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Annual review of biochemistry最新文献

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Emerging Approaches for Studying Lipid Dynamics, Metabolism, and Interactions in Cells. 研究细胞中脂质动力学、代谢和相互作用的新方法。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-18 DOI: 10.1146/annurev-biochem-083024-110827
Lin Luan, Nathan P Frederick, Jeremy M Baskin
{"title":"Emerging Approaches for Studying Lipid Dynamics, Metabolism, and Interactions in Cells.","authors":"Lin Luan, Nathan P Frederick, Jeremy M Baskin","doi":"10.1146/annurev-biochem-083024-110827","DOIUrl":"10.1146/annurev-biochem-083024-110827","url":null,"abstract":"<p><p>Lipids are a major class of biological molecules, the primary components of cellular membranes, and critical signaling molecules that regulate cell biology and physiology. Due to their dynamic behavior within membranes, rapid transport between organelles, and complex and often redundant metabolic pathways, lipids have traditionally been considered among the most challenging biological molecules to study. In recent years, a plethora of tools bridging the chemistry-biology interface has emerged for studying different aspects of lipid biology. Here, we provide an overview of these approaches. We discuss methods for lipid detection, including genetically encoded biosensors, synthetic lipid analogs, and metabolic labeling probes. For targeted manipulation of lipids, we describe pharmacological agents and controllable enzymes, termed membrane editors, that harness optogenetics and chemogenetics. To conclude, we survey techniques for elucidating lipid-protein interactions, including photoaffinity labeling and proximity labeling. Collectively, these strategies are revealing new insights into the regulation, dynamics, and functions of lipids in cell biology.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"417-446"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655884","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
Biochemical Mechanisms of Genetic Recombination and DNA Repair. 基因重组和DNA修复的生化机制。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-28 DOI: 10.1146/annurev-biochem-083024-113931
Vivek B Raina, Aidan Jessop, Eric C Greene
{"title":"Biochemical Mechanisms of Genetic Recombination and DNA Repair.","authors":"Vivek B Raina, Aidan Jessop, Eric C Greene","doi":"10.1146/annurev-biochem-083024-113931","DOIUrl":"10.1146/annurev-biochem-083024-113931","url":null,"abstract":"<p><p>Genetic recombination involves the exchange of genetic material between homologous sequences of DNA. It is employed during meiosis in sexually reproducing organisms or in somatic cells to accurately repair toxic DNA lesions like double-strand breaks and stalled replication forks. In these separate roles, recombination drives genetic diversity by enabling reshuffling of parental genetic information while also serving as a molecular safeguard against the deleterious effects of gross chromosomal rearrangements or mutagenic insults arising for either endogenous or exogenous reasons. In both cases, efficient recombination ensures faithful transmission of genetic information to subsequent generations. In this review, we provide an exploration of the biochemical mechanisms driving genetic recombination, elucidating the molecular intricacies of fundamental processes involved therein with a focus on mechanistic insights gained into these processes using biochemical and single-molecule techniques.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"161-193"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735580","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
Inhibiting Lipopolysaccharide Biogenesis: The More You Know the Further You Go. 抑制脂多糖生物生成：你知道得越多，你走得越远。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 DOI: 10.1146/annurev-biochem-032620-104707
Caitlin B Moffatt, Bailey A Plaman, Sebastian J Rowe, Alessio Caruso, Stephen A Early, Natividad Ruiz, Daniel Kahne
