Pub Date : 2025-08-28DOI: 10.1038/s41594-025-01662-x
Yuqi Yang, Shanshan Wang, Guopeng Wang, Yuke Lian, Lingfeng Xue, Wenhong Jiang, Qiang Guo, Chen Song, Long Li
The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, respectively. However, the mechanisms of protein recognition and sorting in the TOM–TIM23 pathway remain unclear. Here we report cryo-electron microscopy structures of a translocating polypeptide substrate captured in the active TOM–TIM23 supercomplex from Saccharomyces cerevisiae. In the TOM complex, the polypeptide substrate adopts multiple conformations stabilized by hydrophilic residues from distinct regions of the Tom40 channel. In the TIM23 complex, the Tim17 and Mgr2 subunits create the translocation pathway, with a central restriction formed by four highly conserved hydrophobic residues. The substrate primarily interacts with hydrophobic residues along the Tim17–Mgr2 pathway. Substrate hydrophobicity modulates the association of Mgr2 with Tim17, enabling dynamic regulation of protein sorting toward either the matrix or membrane. These findings reveal a sophisticated translocation mechanism of the TOM–TIM23 supercomplex that ensures the efficient import of diverse mitochondrial proteins. Yang et al. uncover the molecular details of how mitochondrial proteins cross the outer and inner mitochondrial membranes, with hydrophobicity guiding them into distinct pathways toward specific destinations.
{"title":"Dynamic TOM–TIM23 supercomplex directs mitochondrial protein translocation and sorting","authors":"Yuqi Yang, Shanshan Wang, Guopeng Wang, Yuke Lian, Lingfeng Xue, Wenhong Jiang, Qiang Guo, Chen Song, Long Li","doi":"10.1038/s41594-025-01662-x","DOIUrl":"10.1038/s41594-025-01662-x","url":null,"abstract":"The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, respectively. However, the mechanisms of protein recognition and sorting in the TOM–TIM23 pathway remain unclear. Here we report cryo-electron microscopy structures of a translocating polypeptide substrate captured in the active TOM–TIM23 supercomplex from Saccharomyces cerevisiae. In the TOM complex, the polypeptide substrate adopts multiple conformations stabilized by hydrophilic residues from distinct regions of the Tom40 channel. In the TIM23 complex, the Tim17 and Mgr2 subunits create the translocation pathway, with a central restriction formed by four highly conserved hydrophobic residues. The substrate primarily interacts with hydrophobic residues along the Tim17–Mgr2 pathway. Substrate hydrophobicity modulates the association of Mgr2 with Tim17, enabling dynamic regulation of protein sorting toward either the matrix or membrane. These findings reveal a sophisticated translocation mechanism of the TOM–TIM23 supercomplex that ensures the efficient import of diverse mitochondrial proteins. Yang et al. uncover the molecular details of how mitochondrial proteins cross the outer and inner mitochondrial membranes, with hydrophobicity guiding them into distinct pathways toward specific destinations.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 11","pages":"2231-2241"},"PeriodicalIF":10.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144910708","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}
Pub Date : 2025-08-27DOI: 10.1038/s41594-025-01660-z
Melanie Arndt, Angela Schweri, Raimund Dutzler
Membrane contact sites are hubs for interorganellar lipid transport within eukaryotic cells. As a principal tether bridging the endoplasmic reticulum (ER) and the plasma membrane in Saccharomyces cerevisiae, the protein IST2 has a major role during lipid transport between both compartments. Here, we show a comprehensive investigation elucidating the structural and mechanistic properties of IST2 and its interaction with the soluble lipid transfer protein OSH6. The ER-embedded transmembrane domain of IST2 is homologous to the TMEM16 family and acts as a constitutively active lipid scramblase. The extended C terminus binds to the plasma membrane and the phosphatidylserine–phosphatidylinositol 4-phosphate exchanger OSH6. Through cellular growth assays and biochemical and structural studies, we characterized the interaction between both proteins and show that OSH6 remains associated with IST2 during lipid shuttling between membranes. These results highlight the role of the IST2–OSH6 complex in lipid trafficking and offer initial insights into the relevance of scramblases for carrier-like lipid transport mechanisms. IST2 serves as a tether between the endoplasmic reticulum and the plasma membrane in yeast. Here, Arndt et al. interrogate its interaction with OSH6, revealing that the two proteins remain associated during lipid shuttling.
