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Annual review of biochemistry最新文献

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Long Noncoding RNAs: Molecular Modalities to Organismal Functions. 长链非编码rna:生物体功能的分子模式。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-062917-012708
John L Rinn, Howard Y Chang
{"title":"Long Noncoding RNAs: Molecular Modalities to Organismal Functions.","authors":"John L Rinn,&nbsp;Howard Y Chang","doi":"10.1146/annurev-biochem-062917-012708","DOIUrl":"https://doi.org/10.1146/annurev-biochem-062917-012708","url":null,"abstract":"<p><p>We have known for decades that long noncoding RNAs (lncRNAs) can play essential functions across most forms of life. The maintenance of chromosome length requires an lncRNA (e.g., hTERC) and two lncRNAs in the ribosome that are required for protein synthesis. Thus, lncRNAs can represent powerful RNA machines. More recently, it has become clear that mammalian genomes encode thousands more lncRNAs. Thus, we raise the question: Which, if any, of these lncRNAs could also represent RNA-based machines? Here we synthesize studies that are beginning to address this question by investigating fundamental properties of lncRNA genes, revealing new insights into the RNA structure-function relationship, determining <i>cis</i>- and <i>trans</i>-acting lncRNAs in vivo, and generating new developments in high-throughput screening used to identify functional lncRNAs. Overall, these findings provide a context toward understanding the molecular grammar underlying lncRNA biology.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"283-308"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-062917-012708","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38070727","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: 153
Synthetic Genomes. 合成基因组。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-013118-110704
Weimin Zhang, Leslie A Mitchell, Joel S Bader, Jef D Boeke
{"title":"Synthetic Genomes.","authors":"Weimin Zhang,&nbsp;Leslie A Mitchell,&nbsp;Joel S Bader,&nbsp;Jef D Boeke","doi":"10.1146/annurev-biochem-013118-110704","DOIUrl":"https://doi.org/10.1146/annurev-biochem-013118-110704","url":null,"abstract":"<p><p>DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"77-101"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-013118-110704","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38071300","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: 40
Structural and Mechanistic Principles of ABC Transporters. ABC转运体的结构和机械原理。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-011520-105201
Christoph Thomas, Robert Tampé
{"title":"Structural and Mechanistic Principles of ABC Transporters.","authors":"Christoph Thomas,&nbsp;Robert Tampé","doi":"10.1146/annurev-biochem-011520-105201","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-105201","url":null,"abstract":"<p><p>ATP-binding cassette (ABC) transporters constitute one of the largest and most ancient protein superfamilies found in all living organisms. They function as molecular machines by coupling ATP binding, hydrolysis, and phosphate release to translocation of diverse substrates across membranes. The substrates range from vitamins, steroids, lipids, and ions to peptides, proteins, polysaccharides, and xenobiotics. ABC transporters undergo substantial conformational changes during substrate translocation. A comprehensive understanding of their inner workings thus requires linking these structural rearrangements to the different functional state transitions. Recent advances in single-particle cryogenic electron microscopy have not only delivered crucial information on the architecture of several medically relevant ABC transporters and their supramolecular assemblies, including the ATP-sensitive potassium channel and the peptide-loading complex, but also made it possible to explore the entire conformational space of these nanomachines under turnover conditions and thereby gain detailed mechanistic insights into their mode of action.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"605-636"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-105201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38071305","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: 189
Checkpoint Responses to DNA Double-Strand Breaks. DNA双链断裂的检查点反应。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-16 DOI: 10.1146/annurev-biochem-011520-104722
David P Waterman, James E Haber, Marcus B Smolka
{"title":"Checkpoint Responses to DNA Double-Strand Breaks.","authors":"David P Waterman, James E Haber, Marcus B Smolka","doi":"10.1146/annurev-biochem-011520-104722","DOIUrl":"10.1146/annurev-biochem-011520-104722","url":null,"abstract":"<p><p>Cells confront DNA damage in every cell cycle. Among the most deleterious types of DNA damage are DNA double-strand breaks (DSBs), which can cause cell lethality if unrepaired or cancers if improperly repaired. In response to DNA DSBs, cells activate a complex DNA damage checkpoint (DDC) response that arrests the cell cycle, reprograms gene expression, and mobilizes DNA repair factors to prevent the inheritance of unrepaired and broken chromosomes. Here we examine the DDC, induced by DNA DSBs, in the budding yeast model system and in mammals.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"103-133"},"PeriodicalIF":12.1,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311309/pdf/nihms-1585581.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37742238","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
Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets. 核糖核苷酸还原酶：核糖核苷酸还原酶：结构、化学和代谢揭示了新的治疗靶点。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-013118-111843
Brandon L Greene, Gyunghoon Kang, Chang Cui, Marina Bennati, Daniel G Nocera, Catherine L Drennan, JoAnne Stubbe
