Pub Date : 2026-03-01Epub Date: 2026-01-14DOI: 10.1016/j.jmb.2026.169640
Xin Li , Nan Liu , Kaiyu Gao , Carina Muyao Gu , Zhihao Cui , Kundi Zhang , Sujuan Xu , Lichuan Gu
Streptococcus mutans, the major causative agent of dental plaque and caries, maintains osmotic balance under hyperosmotic conditions by transporting glycine betaine into the cytoplasm via the BusAB transporter system. This mechanism is coordinated by the c-di-AMP-responsive transcriptional regulator BusR, which represses busAB expression in the absence of osmotic stress. In this study, we systematically characterized the function of BusR in S. mutans UA159. Our experiments showed that deletion of busR resulted not only in high expression of busAB but also in upregulated GlcNAc metabolic genes, specifically nagA/nagB and glmS, which are known to be regulated by transcriptional regulator NagR. The ΔbusR strain utilized GlcNAc as a nutrient more efficiently and exhibited a faster growth rate than the wild-type strain. Combined with results from further experimentation, this suggests that, BusR assumes a dual regulatory role under high-osmolarity conditions: it relieves repression of busAB to increase the transport of the osmoprotectant betaine into cytoplasm, and cooperates with NagR to regulate amino sugar metabolism by regulating the transcription of nagA/nagB and glmS. Consistent with the molecular ruler mechanism previously described for BusR homologs from Streptococcus agalactiae, we observe a similar structural basis that enables BusR to mediate precise, c-di-AMP–dependent modulation of gene transcription. This coordinated regulation of osmoprotection and amino sugar metabolism by BusR may give S. mutans a significant advantage for dealing with osmotic stress within the oral environment.
{"title":"BusR is a Bifunctional Transcription Factor Coordinating Both Osmotic Response and Amino Sugar Metabolism in Streptococcus mutans","authors":"Xin Li , Nan Liu , Kaiyu Gao , Carina Muyao Gu , Zhihao Cui , Kundi Zhang , Sujuan Xu , Lichuan Gu","doi":"10.1016/j.jmb.2026.169640","DOIUrl":"10.1016/j.jmb.2026.169640","url":null,"abstract":"<div><div><em>Streptococcus mutans,</em> the major causative agent of dental plaque and caries, maintains osmotic balance under hyperosmotic conditions by transporting glycine betaine into the cytoplasm via the BusAB transporter system. This mechanism is coordinated by the c-di-AMP-responsive transcriptional regulator BusR, which represses <em>busAB</em> expression in the absence of osmotic stress. In this study, we systematically characterized the function of BusR in <em>S. mutans</em> UA159. Our experiments showed that deletion of <em>busR</em> resulted not only in high expression of <em>busAB</em> but also in upregulated GlcNAc metabolic genes, specifically <em>nagA/nagB</em> and <em>glmS</em>, which are known to be regulated by transcriptional regulator NagR. The Δ<em>busR</em> strain utilized GlcNAc as a nutrient more efficiently and exhibited a faster growth rate than the wild-type strain. Combined with results from further experimentation, this suggests that, BusR assumes a dual regulatory role under high-osmolarity conditions: it relieves repression of <em>busAB</em> to increase the transport of the osmoprotectant betaine into cytoplasm, and cooperates with NagR to regulate amino sugar metabolism by regulating the transcription of <em>nagA/nagB</em> and <em>glmS</em>. Consistent with the molecular ruler mechanism previously described for BusR homologs from <em>Streptococcus agalactiae</em>, we observe a similar structural basis that enables BusR to mediate precise, c-di-AMP–dependent modulation of gene transcription. This coordinated regulation of osmoprotection and amino sugar metabolism by BusR may give <em>S. mutans</em> a significant advantage for dealing with osmotic stress within the oral environment.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169640"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145987699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-10-22DOI: 10.1016/j.jmb.2025.169492
Adam M.B. Allen , Shannon J. McKie , Christian G. Noble , Anthony Maxwell
DNA topoisomerase VI (topo VI) is a type IIB topoisomerase that was originally found in archaea but later found in plants and some other eukaryotes and certain bacteria; claims that it is present in plasmodial parasites have yet to be substantiated. In plants it appears to have an essential role in endoreduplication, but its role in other organisms is less clear. Although topo VI is evolutionarily related to type IIA topoisomerases, it shows a different domain organisation and lacks an exit gate (C gate). Crystal structures of topo VI consolidate these distinctions and show protein cavities and subunit interfaces that are consistent with a double-strand passage mechanism. Single-molecule and ensemble measurements of topo VI reactions show that the rate of DNA relaxation is much slower than with its IIA counterparts, but that it shows a preference for decatenation over relaxation reactions. Radicicol, a known inhibitor of human topo II, also inhibits some topo VI enzymes, and recent drug screens have identified further compounds. Topo VI is ripe for exploitation as a target for herbicides and potentially for antibacterials.
