenosine-to-inosine (A-to-I) editing. Oxidation triggers ADAR1 dimerization at replication forks, enhancing RNA editing of mismatched primers—particularly those caused by ATP misincorporation on d(T+C)-rich centromeric DNA. This A-to-I editing step facilitates more efficient RNA primer degradation by RNase H2, thereby ensuring proper Okazaki fragment maturation. Disruption of ADAR1 oxidation results in increased unligated Okazaki fragments, single-stranded gaps and double-strand breaks, most prominently at centromeres. These findings reveal a role for ROS in safeguarding lagging-strand synthesis by coupling ADAR1 oxidation-induced A-to-I RNA editing to replication fork stability.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145919892","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}
Pub Date : 2026-01-05DOI: 10.1038/s41594-025-01731-1
Kami Ahmad, Matt Wooten, Brittany N. Takushi, Velinda Vidaurre, Xin Chen, Steven Henikoff
In all eukaryotes, DNA replication is coupled to histone synthesis to coordinate chromatin packaging of the genome. Canonical histone genes coalesce in the nucleus into the histone locus body (HLB), where gene transcription and 3′ mRNA processing occurs. Both histone gene transcription and mRNA stability are reduced when DNA replication is inhibited, implying that the HLB senses the rate of DNA synthesis. In Drosophilamelanogaster , the S-phase-induced histone genes are tandemly repeated in an ~100 copy array, whereas, in humans, these histone genes are scattered. In both organisms, these genes coalesce into HLBs. Here, we use a transgenic histone gene reporter and RNA interference in Drosophila to identify canonical H4 histone as a unique repressor of histone synthesis during the G2 phase in germline cells. Using cytology and CUT&Tag chromatin profiling, we find that histone H4 uniquely occupies histone gene promoters in both Drosophila and human cells. Our results suggest that repression of histone genes by soluble histone H4 is a conserved mechanism that coordinates DNA replication with histone synthesis in proliferating cells.
{"title":"Cell-cycle-dependent repression of histone gene transcription by histone H4","authors":"Kami Ahmad, Matt Wooten, Brittany N. Takushi, Velinda Vidaurre, Xin Chen, Steven Henikoff","doi":"10.1038/s41594-025-01731-1","DOIUrl":"https://doi.org/10.1038/s41594-025-01731-1","url":null,"abstract":"In all eukaryotes, DNA replication is coupled to histone synthesis to coordinate chromatin packaging of the genome. Canonical histone genes coalesce in the nucleus into the histone locus body (HLB), where gene transcription and 3′ mRNA processing occurs. Both histone gene transcription and mRNA stability are reduced when DNA replication is inhibited, implying that the HLB senses the rate of DNA synthesis. In <jats:italic>Drosophila</jats:italic> <jats:italic>melanogaster</jats:italic> , the S-phase-induced histone genes are tandemly repeated in an ~100 copy array, whereas, in humans, these histone genes are scattered. In both organisms, these genes coalesce into HLBs. Here, we use a transgenic histone gene reporter and RNA interference in <jats:italic>Drosophila</jats:italic> to identify canonical H4 histone as a unique repressor of histone synthesis during the G2 phase in germline cells. Using cytology and CUT&Tag chromatin profiling, we find that histone H4 uniquely occupies histone gene promoters in both <jats:italic>Drosophila</jats:italic> and human cells. Our results suggest that repression of histone genes by soluble histone H4 is a conserved mechanism that coordinates DNA replication with histone synthesis in proliferating cells.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145902691","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}
Pub Date : 2025-12-15DOI: 10.1038/s41594-025-01718-y
Alexandra G. Chivu, Brent A. Basso, Abderhman Abuhashem, Michelle M. Leger, Gilad Barshad, Edward J. Rice, Albert C. Vill, Wilfred Wong, Shao-Pei Chou, Gopal Chovatiya, Rebecca Brady, Jeramiah J. Smith, Athula H. Wikramanayake, César Arenas-Mena, Ilana L. Brito, Iñaki Ruiz-Trillo, Anna-Katerina Hadjantonakis, John T. Lis, James J. Lewis, Charles G. Danko
Promoter-proximal pausing of RNA polymerase (Pol) II is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here, we analyzed transcription in species across the tree of life. Unicellular eukaryotes display an accumulation of Pol II near transcription start sites, which we propose transitioned to the longer-lived, focused pause observed in metazoans. This transition coincided with the evolution of new subunits in the negative elongation factor (NELF) and 7SK complexes. Depletion of NELF in mammals shifted the promoter-proximal buildup of Pol II from the pause site into the early gene body and compromised transcriptional activation for a set of heat-shock genes. Our work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.
