Pub Date : 2025-11-01DOI: 10.1016/j.tibs.2025.08.007
Łukasz Koziej , Sebastian Glatt
Chemical modifications of rRNA, tRNA, and mRNA play key roles in protein synthesis by affecting the structure of these RNAs, by modulating decoding, and by influencing ribosomal efficiency. Recent advances in sequencing-based detection methods have expanded our ability to map these moieties across RNA molecules in diverse cellular states. In parallel, X-ray crystallography and the advent of high-resolution cryogenic electron microscopy have facilitated the direct visualization of RNA modifications within ribosomes. This review integrates recent structural studies with functional insights to shed light on the roles of RNA modifications in translation. Thereby, we seek to summarize current knowledge about the molecular roles of RNA modifications in gene expression and protein synthesis.
{"title":"Mapping rRNA, tRNA, and mRNA modifications in ribosomes at high resolution","authors":"Łukasz Koziej , Sebastian Glatt","doi":"10.1016/j.tibs.2025.08.007","DOIUrl":"10.1016/j.tibs.2025.08.007","url":null,"abstract":"<div><div>Chemical modifications of rRNA, tRNA, and mRNA play key roles in protein synthesis by affecting the structure of these RNAs, by modulating decoding, and by influencing ribosomal efficiency. Recent advances in sequencing-based detection methods have expanded our ability to map these moieties across RNA molecules in diverse cellular states. In parallel, X-ray crystallography and the advent of high-resolution cryogenic electron microscopy have facilitated the direct visualization of RNA modifications within ribosomes. This review integrates recent structural studies with functional insights to shed light on the roles of RNA modifications in translation. Thereby, we seek to summarize current knowledge about the molecular roles of RNA modifications in gene expression and protein synthesis.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 11","pages":"Pages 1027-1041"},"PeriodicalIF":11.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079207","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 : 2025-11-01DOI: 10.1016/j.tibs.2025.08.003
Thuanny Borba Rios , Mariana Rocha Maximiano , Nelson Gomes de Oliveira Junior , Alessandro S. Nascimento , Octávio Luiz Franco
Antimicrobial peptides (AMPs) have emerged as promising alternatives owing to their broad-spectrum activity and reduced potential for resistance. Recent advances have highlighted the role of peptide self-assembly in enhancing the stability, bioavailability, and efficacy of AMPs. Through non-covalent interactions, self-assembly enables the formation of nanostructures, including nanofibers, nanotubes, and micelles. This process can enhance antimicrobial activity by increasing AMP stability, facilitating membrane interactions, and modulating the mechanisms of bacterial disruption. Physicochemical features, including hydrophobicity, charge distribution, and aromatic interactions, allow the creation of tailored nanostructures with enhanced antimicrobial performance. Furthermore, self-assembled AMPs offer controlled drug release, targeted delivery, and synergistic strategies. This review examines the molecular mechanisms underlying peptide self-assembly and highlights their influence on AMP functionality and potential applications in combating infections.
{"title":"Molecular design drives nanoarchitecture in self-assembling antimicrobial peptides","authors":"Thuanny Borba Rios , Mariana Rocha Maximiano , Nelson Gomes de Oliveira Junior , Alessandro S. Nascimento , Octávio Luiz Franco","doi":"10.1016/j.tibs.2025.08.003","DOIUrl":"10.1016/j.tibs.2025.08.003","url":null,"abstract":"<div><div>Antimicrobial peptides (AMPs) have emerged as promising alternatives owing to their broad-spectrum activity and reduced potential for resistance. Recent advances have highlighted the role of peptide self-assembly in enhancing the stability, bioavailability, and efficacy of AMPs. Through non-covalent interactions, self-assembly enables the formation of nanostructures, including nanofibers, nanotubes, and micelles. This process can enhance antimicrobial activity by increasing AMP stability, facilitating membrane interactions, and modulating the mechanisms of bacterial disruption. Physicochemical features, including hydrophobicity, charge distribution, and aromatic interactions, allow the creation of tailored nanostructures with enhanced antimicrobial performance. Furthermore, self-assembled AMPs offer controlled drug release, targeted delivery, and synergistic strategies. This review examines the molecular mechanisms underlying peptide self-assembly and highlights their influence on AMP functionality and potential applications in combating infections.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 11","pages":"Pages 977-988"},"PeriodicalIF":11.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938090","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 : 2025-11-01DOI: 10.1016/j.tibs.2025.06.010
Domingos F.M. Neto , Rita de Cassia Monteiro-Batista , Adriano Nunes-Nesi , Wagner L. Araújo
Understanding the tissue-specific mitochondrial proteome is essential for advancing understanding of plant biology. In a recent study, Boussardon et al. applied Isolation of Mitochondria Tagged in Specific Cell Types (IMTACT) to investigate mitoproteome dynamics during pollen development. Here, we explore the broader potential of high-purity mitochondrial isolation in elucidating specific roles across tissues and developmental stages.
