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Annual review of biochemistry最新文献

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A Cool Look at Positive-Strand RNA Virus Replication Organelles: New Insights from Cryo–Electron Microscopy 正链 RNA 病毒复制细胞器的酷炫外观：冷冻电子显微镜的新发现
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-052521-115736
Nina L. de Beijer, Eric J. Snijder, Montserrat Bárcena
{"title":"A Cool Look at Positive-Strand RNA Virus Replication Organelles: New Insights from Cryo–Electron Microscopy","authors":"Nina L. de Beijer, Eric J. Snijder, Montserrat Bárcena","doi":"10.1146/annurev-biochem-052521-115736","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-115736","url":null,"abstract":"Positive-strand RNA viruses encompass a variety of established and emerging eukaryotic pathogens. Their genome replication is confined to specialized cytoplasmic membrane compartments known as replication organelles (ROs). These ROs derive from host membranes, transformed into distinct structures such as invaginated spherules or intricate membrane networks including single- and/or double-membrane vesicles. ROs play a vital role in orchestrating viral RNA synthesis and evading detection by innate immune sensors of the host. In recent years, groundbreaking cryo–electron microscopy studies conducted with several prototypic viruses have significantly advanced our understanding of RO structure and function. Notably, these studies unveiled the presence of crown-shaped multimeric viral protein complexes that seem to actively participate in viral RNA synthesis and regulate the release of newly synthesized RNA into the cytosol for translation and packaging. These findings have shed light on novel viral functions and fascinating macromolecular complexes that delineate promising new avenues for future research.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"68 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598961","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
Replication and Transcription of Human Mitochondrial DNA 人类线粒体 DNA 的复制和转录
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-052621-092014
Maria Falkenberg, Nils-Göran Larsson, Claes M. Gustafsson
{"title":"Replication and Transcription of Human Mitochondrial DNA","authors":"Maria Falkenberg, Nils-Göran Larsson, Claes M. Gustafsson","doi":"10.1146/annurev-biochem-052621-092014","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052621-092014","url":null,"abstract":"Mammalian mitochondrial DNA (mtDNA) is replicated and transcribed by phage-like DNA and RNA polymerases, and our understanding of these processes has progressed substantially over the last several decades. Molecular mechanisms have been elucidated by biochemistry and structural biology and essential in vivo roles established by cell biology and mouse genetics. Single molecules of mtDNA are packaged by mitochondrial transcription factor A into mitochondrial nucleoids, and their level of compaction influences the initiation of both replication and transcription. Mutations affecting the molecular machineries replicating and transcribing mtDNA are important causes of human mitochondrial disease, reflecting the critical role of the genome in oxidative phosphorylation system biogenesis. Mechanisms controlling mtDNA replication and transcription still need to be clarified, and future research in this area is likely to open novel therapeutic possibilities for treating mitochondrial dysfunction.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"300 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598798","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
Replication–Transcription Conflicts: A Perpetual War on the Chromosome 复制-转录冲突：染色体上的持久战
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030222-115809
Kaitlyn R. Browning, Houra Merrikh
{"title":"Replication–Transcription Conflicts: A Perpetual War on the Chromosome","authors":"Kaitlyn R. Browning, Houra Merrikh","doi":"10.1146/annurev-biochem-030222-115809","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-115809","url":null,"abstract":"DNA replication and transcription occur in all living cells across all domains of life. Both essential processes occur simultaneously on the same template, leading to conflicts between the macromolecular machines that perform these functions. Numerous studies over the past few decades demonstrate that this is an inevitable problem in both prokaryotic and eukaryotic cells. We have learned that conflicts lead to replication fork reversal, breaks in the DNA, R-loop formation, topological stress, and mutagenesis, and they can ultimately impact evolution. Recent studies have also provided insight into the various mechanisms that mitigate, resolve, and allow tolerance of conflicts and how conflicts result in divergent pathological consequences across divergent species. In this review, we summarize current knowledge regarding the outcomes of encounters between replication and transcription machineries and explore how these clashes are dealt with across species.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"39 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598800","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 Art and Science of Molecular Docking 分子对接的艺术与科学
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030222-120000
Joseph M. Paggi, Ayush Pandit, Ron O. Dror