{"title":"Evolution of promoter-proximal pausing enabled a new layer of transcription control","authors":"Alexandra G. Chivu, Brent A. Basso, Abderhman Abuhashem, Michelle M. Leger, Gilad Barshad, Edward J. Rice, Albert C. Vill, Wilfred Wong, Shao-Pei Chou, Gopal Chovatiya, Rebecca Brady, Jeramiah J. Smith, Athula H. Wikramanayake, César Arenas-Mena, Ilana L. Brito, Iñaki Ruiz-Trillo, Anna-Katerina Hadjantonakis, John T. Lis, James J. Lewis, Charles G. Danko","doi":"10.1038/s41594-025-01718-y","DOIUrl":"https://doi.org/10.1038/s41594-025-01718-y","url":null,"abstract":"Promoter-proximal pausing of RNA polymerase (Pol) II is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here, we analyzed transcription in species across the tree of life. Unicellular eukaryotes display an accumulation of Pol II near transcription start sites, which we propose transitioned to the longer-lived, focused pause observed in metazoans. This transition coincided with the evolution of new subunits in the negative elongation factor (NELF) and 7SK complexes. Depletion of NELF in mammals shifted the promoter-proximal buildup of Pol II from the pause site into the early gene body and compromised transcriptional activation for a set of heat-shock genes. Our work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145759744","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}
Pub Date : 2025-12-09DOI: 10.1038/s41594-025-01728-w
Jianwei Zeng, Yong Fu, Pengge Qian, Wei Huang, Qingwei Niu, Wandy L. Beatty, Alan Brown, L. David Sibley, Rui Zhang
Apicomplexan parasites, responsible for toxoplasmosis, cryptosporidiosis and malaria, invade host cells through a unique gliding motility mechanism powered by actomyosin motors and a dynamic organelle called the conoid. Here, using cryo-electron microscopy, we determined structures of four essential complexes of the Toxoplasma gondii conoid: the preconoidal P2 ring, tubulin-based conoid fibers, and the subpellicular and intraconoidal microtubules. Our analysis identified 40 distinct conoid proteins, several of which are essential for parasite lytic growth, as revealed through genetic disruption studies. Comparative analysis of the tubulin-containing complexes sheds light on their functional specialization by microtubule-associated proteins, while the structure of the preconoidal ring pinpoints the site of actin polymerization and initial translocation, enhancing our mechanistic understanding of gliding motility and, therefore, parasite invasion.