{"title":"DNA Topoisomerase VI: Structure, Function and Mechanism","authors":"Adam M.B. Allen , Shannon J. McKie , Christian G. Noble , Anthony Maxwell","doi":"10.1016/j.jmb.2025.169492","DOIUrl":"10.1016/j.jmb.2025.169492","url":null,"abstract":"<div><div>DNA topoisomerase VI (topo VI) is a type IIB topoisomerase that was originally found in archaea but later found in plants and some other eukaryotes and certain bacteria; claims that it is present in plasmodial parasites have yet to be substantiated. In plants it appears to have an essential role in endoreduplication, but its role in other organisms is less clear. Although topo VI is evolutionarily related to type IIA topoisomerases, it shows a different domain organisation and lacks an exit gate (C gate). Crystal structures of topo VI consolidate these distinctions and show protein cavities and subunit interfaces that are consistent with a double-strand passage mechanism. Single-molecule and ensemble measurements of topo VI reactions show that the rate of DNA relaxation is much slower than with its IIA counterparts, but that it shows a preference for decatenation over relaxation reactions. Radicicol, a known inhibitor of human topo II, also inhibits some topo VI enzymes, and recent drug screens have identified further compounds. Topo VI is ripe for exploitation as a target for herbicides and potentially for antibacterials.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169492"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145367246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-27DOI: 10.1016/j.jmb.2026.169735
Caroline Velez, Aniket Naravane, Victor I Robila, Aakash Saha, Diana Murray, Barry Honig
PrePPI is a structure-based pipeline that predicts protein-protein interactions (PPIs) between two structured domains and between structured domains and short linear motifs (SLiMs) on a proteome-wide scale. Since the 2023 Computational Resource Issue of JMB, the PrePPI website has been significantly expanded and redesigned. The resource now includes interactomes for human, yeast, and E. coli proteomes with 3D models for high-confidence domain-level complexes and PDB templates for most of the SLiM-mediated predicted interactions. A key new addition is derived from the clustering of the PrePPI interactomes based entirely on the structure-based likelihood of an interaction. Remarkably these clusters exhibit functional coherence and provide an unprecedented proteome-wide depiction of the subnetworks of PPIs that underlie biological phenomena. The new website - https://honigcomplab.c2b2.columbia.edu/PrePPI - provides convenient access to these clusters, to structural models for each pairwise complex, and to function annotations for individual proteins, enabling multiple modes of biological discovery.
