Annual review of biochemistry最新文献

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

Mitochondrial DNA Release in Innate Immune Signaling. 先天性免疫信号中的线粒体 DNA 释放

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-032620-104401

Laura E Newman, Gerald S Shadel

{"title":"Mitochondrial DNA Release in Innate Immune Signaling.","authors":"Laura E Newman, Gerald S Shadel","doi":"10.1146/annurev-biochem-032620-104401","DOIUrl":"10.1146/annurev-biochem-032620-104401","url":null,"abstract":"According to the endosymbiotic theory, most of the DNA of the original bacterial endosymbiont has been lost or transferred to the nucleus, leaving a much smaller (∼16 kb in mammals), circular molecule that is the present-day mitochondrial DNA (mtDNA). The ability of mtDNA to escape mitochondria and integrate into the nuclear genome was discovered in budding yeast, along with genes that regulate this process. Mitochondria have emerged as key regulators of innate immunity, and it is now recognized that mtDNA released into the cytoplasm, outside of the cell, or into circulation activates multiple innate immune signaling pathways. Here, we first review the mechanisms through which mtDNA is released into the cytoplasm, including several inducible mitochondrial pores and defective mitophagy or autophagy. Next, we cover how the different forms of released mtDNA activate specific innate immune nucleic acid sensors and inflammasomes. Finally, we discuss how intracellular and extracellular mtDNA release, including circulating cell-free mtDNA that promotes systemic inflammation, are implicated in human diseases, bacterial and viral infections, senescence and aging.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"299-332"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11058562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662511","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

Rubisco Function, Evolution, and Engineering. Rubisco功能，进化和工程。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-040320-101244

Noam Prywes, Naiya R Phillips, Owen T Tuck, Luis E Valentin-Alvarado, David F Savage

{"title":"Rubisco Function, Evolution, and Engineering.","authors":"Noam Prywes, Naiya R Phillips, Owen T Tuck, Luis E Valentin-Alvarado, David F Savage","doi":"10.1146/annurev-biochem-040320-101244","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-101244","url":null,"abstract":"Carbon fixation is the process by which CO2 is converted from a gas into biomass. The Calvin-Benson-Bassham cycle (CBB) is the dominant carbon-consuming pathway on Earth, driving >99.5% of the ∼120 billion tons of carbon that are converted to sugar by plants, algae, and cyanobacteria. The carboxylase enzyme in the CBB, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), fixes one CO2 molecule per turn of the cycle into bioavailable sugars. Despite being critical to the assimilation of carbon, rubisco's kinetic rate is not very fast, limiting flux through the pathway. This bottleneck presents a paradox: Why has rubisco not evolved to be a better catalyst? Many hypothesize that the catalytic mechanism of rubisco is subject to one or more trade-offs and that rubisco variants have been optimized for their native physiological environment. Here, we review the evolution and biochemistry of rubisco through the lens of structure and mechanism in order to understand what trade-offs limit its improvement. We also review the many attempts to improve rubisco itself and thereby promote plant growth.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"385-410"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9670773","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: 7

DNA Fragility and Repair: Some Personal Recollections. DNA的脆弱和修复:一些个人回忆。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-071322-020214

Tomas Robert Lindahl

引用次数: 0

mRNA Regulation by RNA Modifications. 通过 RNA 修饰调节 mRNA。

IF 12.1 1区生物学

Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-04-05 DOI: 10.1146/annurev-biochem-052521-035949

Wendy V Gilbert, Sigrid Nachtergaele

引用次数: 0