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Insights into two modes of TdT action in human V(D)J recombination. TdT在人V(D)J重组中的两种作用模式。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-19 DOI: 10.1016/j.tibs.2026.09.010
Marc Delarue, Michael R Lieber
{"title":"Insights into two modes of TdT action in human V(D)J recombination.","authors":"Marc Delarue, Michael R Lieber","doi":"10.1016/j.tibs.2026.09.010","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.010","url":null,"abstract":"<p><p>Terminal deoxynucleotidyl transferase (TdT) is a DNA polymerase expressed in pre-B and pre-T cells that functions in V(D)J recombination to add random nucleotides in a template-independent (TI) mode at junctions between antigen receptor gene segments. However, cellular, biochemical, and structural studies have also revealed a significant, short-length, template-dependent (TD) mode of TdT, in which it takes instructions from a template strand across a double-strand break. Here, we propose that this can occur through an intrachain fold-back synthesis to generate the short inverted repeats at V(D)J recombination junctions observed in early human lymphoid cells and within the adult human antigen receptor repertoire. This duality is also relevant to the functional and structural flexibility observed during the DNA repair process known as nonhomologous DNA end joining (NHEJ).</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149219894","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
Enzyme proximity sequencing: mapping multidimensional enzyme fitness at scale. 酶接近测序：在规模上绘制多维酶适应度。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-16 DOI: 10.1016/j.tibs.2026.09.008
Rosario Vanella, Marco L Ernst, Huanding Ji, Michael A Nash
{"title":"Enzyme proximity sequencing: mapping multidimensional enzyme fitness at scale.","authors":"Rosario Vanella, Marco L Ernst, Huanding Ji, Michael A Nash","doi":"10.1016/j.tibs.2026.09.008","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.008","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149206293","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
Carbamate post-translational modifications: bridging CO2 biology and protein regulation. 氨基甲酸酯翻译后修饰：桥接CO2生物学和蛋白质调控。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-16 DOI: 10.1016/j.tibs.2026.09.014
Rebecca Marie Dewhurst, George M I Weston, Martin J Cann
{"title":"Carbamate post-translational modifications: bridging CO<sub>2</sub> biology and protein regulation.","authors":"Rebecca Marie Dewhurst, George M I Weston, Martin J Cann","doi":"10.1016/j.tibs.2026.09.014","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.014","url":null,"abstract":"<p><p>Carbon dioxide (CO<sub>2</sub>) is a bioactive gas essential for several physiologically important biological processes, including metabolism, acid-base homoeostasis, and chemosensing. CO<sub>2</sub> can directly modulate these processes by stimulating or inhibiting specific cell signalling pathways, including the nuclear factor-κB, calcium, and Wingless (Wnt) pathways. One mechanism by which CO<sub>2</sub> interacts with proteins to modulate cell signalling is through the reversible and nonenzymatic modification of α- N-terminal and lysine ε-amino groups to form the carbamate post-translational modification (PTM). Identifying carbamate PTMs is technically challenging because these modifications are readily reversible. However, emerging techniques have now made possible their identification and functional characterisation. Here, we review recent advances in experimental and computational methods to identify CO<sub>2</sub>-mediated PTMs.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149206243","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
You can't see what you don't look for: why glycan function remains in the dark. 你看不到你不去寻找的东西：为什么聚糖的功能仍然在黑暗中。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-15 DOI: 10.1016/j.tibs.2026.09.013
Lauren E Richardson, Isabella G Steen, Sagar Dalal, Elisa Fadda, Katherine Wongtrakul-Kish, Nicolle H Packer