{"title":"PrePPI - Structure-based Prediction of Protein-protein Interactomes and Networks.","authors":"Caroline Velez, Aniket Naravane, Victor I Robila, Aakash Saha, Diana Murray, Barry Honig","doi":"10.1016/j.jmb.2026.169735","DOIUrl":"10.1016/j.jmb.2026.169735","url":null,"abstract":"<p><p>PrePPI is a structure-based pipeline that predicts protein-protein interactions (PPIs) between two structured domains and between structured domains and short linear motifs (SLiMs) on a proteome-wide scale. Since the 2023 Computational Resource Issue of JMB, the PrePPI website has been significantly expanded and redesigned. The resource now includes interactomes for human, yeast, and E. coli proteomes with 3D models for high-confidence domain-level complexes and PDB templates for most of the SLiM-mediated predicted interactions. A key new addition is derived from the clustering of the PrePPI interactomes based entirely on the structure-based likelihood of an interaction. Remarkably these clusters exhibit functional coherence and provide an unprecedented proteome-wide depiction of the subnetworks of PPIs that underlie biological phenomena. The new website - https://honigcomplab.c2b2.columbia.edu/PrePPI - provides convenient access to these clusters, to structural models for each pairwise complex, and to function annotations for individual proteins, enabling multiple modes of biological discovery.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169735"},"PeriodicalIF":4.5,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12997520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147324179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2026-02-26DOI: 10.1016/j.jmb.2026.169734
Enes S Arpa, Michael Taschner, Mara De Matos, Stefanie Jonas, David Gatfield
Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway that eliminates transcripts containing premature termination codons (PTCs). Substantial progress has been made in defining the transcript features that mark aberrant translation termination for NMD activation, yet key mechanistic steps remain incompletely understood - including how recruitment of the central NMD factor UPF1 is coupled to the downstream effector phase in which targeted mRNAs are nucleolytically degraded. In metazoans, NMD employs an endonucleolytic route mediated by SMG6, a PIN-domain nuclease, alongside SMG5 and SMG7, which act downstream of PTC recognition. SMG5 has recently been proposed to licence SMG6 activity, yet the molecular basis of this licencing has remained elusive. Here, we combine AlphaFold structural predictions with biochemical assays to investigate interactions among human SMG5, SMG6, and SMG7. Structural models predict a high-confidence interface between SMG5 and SMG6 PIN domains that forms a composite active site: a conserved SMG5 aspartate (D893) complements the SMG6 acidic triad to reinstate the canonical tetrad required for PIN-domain catalysis. In vitro, SMG6 alone exhibits weak endonucleolytic activity, which is enhanced ∼10-fold by the SMG5 PIN domain. Mutational analyses confirm that conserved residues from both proteins are essential for this composite configuration. Our findings reveal that the SMG5 PIN domain, previously considered catalytically inert, plays a critical role in activating SMG6 by completing its active site. This work provides mechanistic insight into the SMG5-dependent licencing step and uncovers a composite PIN nuclease architecture at the heart of the metazoan NMD effector phase.
{"title":"Active Site Assembly by SMG5 as a Mechanism for SMG6 Endonuclease Licencing in Nonsense-mediated mRNA Decay.","authors":"Enes S Arpa, Michael Taschner, Mara De Matos, Stefanie Jonas, David Gatfield","doi":"10.1016/j.jmb.2026.169734","DOIUrl":"10.1016/j.jmb.2026.169734","url":null,"abstract":"<p><p>Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway that eliminates transcripts containing premature termination codons (PTCs). Substantial progress has been made in defining the transcript features that mark aberrant translation termination for NMD activation, yet key mechanistic steps remain incompletely understood - including how recruitment of the central NMD factor UPF1 is coupled to the downstream effector phase in which targeted mRNAs are nucleolytically degraded. In metazoans, NMD employs an endonucleolytic route mediated by SMG6, a PIN-domain nuclease, alongside SMG5 and SMG7, which act downstream of PTC recognition. SMG5 has recently been proposed to licence SMG6 activity, yet the molecular basis of this licencing has remained elusive. Here, we combine AlphaFold structural predictions with biochemical assays to investigate interactions among human SMG5, SMG6, and SMG7. Structural models predict a high-confidence interface between SMG5 and SMG6 PIN domains that forms a composite active site: a conserved SMG5 aspartate (D893) complements the SMG6 acidic triad to reinstate the canonical tetrad required for PIN-domain catalysis. In vitro, SMG6 alone exhibits weak endonucleolytic activity, which is enhanced ∼10-fold by the SMG5 PIN domain. Mutational analyses confirm that conserved residues from both proteins are essential for this composite configuration. Our findings reveal that the SMG5 PIN domain, previously considered catalytically inert, plays a critical role in activating SMG6 by completing its active site. This work provides mechanistic insight into the SMG5-dependent licencing step and uncovers a composite PIN nuclease architecture at the heart of the metazoan NMD effector phase.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169734"},"PeriodicalIF":4.5,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147321137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-16DOI: 10.1016/j.jmb.2026.169718