{"title":"Atomic models of the Toxoplasma cell invasion machinery","authors":"Jianwei Zeng, Yong Fu, Pengge Qian, Wei Huang, Qingwei Niu, Wandy L. Beatty, Alan Brown, L. David Sibley, Rui Zhang","doi":"10.1038/s41594-025-01728-w","DOIUrl":"https://doi.org/10.1038/s41594-025-01728-w","url":null,"abstract":"Apicomplexan parasites, responsible for toxoplasmosis, cryptosporidiosis and malaria, invade host cells through a unique gliding motility mechanism powered by actomyosin motors and a dynamic organelle called the conoid. Here, using cryo-electron microscopy, we determined structures of four essential complexes of the Toxoplasma gondii conoid: the preconoidal P2 ring, tubulin-based conoid fibers, and the subpellicular and intraconoidal microtubules. Our analysis identified 40 distinct conoid proteins, several of which are essential for parasite lytic growth, as revealed through genetic disruption studies. Comparative analysis of the tubulin-containing complexes sheds light on their functional specialization by microtubule-associated proteins, while the structure of the preconoidal ring pinpoints the site of actin polymerization and initial translocation, enhancing our mechanistic understanding of gliding motility and, therefore, parasite invasion.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145705135","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}
Pub Date : 2025-12-08DOI: 10.1038/s41594-025-01723-1
Tao Li,Ji Chen,Hao Li,Hong Cao,Sheng-You Huang
Cryo-electron microscopy (cryo-EM) has become the mainstream technique for macromolecular structure determination. However, because of intrinsic resolution heterogeneity, accurate modeling of all-atom structure from cryo-EM maps remains challenging even for maps at near-atomic resolution. Addressing the challenge, we present EMProt, a fully automated method for accurate protein structure determination from cryo-EM maps by efficiently integrating map information and structure prediction with a three-track attention network. EMProt is extensively evaluated on a diverse test set of 177 experimental cryo-EM maps with up to 54 chains in a case at <4-Å resolution, and compared to state-of-the-art methods including DeepMainmast, ModelAngelo, phenix.dock_and_rebuild and AlphaFold3. It is shown that EMProt greatly outperforms the existing methods in recovering the protein structure and building the complete structure. In addition, the built models by EMrot exhibit a high accuracy in model-to-map fit and structure validations.
{"title":"EMProt improves structure determination from cryo-EM maps.","authors":"Tao Li,Ji Chen,Hao Li,Hong Cao,Sheng-You Huang","doi":"10.1038/s41594-025-01723-1","DOIUrl":"https://doi.org/10.1038/s41594-025-01723-1","url":null,"abstract":"Cryo-electron microscopy (cryo-EM) has become the mainstream technique for macromolecular structure determination. However, because of intrinsic resolution heterogeneity, accurate modeling of all-atom structure from cryo-EM maps remains challenging even for maps at near-atomic resolution. Addressing the challenge, we present EMProt, a fully automated method for accurate protein structure determination from cryo-EM maps by efficiently integrating map information and structure prediction with a three-track attention network. EMProt is extensively evaluated on a diverse test set of 177 experimental cryo-EM maps with up to 54 chains in a case at <4-Å resolution, and compared to state-of-the-art methods including DeepMainmast, ModelAngelo, phenix.dock_and_rebuild and AlphaFold3. It is shown that EMProt greatly outperforms the existing methods in recovering the protein structure and building the complete structure. In addition, the built models by EMrot exhibit a high accuracy in model-to-map fit and structure validations.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145704660","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}
Pub Date : 2025-12-05DOI: 10.1038/s41594-025-01717-z
Carlos Riechmann, Cara J. Ellison, Jake W. Anderson, Kay Hofmann, Peter Sarkies, Paul R. Elliott
In mammals, ubiquitylation is orchestrated by the canonical ubiquitin-activating E1 enzyme UBA1 and the orthogonal E1 UBA6. Growing evidence underscores the essentiality of both E1s, which differentiate between 29 active ubiquitin-conjugating enzymes (E2s). The mechanisms governing this distinction have remained unclear. Here we establish a framework for ubiquitin E1–E2 specificity. Focusing on UBA6-controlled ubiquitylation cascades, we reveal that BIRC6, a UBA6-exclusive E2, gains priority over all other UBA6-competent E2s, underpinning the functional importance of defined UBA6–BIRC6 ubiquitylation events in regulating cell death, embryogenesis and autophagy. By capturing BIRC6 receiving ubiquitin from UBA6 in different states, we observe BIRC6 engaging with the UBA6 ubiquitin fold domain, driving an exceptionally high-affinity interaction that is modulated by the UBA6 Cys-Cap loop. Using this interaction as a template, we demonstrate how to confer activity between E2s and their noncognate E1, providing a tool to delineate E1–E2-dependent pathways. Lastly, we explain how BIRC6 priority does not lead to inhibition of UBA6, through a bespoke thioester switch mechanism that disengages BIRC6 upon receiving ubiquitin. Our findings propose a concept of hierarchy of E2 activity with cognate E1s, which may explain how ubiquitin E1s can each function with over a dozen E2s and orchestrate E2-specific cellular functions.
