Pub Date : 2025-09-01DOI: 10.1016/S0968-0004(25)00199-9
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/S0968-0004(25)00199-9","DOIUrl":"10.1016/S0968-0004(25)00199-9","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Pages i-ii"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005043","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 : 2025-09-01DOI: 10.1016/j.tibs.2025.06.012
Fei Qu , Yuan Liu
N6-methyladenosine (m6A) is the most abundant epitranscriptomic mark on mRNA and plays crucial roles in gene expression, cell differentiation, stress responses, and cancer and neurodegenerative diseases. Recent studies have further revealed a new role of m6A-modified coding and noncoding RNAs in regulating DNA repair and modulating genome stability. In this review, we first discuss the roles of m6A modification in regulating RNA stability and splicing of DNA repair genes, as well as its roles in guiding DNA repair. We then discuss the crosstalk between m6A-modified RNA and DNA damage and repair, highlighting several outstanding questions.
{"title":"The crosstalk of m6A-modified RNA with DNA damage repair","authors":"Fei Qu , Yuan Liu","doi":"10.1016/j.tibs.2025.06.012","DOIUrl":"10.1016/j.tibs.2025.06.012","url":null,"abstract":"<div><div><em>N</em><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is the most abundant epitranscriptomic mark on mRNA and plays crucial roles in gene expression, cell differentiation, stress responses, and cancer and neurodegenerative diseases. Recent studies have further revealed a new role of m<sup>6</sup>A-modified coding and noncoding RNAs in regulating DNA repair and modulating genome stability. In this review, we first discuss the roles of m<sup>6</sup>A modification in regulating RNA stability and splicing of DNA repair genes, as well as its roles in guiding DNA repair. We then discuss the crosstalk between m<sup>6</sup>A-modified RNA and DNA damage and repair, highlighting several outstanding questions.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Pages 822-833"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688505","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 : 2025-09-01DOI: 10.1016/S0968-0004(25)00202-6
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/S0968-0004(25)00202-6","DOIUrl":"10.1016/S0968-0004(25)00202-6","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Page e1"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005044","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 : 2025-09-01DOI: 10.1016/j.tibs.2025.06.014
Jennifer L. DuBois
Science is not a list of facts in a textbook, but rather a living series of stories spanning the history of human thought and continuing to this day. Understanding how scientific consensus evolves helps mitigate distrust of research among the general public.
{"title":"Epic science","authors":"Jennifer L. DuBois","doi":"10.1016/j.tibs.2025.06.014","DOIUrl":"10.1016/j.tibs.2025.06.014","url":null,"abstract":"<div><div>Science is not a list of facts in a textbook, but rather a living series of stories spanning the history of human thought and continuing to this day. Understanding how scientific consensus evolves helps mitigate distrust of research among the general public.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Pages 735-737"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688504","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 : 2025-09-01DOI: 10.1016/j.tibs.2025.06.009
Haleigh C. Wooters , Neil C. Nimmagadda , Alicia M. Darnell , Gustavo M. Silva
It has become evident that a complex code of ribosome ubiquitination regulates protein synthesis, particularly in stress conditions. Ubiquitin is known largely for its role in protein stability; however, new high-throughput screening and advances in proteomics are underscoring its novel role as a master regulator of ribosome function. Still, much remains to be discovered about how this code acts and supports translation reprogramming in a context-specific manner. Here we discuss the nature of this code, the dynamics of site-specific ribosome ubiquitination, and the unique roles that multiple enzymes play in defining the translatome and cotranslational quality control pathways. We also provide insights on the importance of unraveling this code to understand the physiological impact of modified ribosome subpopulations in cellular stress and human disease.
{"title":"The ribosome ubiquitination code: fine-tuning translation under stress","authors":"Haleigh C. Wooters , Neil C. Nimmagadda , Alicia M. Darnell , Gustavo M. Silva","doi":"10.1016/j.tibs.2025.06.009","DOIUrl":"10.1016/j.tibs.2025.06.009","url":null,"abstract":"<div><div>It has become evident that a complex code of ribosome ubiquitination regulates protein synthesis, particularly in stress conditions. Ubiquitin is known largely for its role in protein stability; however, new high-throughput screening and advances in proteomics are underscoring its novel role as a master regulator of ribosome function. Still, much remains to be discovered about how this code acts and supports translation reprogramming in a context-specific manner. Here we discuss the nature of this code, the dynamics of site-specific ribosome ubiquitination, and the unique roles that multiple enzymes play in defining the translatome and cotranslational quality control pathways. We also provide insights on the importance of unraveling this code to understand the physiological impact of modified ribosome subpopulations in cellular stress and human disease.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Pages 766-778"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615699","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 : 2025-09-01DOI: 10.1016/j.tibs.2025.05.009
Robyn Duttenhefner , Subeksha Subedi , Sangita C. Sinha
Cook et al. show that the VPS15 pseudokinase domain binds GTP and sequesters its covalently-linked N-terminal myristate. Together, this enforces VPS15 conformations that interact with and stabilize inactive VPS34 kinase domain conformations. Myristate release disrupts this inhibitory interaction and also helps dock VPS34 on membranes to catalyze phosphatidylinositol-3-phophate (PI3P) production.