Nigam Padhiar, Nathan Clement, Upendra Katneni, Patrick Dopler, Tigran Ghazanchyan, Luis Santana-Quintero, Anton Golikov, Michael DiCuccio, Haim Bar, Anton A Komar, Chava Kimchi-Sarfaty
Cell lines are essential tools for studying biological mechanisms, advancing pre-clinical drug discovery and supporting biologics production. To further research in these fields, we introduce the Cell Lines CoCoPUTs (Codon and Codon Pair Usage Tables, https://dnahive.fda.gov/hivecuts/cell-lines/), a comprehensive resource of transcriptomic-weighted codon and codon-pair usages for 1866 unique cell lines derived from two cancer databases, Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), and the Human Protein Atlas (HPA) database. Despite differences in the number of cell lines in each database and platforms used for the analysis (microarray vs RNA-Seq), codon usage distributions were broadly similar for all overlapping cell lines across three databases. Application of unsupervised machine learning approaches, including hierarchical and spectral clustering, for the analysis of 1355 cell lines of non-metastatic origin yielded more distinct clusters based on codon-pair usage over codon usage. However, distance-based comparisons indicated that codon usage often yields equal or smaller within-group distances than codon-pair usage and that cell lines are, on average, closer to their site of origin than to their disease phenotype.
{"title":"Cell Lines CoCoPUTs: A Database of Codon and Codon-pair Usage Frequencies in Cell Lines.","authors":"Nigam Padhiar, Nathan Clement, Upendra Katneni, Patrick Dopler, Tigran Ghazanchyan, Luis Santana-Quintero, Anton Golikov, Michael DiCuccio, Haim Bar, Anton A Komar, Chava Kimchi-Sarfaty","doi":"10.1016/j.jmb.2026.169718","DOIUrl":"10.1016/j.jmb.2026.169718","url":null,"abstract":"<p><p>Cell lines are essential tools for studying biological mechanisms, advancing pre-clinical drug discovery and supporting biologics production. To further research in these fields, we introduce the Cell Lines CoCoPUTs (Codon and Codon Pair Usage Tables, https://dnahive.fda.gov/hivecuts/cell-lines/), a comprehensive resource of transcriptomic-weighted codon and codon-pair usages for 1866 unique cell lines derived from two cancer databases, Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), and the Human Protein Atlas (HPA) database. Despite differences in the number of cell lines in each database and platforms used for the analysis (microarray vs RNA-Seq), codon usage distributions were broadly similar for all overlapping cell lines across three databases. Application of unsupervised machine learning approaches, including hierarchical and spectral clustering, for the analysis of 1355 cell lines of non-metastatic origin yielded more distinct clusters based on codon-pair usage over codon usage. However, distance-based comparisons indicated that codon usage often yields equal or smaller within-group distances than codon-pair usage and that cell lines are, on average, closer to their site of origin than to their disease phenotype.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169718"},"PeriodicalIF":4.5,"publicationDate":"2026-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146218158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-15Epub Date: 2026-01-23DOI: 10.1016/j.jmb.2026.169651
Xiaoci Hu, Ana Vila Verde
Proteins of halophilic microorganisms thrive in high-salt environments. Compared to mesophilic proteins, they are enriched in acidic residues and small polar/apolar amino acids while being depleted in large hydrophobic residues, features that strongly influence their structure and stability. Here we critically examine experimental and computational studies investigating the mechanistic connection between the halophilic proteome and thermodynamic stability of halophilic proteins as a function of salt concentration. A defining feature of halophilic proteins is their highly negative surface charge, arising from abundant acidic residues. Some studies suggest this property is essential to ensure proteins remain folded at high salt concentrations, while others argue that a net negative protein charge might always be destabilizing. Alternative views propose that reducing solvent-exposed hydrophobic surface area is more critical than charge for stability at high salt concentrations. Advancing our understanding on this topic will require addressing multiple knowledge gaps. The unfolded states of both protein classes remain poorly characterized, leaving differences in local and non-local entropy contributions between the folded and the unfolded states to salt-dependent protein stability largely unexplored. Packing, cation-carbonyl and hydrophobic SASA differences between both protein classes are also insufficiently quantified. Atomistic molecular dynamics simulations with explicit solvent can advantageously be used to investigate these issues. Simultaneously, theoretical frameworks to understand how small perturbations in protein composition impact its stability as a function of salt concentration need to be expanded to include these contributions, which to date have been neglected, to fully understand how a halophilic proteome impacts salt-dependent stability.
