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Annual review of biochemistry最新文献

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Zona Pellucida Proteins, Fibrils, and Matrix. 透明带蛋白、原纤维和基质。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-011520-105310
Eveline S Litscher, Paul M Wassarman
{"title":"Zona Pellucida Proteins, Fibrils, and Matrix.","authors":"Eveline S Litscher,&nbsp;Paul M Wassarman","doi":"10.1146/annurev-biochem-011520-105310","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-105310","url":null,"abstract":"<p><p>The zona pellucida (ZP) is an extracellular matrix that surrounds all mammalian oocytes, eggs, and early embryos and plays vital roles during oogenesis, fertilization, and preimplantation development. The ZP is composed of three or four glycosylated proteins, ZP1-4, that are synthesized, processed, secreted, and assembled into long, cross-linked fibrils by growing oocytes. ZP proteins have an immunoglobulin-like three-dimensional structure and a ZP domain that consists of two subdomains, ZP-N and ZP-C, with ZP-N of ZP2 and ZP3 required for fibril assembly. A ZP2-ZP3 dimer is located periodically along ZP fibrils that are cross-linked by ZP1, a protein with a proline-rich N terminus. Fibrils in the inner and outer regions of the ZP are oriented perpendicular and parallel to the oolemma, respectively, giving the ZP a multilayered appearance. Upon fertilization of eggs, modification of ZP2 and ZP3 results in changes in the ZP's physical and biological properties that have important consequences. Certain structural features of ZP proteins suggest that they may be amyloid-like proteins.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"695-715"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-105310","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38070731","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: 34
Standing on the Shoulders of Viruses. 站在病毒的肩膀上
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-011320-103928
Ari Helenius
{"title":"Standing on the Shoulders of Viruses.","authors":"Ari Helenius","doi":"10.1146/annurev-biochem-011320-103928","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011320-103928","url":null,"abstract":"<p><p>My coworkers and I have used animal viruses and their interaction with host cells to investigate cellular processes difficult to study by other means. This approach has allowed us to branch out in many directions, including membrane protein characterization, endocytosis, secretion, protein folding, quality control, and glycobiology. At the same time, our aim has been to employ cell biological approaches to expand the fundamental understanding of animal viruses and their pathogenic lifestyles. We have studied mechanisms of host cell entry and the uncoating of incoming viruses as well as the synthesis, folding, maturation, and intracellular movement of viral proteins and molecular assemblies. I have had the privilege to work in institutions in four different countries. The early years in Finland (the University of Helsinki) were followed by 6 years in Germany (European Molecular Biology Laboratory), 16 years in the United States (Yale School of Medicine), and 16 years in Switzerland (ETH Zurich).</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"21-43"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011320-103928","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38071304","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
Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming. 转录编程中多聚酶和三叉轴的动态竞争
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-01-13 DOI: 10.1146/annurev-biochem-120219-103641
Mitzi I Kuroda, Hyuckjoon Kang, Sandip De, Judith A Kassis
{"title":"Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming.","authors":"Mitzi I Kuroda, Hyuckjoon Kang, Sandip De, Judith A Kassis","doi":"10.1146/annurev-biochem-120219-103641","DOIUrl":"10.1146/annurev-biochem-120219-103641","url":null,"abstract":"<p><p>Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"235-253"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311296/pdf/nihms-1575141.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37533775","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 Proteases: Multifaceted Regulators of Mitochondrial Plasticity. 线粒体蛋白酶:线粒体可塑性的多方面调节因子。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-02-19 DOI: 10.1146/annurev-biochem-062917-012739
Soni Deshwal, Kai Uwe Fiedler, Thomas Langer
{"title":"Mitochondrial Proteases: Multifaceted Regulators of Mitochondrial Plasticity.","authors":"Soni Deshwal,&nbsp;Kai Uwe Fiedler,&nbsp;Thomas Langer","doi":"10.1146/annurev-biochem-062917-012739","DOIUrl":"https://doi.org/10.1146/annurev-biochem-062917-012739","url":null,"abstract":"<p><p>Mitochondria are essential metabolic hubs that dynamically adapt to physiological demands. More than 40 proteases residing in different compartments of mitochondria, termed mitoproteases, preserve mitochondrial proteostasis and are emerging as central regulators of mitochondrial plasticity. These multifaceted enzymes limit the accumulation of short-lived, regulatory proteins within mitochondria, modulate the activity of mitochondrial proteins by protein processing, and mediate the degradation of damaged proteins. Various signaling cascades coordinate the activity of mitoproteases to preserve mitochondrial homeostasis and ensure cell survival. Loss of mitoproteases severely impairs the functional integrity of mitochondria, is associated with aging, and causes pleiotropic diseases. Understanding the dual function of mitoproteases as regulatory and quality control enzymes will help unravel the role of mitochondrial plasticity in aging and disease.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"501-528"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-062917-012739","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37656954","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: 101
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
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