{"title":"Structural basis for lipid transport at membrane contact sites by the IST2–OSH6 complex","authors":"Melanie Arndt, Angela Schweri, Raimund Dutzler","doi":"10.1038/s41594-025-01660-z","DOIUrl":"10.1038/s41594-025-01660-z","url":null,"abstract":"Membrane contact sites are hubs for interorganellar lipid transport within eukaryotic cells. As a principal tether bridging the endoplasmic reticulum (ER) and the plasma membrane in Saccharomyces cerevisiae, the protein IST2 has a major role during lipid transport between both compartments. Here, we show a comprehensive investigation elucidating the structural and mechanistic properties of IST2 and its interaction with the soluble lipid transfer protein OSH6. The ER-embedded transmembrane domain of IST2 is homologous to the TMEM16 family and acts as a constitutively active lipid scramblase. The extended C terminus binds to the plasma membrane and the phosphatidylserine–phosphatidylinositol 4-phosphate exchanger OSH6. Through cellular growth assays and biochemical and structural studies, we characterized the interaction between both proteins and show that OSH6 remains associated with IST2 during lipid shuttling between membranes. These results highlight the role of the IST2–OSH6 complex in lipid trafficking and offer initial insights into the relevance of scramblases for carrier-like lipid transport mechanisms. IST2 serves as a tether between the endoplasmic reticulum and the plasma membrane in yeast. Here, Arndt et al. interrogate its interaction with OSH6, revealing that the two proteins remain associated during lipid shuttling.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 11","pages":"2219-2230"},"PeriodicalIF":10.1,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01660-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144905916","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}
Pub Date : 2025-08-27DOI: 10.1038/s41594-025-01675-6
Dermot Harnett, Mateusz C. Ambrozkiewicz, Ulrike Zinnall, Alexandra Rusanova, Ekaterina Borisova, Amelie N. Drescher, Marta Couce-Iglesias, Gabriel Villamil, Rike Dannenberg, Koshi Imami, Agnieszka Münster-Wandowski, Beatrix Fauler, Thorsten Mielke, Matthias Selbach, Markus Landthaler, Christian M. T. Spahn, Victor Tarabykin, Uwe Ohler, Matthew L. Kraushar
{"title":"Author Correction: A critical period of translational control during brain development at codon resolution","authors":"Dermot Harnett, Mateusz C. Ambrozkiewicz, Ulrike Zinnall, Alexandra Rusanova, Ekaterina Borisova, Amelie N. Drescher, Marta Couce-Iglesias, Gabriel Villamil, Rike Dannenberg, Koshi Imami, Agnieszka Münster-Wandowski, Beatrix Fauler, Thorsten Mielke, Matthias Selbach, Markus Landthaler, Christian M. T. Spahn, Victor Tarabykin, Uwe Ohler, Matthew L. Kraushar","doi":"10.1038/s41594-025-01675-6","DOIUrl":"10.1038/s41594-025-01675-6","url":null,"abstract":"","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 9","pages":"1838-1838"},"PeriodicalIF":10.1,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12440796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961726","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}
Pub Date : 2025-08-25DOI: 10.1038/s41594-025-01647-w
Masahiro Nagano, Bo Hu, Kosuke Ogata, Fumiya Umemura, Yukiko Ishikura, Shinnosuke Suzuki, Christos C. Katsifis, Masanori Yoshinaga, Gabriele Litos, Kota Nagasaka, Wen Tang, Yoshiaki Nosaka, Hiromichi Sasada, Hanbo Wang, Daichi Kondo, Yoshitaka Katou, Ken Mizuta, Yukihiro Yabuta, Hiroshi Ohta, Francisca Nathalia de Luna Vitorino, Hiroshi Arima, Takafumi Ichikawa, Michele Gabriele, Jacek Majewski, Benjamin A. Garcia, Osamu Takeuchi, Shosei Yoshida, Anders S. Hansen, Jan-Michael Peters, Yasushi Ishihama, Mitinori Saitou
Germ cells are unique in that they tailor chromatin toward generating totipotency. Accordingly, mammalian spermatogonia, including spermatogonial stem cells that constitute the source for male gametes, acquire distinctive chromatin organization with weak insulation, but the underlying mechanism remains unknown. Here we show that STAG3, so far known to exclusively form meiotic cohesins, generates a mitotic cohesin for male germline nucleome programming in mice. Owing to its shorter chromatin residence, STAG3–cohesin attenuates topologically associating domains, rewires enhancer–promoter and Polycomb-mediated repressive interactions, and facilitates finer and more strengthened compartments, establishing a distinctive spermatogonial nucleome. Moreover, in the absence of STAG3–cohesin, spermatogonial stem cells show an impaired differentiation priming for spermatogenesis. Mitotic STAG3–cohesin is also expressed in human B cells and their malignant variations, promoting their propagation. Our findings on mitotic STAG3–cohesin elucidate a principle of male germline nucleome programming, demonstrate an unexpected mitotic role for STAG3 and might potentially improve understanding of human malignancies. Nagano et al. identify the third mitotic cohesin complex, STAG3–cohesin, which, with its unique biophysical properties, weakens insulation and rewires regulatory interactions of spermatogonial stem cells, shaping the male germline nucleome.