{"title":"Electrolyte–amino acid interplay in the stability mechanisms of halophilic proteins","authors":"Xiaoci Hu, Ana Vila Verde","doi":"10.1016/j.jmb.2026.169651","DOIUrl":"10.1016/j.jmb.2026.169651","url":null,"abstract":"<div><div>Proteins of halophilic microorganisms thrive in high-salt environments. Compared to mesophilic proteins, they are enriched in acidic residues and small polar/apolar amino acids while being depleted in large hydrophobic residues, features that strongly influence their structure and stability. Here we critically examine experimental and computational studies investigating the mechanistic connection between the halophilic proteome and thermodynamic stability of halophilic proteins as a function of salt concentration. A defining feature of halophilic proteins is their highly negative surface charge, arising from abundant acidic residues. Some studies suggest this property is essential to ensure proteins remain folded at high salt concentrations, while others argue that a net negative protein charge might always be destabilizing. Alternative views propose that reducing solvent-exposed hydrophobic surface area is more critical than charge for stability at high salt concentrations. Advancing our understanding on this topic will require addressing multiple knowledge gaps. The unfolded states of both protein classes remain poorly characterized, leaving differences in local and non-local entropy contributions between the folded and the unfolded states to salt-dependent protein stability largely unexplored. Packing, cation-carbonyl and hydrophobic SASA differences between both protein classes are also insufficiently quantified. Atomistic molecular dynamics simulations with explicit solvent can advantageously be used to investigate these issues. Simultaneously, theoretical frameworks to understand how small perturbations in protein composition impact its stability as a function of salt concentration need to be expanded to include these contributions, which to date have been neglected, to fully understand how a halophilic proteome impacts salt-dependent stability.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 4","pages":"Article 169651"},"PeriodicalIF":4.5,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-15Epub Date: 2025-09-11DOI: 10.1016/j.jmb.2025.169435
Satoshi Akanuma
Understanding how proteins have evolved to adapt their stability and function to changing temperatures remains a central question in molecular biology. While structural analyses, site-directed mutagenesis, and directed evolution have yielded valuable insights, ancestral sequence reconstruction (ASR) has recently emerged as a powerful tool for addressing the drivers behind protein evolution. Specifically, by enabling the inference and experimental characterization of reconstructed ancient proteins, ASR provides unique perspectives on the molecular mechanisms underlying both thermostability and low-temperature-adaptation. This review outlines the historical development of research on protein temperature adaptation and highlights the role of ASR in advancing the field. Selected case studies illustrate how ASR has uncovered structural and dynamic features associated with extreme thermostability or enhanced activity at low temperatures. Common sources of uncertainty in ASR and how they can be addressed are also discussed. Finally, the broader potential of ASR is described, both for elucidating early evolutionary processes and for guiding the design of enzymes useful for industrial applications.
