Annual review of biochemistry最新文献

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Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. 真核细胞DNA和RNA成像揭示基因表达的时空动态。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-16 DOI: 10.1146/annurev-biochem-011520-104955
Hanae Sato, Sulagna Das, Robert H Singer, Maria Vera
{"title":"Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression.","authors":"Hanae Sato,&nbsp;Sulagna Das,&nbsp;Robert H Singer,&nbsp;Maria Vera","doi":"10.1146/annurev-biochem-011520-104955","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-104955","url":null,"abstract":"<p><p>This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"159-187"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-104955","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37741794","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: 32
Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data. 光系统II中水氧化机理的最新认识及其与XFEL数据的关系。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-24 DOI: 10.1146/annurev-biochem-011520-104801
Nicholas Cox, Dimitrios A Pantazis, Wolfgang Lubitz
{"title":"Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data.","authors":"Nicholas Cox,&nbsp;Dimitrios A Pantazis,&nbsp;Wolfgang Lubitz","doi":"10.1146/annurev-biochem-011520-104801","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-104801","url":null,"abstract":"<p><p>The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn<sub>4</sub>CaO<sub>x</sub> complex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"795-820"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-104801","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37768801","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: 91
Biosynthesis and Export of Bacterial Glycolipids. 细菌糖脂的生物合成和输出。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-011520-104707
Christopher A Caffalette, Jeremi Kuklewicz, Nicholas Spellmon, Jochen Zimmer
{"title":"Biosynthesis and Export of Bacterial Glycolipids.","authors":"Christopher A Caffalette,&nbsp;Jeremi Kuklewicz,&nbsp;Nicholas Spellmon,&nbsp;Jochen Zimmer","doi":"10.1146/annurev-biochem-011520-104707","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-104707","url":null,"abstract":"Complex carbohydrates are essential for many biological processes, from protein quality control to cell recognition, energy storage, and cell wall formation. Many of these processes are performed in topologically extracellular compartments or on the cell surface; hence, diverse secretion systems evolved to transport the hydrophilic molecules to their sites of action. Polyprenyl lipids serve as ubiquitous anchors and facilitators of these transport processes. Here, we summarize and compare bacterial biosynthesis pathways relying on the recognition and transport of lipid-linked complex carbohydrates. In particular, we compare transporters implicated in O antigen and capsular polysaccharide biosyntheses with those facilitating teichoic acid and N-linked glycan transport. Further, we discuss recent insights into the generation, recognition, and recycling of polyprenyl lipids.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"741-768"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-104707","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38070730","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: 18
Structure and Mechanism of P-Type ATPase Ion Pumps. p型atp酶离子泵的结构与机理。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-12-24 DOI: 10.1146/annurev-biochem-010611-112801
Mateusz Dyla, Magnus Kjærgaard, Hanne Poulsen, Poul Nissen
{"title":"Structure and Mechanism of P-Type ATPase Ion Pumps.","authors":"Mateusz Dyla,&nbsp;Magnus Kjærgaard,&nbsp;Hanne Poulsen,&nbsp;Poul Nissen","doi":"10.1146/annurev-biochem-010611-112801","DOIUrl":"https://doi.org/10.1146/annurev-biochem-010611-112801","url":null,"abstract":"<p><p>P-type ATPases are found in all kingdoms of life and constitute a wide range of cation transporters, primarily for H<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup>, Ca<sup>2+</sup>, and transition metal ions such as Cu(I), Zn(II), and Cd(II). They have been studied through a wide range of techniques, and research has gained very significant insight on their transport mechanism and regulation. Here, we review the structure, function, and dynamics of P2-ATPases including Ca<sup>2+</sup>-ATPases and Na,K-ATPase. We highlight mechanisms of functional transitions that are associated with ion exchange on either side of the membrane and how the functional cycle is regulated by interaction partners, autoregulatory domains, and off-cycle states. Finally, we discuss future perspectives based on emerging techniques and insights.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"583-603"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-010611-112801","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37488766","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: 83
Anti-CRISPRs: Protein Inhibitors of CRISPR-Cas Systems. 抗 CRISPRs:CRISPR-Cas系统的蛋白质抑制剂。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-18 DOI: 10.1146/annurev-biochem-011420-111224
Alan R Davidson, Wang-Ting Lu, Sabrina Y Stanley, Jingrui Wang, Marios Mejdani, Chantel N Trost, Brian T Hicks, Jooyoung Lee, Erik J Sontheimer
