Annual review of biochemistry最新文献_第10页

Site-Specific Self-Catalyzed DNA Depurination: A Biological Mechanism That Leads to Mutations and Creates Sequence Diversity. 位点特异性自催化DNA去纯化:导致突变和创造序列多样性的生物学机制。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 DOI: 10.1146/annurev-biochem-070611-095951

Jacques R Fresco, Olga Amosova

{"title":"Site-Specific Self-Catalyzed DNA Depurination: A Biological Mechanism That Leads to Mutations and Creates Sequence Diversity.","authors":"Jacques R Fresco, Olga Amosova","doi":"10.1146/annurev-biochem-070611-095951","DOIUrl":"https://doi.org/10.1146/annurev-biochem-070611-095951","url":null,"abstract":"Self-catalyzed DNA depurination is a sequence-specific physiological mechanism mediated by spontaneous extrusion of a stem-loop catalytic intermediate. Hydrolysis of the 5'G residue of the 5'GA/TGG loop and of the first 5'A residue of the 5'GAGA loop, together with particular first stem base pairs, specifies their hydrolysis without involving protein, cofactor, or cation. As such, this mechanism is the only known DNA catalytic activity exploited by nature. The consensus sequences for self-depurination of such G- and A-loop residues occur in all genomes examined across the phyla, averaging one site every 2,000-4,000 base pairs. Because apurinic sites are subject to error-prone repair, leading to substitution and short frameshift mutations, they are both a source of genome damage and a means for creating sequence diversity. Their marked overrepresentation in genomes, and largely unchanging density from the lowest to the highest organisms, indicate their selection over the course of evolution. The mutagenicity at such sites in many human genes is associated with loss of function of key proteins responsible for diverse diseases.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"86 ","pages":"461-484"},"PeriodicalIF":16.6,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-070611-095951","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35122172","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: 9

The Ubiquitin System, Autophagy, and Regulated Protein Degradation. 泛素系统，自噬和调节蛋白降解。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 DOI: 10.1146/annurev-biochem-061516-044859

Alexander Varshavsky

引用次数: 255

Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA. 环GMP-AMP作为细胞胞质DNA先天免疫信号的内源性第二信使。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 Epub Date: 2017-04-07 DOI: 10.1146/annurev-biochem-061516-044813

Kazuki Kato, Hiroki Omura, Ryuichiro Ishitani, Osamu Nureki

{"title":"Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA.","authors":"Kazuki Kato, Hiroki Omura, Ryuichiro Ishitani, Osamu Nureki","doi":"10.1146/annurev-biochem-061516-044813","DOIUrl":"https://doi.org/10.1146/annurev-biochem-061516-044813","url":null,"abstract":"The innate immune system functions as the first line of defense against invading bacteria and viruses. In this context, the cGAS/STING [cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase/STING] signaling axis perceives the nonself DNA associated with bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. In this pathway, the noncanonical cyclic dinucleotide 2',3'-cyclic GMP-AMP (2',3'-cGAMP) functions as a second messenger for signal transduction: 2',3'-cGAMP is produced by the enzyme cGAS upon its recognition of double-stranded DNA, and then the 2',3'-cGAMP is recognized by the receptor STING to induce the phosphorylation of downstream factors, including TBK1 (TANK binding kinase 1) and IRF3 (interferon regulatory factor 3). Numerous crystal structures of the components of this cGAS/STING signaling axis have been reported and these clarify the structural basis for their signal transduction mechanisms. In this review, we summarize recent progress made in the structural dissection of this signaling pathway and indicate possible directions of forthcoming research.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"86 ","pages":"541-566"},"PeriodicalIF":16.6,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-061516-044813","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34906424","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: 638

Multiple Functions and Regulation of Mammalian Peroxiredoxins. 哺乳动物过氧化物还毒素的多种功能及其调控。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 Epub Date: 2017-02-02 DOI: 10.1146/annurev-biochem-060815-014431

Sue Goo Rhee, In Sup Kil

{"title":"Multiple Functions and Regulation of Mammalian Peroxiredoxins.","authors":"Sue Goo Rhee, In Sup Kil","doi":"10.1146/annurev-biochem-060815-014431","DOIUrl":"https://doi.org/10.1146/annurev-biochem-060815-014431","url":null,"abstract":"Peroxiredoxins (Prxs) constitute a major family of peroxidases, with mammalian cells expressing six Prx isoforms (PrxI to PrxVI). Cells produce hydrogen peroxide (H2O2) at various intracellular locations where it can serve as a signaling molecule. Given that Prxs are abundant and possess a structure that renders the cysteine (Cys) residue at the active site highly sensitive to oxidation by H2O2, the signaling function of this oxidant requires extensive and highly localized regulation. Recent findings on the reversible regulation of PrxI through phosphorylation at the centrosome and on the hyperoxidation of the Cys at the active site of PrxIII in mitochondria are described in this review as examples of such local regulation of H2O2 signaling. Moreover, their high affinity for and sensitivity to oxidation by H2O2 confer on Prxs the ability to serve as sensors and transducers of H2O2 signaling through transfer of their oxidation state to bound effector proteins.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"86 ","pages":"749-775"},"PeriodicalIF":16.6,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-060815-014431","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34756229","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: 202

