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The emerging roles of S-acylation in autophagy. s -酰化在自噬中的新作用。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-26 DOI: 10.1016/j.tibs.2025.02.007
Jia Yao, Chunyang Xie, Aimin Yang
{"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":"https://doi.org/10.1016/j.tibs.2025.02.007","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-03-26","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}
引用次数: 0
AID/APOBEC: an expanding repertoire of targets and functions. AID/APOBEC：目标和职能的扩展曲目。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-24 DOI: 10.1016/j.tibs.2025.02.006
Lucyna Budzko, Aleksandra Mierzwa, Marek Figlerowicz
{"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":"https://doi.org/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":""},"PeriodicalIF":11.6,"publicationDate":"2025-03-24","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}
引用次数: 0
Thermal proteome profiling of protein-centric interactions and modifications. 蛋白质中心相互作用和修饰的热蛋白质组分析。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-17 DOI: 10.1016/j.tibs.2025.02.002
Zhenghui Chen, Anhui Wang, Yiqun Geng
{"title":"Thermal proteome profiling of protein-centric interactions and modifications.","authors":"Zhenghui Chen, Anhui Wang, Yiqun Geng","doi":"10.1016/j.tibs.2025.02.002","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.02.002","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655572","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}
引用次数: 0
Stress responses induced by perturbation of the ubiquitin–proteasome system 泛素-蛋白酶体系统扰动诱导的应激反应。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-01 DOI: 10.1016/j.tibs.2024.12.011
Mamta Rai , Liam C. Hunt , Fabio Demontis
{"title":"Stress responses induced by perturbation of the ubiquitin–proteasome system","authors":"Mamta Rai ,&nbsp;Liam C. Hunt ,&nbsp;Fabio Demontis","doi":"10.1016/j.tibs.2024.12.011","DOIUrl":"10.1016/j.tibs.2024.12.011","url":null,"abstract":"<div><div>The ubiquitin–proteasome system is key for proteostasis and its disruption can induce several cellular adaptations. Here, we summarize the range of cellular responses that are induced by perturbation of distinct components of the ubiquitin–proteasome system, and how proteasome stress in a tissue can induce systemic responses in distant tissues.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 3","pages":"Pages 175-178"},"PeriodicalIF":11.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942328","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}
引用次数: 0
Regulating Nrf2 activity: ubiquitin ligases and signaling molecules in redox homeostasis 调控Nrf2活性：氧化还原稳态中的泛素连接酶和信号分子。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-01 DOI: 10.1016/j.tibs.2024.12.010
John D. Hayes , Sharadha Dayalan Naidu , Albena T. Dinkova-Kostova
{"title":"Regulating Nrf2 activity: ubiquitin ligases and signaling molecules in redox homeostasis","authors":"John D. Hayes ,&nbsp;Sharadha Dayalan Naidu ,&nbsp;Albena T. Dinkova-Kostova","doi":"10.1016/j.tibs.2024.12.010","DOIUrl":"10.1016/j.tibs.2024.12.010","url":null,"abstract":"<div><div>Transcription factor NF-E2 p45-related factor 2 (Nrf2) orchestrates defenses against oxidants and thiol-reactive electrophiles. It is controlled at the protein stability level by several E3 ubiquitin ligases (CRL3<sup>Keap1</sup>, CRL4<sup>DCAF11</sup>, SCF<sup>β-TrCP</sup>, and Hrd1). CRL3<sup>Keap1</sup> is of the greatest importance because it constitutively targets Nrf2 for proteasomal degradation under homeostatic conditions but is prevented from doing so by oxidative stressors. Repression of Nrf2 by CRL3<sup>Keap1</sup> is attenuated by SQSTM1/p62, and this is reinforced by phosphorylation of SQSTM1/p62. Repression by SCF<sup>β-TrCP</sup> requires phosphorylation of Nrf2 by GSK3, the activity of which is inhibited by PKB/Akt and other kinases. We discuss how Nrf2 activity is controlled by the ubiquitin ligases under different circumstances. We also describe endogenous signaling molecules that inactivate CRL3<sup>Keap1</sup> to alleviate stress and restore homeostasis.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 3","pages":"Pages 179-205"},"PeriodicalIF":11.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057630","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}
引用次数: 0
Journey to the past: molecular de-extinction enables the discovery of ancient β-defensins and highlights their evolutionary history 过去的旅程：分子去灭绝使发现古代β-防御素和突出他们的进化史。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-01 DOI: 10.1016/j.tibs.2024.12.002
Françoise Gosti
{"title":"Journey to the past: molecular de-extinction enables the discovery of ancient β-defensins and highlights their evolutionary history","authors":"Françoise Gosti","doi":"10.1016/j.tibs.2024.12.002","DOIUrl":"10.1016/j.tibs.2024.12.002","url":null,"abstract":"<div><div>Molecular de-extinction is an innovative science aiming to discover, synthesize, and characterize molecules throughout evolution. Recent work by <span><span>Ferreira <em>et al</em>.</span><svg><path></path></svg></span> involved mining ancient genomes to search for antimicrobial defensins. They discovered six ancient β-defensins, revealing their evolutionary history and uncovering their structural and biochemical properties, which could feed medical applications.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 3","pages":"Pages 173-174"},"PeriodicalIF":11.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891261","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}
引用次数: 0
Mechanisms and rationales of SAM homeostasis SAM稳态的机制和原理。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-01 DOI: 10.1016/j.tibs.2024.12.009
Zheng Xing , Benjamin P. Tu