{"title":"The mitotic STAG3–cohesin complex shapes male germline nucleome","authors":"Masahiro Nagano, Bo Hu, Kosuke Ogata, Fumiya Umemura, Yukiko Ishikura, Shinnosuke Suzuki, Christos C. Katsifis, Masanori Yoshinaga, Gabriele Litos, Kota Nagasaka, Wen Tang, Yoshiaki Nosaka, Hiromichi Sasada, Hanbo Wang, Daichi Kondo, Yoshitaka Katou, Ken Mizuta, Yukihiro Yabuta, Hiroshi Ohta, Francisca Nathalia de Luna Vitorino, Hiroshi Arima, Takafumi Ichikawa, Michele Gabriele, Jacek Majewski, Benjamin A. Garcia, Osamu Takeuchi, Shosei Yoshida, Anders S. Hansen, Jan-Michael Peters, Yasushi Ishihama, Mitinori Saitou","doi":"10.1038/s41594-025-01647-w","DOIUrl":"10.1038/s41594-025-01647-w","url":null,"abstract":"Germ cells are unique in that they tailor chromatin toward generating totipotency. Accordingly, mammalian spermatogonia, including spermatogonial stem cells that constitute the source for male gametes, acquire distinctive chromatin organization with weak insulation, but the underlying mechanism remains unknown. Here we show that STAG3, so far known to exclusively form meiotic cohesins, generates a mitotic cohesin for male germline nucleome programming in mice. Owing to its shorter chromatin residence, STAG3–cohesin attenuates topologically associating domains, rewires enhancer–promoter and Polycomb-mediated repressive interactions, and facilitates finer and more strengthened compartments, establishing a distinctive spermatogonial nucleome. Moreover, in the absence of STAG3–cohesin, spermatogonial stem cells show an impaired differentiation priming for spermatogenesis. Mitotic STAG3–cohesin is also expressed in human B cells and their malignant variations, promoting their propagation. Our findings on mitotic STAG3–cohesin elucidate a principle of male germline nucleome programming, demonstrate an unexpected mitotic role for STAG3 and might potentially improve understanding of human malignancies. Nagano et al. identify the third mitotic cohesin complex, STAG3–cohesin, which, with its unique biophysical properties, weakens insulation and rewires regulatory interactions of spermatogonial stem cells, shaping the male germline nucleome.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 11","pages":"2203-2218"},"PeriodicalIF":10.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900404","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}
Pub Date : 2025-08-25DOI: 10.1038/s41594-025-01607-4
M. Broc, M. V. Cherrier, A. Uzel, R. Arias-Cartin, P. Arnoux, G. Brasseur, F. Seduk, B. Guigliarelli, P. Legrand, F. Pierrel, G. Schoehn, M. J. Maté, L. Martin, S. Grimaldi, Y. Nicolet, A. Magalon, A. Walburger
Redox processes are at the heart of energetic metabolism that drives life on earth. By extension, complex and efficient electron transfer wires are necessary to connect the various metabolic pathways that are often located in distinct cellular compartments. Here, we uncovered a structural module that enables channeling of quinones from the membrane to various water-soluble redox catalytic units in prokaryotes. Using X-ray crystallography and cryo-electron microscopy, we determined the structure of the unusual bacterial formate dehydrogenase ForCE that contains four ForC catalytic subunits docked around a membrane-associated tetrameric ForE central scaffold. In the latter, a conserved domain that we propose to name helical membrane plugin (HMP) was identified as essential to link formate oxidation, in Bacillus subtilis, to the aerobic respiratory chain. Our bioinformatic analysis indicates that this HMP is associated with different quinone-reducing oxidoreductases, highlighting its broad importance as a functional unit to wire electrons between a given catalytic redox center and the quinone pool. Here, the authors describe a tubular module connecting oxidoreductases to the membrane. This system, found in many microorganisms, reveals a distinct mode of membrane anchoring and an electron transfer mechanism involved in energy conservation.