{"title":"Learning About Protein Stability and Functional Activity From Ancestral Reconstruction","authors":"Satoshi Akanuma","doi":"10.1016/j.jmb.2025.169435","DOIUrl":"10.1016/j.jmb.2025.169435","url":null,"abstract":"<div><div>Understanding how proteins have evolved to adapt their stability and function to changing temperatures remains a central question in molecular biology. While structural analyses, site-directed mutagenesis, and directed evolution have yielded valuable insights, ancestral sequence reconstruction (ASR) has recently emerged as a powerful tool for addressing the drivers behind protein evolution. Specifically, by enabling the inference and experimental characterization of reconstructed ancient proteins, ASR provides unique perspectives on the molecular mechanisms underlying both thermostability and low-temperature-adaptation. This review outlines the historical development of research on protein temperature adaptation and highlights the role of ASR in advancing the field. Selected case studies illustrate how ASR has uncovered structural and dynamic features associated with extreme thermostability or enhanced activity at low temperatures. Common sources of uncertainty in ASR and how they can be addressed are also discussed. Finally, the broader potential of ASR is described, both for elucidating early evolutionary processes and for guiding the design of enzymes useful for industrial applications.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 4","pages":"Article 169435"},"PeriodicalIF":4.5,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-15Epub Date: 2025-11-26DOI: 10.1016/j.jmb.2025.169565
Alexander Vologodskii
This review focuses on a fundamental problem faced by hyperthermophiles that grow at temperatures above 95 °C. At such high temperatures, both linear and open circular DNA denature, leading to strand separation and loss of the double-helical structure. One strategy to prevent denaturation is to maintain DNA in a closed circular form, where the topological constraint on DNA conformations increases the melting temperature by 30–40 °C. However, this conformational restriction is lost when a single-stranded break occurs – a common type of DNA lesion. In hyperthermophiles, circular DNA containing a single-stranded nick begins to unwind and partially denature. Although DNA-bound proteins can slow this process, they protect only a fraction of the double helix. As a result, repairing such damage requires not only restoration of the strand integrity but also restoration of the original linking number between complementary strands. Reverse gyrase, a thermophile-specific enzyme that catalyzes positive supercoiling in closed circular DNA, fulfills this essential role in the DNA repair pathway.
{"title":"Repair of Single-Stranded Breaks in Hyperthermophilic DNA","authors":"Alexander Vologodskii","doi":"10.1016/j.jmb.2025.169565","DOIUrl":"10.1016/j.jmb.2025.169565","url":null,"abstract":"<div><div>This review focuses on a fundamental problem faced by hyperthermophiles that grow at temperatures above 95 °C. At such high temperatures, both linear and open circular DNA denature, leading to strand separation and loss of the double-helical structure. One strategy to prevent denaturation is to maintain DNA in a closed circular form, where the topological constraint on DNA conformations increases the melting temperature by 30–40 °C. However, this conformational restriction is lost when a single-stranded break occurs – a common type of DNA lesion. In hyperthermophiles, circular DNA containing a single-stranded nick begins to unwind and partially denature. Although DNA-bound proteins can slow this process, they protect only a fraction of the double helix. As a result, repairing such damage requires not only restoration of the strand integrity but also restoration of the original linking number between complementary strands. Reverse gyrase, a thermophile-specific enzyme that catalyzes positive supercoiling in closed circular DNA, fulfills this essential role in the DNA repair pathway.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 4","pages":"Article 169565"},"PeriodicalIF":4.5,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145627103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-15Epub Date: 2025-08-21DOI: 10.1016/j.jmb.2025.169403
Olga Zhaxybayeva , Camilla L. Nesbø
Horizontal (or lateral) gene transfer – an acquisition of genetic material not associated with the organismal reproduction – is known to alter genomes of most, if not all, living organisms. There is mounting evidence for the importance of gene exchange in organismal adaptations to new or changing environmental conditions. In comparison to accumulation of de novo mutations, acquisition of a gene already beneficial in the environment is fast and less costly, and thus an advantageous, way to adjust to survival and growth in new conditions. Adaptation to extreme environments at the boundaries of habitat conditions beyond which cellular integrity, metabolism and growth are not possible, is not an exception. Here we review the impact of horizontal gene transfer on organismal adaptations to natural and human-made extreme environments. This includes thermophiles living at high temperatures, psychrophiles found at low temperatures, acidophiles inhabiting high acidity environments, alkaliphiles thriving at high pH, halophiles found in high salt environments, xerophiles that can tolerate extremely low water availability, oligotrophes thriving at low nutrient availability, piezophiles inhabiting high pressure environments, and organisms that can withstand high levels of ionizing radiation. We also discuss the challenges and future directions for deciphering genetic determinants and horizontal gene transfer events of extremophiles’ adaptations.