{"title":"CryoEM provides detailed insights into how VPS15 regulates VPS34 activity","authors":"Robyn Duttenhefner , Subeksha Subedi , Sangita C. Sinha","doi":"10.1016/j.tibs.2025.05.009","DOIUrl":"10.1016/j.tibs.2025.05.009","url":null,"abstract":"<div><div><span><span>Cook <em>et al</em>.</span><svg><path></path></svg></span><span> show that the VPS15<span> pseudokinase domain binds GTP and sequesters its covalently-linked N-terminal myristate<span>. Together, this enforces VPS15 conformations that interact with and stabilize inactive VPS34 kinase domain conformations. Myristate release disrupts this inhibitory interaction and also helps dock VPS34 on membranes to catalyze phosphatidylinositol-3-phophate (PI3P) production.</span></span></span></div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Pages 741-743"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332149","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 : 2025-09-01DOI: 10.1016/j.tibs.2025.06.007
Anna Brennan , Taylor R. Church , Seth S. Margolis
The proteasome is an essential protein complex in all cells. Proteasomes have two main functions: protein degradation and peptide generation. While proteasome-dependent protein degradation removes proteins and is critical for cellular function, the newly generated proteasome-derived peptides, which range in size and sequence, are emerging as essential cellular effector molecules: they are expressed on MHC-I in the immune system, function as novel modulators of neuronal signaling, are involved in innate immunity and intracellular signaling, and can be metabolized further for important cellular processes. Here, we take a comprehensive look at the mechanics behind proteasome-mediated peptide generation; the function of proteasome-derived peptides in signaling and metabolism relevant to cellular biology, health, and disease; and the techniques enabling these studies.
{"title":"Proteasome-derived peptides: separating the trash from the recycling","authors":"Anna Brennan , Taylor R. Church , Seth S. Margolis","doi":"10.1016/j.tibs.2025.06.007","DOIUrl":"10.1016/j.tibs.2025.06.007","url":null,"abstract":"<div><div>The proteasome is an essential protein complex in all cells. Proteasomes have two main functions: protein degradation and peptide generation. While proteasome-dependent protein degradation removes proteins and is critical for cellular function, the newly generated proteasome-derived peptides, which range in size and sequence, are emerging as essential cellular effector molecules: they are expressed on MHC-I in the immune system, function as novel modulators of neuronal signaling, are involved in innate immunity and intracellular signaling, and can be metabolized further for important cellular processes. Here, we take a comprehensive look at the mechanics behind proteasome-mediated peptide generation; the function of proteasome-derived peptides in signaling and metabolism relevant to cellular biology, health, and disease; and the techniques enabling these studies.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Pages 779-794"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625109","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 : 2025-09-01DOI: 10.1016/j.tibs.2025.02.007
Jia Yao , Chunyang Xie , Aimin Yang
Autophagy is an intracellular degradation system that delivers cytoplasmic materials to the lysosome. S-acylation, a reversible post-translational modification that attaches long-chain fatty acids to cysteine residues within proteins, has recently emerged as an important regulatory mechanism for autophagy. In this forum article, we review and discuss the emerging roles of S-acylation in autophagy.
{"title":"The emerging roles of S-acylation in autophagy","authors":"Jia Yao , Chunyang Xie , Aimin Yang","doi":"10.1016/j.tibs.2025.02.007","DOIUrl":"10.1016/j.tibs.2025.02.007","url":null,"abstract":"<div><div><span>Autophagy is an intracellular degradation system that delivers cytoplasmic materials to the lysosome. </span><em>S</em>-acylation, a reversible post-translational modification that attaches long-chain fatty acids to cysteine residues within proteins, has recently emerged as an important regulatory mechanism for autophagy. In this forum article, we review and discuss the emerging roles of <em>S</em>-acylation in autophagy.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 9","pages":"Pages 744-747"},"PeriodicalIF":11.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727509","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 : 2025-08-01Epub Date: 2025-03-24DOI: 10.1016/j.tibs.2025.02.006
Lucyna Budzko, Aleksandra Mierzwa, Marek Figlerowicz
Deaminases belonging to the AID/APOBEC family are known as ssDNA and mRNA mutators involved in innate/adaptive immunity, mRNA editing, genome stabilization by restricting retrotransposons, and carcinogenesis. Recent studies suggest that the repertoire of AID/APOBEC targets is more diverse than previously thought and imply a broader biological impact of these proteins.
{"title":"AID/APOBEC: an expanding repertoire of targets and functions.","authors":"Lucyna Budzko, Aleksandra Mierzwa, Marek Figlerowicz","doi":"10.1016/j.tibs.2025.02.006","DOIUrl":"10.1016/j.tibs.2025.02.006","url":null,"abstract":"<p><p>Deaminases belonging to the AID/APOBEC family are known as ssDNA and mRNA mutators involved in innate/adaptive immunity, mRNA editing, genome stabilization by restricting retrotransposons, and carcinogenesis. Recent studies suggest that the repertoire of AID/APOBEC targets is more diverse than previously thought and imply a broader biological impact of these proteins.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"642-645"},"PeriodicalIF":11.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708066","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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