{"title":"A scaffold for quinone channeling between membrane and soluble bacterial oxidoreductases","authors":"M. Broc, M. V. Cherrier, A. Uzel, R. Arias-Cartin, P. Arnoux, G. Brasseur, F. Seduk, B. Guigliarelli, P. Legrand, F. Pierrel, G. Schoehn, M. J. Maté, L. Martin, S. Grimaldi, Y. Nicolet, A. Magalon, A. Walburger","doi":"10.1038/s41594-025-01607-4","DOIUrl":"10.1038/s41594-025-01607-4","url":null,"abstract":"Redox processes are at the heart of energetic metabolism that drives life on earth. By extension, complex and efficient electron transfer wires are necessary to connect the various metabolic pathways that are often located in distinct cellular compartments. Here, we uncovered a structural module that enables channeling of quinones from the membrane to various water-soluble redox catalytic units in prokaryotes. Using X-ray crystallography and cryo-electron microscopy, we determined the structure of the unusual bacterial formate dehydrogenase ForCE that contains four ForC catalytic subunits docked around a membrane-associated tetrameric ForE central scaffold. In the latter, a conserved domain that we propose to name helical membrane plugin (HMP) was identified as essential to link formate oxidation, in Bacillus subtilis, to the aerobic respiratory chain. Our bioinformatic analysis indicates that this HMP is associated with different quinone-reducing oxidoreductases, highlighting its broad importance as a functional unit to wire electrons between a given catalytic redox center and the quinone pool. Here, the authors describe a tubular module connecting oxidoreductases to the membrane. This system, found in many microorganisms, reveals a distinct mode of membrane anchoring and an electron transfer mechanism involved in energy conservation.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 11","pages":"2196-2202"},"PeriodicalIF":10.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900405","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}
Pub Date : 2025-08-25DOI: 10.1038/s41594-025-01633-2
Luca Mariani, Xiao Liu, Kwangwoon Lee, Stephen S. Gisselbrecht, Philip A. Cole, Martha L. Bulyk
Cell fates are controlled by ‘pioneers’, sequence-specific transcription factors (TFs) that bind recognition motifs on nucleosomes (‘pioneer binding’). Pioneers occupy a minority of their recognition sequences in the genome, suggesting that the sequence context regulates their binding. Here we developed PIONEAR–seq, a high-throughput biochemical assay to characterize pioneer binding. We used PIONEAR–seq to assay 11 human TFs for binding to nucleosomes based on Widom 601 versus genomic sequences. We found that pioneer binding, while mediated primarily by the recognition motifs of TFs, is regulated by the broader nucleosome sequence context. Certain TFs, found to be dyad or periodic binders on nucleosomes assembled on synthetic sequences, exhibited end binding to nucleosomes based on genomic sequences. We propose a model where the local bendability of the DNA sequence in nucleosomes is involved in positioning pioneer binding, and thus represents another cis-regulatory layer in eukaryotic genomes. The authors present PIONEAR–seq technology to assay in vitro binding of pioneer transcription factors to nucleosomes. The PIONEAR–seq data reveal that a nucleosome’s broader sequence context regulates the interactions of pioneer transcription factors via DNA bendability.