{"title":"The Art and Science of Molecular Docking","authors":"Joseph M. Paggi, Ayush Pandit, Ron O. Dror","doi":"10.1146/annurev-biochem-030222-120000","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-120000","url":null,"abstract":"Molecular docking has become an essential part of a structural biologist's and medicinal chemist's toolkits. Given a chemical compound and the three-dimensional structure of a molecular target—for example, a protein—docking methods fit the compound into the target, predicting the compound's bound structure and binding energy. Docking can be used to discover novel ligands for a target by screening large virtual compound libraries. Docking can also provide a useful starting point for structure-based ligand optimization or for investigating a ligand's mechanism of action. Advances in computational methods, including both physics-based and machine learning approaches, as well as in complementary experimental techniques, are making docking an even more powerful tool. We review how docking works and how it can drive drug discovery and biological research. We also describe its current limitations and ongoing efforts to overcome them.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"103 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599105","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
How Natural Enzymes and Synthetic Ribozymes Generate Methylated Nucleotides in RNA 天然酶和合成核糖酶如何在 RNA 中生成甲基化核苷酸
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030222-112310
Claudia Höbartner, Katherine E. Bohnsack, Markus T. Bohnsack
{"title":"How Natural Enzymes and Synthetic Ribozymes Generate Methylated Nucleotides in RNA","authors":"Claudia Höbartner, Katherine E. Bohnsack, Markus T. Bohnsack","doi":"10.1146/annurev-biochem-030222-112310","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-112310","url":null,"abstract":"Methylation of RNA nucleotides represents an important layer of gene expression regulation, and perturbation of the RNA methylome is associated with pathophysiology. In cells, RNA methylations are installed by RNA methyltransferases (RNMTs) that are specialized to catalyze particular types of methylation (ribose or different base positions). Furthermore, RNMTs must specifically recognize their appropriate target RNAs within the RNA-dense cellular environment. Some RNMTs are catalytically active alone and achieve target specificity via recognition of sequence motifs and/or RNA structures. Others function together with protein cofactors that can influence stability, <jats:italic>S</jats:italic>-adenosyl-L-methionine binding, and RNA affinity as well as aiding specific recruitment and catalytic activity. Association of RNMTs with guide RNAs represents an alternative mechanism to direct site-specific methylation by an RNMT that lacks intrinsic specificity. Recently, ribozyme-catalyzed methylation of RNA has been achieved in vitro, and here, we compare these different strategies for RNA methylation from structural and mechanistic perspectives.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"57 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598795","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
Natural and Engineered Guide RNA–directed Transposition with CRISPR-Associated Tn7-like Transposons 利用 CRISPR 相关 Tn7 类转座子进行天然和工程化的引导 RNA 定向转座
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030122-041908
Shan-Chi Hsieh, Joseph E. Peters
{"title":"Natural and Engineered Guide RNA–directed Transposition with CRISPR-Associated Tn7-like Transposons","authors":"Shan-Chi Hsieh, Joseph E. Peters","doi":"10.1146/annurev-biochem-030122-041908","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030122-041908","url":null,"abstract":"CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated nuclease) defense systems have been naturally coopted for guide RNA–directed transposition on multiple occasions. In all cases, cooption occurred with diverse elements related to the bacterial transposon Tn7. Tn7 tightly controls transposition; the transposase is activated only when special targets are recognized by dedicated target-site selection proteins. Tn7 and the Tn7-like elements that coopted CRISPR–Cas systems evolved complementary targeting pathways: one that recognizes a highly conserved site in the chromosome and a second pathway that targets mobile plasmids capable of cell-to-cell transfer. Tn7 and Tn7-like elements deliver a single integration into the site they recognize and also control the orientation of the integration event, providing future potential for use as programmable gene-integration tools. Early work has shown that guide RNA–directed transposition systems can be adapted to diverse hosts, even within microbial communities, suggesting great potential for engineering these systems as powerful gene-editing tools.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"59 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598805","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 Story of RNA Unfolded: The Molecular Function of DEAD- and DExH-Box ATPases and Their Complex Relationship with Membraneless Organelles RNA 展开的故事：DEAD-和DExH-Box ATP酶的分子功能及其与无膜细胞器的复杂关系
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-052521-121259
Kerstin Dörner, Maria Hondele
{"title":"The Story of RNA Unfolded: The Molecular Function of DEAD- and DExH-Box ATPases and Their Complex Relationship with Membraneless Organelles","authors":"Kerstin Dörner, Maria Hondele","doi":"10.1146/annurev-biochem-052521-121259","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-121259","url":null,"abstract":"DEAD- and DExH-box ATPases (DDX/DHXs) are abundant and highly conserved cellular enzymes ubiquitously involved in RNA processing. By remodeling RNA–RNA and RNA–protein interactions, they often function as gatekeepers that control the progression of diverse RNA maturation steps. Intriguingly, most DDX/DHXs localize to membraneless organelles (MLOs) such as nucleoli, nuclear speckles, stress granules, or processing bodies. Recent findings suggest not only that localization to MLOs can promote interaction between DDX/DHXs and their targets but also that DDX/DHXs are key regulators of MLO formation and turnover through their condensation and ATPase activity. In this review, we describe the molecular function of DDX/DHXs in ribosome biogenesis, messenger RNA splicing, export, translation, and storage or decay as well as their association with prominent MLOs. We discuss how the enzymatic function of DDX/DHXs in RNA processing is linked to DDX/DHX condensation, the accumulation of ribonucleoprotein particles and MLO dynamics. Future research will reveal how these processes orchestrate the RNA life cycle in MLO space and DDX/DHX time.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"8 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599015","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 Endo-Lysosomal Damage Response 内溶酶体损伤反应