{"title":"UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6","authors":"Carlos Riechmann, Cara J. Ellison, Jake W. Anderson, Kay Hofmann, Peter Sarkies, Paul R. Elliott","doi":"10.1038/s41594-025-01717-z","DOIUrl":"https://doi.org/10.1038/s41594-025-01717-z","url":null,"abstract":"In mammals, ubiquitylation is orchestrated by the canonical ubiquitin-activating E1 enzyme UBA1 and the orthogonal E1 UBA6. Growing evidence underscores the essentiality of both E1s, which differentiate between 29 active ubiquitin-conjugating enzymes (E2s). The mechanisms governing this distinction have remained unclear. Here we establish a framework for ubiquitin E1–E2 specificity. Focusing on UBA6-controlled ubiquitylation cascades, we reveal that BIRC6, a UBA6-exclusive E2, gains priority over all other UBA6-competent E2s, underpinning the functional importance of defined UBA6–BIRC6 ubiquitylation events in regulating cell death, embryogenesis and autophagy. By capturing BIRC6 receiving ubiquitin from UBA6 in different states, we observe BIRC6 engaging with the UBA6 ubiquitin fold domain, driving an exceptionally high-affinity interaction that is modulated by the UBA6 Cys-Cap loop. Using this interaction as a template, we demonstrate how to confer activity between E2s and their noncognate E1, providing a tool to delineate E1–E2-dependent pathways. Lastly, we explain how BIRC6 priority does not lead to inhibition of UBA6, through a bespoke thioester switch mechanism that disengages BIRC6 upon receiving ubiquitin. Our findings propose a concept of hierarchy of E2 activity with cognate E1s, which may explain how ubiquitin E1s can each function with over a dozen E2s and orchestrate E2-specific cellular functions.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"127 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145680235","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}
Pub Date : 2025-12-03DOI: 10.1038/s41594-025-01726-y
Joseph B. Bridgers, Andreas Carlström, Dawafuti Sherpa, Mary T. Couvillion, Urška Rovšnik, Jingjing Gao, Bowen Wan, Sichen Shao, Martin Ott, L. Stirling Churchman
Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In Saccharomycescerevisiae , nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats using selective mitoribosome profiling and cryo-electron microscopy (cryo-EM) structural analysis. These analyses show that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA–mitoribosome footprints indicate that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA–TA complexes bound to mitoribosomes stalled in the post-initiation, pre-elongation state revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5′ untranslated region of the client mRNA and the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons.
{"title":"Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation","authors":"Joseph B. Bridgers, Andreas Carlström, Dawafuti Sherpa, Mary T. Couvillion, Urška Rovšnik, Jingjing Gao, Bowen Wan, Sichen Shao, Martin Ott, L. Stirling Churchman","doi":"10.1038/s41594-025-01726-y","DOIUrl":"https://doi.org/10.1038/s41594-025-01726-y","url":null,"abstract":"Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In <jats:italic>Saccharomyces</jats:italic> <jats:italic>cerevisiae</jats:italic> , nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats using selective mitoribosome profiling and cryo-electron microscopy (cryo-EM) structural analysis. These analyses show that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA–mitoribosome footprints indicate that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA–TA complexes bound to mitoribosomes stalled in the post-initiation, pre-elongation state revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5′ untranslated region of the client mRNA and the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145664480","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}
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