了解组织特异性线粒体蛋白质组对于提高对植物生物学的理解至关重要。在最近的一项研究中，Boussardon等人采用了IMTACT （Isolation of Mitochondria Tagged In Specific Cell Types）技术来研究花粉发育过程中的线粒体蛋白质动力学。在这里，我们探索高纯度线粒体分离在阐明组织和发育阶段的特定作用方面的更广泛潜力。
{"title":"Cell-specific mitoproteomics reveals mitochondrial plasticity and applications","authors":"Domingos F.M. Neto , Rita de Cassia Monteiro-Batista , Adriano Nunes-Nesi , Wagner L. Araújo","doi":"10.1016/j.tibs.2025.06.010","DOIUrl":"10.1016/j.tibs.2025.06.010","url":null,"abstract":"<div><div>Understanding the tissue-specific mitochondrial proteome is essential for advancing understanding of plant biology. In a recent study, <span><span>Boussardon <em>et al</em>.</span><svg><path></path></svg></span> applied Isolation of Mitochondria Tagged in Specific Cell Types (IMTACT) to investigate mitoproteome dynamics during pollen development. Here, we explore the broader potential of high-purity mitochondrial isolation in elucidating specific roles across tissues and developmental stages.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 11","pages":"Pages 953-955"},"PeriodicalIF":11.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525854","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 : 2025-11-01DOI: 10.1016/j.tibs.2025.08.010
Yinfeng Xu (许银丰) , Wei Wan (万伟)
The cyclic GMP-AMP (cGAMP) synthase (cGAS)–stimulator of interferon (IFN) genes (STING) pathway detects cytoplasmic DNA and elicits the innate immune response. Several recent studies show that cGAS–STING signaling not only terminates at the lysosome but also regulates lysosomal function. Here, we discuss the interplay of the cGAS–STING pathway with the lysosome.
{"title":"The interplay of the cGAS–STING pathway with the lysosome","authors":"Yinfeng Xu (许银丰) , Wei Wan (万伟)","doi":"10.1016/j.tibs.2025.08.010","DOIUrl":"10.1016/j.tibs.2025.08.010","url":null,"abstract":"<div><div>The cyclic GMP-AMP (cGAMP) synthase (cGAS)–stimulator of interferon (IFN) genes (STING) pathway detects cytoplasmic DNA and elicits the innate immune response. Several recent studies show that cGAS–STING signaling not only terminates at the lysosome but also regulates lysosomal function. Here, we discuss the interplay of the cGAS–STING pathway with the lysosome.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 11","pages":"Pages 956-959"},"PeriodicalIF":11.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136057","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 : 2025-10-01DOI: 10.1016/S0968-0004(25)00227-0
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/S0968-0004(25)00227-0","DOIUrl":"10.1016/S0968-0004(25)00227-0","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 10","pages":"Pages i-ii"},"PeriodicalIF":11.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145204411","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 : 2025-10-01DOI: 10.1016/S0968-0004(25)00230-0
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/S0968-0004(25)00230-0","DOIUrl":"10.1016/S0968-0004(25)00230-0","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 10","pages":"Page e1"},"PeriodicalIF":11.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145204366","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 : 2025-10-01DOI: 10.1016/j.tibs.2025.08.002
Naama Rotenberg , Noam Y. Bentolila , Julia M. Shifman
Matrix metalloproteinases (MMPs) are a family of 23 zinc-dependent proteases involved in extracellular matrix (ECM) remodeling and are implicated in diseases such as cancer, arthritis, and cardiovascular disorders. Broad-spectrum MMP inhibitors (MMPIs) have proven counterproductive due to the protective roles of certain MMPs and their expression in healthy tissues. Recent advances in protein engineering have enabled the development of highly specific protein-based MMPIs that precisely target individual MMPs. These engineered proteins, often derived from antibody fragments or endogenous MMPIs, offer enhanced selectivity, reduced off-target effects, and improved therapeutic efficacy. This review highlights novel strategies for the precise targeting of MMPs using engineered proteins and discusses their potential to transform diagnostics and treatment of MMP-driven diseases.