{"title":"Inhibiting Lipopolysaccharide Biogenesis: The More You Know the Further You Go.","authors":"Caitlin B Moffatt, Bailey A Plaman, Sebastian J Rowe, Alessio Caruso, Stephen A Early, Natividad Ruiz, Daniel Kahne","doi":"10.1146/annurev-biochem-032620-104707","DOIUrl":"10.1146/annurev-biochem-032620-104707","url":null,"abstract":"<p><p>Gram-negative bacteria are intrinsically resistant to many antibiotics because they are surrounded by an outer membrane that creates a robust permeability barrier. The outer membrane has an unusual asymmetric structure with a periplasmic leaflet composed of phospholipids and an outer leaflet composed of lipopolysaccharides. Because lipid biosynthesis is completed in the inner membrane of these didermic bacteria, these components must be transported across the cell envelope and properly assembled to expand the outer membrane during growth and division. Lipopolysaccharide molecules are transported over a multi-protein transenvelope bridge that is powered by ATP hydrolysis in the cytoplasm. This review discusses how this bridge is assembled and functions and how lipopolysaccharide transport is regulated to ensure balanced growth of all envelope layers. A combination of approaches and new experimental tools have significantly advanced our understanding of this molecular machine and contributed to the development of new antimicrobials that interfere with transport.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"94 1","pages":"137-160"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144336260","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
A Lipid-Raft Theory of Alzheimer's Disease. 阿尔茨海默病的脂质筏理论
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2024-10-30 DOI: 10.1146/annurev-biochem-052024-115455
Ari Rappoport
{"title":"A Lipid-Raft Theory of Alzheimer's Disease.","authors":"Ari Rappoport","doi":"10.1146/annurev-biochem-052024-115455","DOIUrl":"10.1146/annurev-biochem-052024-115455","url":null,"abstract":"<p><p>I present a theory of Alzheimer's disease (AD) that explains its symptoms, pathology, and risk factors. To do this, I introduce a new theory of brain plasticity that elucidates the physiological roles of AD-related agents. New events generate synaptic and branching candidates competing for long-term enhancement. Competition resolution crucially depends on the formation of membrane lipid rafts, which requires astrocyte-produced cholesterol. Sporadic AD is caused by impaired formation of plasma-membrane lipid rafts, preventing the conversion of short- to long-term memory and yielding excessive tau phosphorylation, intracellular cholesterol accumulation, synaptic dysfunction, and neurodegeneration. Amyloid β (Aβ) production is promoted by cholesterol during the switch to competition resolution, and cholesterol accumulation stimulates chronic Aβ production, secretion, and aggregation. The theory addresses all of the major established facts known about the disease and is supported by strong evidence.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"387-416"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543236","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
Topoisomerase Regulation of Cancer Gene Expression. 拓扑异构酶对肿瘤基因表达的调控。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-18 DOI: 10.1146/annurev-biochem-091724-010717
Laura Baranello, Fedor Kouzine, David Levens
{"title":"Topoisomerase Regulation of Cancer Gene Expression.","authors":"Laura Baranello, Fedor Kouzine, David Levens","doi":"10.1146/annurev-biochem-091724-010717","DOIUrl":"10.1146/annurev-biochem-091724-010717","url":null,"abstract":"<p><p>Under hyperproliferative conditions, escalation of genomic activity provokes high levels of DNA mechanical stress. Cancer cells cope with this stress through topoisomerase activity. Topoisomerases support genome-wide programs, including those driven by oncogenes and tumor suppressors, by adjusting the supercoiling and by interacting with the regulatory complexes involved in transcription, replication, and chromatin transactions. Topoisomerases also manage DNA conformational alterations that control gene activity. However, when the topological stress from oncogene-driven processes exceeds topoisomerase capacity, aberrant structures associated with DNA damage arise. These abnormalities include R-loop formation during transcription and replication. Excessive supercoiling also creates transcription-replication conflicts triggering DNA damage. Topoisomerase catalytic failure elicits topological dysregulation and DNA damage. This damage contributes further to tumorigenesis and tumor progression. The roles of topoisomerases in various genetic processes have been widely described, but the cancer-specific functions of topoisomerases are incompletely understood. Here, we summarize the crucial roles played by topoisomerases in cancer.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"333-359"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655566","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