{"title":"DNA bendability regulates transcription factor binding to nucleosomes","authors":"Luca Mariani, Xiao Liu, Kwangwoon Lee, Stephen S. Gisselbrecht, Philip A. Cole, Martha L. Bulyk","doi":"10.1038/s41594-025-01633-2","DOIUrl":"10.1038/s41594-025-01633-2","url":null,"abstract":"Cell fates are controlled by ‘pioneers’, sequence-specific transcription factors (TFs) that bind recognition motifs on nucleosomes (‘pioneer binding’). Pioneers occupy a minority of their recognition sequences in the genome, suggesting that the sequence context regulates their binding. Here we developed PIONEAR–seq, a high-throughput biochemical assay to characterize pioneer binding. We used PIONEAR–seq to assay 11 human TFs for binding to nucleosomes based on Widom 601 versus genomic sequences. We found that pioneer binding, while mediated primarily by the recognition motifs of TFs, is regulated by the broader nucleosome sequence context. Certain TFs, found to be dyad or periodic binders on nucleosomes assembled on synthetic sequences, exhibited end binding to nucleosomes based on genomic sequences. We propose a model where the local bendability of the DNA sequence in nucleosomes is involved in positioning pioneer binding, and thus represents another cis-regulatory layer in eukaryotic genomes. The authors present PIONEAR–seq technology to assay in vitro binding of pioneer transcription factors to nucleosomes. The PIONEAR–seq data reveal that a nucleosome’s broader sequence context regulates the interactions of pioneer transcription factors via DNA bendability.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 11","pages":"2185-2195"},"PeriodicalIF":10.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900574","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}
Pub Date : 2025-08-25DOI: 10.1038/s41594-025-01625-2
Samuel P. Berry, Rachelle Gaudet
Protein sequence signatures suggest that eons ago, a bacterial glutamate transporter lost its sodium coupling to make way for a shift to proton coupling. A study now maps this ancient transition in biochemical and structural detail to better understand how secondary transporters control their energetics.
{"title":"A structural window into the evolution of secondary transport mechanisms","authors":"Samuel P. Berry, Rachelle Gaudet","doi":"10.1038/s41594-025-01625-2","DOIUrl":"10.1038/s41594-025-01625-2","url":null,"abstract":"Protein sequence signatures suggest that eons ago, a bacterial glutamate transporter lost its sodium coupling to make way for a shift to proton coupling. A study now maps this ancient transition in biochemical and structural detail to better understand how secondary transporters control their energetics.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 12","pages":"2377-2379"},"PeriodicalIF":10.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900402","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}
Pub Date : 2025-08-25DOI: 10.1038/s41594-025-01652-z
Krishna D. Reddy, Burha Rasool, Farideh Badichi Akher, Nemanja Kutlešić, Swati Pant, Olga Boudker
Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to changing environments and needs. The bases of such diversification and, thus, principles of ion coupling are unexplored. Here, using phylogenetics and ancestral protein reconstruction, we investigated sodium-coupled transport in prokaryotic glutamate transporters, a mechanism ubiquitous across life domains and critical to neurotransmitter recycling in humans by excitatory amino acid transporters from the solute carrier 1 family. By inferring ancestral prokaryotic transporter sequences during a change in the ion-coupling mechanism, we found an evolutionary transition from sodium-dependent to independent substrate binding and transport. Structural and functional experiments on ancestral transporters suggest that the transition involved allosteric mutations, rendering sodium binding dispensable without affecting the ion-binding sites. Allosteric tuning of transporters’ energy landscapes might be a widespread route of their functional diversification. Reddy et al. used ancestral protein reconstruction, cryo-electron microscopy and functional assays to elucidate how a secondary active transporter evolved to harness the energy of sodium gradients to power the concentrative uptake of its substrate.
