Annual review of biochemistry最新文献_第5页

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, S-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

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

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, Anouk M Olthof, Jesper Q Svejstrup","doi":"10.1146/annurev-biochem-052621-091205","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052621-091205","url":null,"abstract":"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.","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

Molecular Mechanisms of Transcription-Coupled Repair. 转录偶联修复的分子机制。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-041522-034232

Christopher P Selby, Laura A Lindsey-Boltz, Wentao Li, Aziz Sancar

{"title":"Molecular Mechanisms of Transcription-Coupled Repair.","authors":"Christopher P Selby, Laura A Lindsey-Boltz, Wentao Li, Aziz Sancar","doi":"10.1146/annurev-biochem-041522-034232","DOIUrl":"https://doi.org/10.1146/annurev-biochem-041522-034232","url":null,"abstract":"Transcription-coupled repair (TCR), discovered as preferential nucleotide excision repair of UV-induced cyclobutane pyrimidine dimers located in transcribed mammalian genes compared to those in nontranscribed regions of the genome, is defined as faster repair of the transcribed strand versus the nontranscribed strand in transcribed genes. The phenomenon, universal in model organisms including Escherichia coli, yeast, Arabidopsis, mice, and humans, involves a translocase that interacts with both RNA polymerase stalled at damage in the transcribed strand and nucleotide excision repair proteins to accelerate repair. Drosophila, a notable exception, exhibits TCR but lacks an obvious TCR translocase. Mutations inactivating TCR genes cause increased damage-induced mutagenesis in E. coli and severe neurological and UV sensitivity syndromes in humans. To date, only E. coli TCR has been reconstituted in vitro with purified proteins. Detailed investigations of TCR using genome-wide next-generation sequencing methods, cryo-electron microscopy, single-molecule analysis, and other approaches have revealed fascinating mechanisms.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"115-144"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662513","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

3'-End Processing of Eukaryotic mRNA: Machinery, Regulation, and Impact on Gene Expression. 真核 mRNA 的 3'-End 处理：机械、调控和对基因表达的影响。

IF 12.1 1区生物学

Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-03-31 DOI: 10.1146/annurev-biochem-052521-012445

Vytautė Boreikaitė, Lori A Passmore

引用次数: 0

Thiolase: A Versatile Biocatalyst Employing Coenzyme A-Thioester Chemistry for Making and Breaking C-C Bonds. 硫醇酶:一种多功能生物催化剂，利用辅酶A-硫酯化学来制造和破坏C-C键。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-052521-033746

Rajesh K Harijan, Subhadra Dalwani, Tiila-Riikka Kiema, Rajaram Venkatesan, Rik K Wierenga

{"title":"Thiolase: A Versatile Biocatalyst Employing Coenzyme A-Thioester Chemistry for Making and Breaking C-C Bonds.","authors":"Rajesh K Harijan, Subhadra Dalwani, Tiila-Riikka Kiema, Rajaram Venkatesan, Rik K Wierenga","doi":"10.1146/annurev-biochem-052521-033746","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-033746","url":null,"abstract":"Thiolases are CoA-dependent enzymes that catalyze the thiolytic cleavage of 3-ketoacyl-CoA, as well as its reverse reaction, which is the thioester-dependent Claisen condensation reaction. Thiolases are dimers or tetramers (dimers of dimers). All thiolases have two reactive cysteines: (a) a nucleophilic cysteine, which forms a covalent intermediate, and (b) an acid/base cysteine. The best characterized thiolase is the Zoogloea ramigera thiolase, which is a bacterial biosynthetic thiolase belonging to the CT-thiolase subfamily. The thiolase active site is also characterized by two oxyanion holes, two active site waters, and four catalytic loops with characteristic amino acid sequence fingerprints. Three thiolase subfamilies can be identified, each characterized by a unique sequence fingerprint for one of their catalytic loops, which causes unique active site properties. Recent insights concerning the thiolase reaction mechanism, as obtained from recent structural studies, as well as from classical and recent enzymological studies, are addressed, and open questions are discussed.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"351-384"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10044966","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: 1

Mechanism of Radical Initiation in the Radical SAM Enzyme Superfamily. 自由基SAM酶超家族中自由基起始机制研究。

IF 12.1 1区生物学

Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-04-04 DOI: 10.1146/annurev-biochem-052621-090638

Brian M Hoffman, William E Broderick, Joan B Broderick

{"title":"Mechanism of Radical Initiation in the Radical SAM Enzyme Superfamily.","authors":"Brian M Hoffman, William E Broderick, Joan B Broderick","doi":"10.1146/annurev-biochem-052621-090638","DOIUrl":"10.1146/annurev-biochem-052621-090638","url":null,"abstract":"Radical S-adenosylmethionine (SAM) enzymes use a site-differentiated [4Fe-4S] cluster and SAM to initiate radical reactions through liberation of the 5'-deoxyadenosyl (5'-dAdo•) radical. They form the largest enzyme superfamily, with more than 700,000 unique sequences currently, and their numbers continue to grow as a result of ongoing bioinformatics efforts. The range of extremely diverse, highly regio- and stereo-specific reactions known to be catalyzed by radical SAM superfamily members is remarkable. The common mechanism of radical initiation in the radical SAM superfamily is the focus of this review. Most surprising is the presence of an organometallic intermediate, Ω, exhibiting an Fe-C5'-adenosyl bond. Regioselective reductive cleavage of the SAM S-C5' bond produces 5'-dAdo• to form Ω, with the regioselectivity originating in the Jahn-Teller effect. Ω liberates the free 5'-dAdo• as the catalytically active intermediate through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12, which was once viewed as biology's choice of radical generator.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"333-349"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10759928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662524","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