Endothelial Glycocalyx Turnover in Vascular Health and Disease: Rethinking Endothelial Dysfunction. 血管健康与疾病中的内皮糖萼转换：对内皮功能障碍的再思考。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-25 DOI: 10.1146/annurev-biochem-032620-104745
Alejandro Gomez Toledo, Gregory J Golden, Richard D Cummings, Johan Malmström, Jeffrey D Esko
{"title":"Endothelial Glycocalyx Turnover in Vascular Health and Disease: Rethinking Endothelial Dysfunction.","authors":"Alejandro Gomez Toledo, Gregory J Golden, Richard D Cummings, Johan Malmström, Jeffrey D Esko","doi":"10.1146/annurev-biochem-032620-104745","DOIUrl":"10.1146/annurev-biochem-032620-104745","url":null,"abstract":"<p><p>The endothelial glycocalyx, a glycan-rich layer on the luminal surface of endothelial cells lining blood and lymphatic vessels, plays a crucial role in vascular homeostasis by regulating vascular permeability, immune cell trafficking, and vascular tone. Dysregulated endothelial glycocalyx turnover-whether through altered synthesis, intracellular degradation, or shedding-contributes to endothelial dysfunction in conditions such as sepsis, ischemic events, and chronic inflammatory disorders including diabetes and atherosclerosis. In this review, we examine the structure, function, and turnover of the endothelial glycocalyx, emphasizing how pathological changes in its turnover drive vascular dysfunction. We also highlight diagnostic approaches to evaluate dysregulated endothelial glycocalyx turnover in connection with vascular diseases and discuss therapeutic strategies aimed at preventing endothelial glycocalyx degradation and restoring endothelial function.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"561-586"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708246","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
Electron Transport Across Bacterial Cell Envelopes. 细菌细胞膜上的电子传递。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-17 DOI: 10.1146/annurev-biochem-052621-092202
Joshua A J Burton, Marcus J Edwards, David J Richardson, Thomas A Clarke
{"title":"Electron Transport Across Bacterial Cell Envelopes.","authors":"Joshua A J Burton, Marcus J Edwards, David J Richardson, Thomas A Clarke","doi":"10.1146/annurev-biochem-052621-092202","DOIUrl":"10.1146/annurev-biochem-052621-092202","url":null,"abstract":"<p><p>Extracellular electron transfer is an ancient and ubiquitous process that is used by a range of microorganisms to exchange electrons between the cell and environment. These electron transfer reactions can impact the solubility and speciation of redox-active molecules in the environment, such as metal oxides, while allowing bacteria to survive in areas of limited nutrient availability. Controlled transfer of electrons across the cell envelope requires assembly of electron transport chains that must pass through the outer membrane of Gram-negative bacteria or the S-layer of Gram-positive bacteria, but the mechanisms used by bacteria are still far from understood. Here, we review the literature surrounding characterized extracellular electron transfer pathways and use protein modeling tools to investigate novel electron transfer proteins and protein complexes. While these protein models are hypothetical, they provide new insight into features that may explain how extracellular electron transfer complexes interact with a range of different environmental substrates.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"89-109"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647213","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
Exploiting Covalent Chemical Labeling with Self-Labeling Proteins. 利用自标记蛋白开发共价化学标记。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-19 DOI: 10.1146/annurev-biochem-030222-121016
Nicola Porzberg, Klara Gries, Kai Johnsson
{"title":"Exploiting Covalent Chemical Labeling with Self-Labeling Proteins.","authors":"Nicola Porzberg, Klara Gries, Kai Johnsson","doi":"10.1146/annurev-biochem-030222-121016","DOIUrl":"10.1146/annurev-biochem-030222-121016","url":null,"abstract":"<p><p>The visualization and manipulation of proteins in live cells are critical for studying complex biological processes. Self-labeling proteins do so by enabling the specific and covalent attachment of synthetic probes, offering unprecedented flexibility in the chemical labeling of proteins in live cells and in vivo. By combining the excellent photophysical properties of synthetic dyes with genetic targetability, these tags provide a modular and innovative toolbox for live-cell and high-resolution fluorescence imaging. In this review, we explore the development and diverse applications of the key self-labeling protein technologies, HaloTag7, SNAP-tag, and CLIP-tag, as well as the covalent trimethoprim (TMP)-tag. We discuss recent innovations in both protein engineering and substrate design that have introduced new functionalities to enable multiplexed imaging, super-resolution microscopy, and the design of novel biosensors and recorders.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"29-58"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662109","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