{"title":"You can't see what you don't look for: why glycan function remains in the dark.","authors":"Lauren E Richardson, Isabella G Steen, Sagar Dalal, Elisa Fadda, Katherine Wongtrakul-Kish, Nicolle H Packer","doi":"10.1016/j.tibs.2026.09.013","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.013","url":null,"abstract":"<p><p>A weakness in glycobiology research is the insufficient integration of approaches used to connect glycan structure to function. From glycogene knockouts to understanding glycan structures, dynamics, and interactions, to determining whether a single glycan structure underlies a specific cellular function, no single approach provides sufficient information to establish these relationships. We argue that resolving glycan structure-function relationships requires the integration of complementary approaches spanning genetics, analytical glycomics, glycoengineering, structural biology, and computational modelling. The field stands at a transition point: from cataloguing glycan structures to understanding their diverse roles in regulating the biology of health and disease. Such an integrated approach will be critical for translating structural glycan information into mechanistic insights and, ultimately, informed glycoengineering and therapeutic design.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149190387","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
Thiol reactivity: lost in the crowd? 硫醇反应性：迷失在人群中？
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-12 DOI: 10.1016/j.tibs.2026.09.011
Eduardo Fuentes-Lemus, Michael J Davies
{"title":"Thiol reactivity: lost in the crowd?","authors":"Eduardo Fuentes-Lemus, Michael J Davies","doi":"10.1016/j.tibs.2026.09.011","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.011","url":null,"abstract":"<p><p>Predictions of cysteine reactivity rely heavily on acidity (pK<sub>a</sub>) data from dilute solutions. However, the intracellular milieu is crowded and dynamic, with substrates, cofactors, and metabolites that modulate reactivity, thereby affecting cell signaling and metabolic adaptation. This forum argues that Cys pK<sub>a</sub> values are necessary but insufficient, proposing an integrated, microenvironment-dependent framework.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149163661","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
Metabolic enzymes moonlighting as protein kinases and phosphatases. 代谢酶兼有蛋白激酶和磷酸酶的作用。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-09 DOI: 10.1016/j.tibs.2026.09.006
Min Li, Guijun Liu, Li Yuan, Zhimin Lu
{"title":"Metabolic enzymes moonlighting as protein kinases and phosphatases.","authors":"Min Li, Guijun Liu, Li Yuan, Zhimin Lu","doi":"10.1016/j.tibs.2026.09.006","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.006","url":null,"abstract":"<p><p>Protein phosphorylation is a central and reversible mechanism regulating virtually all cellular processes and is classically mediated by the canonical protein kinome and phosphatome. However, beyond their traditional roles as metabolic catalysts, a subset of metabolic enzymes also exhibits noncanonical 'moonlighting' activities as protein kinases or phosphatases, directly linking metabolic states to phosphorylation-dependent signaling. These unexpected functions of enzymes involved in glucose, fructose, lipid, nucleotide, and creatine metabolism influence a broad spectrum of cellular processes, including chromatin remodeling, transcription, cell cycle progression, metabolism, autophagy, cell survival and death, and immune responses. As a result, metabolic enzymes are increasingly recognized as key regulators that bridge cellular metabolism and signaling networks, with important implications for both normal physiology and disease.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147029","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
Roots turn decay into a chemical map. 根将腐烂转化为化学地图。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-08 DOI: 10.1016/j.tibs.2026.09.009
Yuting Lei, Lingfei Hu
{"title":"Roots turn decay into a chemical map.","authors":"Yuting Lei, Lingfei Hu","doi":"10.1016/j.tibs.2026.09.009","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.009","url":null,"abstract":"<p><p>Roots navigate soils where abiotic cues intersect with microbial activity. How they extract directional information from microbial processes remains unclear. Bao et al. identify saprotropism, whereby decay-generated pH gradients steer roots via the root meristem growth factor (RGF)-RGF receptor-abscisic acid signaling, revealing how ecological complexity shapes developmental decisions.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149134533","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