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030222-102505
Hemmo Meyer, Bojana Kravic
{"title":"The Endo-Lysosomal Damage Response","authors":"Hemmo Meyer, Bojana Kravic","doi":"10.1146/annurev-biochem-030222-102505","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-102505","url":null,"abstract":"Lysosomes are the degradative endpoints of material delivered by endocytosis and autophagy and are therefore particularly prone to damage. Membrane permeabilization or full rupture of lysosomal or late endosomal compartments is highly deleterious because it threatens cellular homeostasis and can elicit cell death and inflammatory signaling. Cells have developed a complex response to endo-lysosomal damage that largely consists of three branches. Initially, a number of repair pathways are activated to restore the integrity of the lysosomal membrane. If repair fails or if damage is too extensive, lysosomes are isolated and degraded by a form of selective autophagy termed lysophagy. Meanwhile, an mTORC1-governed signaling cascade drives biogenesis and regeneration of new lysosomal components to reestablish the full lysosomal capacity of the cell. This damage response is vital to counteract the effects of various conditions, including neurodegeneration and infection, and can constitute a critical vulnerability in cancer cells.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"97 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599092","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
Structural Biochemistry of Muscle Contraction. 肌肉收缩的结构生物化学。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-052521-042909
Zhexin Wang, Stefan Raunser
{"title":"Structural Biochemistry of Muscle Contraction.","authors":"Zhexin Wang,&nbsp;Stefan Raunser","doi":"10.1146/annurev-biochem-052521-042909","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-042909","url":null,"abstract":"<p><p>Muscles are essential for movement and heart function. Contraction and relaxation of muscles rely on the sliding of two types of filaments-the thin filament and the thick myosin filament. The thin filament is composed mainly of filamentous actin (F-actin), tropomyosin, and troponin. Additionally, several other proteins are involved in the contraction mechanism, and their malfunction can lead to diverse muscle diseases, such as cardiomyopathies. We review recent high-resolution structural data that explain the mechanism of action of muscle proteins at an unprecedented level of molecular detail. We focus on the molecular structures of the components of the thin and thick filaments and highlight the mechanisms underlying force generation through actin-myosin interactions, as well as Ca<sup>2+</sup>-dependent regulation via the dihydropyridine receptor, the ryanodine receptor, and troponin. We particularly emphasize the impact of cryo-electron microscopy and cryo-electron tomography in leading muscle research into a new era.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"411-433"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662512","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: 3
Transcription-Coupled Nucleotide Excision Repair and the Transcriptional Response to UV-Induced DNA Damage. 转录偶联核苷酸切除修复和紫外线诱导DNA损伤的转录反应。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-052621-091205
Nicolás Nieto Moreno, Anouk M Olthof, Jesper Q Svejstrup
{"title":"Transcription-Coupled Nucleotide Excision Repair and the Transcriptional Response to UV-Induced DNA Damage.","authors":"Nicolás Nieto Moreno,&nbsp;Anouk M Olthof,&nbsp;Jesper Q Svejstrup","doi":"10.1146/annurev-biochem-052621-091205","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052621-091205","url":null,"abstract":"<p><p>Ultraviolet (UV) irradiation and other genotoxic stresses induce bulky DNA lesions, which threaten genome stability and cell viability. Cells have evolved two main repair pathways to remove such lesions: global genome nucleotide excision repair (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER). The modes by which these subpathways recognize DNA lesions are distinct, but they converge onto the same downstream steps for DNA repair. Here, we first summarize the current understanding of these repair mechanisms, specifically focusing on the roles of stalled RNA polymerase II, Cockayne syndrome protein B (CSB), CSA and UV-stimulated scaffold protein A (UVSSA) in TC-NER. We also discuss the intriguing role of protein ubiquitylation in this process. Additionally, we highlight key aspects of the effect of UV irradiation on transcription and describe the role of signaling cascades in orchestrating this response. Finally, we describe the pathogenic mechanisms underlying xeroderma pigmentosum and Cockayne syndrome, the two main diseases linked to mutations in NER factors.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"81-113"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9671476","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: 6
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