Assembly and Dynamics of Transcription Initiation Complexes. 转录起始复合物的组装和动力学。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-25 DOI: 10.1146/annurev-biochem-072324-035226
Meagan N Esbin, Trinity Cookis, Sathvik Anantakrishnan, Abrar A Abidi, Jonathan Karr, Claudia Cattoglio, Xavier Darzacq, Robert Tjian
{"title":"Assembly and Dynamics of Transcription Initiation Complexes.","authors":"Meagan N Esbin, Trinity Cookis, Sathvik Anantakrishnan, Abrar A Abidi, Jonathan Karr, Claudia Cattoglio, Xavier Darzacq, Robert Tjian","doi":"10.1146/annurev-biochem-072324-035226","DOIUrl":"10.1146/annurev-biochem-072324-035226","url":null,"abstract":"<p><p>Gene expression is essential for life and development, allowing the cell to modulate mRNA production in response to intrinsic and extracellular cues. Initiation of gene transcription requires a highly regulated molecular process to assemble multisubunit complexes into the preinitiation complex (PIC). Attempts to visualize these processes have been driven largely by electron microscopy, with near atomic-level resolution producing static snapshots complemented by low-resolution fluorescence cell imaging. Here, we review how new advances in superresolution single-molecule imaging in live cells can track transcription across vast spatiotemporal scales. We discuss how recent imaging research has fundamentally recast our understanding of PIC assembly from a stable, ordered process to one constantly in flux, dominated by multivalent weak interactions. We also discuss future advancements that will further expand our ability to measure PIC assembly in concert with cellular behavior, predict complex interactions computationally, and target undruggable transcription factors to treat human disease.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"305-331"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708186","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
Heme Oxygenase-Like Metalloenzymes. 血红素加氧酶样金属酶。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2025-06-01 Epub Date: 2025-03-27 DOI: 10.1146/annurev-biochem-030122-043608
Sarah R Pope, Molly J McBride, Mrutyunjay A Nair, Xavier E Salas-Solá, Carsten Krebs, J Martin Bollinger, Amie K Boal
{"title":"Heme Oxygenase-Like Metalloenzymes.","authors":"Sarah R Pope, Molly J McBride, Mrutyunjay A Nair, Xavier E Salas-Solá, Carsten Krebs, J Martin Bollinger, Amie K Boal","doi":"10.1146/annurev-biochem-030122-043608","DOIUrl":"10.1146/annurev-biochem-030122-043608","url":null,"abstract":"<p><p>Heme oxygenase (HO)-like metalloenzymes are an emerging protein superfamily diverse in reaction outcome and mechanism. Found primarily in bacterial biosynthetic pathways, members conserve a flexible protein scaffold shared with the heme catabolic enzyme, HO, and a set of metal-binding residues. Most HO-like metalloenzymes assemble a diiron cluster, although manganese-iron and mononuclear iron cofactors can also be accommodated. In the canonical HO-like diiron oxygenases/oxidases (HDOs), an Fe<sub>2</sub>(II/II) complex reacts with O<sub>2</sub> to form a peroxo-Fe<sub>2</sub>(III/III) intermediate (<b>P</b>), common to all HDOs studied to date. The HO-like scaffold confers both distinctive metal-binding properties, allowing for dynamic cofactor assembly and disassembly, and unusual reactivity to its associated metallocofactor. These features may prove to be important in HDO-mediated catalysis of the fragmentation and rearrangement reactions that remain unprecedented among other dinuclear iron enzymes. Much of the sequence space in the HO-like metalloenzyme superfamily remains unexplored, offering exciting opportunities for the discovery of new mechanisms and reactivities.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"59-88"},"PeriodicalIF":12.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727519","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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