{"title":"Engineered protein inhibitors for precise targeting of matrix metalloproteinases","authors":"Naama Rotenberg , Noam Y. Bentolila , Julia M. Shifman","doi":"10.1016/j.tibs.2025.08.002","DOIUrl":"10.1016/j.tibs.2025.08.002","url":null,"abstract":"<div><div>Matrix metalloproteinases (MMPs) are a family of 23 zinc-dependent proteases involved in extracellular matrix (ECM) remodeling and are implicated in diseases such as cancer, arthritis, and cardiovascular disorders. Broad-spectrum MMP inhibitors (MMPIs) have proven counterproductive due to the protective roles of certain MMPs and their expression in healthy tissues. Recent advances in protein engineering have enabled the development of highly specific protein-based MMPIs that precisely target individual MMPs. These engineered proteins, often derived from antibody fragments or endogenous MMPIs, offer enhanced selectivity, reduced off-target effects, and improved therapeutic efficacy. This review highlights novel strategies for the precise targeting of MMPs using engineered proteins and discusses their potential to transform diagnostics and treatment of MMP-driven diseases.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 10","pages":"Pages 919-930"},"PeriodicalIF":11.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038867","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 : 2025-10-01DOI: 10.1016/j.tibs.2025.05.008
Lien B. Lai , Jane E. Jackman , Charles J. Daniels , Venkat Gopalan
Mitochondrial tRNA processing is a chronicle of molecular adaptability. The processing of structurally compromised tRNAs is unexpectedly rescued by a multienzyme complex shaped by constructive neutral evolution. This striking example of biological complexity arising from nonadaptive mechanisms showcases how a potential vulnerability is transformed into a robust, if precarious, innovation.
{"title":"Mitochondrial tRNA processing: a neutral evolutionary ratchet innovation","authors":"Lien B. Lai , Jane E. Jackman , Charles J. Daniels , Venkat Gopalan","doi":"10.1016/j.tibs.2025.05.008","DOIUrl":"10.1016/j.tibs.2025.05.008","url":null,"abstract":"<div><div>Mitochondrial tRNA processing is a chronicle of molecular adaptability. The processing of structurally compromised tRNAs is unexpectedly rescued by a multienzyme complex shaped by constructive neutral evolution. This striking example of biological complexity arising from nonadaptive mechanisms showcases how a potential vulnerability is transformed into a robust, if precarious, innovation.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 10","pages":"Pages 842-844"},"PeriodicalIF":11.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525856","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 : 2025-10-01DOI: 10.1016/j.tibs.2025.08.001
Michela Ghitti , Liam Sean Colley , Malisa Vittoria Mantonico , Giovanna Musco , Marco Emilio Bianchi
HMGB1, a multitasking protein, is scrutinized here through the lens of the 'fuzzy interactions' driven by its intrinsically disordered regions (IDRs). Although the multiple intracellular and extracellular functions of this protein have been studied for decades, viewing HMGB1 as fuzzy and dynamic provides a novel perspective. Recent breakthroughs emphasize the crucial role of its IDRs, especially the acidic C-terminal tail, in mediating dynamic multivalent interactions. This fuzziness enables HMGB1 to modulate DNA and chromatin binding, to chaperone other proteins such as p53, and to tune inflammatory signals via receptors such as TLR4 and CXCR4. Understanding the fuzzy nature of HMGB1 unlocks new therapeutic strategies targeting both its structured and unstructured regions to tackle a range of diseases.
{"title":"Intrinsic disorder and fuzzy interactions drive multiple functions of HMGB1","authors":"Michela Ghitti , Liam Sean Colley , Malisa Vittoria Mantonico , Giovanna Musco , Marco Emilio Bianchi","doi":"10.1016/j.tibs.2025.08.001","DOIUrl":"10.1016/j.tibs.2025.08.001","url":null,"abstract":"<div><div>HMGB1, a multitasking protein, is scrutinized here through the lens of the 'fuzzy interactions' driven by its intrinsically disordered regions (IDRs). Although the multiple intracellular and extracellular functions of this protein have been studied for decades, viewing HMGB1 as fuzzy and dynamic provides a novel perspective. Recent breakthroughs emphasize the crucial role of its IDRs, especially the acidic C-terminal tail, in mediating dynamic multivalent interactions. This fuzziness enables HMGB1 to modulate DNA and chromatin binding, to chaperone other proteins such as p53, and to tune inflammatory signals via receptors such as TLR4 and CXCR4. Understanding the fuzzy nature of HMGB1 unlocks new therapeutic strategies targeting both its structured and unstructured regions to tackle a range of diseases.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 10","pages":"Pages 906-918"},"PeriodicalIF":11.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938131","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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