Mechanisms of Autophagy Initiation. 自噬起始机制。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 Epub Date: 2017-03-15 DOI: 10.1146/annurev-biochem-061516-044820

James H Hurley, Lindsey N Young

{"title":"Mechanisms of Autophagy Initiation.","authors":"James H Hurley, Lindsey N Young","doi":"10.1146/annurev-biochem-061516-044820","DOIUrl":"https://doi.org/10.1146/annurev-biochem-061516-044820","url":null,"abstract":"Autophagy is the process of cellular self-eating by a double-membrane organelle, the autophagosome. A range of signaling processes converge on two protein complexes to initiate autophagy: the ULK1 (unc51-like autophagy activating kinase 1) protein kinase complex and the PI3KC3-C1 (class III phosphatidylinositol 3-kinase complex I) lipid kinase complex. Some 90% of the mass of these large protein complexes consists of noncatalytic domains and subunits, and the ULK1 complex has essential noncatalytic activities. Structural studies of these complexes have shed increasing light on the regulation of their catalytic and noncatalytic activities in autophagy initiation. The autophagosome is thought to nucleate from vesicles containing the integral membrane protein Atg9 (autophagy-related 9), COPII (coat protein complex II) vesicles, and possibly other sources. In the wake of reconstitution and super-resolution imaging studies, we are beginning to understand how the ULK1 and PI3KC3-C1 complexes might coordinate the nucleation and fusion of Atg9 and COPII vesicles at the start of autophagosome biogenesis.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"86 ","pages":"225-244"},"PeriodicalIF":16.6,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-061516-044820","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34818687","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: 462

Teaching Old Dyes New Tricks: Biological Probes Built from Fluoresceins and Rhodamines. 教授旧染料的新技巧:荧光素和罗丹明构建的生物探针。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 Epub Date: 2017-04-07 DOI: 10.1146/annurev-biochem-061516-044839

Luke D Lavis

引用次数: 150

Proteasomal and Autophagic Degradation Systems. 蛋白酶体和自噬降解系统。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 Epub Date: 2017-05-01 DOI: 10.1146/annurev-biochem-061516-044908

Ivan Dikic

引用次数: 699

Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching. 用概念和实验工具理解非线性生化网络中的空间效应和传输现象--以斑状开关为例证

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 DOI: 10.1146/annurev-biochem-060815-014207

Rebecca R Pompano, Andrew H Chiang, Christian J Kastrup, Rustem F Ismagilov

{"title":"Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching.","authors":"Rebecca R Pompano, Andrew H Chiang, Christian J Kastrup, Rustem F Ismagilov","doi":"10.1146/annurev-biochem-060815-014207","DOIUrl":"10.1146/annurev-biochem-060815-014207","url":null,"abstract":"Many biochemical systems are spatially heterogeneous and exhibit nonlinear behaviors, such as state switching in response to small changes in the local concentration of diffusible molecules. Systems as varied as blood clotting, intracellular calcium signaling, and tissue inflammation are all heavily influenced by the balance of rates of reaction and mass transport phenomena including flow and diffusion. Transport of signaling molecules is also affected by geometry and chemoselective confinement via matrix binding. In this review, we use a phenomenon referred to as patchy switching to illustrate the interplay of nonlinearities, transport phenomena, and spatial effects. Patchy switching describes a change in the state of a network when the local concentration of a diffusible molecule surpasses a critical threshold. Using patchy switching as an example, we describe conceptual tools from nonlinear dynamics and chemical engineering that make testable predictions and provide a unifying description of the myriad possible experimental observations. We describe experimental microfluidic and biochemical tools emerging to test conceptual predictions by controlling transport phenomena and spatial distribution of diffusible signals, and we highlight the unmet need for in vivo tools.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"86 ","pages":"333-356"},"PeriodicalIF":16.6,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10852032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35122173","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

Systems Biology of Metabolism. 代谢系统生物学。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 Epub Date: 2017-03-08 DOI: 10.1146/annurev-biochem-061516-044757

Jens Nielsen

引用次数: 123

Mitochondrial Machineries for Protein Import and Assembly. 用于蛋白质进口和组装的线粒体机器。

IF 16.6 1区生物学

Annual review of biochemistry Pub Date : 2017-06-20 Epub Date: 2017-03-15 DOI: 10.1146/annurev-biochem-060815-014352

Nils Wiedemann, Nikolaus Pfanner

引用次数: 578