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Unlocking the protein code: how our organs age across a lifetime 解开蛋白质密码：我们的器官在一生中是如何衰老的。
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-12-01 Epub Date: 2025-11-18 DOI: 10.1016/j.tibs.2025.10.002
Dongxue Wang (王冬雪) , Jing Yang (杨靖)
{"title":"Unlocking the protein code: how our organs age across a lifetime","authors":"Dongxue Wang (王冬雪) ,&nbsp;Jing Yang (杨靖)","doi":"10.1016/j.tibs.2025.10.002","DOIUrl":"10.1016/j.tibs.2025.10.002","url":null,"abstract":"<div><div>A recent study by <span><span>Ding <em>et al.</em></span><svg><path></path></svg></span> harnesses cutting-edge proteomics to explore protein changes linked to human aging over 50 years across 12 tissues and plasma. It uncovered asynchronous aging clocks in different organs, redefining aging as a coordinated, targetable network.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 12","pages":"Pages 1049-1050"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145547578","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
MitoTraP: mitochondrial protection for cellular proteostasis MitoTraP：线粒体保护细胞蛋白质静止。
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-12-01 Epub Date: 2025-08-27 DOI: 10.1016/j.tibs.2025.08.004
Michaela Oborská-Oplová , Michael A. Ruoss , Vikram G. Panse
{"title":"MitoTraP: mitochondrial protection for cellular proteostasis","authors":"Michaela Oborská-Oplová ,&nbsp;Michael A. Ruoss ,&nbsp;Vikram G. Panse","doi":"10.1016/j.tibs.2025.08.004","DOIUrl":"10.1016/j.tibs.2025.08.004","url":null,"abstract":"<div><div>Cells depend on the efficient import of thousands of nuclear-encoded mitochondrial proteins to maintain mitochondrial function. A new study by <span><span>Flohr <em>et al</em></span><svg><path></path></svg></span><em>.</em> reveals a quality control strategy that traps a subset of mitochondrial precursors in the intermembrane space during energy stress, preventing their toxic accumulation in the cytosol or nucleus.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 12","pages":"Pages 1047-1048"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938166","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
The Integrator–PP2A complex integrates promoter-proximal premature termination with chromatin context and genome maintenance 整合子- pp2a复合体将启动子-近端过早终止与染色质背景和基因组维持结合起来。
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-12-01 Epub Date: 2025-10-10 DOI: 10.1016/j.tibs.2025.09.006
Aixia Song , Danyi Lu , Fei Xavier Chen
{"title":"The Integrator–PP2A complex integrates promoter-proximal premature termination with chromatin context and genome maintenance","authors":"Aixia Song ,&nbsp;Danyi Lu ,&nbsp;Fei Xavier Chen","doi":"10.1016/j.tibs.2025.09.006","DOIUrl":"10.1016/j.tibs.2025.09.006","url":null,"abstract":"<div><div>Well-regulated transcription is essential for maintaining cellular homeostasis and genome integrity. The Integrator–PP2A complex has emerged as a major regulator of transcription by stimulating promoter-proximal termination of RNA polymerase II (Pol II). By employing dual catalytic activities, Integrator–PP2A shapes transcriptional output, limits aberrant RNA production, and suppresses R-loop–associated genome instability. Integrator–PP2A is highly modular, enabling dynamic interactions with transcription factors and epigenetic modifiers in distinct chromatin contexts and serving as a molecular hub that links transcriptional regulation to RNA quality control, chromatin state, and genome surveillance. Here, we review recent insights into the composition, mechanisms, and regulatory functions of this complex, which together establish its broad roles across both coding and noncoding transcriptional programs.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 12","pages":"Pages 1118-1130"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273483","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
Advisory Board and Contents 咨询委员会及内容
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-12-01 Epub Date: 2025-12-04 DOI: 10.1016/S0968-0004(25)00281-6
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/S0968-0004(25)00281-6","DOIUrl":"10.1016/S0968-0004(25)00281-6","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 12","pages":"Page i"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145665542","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
Decoding protein structures with residue interaction networks 用残基相互作用网络解码蛋白质结构。
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-12-01 Epub Date: 2025-09-05 DOI: 10.1016/j.tibs.2025.08.006
Sol C. Begue , Emanuela Leonardi , Silvio C.E. Tosatto
{"title":"Decoding protein structures with residue interaction networks","authors":"Sol C. Begue ,&nbsp;Emanuela Leonardi ,&nbsp;Silvio C.E. Tosatto","doi":"10.1016/j.tibs.2025.08.006","DOIUrl":"10.1016/j.tibs.2025.08.006","url":null,"abstract":"<div><div>The rise of AlphaFold and similar structure predictors has made it possible to determine the 3D structure of almost any protein from its amino acid sequence. Residue interaction networks (RINs), graphs where residues are represented as nodes and interactions as edges, provide a powerful framework for analyzing and interpreting this surge in structural data. Here, we provide a comprehensive introduction to RINs, exploring different approaches to constructing and analyzing them, including their integration with molecular dynamics (MD) simulations and artificial intelligence (AI). To illustrate their versatility, we present different case studies where RINs have been applied to investigate thermostability, allosterism, post-translational modifications (PTMs), homology, and evolution. Finally, we discuss future directions for RINs, emphasizing opportunities for refinement and broader integration into structural biology.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 12","pages":"Pages 1072-1085"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008056","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