{"title":"Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters","authors":"Krishna D. Reddy, Burha Rasool, Farideh Badichi Akher, Nemanja Kutlešić, Swati Pant, Olga Boudker","doi":"10.1038/s41594-025-01652-z","DOIUrl":"10.1038/s41594-025-01652-z","url":null,"abstract":"Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to changing environments and needs. The bases of such diversification and, thus, principles of ion coupling are unexplored. Here, using phylogenetics and ancestral protein reconstruction, we investigated sodium-coupled transport in prokaryotic glutamate transporters, a mechanism ubiquitous across life domains and critical to neurotransmitter recycling in humans by excitatory amino acid transporters from the solute carrier 1 family. By inferring ancestral prokaryotic transporter sequences during a change in the ion-coupling mechanism, we found an evolutionary transition from sodium-dependent to independent substrate binding and transport. Structural and functional experiments on ancestral transporters suggest that the transition involved allosteric mutations, rendering sodium binding dispensable without affecting the ion-binding sites. Allosteric tuning of transporters’ energy landscapes might be a widespread route of their functional diversification. Reddy et al. used ancestral protein reconstruction, cryo-electron microscopy and functional assays to elucidate how a secondary active transporter evolved to harness the energy of sodium gradients to power the concentrative uptake of its substrate.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 12","pages":"2564-2574"},"PeriodicalIF":10.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-025-01652-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900403","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}
Pub Date : 2025-08-22DOI: 10.1038/s41594-025-01644-z
Adel Atari, Haoyang Jiang, Roger A. Greenberg
DNA double-strand breaks (DSBs) are a severe threat to genome stability, as DSB-repair mechanisms with low fidelity contribute to loss of genome integrity. Break-induced replication (BIR) is a crucial DSB-repair pathway when classical homologous recombination mechanisms fail. BIR is often triggered by stalled or collapsed replication forks, following extensive end resection that generates a single-stranded DNA substrate, which can engage either canonical homology-driven BIR, or microhomology-mediated BIR (mmBIR), which requires shorter sequence homologies than does canonical BIR. BIR is a double-edged sword: it is necessary for DSB repair, but is also culpable for introducing mutations and structural variations that are linked to cancer and genetic disorders. In this Review, we discuss BIR regulation in mammalian cells, and the role of BIR in telomere maintenance and in human disease, as well as in genome engineering. We highlight emerging findings in these areas and advances in technologies that have enabled their discovery and reshape our understanding of this enigmatic repair mechanism. Break-induced replication (BIR) is a crucial DNA double-strand break-repair pathway, but it also introduces mutations linked to cancer and genetic disorders. This Review discusses BIR regulation in mammalian cells, its roles in human disease and its potential uses in genome engineering.
{"title":"Mechanisms and genomic implications of break-induced replication","authors":"Adel Atari, Haoyang Jiang, Roger A. Greenberg","doi":"10.1038/s41594-025-01644-z","DOIUrl":"10.1038/s41594-025-01644-z","url":null,"abstract":"DNA double-strand breaks (DSBs) are a severe threat to genome stability, as DSB-repair mechanisms with low fidelity contribute to loss of genome integrity. Break-induced replication (BIR) is a crucial DSB-repair pathway when classical homologous recombination mechanisms fail. BIR is often triggered by stalled or collapsed replication forks, following extensive end resection that generates a single-stranded DNA substrate, which can engage either canonical homology-driven BIR, or microhomology-mediated BIR (mmBIR), which requires shorter sequence homologies than does canonical BIR. BIR is a double-edged sword: it is necessary for DSB repair, but is also culpable for introducing mutations and structural variations that are linked to cancer and genetic disorders. In this Review, we discuss BIR regulation in mammalian cells, and the role of BIR in telomere maintenance and in human disease, as well as in genome engineering. We highlight emerging findings in these areas and advances in technologies that have enabled their discovery and reshape our understanding of this enigmatic repair mechanism. Break-induced replication (BIR) is a crucial DNA double-strand break-repair pathway, but it also introduces mutations linked to cancer and genetic disorders. This Review discusses BIR regulation in mammalian cells, its roles in human disease and its potential uses in genome engineering.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"32 10","pages":"1871-1882"},"PeriodicalIF":10.1,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900458","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}
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