{"title":"Anti-CRISPRs: Protein Inhibitors of CRISPR-Cas Systems.","authors":"Alan R Davidson, Wang-Ting Lu, Sabrina Y Stanley, Jingrui Wang, Marios Mejdani, Chantel N Trost, Brian T Hicks, Jooyoung Lee, Erik J Sontheimer","doi":"10.1146/annurev-biochem-011420-111224","DOIUrl":"10.1146/annurev-biochem-011420-111224","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR) together with their accompanying <i>cas</i> (CRISPR-associated) genes are found frequently in bacteria and archaea, serving to defend against invading foreign DNA, such as viral genomes. CRISPR-Cas systems provide a uniquely powerful defense because they can adapt to newly encountered genomes. The adaptive ability of these systems has been exploited, leading to their development as highly effective tools for genome editing. The widespread use of CRISPR-Cas systems has driven a need for methods to control their activity. This review focuses on anti-CRISPRs (Acrs), proteins produced by viruses and other mobile genetic elements that can potently inhibit CRISPR-Cas systems. Discovered in 2013, there are now 54 distinct families of these proteins described, and the functional mechanisms of more than a dozen have been characterized in molecular detail. The investigation of Acrs is leading to a variety of practical applications and is providing exciting new insight into the biology of CRISPR-Cas systems.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"309-332"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011420-111224","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37749621","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: 76
Evaluating Enhancer Function and Transcription. 评估增强子功能和转录。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-20 DOI: 10.1146/annurev-biochem-011420-095916
Andrew Field, Karen Adelman
{"title":"Evaluating Enhancer Function and Transcription.","authors":"Andrew Field,&nbsp;Karen Adelman","doi":"10.1146/annurev-biochem-011420-095916","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011420-095916","url":null,"abstract":"<p><p>Cell-type- and condition-specific profiles of gene expression require coordination between protein-coding gene promoters and <i>cis</i>-regulatory sequences called enhancers. Enhancers can stimulate gene activity at great genomic distances from their targets, raising questions about how enhancers communicate with specific gene promoters and what molecular mechanisms underlie enhancer function. Characterization of enhancer loci has identified the molecular features of active enhancers that accompany the binding of transcription factors and local opening of chromatin. These characteristics include coactivator recruitment, histone modifications, and noncoding RNA transcription. However, it remains unclear which of these features functionally contribute to enhancer activity. Here, we discuss what is known about how enhancers regulate their target genes and how enhancers and promoters communicate. Further, we describe recent data demonstrating many similarities between enhancers and the gene promoters they control, and we highlight unanswered questions in the field, such as the potential roles of transcription at enhancers.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"213-234"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011420-095916","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37758156","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: 99
Quantifying Target Occupancy of Small Molecules Within Living Cells. 活细胞内小分子目标占用的定量分析。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-24 DOI: 10.1146/annurev-biochem-011420-092302
M B Robers, R Friedman-Ohana, K V M Huber, L Kilpatrick, J D Vasta, B-T Berger, C Chaudhry, S Hill, S Müller, S Knapp, K V Wood
{"title":"Quantifying Target Occupancy of Small Molecules Within Living Cells.","authors":"M B Robers,&nbsp;R Friedman-Ohana,&nbsp;K V M Huber,&nbsp;L Kilpatrick,&nbsp;J D Vasta,&nbsp;B-T Berger,&nbsp;C Chaudhry,&nbsp;S Hill,&nbsp;S Müller,&nbsp;S Knapp,&nbsp;K V Wood","doi":"10.1146/annurev-biochem-011420-092302","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011420-092302","url":null,"abstract":"<p><p>The binding affinity and kinetics of target engagement are fundamental to establishing structure-activity relationships (SARs) for prospective therapeutic agents. Enhancing these binding parameters for operative targets, while minimizing binding to off-target sites, can translate to improved drug efficacy and a widened therapeutic window. Compound activity is typically assessed through modulation of an observed phenotype in cultured cells. Quantifying the corresponding binding properties under common cellular conditions can provide more meaningful interpretation of the cellular SAR analysis. Consequently, methods for assessing drug binding in living cells have advanced and are now integral to medicinal chemistry workflows. In this review, we survey key technological advancements that support quantitative assessments of target occupancy in cultured cells, emphasizing generalizable methodologies able to deliver analytical precision that heretofore required reductionist biochemical approaches.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"557-581"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011420-092302","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37768803","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: 28
How Does the Ribosome Fold the Proteome? 核糖体如何折叠蛋白质组?