Intramembrane proteolysis: principles of substrate recognition and membrane protein fate. 膜内蛋白水解：底物识别和膜蛋白命运的原理。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-05 DOI: 10.1016/j.tibs.2026.09.005
Dönem Avci, Susanne S Steigleder, Marius K Lemberg
{"title":"Intramembrane proteolysis: principles of substrate recognition and membrane protein fate.","authors":"Dönem Avci, Susanne S Steigleder, Marius K Lemberg","doi":"10.1016/j.tibs.2026.09.005","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.005","url":null,"abstract":"<p><p>Intramembrane proteases catalyze peptide bond hydrolysis within cellular membranes, regulating processes including signaling, protein quality control, and membrane protein turnover. Recent advances in cryo-electron microscopy, biochemistry, and molecular dynamics simulations have transformed our understanding of how these enzymes recognize and process substrates within the lipid bilayer. Here, we discuss how dynamic interactions among proteases, substrates, and membranes govern substrate recognition. Structural and biophysical studies reveal how conformational dynamics, membrane remodeling, and specific protease-substrate interactions enable processing of membrane-embedded substrates. Studies of rhomboid pseudoproteases further suggest that transmembrane-domain recognition represents a conserved principle of membrane protein processing that extends beyond proteolysis itself. Finally, we consider how recognition determines membrane protein fate, linking protease activity to signaling, proteostasis, and nonproteolytic scaffolding functions.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102322","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 protein tyrosine phosphatase interactome: beyond catalytic activity. 蛋白酪氨酸磷酸酶相互作用组：超越催化活性。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-02 DOI: 10.1016/j.tibs.2026.09.001
Adina-Gabriela Vasilescu, Andrei-Mihai Vasilescu, Andra-Elena Coșoreanu-Șulea, Ștefan-Eugen Szedlacsek
{"title":"The protein tyrosine phosphatase interactome: beyond catalytic activity.","authors":"Adina-Gabriela Vasilescu, Andrei-Mihai Vasilescu, Andra-Elena Coșoreanu-Șulea, Ștefan-Eugen Szedlacsek","doi":"10.1016/j.tibs.2026.09.001","DOIUrl":"https://doi.org/10.1016/j.tibs.2026.09.001","url":null,"abstract":"<p><p>Protein tyrosine phosphatases (PTPs) are increasingly recognized as regulators of signaling networks rather than mere antagonists of kinases. Interactome-level analyses reveal that many PTPs function as scaffolds that organize spatially constrained signaling complexes, thereby influencing context-dependent signaling outputs. Focusing on representative nonreceptor PTPs (SHP-2, PTPN23, and PTPN13) and receptor PTPs (PTPRM and PTPRK), this review integrates methodological advances that enable increasingly detailed mapping of PTP-centered interactomes. Across cancer, neurobiology, and immune signaling, changes in these assemblies link scaffold function to disease phenotypes. This framework highlights PTP scaffold functions beyond catalysis and emerging therapeutic strategies targeting protein-protein interactions and scaffold-dependent mechanisms.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":14.4,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102469","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
RAF-like protein kinase signaling modules control plant proton pump activity raf样蛋白激酶信号模块控制植物质子泵活性。
IF 14.4 1区 生物学
Trends in Biochemical Sciences Pub Date : 2026-10-01 Epub Date: 2026-08-15 DOI: 10.1016/j.tibs.2026.07.015
Paul E. Verslues
{"title":"RAF-like protein kinase signaling modules control plant proton pump activity","authors":"Paul E. Verslues","doi":"10.1016/j.tibs.2026.07.015","DOIUrl":"10.1016/j.tibs.2026.07.015","url":null,"abstract":"<div><div>Proton extrusion by plasma membrane autoinhibited H<sup>+</sup> ATPases (AHAs) enables stomatal opening and plant cell expansion. <span><span>Takase <em>et al</em>.</span><svg><path></path></svg></span> demonstrated that heterocomplexes of C5 and C7 RAF-like kinases activate AHAs. The modular nature of C5–C7 RAF complexes allows cell-type-specific responses to stimuli, such as stomatal guard-cell CO<sub>2</sub> levels.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"51 10","pages":"Pages 981-983"},"PeriodicalIF":14.4,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148757209","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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