{"title":"Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets.","authors":"Brandon L Greene, Gyunghoon Kang, Chang Cui, Marina Bennati, Daniel G Nocera, Catherine L Drennan, JoAnne Stubbe","doi":"10.1146/annurev-biochem-013118-111843","DOIUrl":"10.1146/annurev-biochem-013118-111843","url":null,"abstract":"<p><p>Ribonucleotide reductases (RNRs) catalyze the de novo conversion of nucleotides to deoxynucleotides in all organisms, controlling their relative ratios and abundance. In doing so, they play an important role in fidelity of DNA replication and repair. RNRs' central role in nucleic acid metabolism has resulted in five therapeutics that inhibit human RNRs. In this review, we discuss the structural, dynamic, and mechanistic aspects of RNR activity and regulation, primarily for the human and <i>Escherichia coli</i> class Ia enzymes. The unusual radical-based organic chemistry of nucleotide reduction, the inorganic chemistry of the essential metallo-cofactor biosynthesis/maintenance, the transport of a radical over a long distance, and the dynamics of subunit interactions all present distinct entry points toward RNR inhibition that are relevant for drug discovery. We describe the current mechanistic understanding of small molecules that target different elements of RNR function, including downstream pathways that lead to cell cytotoxicity. We conclude by summarizing novel and emergent RNR targeting motifs for cancer and antibiotic therapeutics.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"45-75"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316142/pdf/nihms-1063546.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38070728","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
Detection and Degradation of Stalled Nascent Chains via Ribosome-Associated Quality Control. 通过核糖体相关质量控制检测和降解停滞新生链。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-013118-110729
Cole S Sitron, Onn Brandman
{"title":"Detection and Degradation of Stalled Nascent Chains via Ribosome-Associated Quality Control.","authors":"Cole S Sitron,&nbsp;Onn Brandman","doi":"10.1146/annurev-biochem-013118-110729","DOIUrl":"10.1146/annurev-biochem-013118-110729","url":null,"abstract":"<p><p>Stalled protein synthesis produces defective nascent chains that can harm cells. In response, cells degrade these nascent chains via a process called ribosome-associated quality control (RQC). Here, we review the irregularities in the translation process that cause ribosomes to stall as well as how cells use RQC to detect stalled ribosomes, ubiquitylate their tethered nascent chains, and deliver the ubiquitylated nascent chains to the proteasome. We additionally summarize how cells respond to RQC failure.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"417-442"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-013118-110729","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38070734","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: 49
HLAs, TCRs, and KIRs, a Triumvirate of Human Cell-Mediated Immunity. hla, tcr和kir，人类细胞介导免疫的三驾马车。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-011520-102754
Zakia Djaoud, Peter Parham
{"title":"HLAs, TCRs, and KIRs, a Triumvirate of Human Cell-Mediated Immunity.","authors":"Zakia Djaoud,&nbsp;Peter Parham","doi":"10.1146/annurev-biochem-011520-102754","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-102754","url":null,"abstract":"<p><p>In all human cells, human leukocyte antigen (HLA) class I glycoproteins assemble with a peptide and take it to the cell surface for surveillance by lymphocytes. These include natural killer (NK) cells and γδ T cells of innate immunity and αβ T cells of adaptive immunity. In healthy cells, the presented peptides derive from human proteins, to which lymphocytes are tolerant. In pathogen-infected cells, HLA class I expression is perturbed. Reduced HLA class I expression is detected by KIR and CD94:NKG2A receptors of NK cells. Almost any change in peptide presentation can be detected by αβ CD8<sup>+</sup> T cells. In responding to extracellular pathogens, HLA class II glycoproteins, expressed by specialized antigen-presenting cells, present peptides to αβ CD4<sup>+</sup> T cells. In comparison to the families of major histocompatibility complex (MHC) class I, MHC class II and αβ T cell receptors, the antigenic specificity of the γδ T cell receptors is incompletely understood.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"717-739"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-102754","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38071302","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: 41
Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. 兼性异染色质形成的分子机制:一个x染色体的视角。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-07-07 DOI: 10.1146/annurev-biochem-062917-012655
Jan J Żylicz, Edith Heard
{"title":"Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective.","authors":"Jan J Żylicz,&nbsp;Edith Heard","doi":"10.1146/annurev-biochem-062917-012655","DOIUrl":"https://doi.org/10.1146/annurev-biochem-062917-012655","url":null,"abstract":"<p><p>Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong <i>trans</i> activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (<i>Hox</i>) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (<i>Hox</i> clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"255-282"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-062917-012655","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37811770","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: 45
ADP-ribosylation. ADP-ribosylation。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-02-02 DOI: 10.32388/tr7tjc
K. Ueda, O. Hayaishi
{"title":"ADP-ribosylation.","authors":"K. Ueda, O. Hayaishi","doi":"10.32388/tr7tjc","DOIUrl":"https://doi.org/10.32388/tr7tjc","url":null,"abstract":"","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"54 1","pages":"73-100"},"PeriodicalIF":16.6,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43345124","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: 239
Chromatin. 染色质。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-02-02 DOI: 10.32388/s9htxi
T. Igo-Kemenes, W. Hörz, H. Zachau
{"title":"Chromatin.","authors":"T. Igo-Kemenes, W. Hörz, H. Zachau","doi":"10.32388/s9htxi","DOIUrl":"https://doi.org/10.32388/s9htxi","url":null,"abstract":"The approximate shape of the chromatin subunit called the nucleosome is now known, but its internal architecture is not well understood. Recent studies reveal details of the organisation of DNA within the nucleosome, and show that the arginine-rich histones are essential to DNA folding. Nucleosomes or structures related to them seem to be present at points of DNA replication and transcription; interactions within and between nucleosomes are likely to play a critical part in these processes.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"51 1","pages":"89-121"},"PeriodicalIF":16.6,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45979970","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
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