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-062917-012226
Anaïs M E Cassaignau, Lisa D Cabrita, John Christodoulou
{"title":"How Does the Ribosome Fold the Proteome?","authors":"Anaïs M E Cassaignau,&nbsp;Lisa D Cabrita,&nbsp;John Christodoulou","doi":"10.1146/annurev-biochem-062917-012226","DOIUrl":"https://doi.org/10.1146/annurev-biochem-062917-012226","url":null,"abstract":"<p><p>Folding of polypeptides begins during their synthesis on ribosomes. This process has evolved as a means for the cell to maintain proteostasis, by mitigating the risk of protein misfolding and aggregation. The capacity to now depict this cellular feat at increasingly higher resolution is providing insight into the mechanistic determinants that promote successful folding. Emerging from these studies is the intimate interplay between protein translation and folding, and within this the ribosome particle is the key player. Its unique structural properties provide a specialized scaffold against which nascent polypeptides can begin to form structure in a highly coordinated, co-translational manner. Here, we examine how, as a macromolecular machine, the ribosome modulates the intrinsic dynamic properties of emerging nascent polypeptide chains and guides them toward their biologically active structures.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"389-415"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-062917-012226","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38071301","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: 36
Molecular Mechanisms of Natural Rubber Biosynthesis. 天然橡胶生物合成的分子机制。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-30 DOI: 10.1146/annurev-biochem-013118-111107
Satoshi Yamashita, Seiji Takahashi
{"title":"Molecular Mechanisms of Natural Rubber Biosynthesis.","authors":"Satoshi Yamashita,&nbsp;Seiji Takahashi","doi":"10.1146/annurev-biochem-013118-111107","DOIUrl":"https://doi.org/10.1146/annurev-biochem-013118-111107","url":null,"abstract":"<p><p>Natural rubber (NR), principally comprising <i>cis</i>-1,4-polyisoprene, is an industrially important natural hydrocarbon polymer because of its unique physical properties, which render it suitable for manufacturing items such as tires. Presently, industrial NR production depends solely on latex obtained from the Pará rubber tree, <i>Hevea brasiliensis</i>. In latex, NR is enclosed in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The similarity of the basic carbon skeleton structure between NR and dolichols and polyprenols, which are found in most organisms, suggests that the NR biosynthetic pathway is related to the polyisoprenoid biosynthetic pathway and that rubber transferase, which is the key enzyme in NR biosynthesis, belongs to the <i>cis</i>-prenyltransferase family. Here, we review recent progress in the elucidation of molecular mechanisms underlying NR biosynthesis through the identification of the enzymes that are responsible for the formation of the NR backbone structure.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"821-851"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-013118-111107","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37784516","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: 47
Christopher Dobson, 1949-2019: Mentor, Friend, Scientist Extraordinaire. 克里斯托弗·多布森,1949-2019:导师、朋友、非凡的科学家。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-04-28 DOI: 10.1146/annurev-biochem-011520-105226
Carol V Robinson
{"title":"Christopher Dobson, 1949-2019: Mentor, Friend, Scientist Extraordinaire.","authors":"Carol V Robinson","doi":"10.1146/annurev-biochem-011520-105226","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-105226","url":null,"abstract":"<p><p>It is impossible to do justice in one review article to a researcher of the stature of Christopher Dobson. His career spanned almost five decades, resulting in more than 870 publications and a legacy that will continue to influence the lives of many for decades to come. In this review, I have attempted to capture Chris's major contributions: his early work, dedicated to understanding protein-folding mechanisms; his collaborative work with physicists to understand the process of protein aggregation; and finally, his later career in which he developed strategies to prevent misfolding. However, it is not only this body of work but also the man himself who inspired an entire generation of scientists through his patience, ability to mentor, and innate generosity. These qualities remain a hallmark of the way in which he conducted his research-research that will leave a lasting imprint on science.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"1-19"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-105226","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37880117","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: 2
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