{"title":"Mechanisms and rationales of SAM homeostasis","authors":"Zheng Xing ,&nbsp;Benjamin P. Tu","doi":"10.1016/j.tibs.2024.12.009","DOIUrl":"10.1016/j.tibs.2024.12.009","url":null,"abstract":"<div><div><em>S</em>-Adenosylmethionine (SAM) is the primary methyl donor for numerous cellular methylation reactions. Its central role in methylation and involvement with many pathways link its availability to the regulation of cellular processes, the dysregulation of which can contribute to disease states, such as cancer or neurodegeneration. Emerging evidence indicates that intracellular SAM levels are maintained within an optimal range by a variety of homeostatic mechanisms. This suggests that the need to maintain SAM homeostasis represents a significant evolutionary pressure across all kingdoms of life. Here, we review how SAM controls cellular functions at the molecular level and discuss strategies to maintain SAM homeostasis. We propose that SAM exerts a broad and underappreciated influence in cellular regulation that remains to be fully elucidated.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 3","pages":"Pages 242-254"},"PeriodicalIF":11.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998216","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}
引用次数: 0
Glucokinase: from allosteric glucose sensing to disease variants 葡萄糖激酶：从变构葡萄糖感应到疾病变异。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-01 DOI: 10.1016/j.tibs.2024.12.007
Sarah Gersing , Torben Hansen , Kresten Lindorff-Larsen , Rasmus Hartmann-Petersen
{"title":"Glucokinase: from allosteric glucose sensing to disease variants","authors":"Sarah Gersing ,&nbsp;Torben Hansen ,&nbsp;Kresten Lindorff-Larsen ,&nbsp;Rasmus Hartmann-Petersen","doi":"10.1016/j.tibs.2024.12.007","DOIUrl":"10.1016/j.tibs.2024.12.007","url":null,"abstract":"<div><div>Human glucokinase (GCK) functions as a glucose sensor in the pancreas and liver, where GCK activity regulates insulin secretion and glycogen synthesis, respectively. GCK’s low affinity for glucose and the sigmoidal substrate dependency of enzymatic turnover enables it to act as a sensor that makes cells responsive to changes in circulating glucose levels. Its unusual kinetic properties are intrinsically linked to the enzyme’s conformational dynamics. Accordingly, genetic variants that alter the dynamics or other aspects of GCK function are linked to three glucose homeostasis diseases. In this review, we describe the enzyme GCK, focusing on its role as a glucose sensor, its unusual kinetic properties, and recent large-scale efforts to assess GCK variant effects.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 3","pages":"Pages 255-266"},"PeriodicalIF":11.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926132","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}
引用次数: 0
Z-DNA at the crossroads: untangling its role in genome dynamics 十字路口的Z-DNA：解开它在基因组动力学中的作用。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-01 DOI: 10.1016/j.tibs.2025.01.001
Vinodh J. Sahayasheela , Mitsuharu Ooga , Tomotaka Kumagai , Hiroshi Sugiyama
{"title":"Z-DNA at the crossroads: untangling its role in genome dynamics","authors":"Vinodh J. Sahayasheela ,&nbsp;Mitsuharu Ooga ,&nbsp;Tomotaka Kumagai ,&nbsp;Hiroshi Sugiyama","doi":"10.1016/j.tibs.2025.01.001","DOIUrl":"10.1016/j.tibs.2025.01.001","url":null,"abstract":"<div><div>DNA can fold into noncanonical left-handed Z-DNA conformation beyond the right-handed B-DNA. While its crystal structure was discovered nearly four decades ago, it was predominantly considered a structural curiosity. Recent evidence suggests that Z-DNA formation occurs in nuclear and mitochondrial DNA (mtDNA), with significant biological implications. However, our understanding of its roles remains in its infancy, primarily due to a lack of study tools. In this review we summarize the structure and function of Z-DNA within the genome while addressing the difficulties associated with identifying and investigating its role(s). We then critically evaluate several intracellular factors that can modulate and regulate Z-DNA. Additionally, we discuss the recent technological and methodological advances that may overcome the challenges and enhance our understanding of Z-DNA.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 3","pages":"Pages 267-279"},"PeriodicalIF":11.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057633","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}
引用次数: 0
PARPs and ADP-ribosylation-mediated biomolecular condensates: determinants, dynamics, and disease implications PARPs和adp核糖基化介导的生物分子凝聚物：决定因素、动力学和疾病意义。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-03-01 DOI: 10.1016/j.tibs.2024.12.013
Hongrui Liu , Meenakshi Pillai , Anthony K.L. Leung
{"title":"PARPs and ADP-ribosylation-mediated biomolecular condensates: determinants, dynamics, and disease implications","authors":"Hongrui Liu ,&nbsp;Meenakshi Pillai ,&nbsp;Anthony K.L. Leung","doi":"10.1016/j.tibs.2024.12.013","DOIUrl":"10.1016/j.tibs.2024.12.013","url":null,"abstract":"<div><div>Biomolecular condensates are cellular compartments that selectively enrich proteins and other macromolecules despite lacking enveloping membranes. These compartments often form through phase separation triggered by multivalent nucleic acids. Emerging data have revealed that poly(ADP-ribose) (PAR), a nucleic acid-based protein modification catalyzed by ADP-ribosyltransferases (commonly known as PARPs), plays a crucial role in this process. This review focuses on the role of PARPs and ADP-ribosylation, and explores the principles and mechanisms by which PAR regulates condensate formation, dissolution, and dynamics. Future studies with advanced tools to examine PAR binding sites, substrate interactions, PAR length and structure, and transitions from condensates to aggregates will be key to unraveling the complexity of ADP-ribosylation in health and disease, including cancer, viral infection, and neurodegeneration.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 3","pages":"Pages 224-241"},"PeriodicalIF":11.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143373631","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}
引用次数: 0
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