Zn2+ transients and signaling in mammalian systems 哺乳动物系统中的Zn2+瞬态和信号传导。
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-12-01 Epub Date: 2025-10-04 DOI: 10.1016/j.tibs.2025.09.002
Ananya Rakshit , Amy E. Palmer
{"title":"Zn2+ transients and signaling in mammalian systems","authors":"Ananya Rakshit ,&nbsp;Amy E. Palmer","doi":"10.1016/j.tibs.2025.09.002","DOIUrl":"10.1016/j.tibs.2025.09.002","url":null,"abstract":"<div><div>Labile zinc (Zn<sup>2+</sup>) represents an important fraction of the total intracellular zinc pool that is readily available for binding. The signaling function of labile Zn<sup>2+</sup> lies in its dynamic nature. Fluctuations in labile Zn<sup>2+</sup> concentrations caused by either endogenous or exogenous stimuli can transiently influence cellular microenvironments, leading to modulation of signaling pathways. In this review, we focus on recent findings of zinc transients that influence cellular processes in mammalian systems. We highlight different types of zinc transients and how cellular zinc status plays regulatory roles in early development, gene expression, and kinase or neuronal signaling. Although the molecular mechanism behind how zinc transients activate signaling cascades is not clear in all cases, charting these interactions is the first step in the process.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 12","pages":"Pages 1086-1101"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231191","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
Drug ubiquitination: an unwelcome mode of action or a novel modality 药物泛素化：一种不受欢迎的作用方式或一种新的方式。
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-12-01 Epub Date: 2025-10-29 DOI: 10.1016/j.tibs.2025.10.004
Richard A. de Heiden , Monique P.C. Mulder
{"title":"Drug ubiquitination: an unwelcome mode of action or a novel modality","authors":"Richard A. de Heiden ,&nbsp;Monique P.C. Mulder","doi":"10.1016/j.tibs.2025.10.004","DOIUrl":"10.1016/j.tibs.2025.10.004","url":null,"abstract":"<div><div>Recent reports by <span><span>Orth, Pohl, <em>et al.</em></span><svg><path></path></svg></span> and <span><span>Li, Garcia-Rivera <em>et al.</em></span><svg><path></path></svg></span> show that ubiquitin can mark drug-like molecules in cells. This non-canonical ubiquitination, initially discovered with proposed small-molecule HUWE1 inhibitors and a synthesis library component, respectively, offers a versatile chemical tool for probing protein regulation and developing new therapeutics.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 12","pages":"Pages 1045-1046"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145399472","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
Subscription and Copyright Information 订阅及版权资料
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-11-01 Epub Date: 2025-11-14 DOI: 10.1016/S0968-0004(25)00256-7
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/S0968-0004(25)00256-7","DOIUrl":"10.1016/S0968-0004(25)00256-7","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 11","pages":"Page e1"},"PeriodicalIF":11.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145500136","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
Advisory Board and Contents 咨询委员会及内容
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-11-01 Epub Date: 2025-11-14 DOI: 10.1016/S0968-0004(25)00253-1
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/S0968-0004(25)00253-1","DOIUrl":"10.1016/S0968-0004(25)00253-1","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 11","pages":"Pages i-ii"},"PeriodicalIF":11.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145500130","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
Mining the gut microbiota for defluorination activity 挖掘肠道微生物群的除氟活性。
IF 11 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-11-01 Epub Date: 2025-07-18 DOI: 10.1016/j.tibs.2025.07.003
Camille V. Goemans
{"title":"Mining the gut microbiota for defluorination activity","authors":"Camille V. Goemans","doi":"10.1016/j.tibs.2025.07.003","DOIUrl":"10.1016/j.tibs.2025.07.003","url":null,"abstract":"<div><div>The gut microbiota harbors a vast array of enzymes, many with unknown functions. In a recent study, <span><span>Probst <em>et al.</em></span><svg><path></path></svg></span> mined this ecosystem to identify potential defluorinating enzymes. Combining molecular dynamics, alanine scanning, and machine learning, they uncovered molecular features critical for defluorination enzymatic activity in human gut microbes.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 11","pages":"Pages 951-952"},"PeriodicalIF":11.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666758","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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