{"title":"Impact of Horizontal Gene Transfer on Adaptations to Extreme Environments","authors":"Olga Zhaxybayeva , Camilla L. Nesbø","doi":"10.1016/j.jmb.2025.169403","DOIUrl":"10.1016/j.jmb.2025.169403","url":null,"abstract":"<div><div>Horizontal (or lateral) gene transfer – an acquisition of genetic material not associated with the organismal reproduction – is known to alter genomes of most, if not all, living organisms. There is mounting evidence for the importance of gene exchange in organismal adaptations to new or changing environmental conditions. In comparison to accumulation of <em>de novo</em> mutations, acquisition of a gene already beneficial in the environment is fast and less costly, and thus an advantageous, way to adjust to survival and growth in new conditions. Adaptation to extreme environments at the boundaries of habitat conditions beyond which cellular integrity, metabolism and growth are not possible, is not an exception. Here we review the impact of horizontal gene transfer on organismal adaptations to natural and human-made extreme environments<em>.</em> This includes thermophiles living at high temperatures, psychrophiles found at low temperatures, acidophiles inhabiting high acidity environments, alkaliphiles thriving at high pH, halophiles found in high salt environments, xerophiles that can tolerate extremely low water availability, oligotrophes thriving at low nutrient availability, piezophiles inhabiting high pressure environments, and organisms that can withstand high levels of ionizing radiation. We also discuss the challenges and future directions for deciphering genetic determinants and horizontal gene transfer events of extremophiles’ adaptations.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 4","pages":"Article 169403"},"PeriodicalIF":4.5,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-15Epub Date: 2025-11-10DOI: 10.1016/j.jmb.2025.169537
Raechell , Wei-Ven Tee , Bingxue Dong , Enrico Guarnera , Igor N. Berezovsky
The thermodynamic stability of proteins and regulation of their functional activity can be described within the energy landscape framework, where the former is provided by a unique native conformational ensemble separated by an energy gap from misfolded structures, and the latter is based on conformational transitions between structural states in the native ensemble. This work investigates the relationship between fundamentals of structural stability and dynamics-driven allosteric regulation. We describe here general proteomic trends and fold/function-specific determinants of protein stability. The intricate relationship between stability and allostery has been observed, showing how requirements on stability and thermal adaptation drive and shape the protein’s “structural platform”, while complementary sequence-structure determinants control the allosteric signaling and regulation. We illustrate our findings using four groups of proteins – inorganic pyrophosphatase and β-glucosidase representing hydrolases, the CheY signaling protein, and adenylate kinase – obtained from host organisms spanning from psychrophiles to hyperthermophiles. We also show that allosteric effects of mutations in adenylate kinase account for experimentally observed changes in organismal fitness expressed in bacterial growth rates. Epistasis arising from the effects of these mutations is another important phenomenon, resulting in unexpected non-additive changes in fitness that could not be explained by the stability changes alone. The findings in this work and options for further investigations of the stability-signaling relationship are provided by the sequence-dependent model of allostery employed here and implemented in AlloSigMA 3 – the latest update of our AlloSigMA web-server (https://allosigma.bii.a-star.edu.sg).
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