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The Hsp70 and JDP proteins: Structure-function perspective on molecular chaperone activity. Hsp70和JDP蛋白：分子伴侣活性的结构-功能视角。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-09-29 DOI: 10.1016/bs.enz.2023.07.008
Szymon J Ciesielski, Cameron Young, Elena J Ciesielska, Grzegorz L Ciesielski
{"title":"The Hsp70 and JDP proteins: Structure-function perspective on molecular chaperone activity.","authors":"Szymon J Ciesielski, Cameron Young, Elena J Ciesielska, Grzegorz L Ciesielski","doi":"10.1016/bs.enz.2023.07.008","DOIUrl":"10.1016/bs.enz.2023.07.008","url":null,"abstract":"<p><p>Proteins are the most structurally diverse cellular biomolecules that act as molecular machines driving essential activities of all living organisms. To be functional, most of the proteins need to fold into a specific three-dimensional structure, which on one hand should be stable enough to oppose disruptive conditions and on the other hand flexible enough to allow conformational dynamics necessary for their biological functions. This compromise between stability and dynamics makes proteins susceptible to stress-induced misfolding and aggregation. Moreover, the folding process itself is intrinsically prone to conformational errors. Molecular chaperones are proteins that mitigate folding defects and maintain the structural integrity of the cellular proteome. Promiscuous Hsp70 chaperones are central to these processes and their activity depends on the interaction with obligatory J-domain protein (JDP) partners. In this review, we discuss structural aspects of Hsp70s, JDPs, and their interaction in the context of biological activities.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"54 ","pages":"221-245"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72015668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Perspectives on ATP-dependent chromatin remodeling. ATP依赖性染色质重塑的展望。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-04-19 DOI: 10.1016/bs.enz.2023.03.002
James T Kadonaga
{"title":"Perspectives on ATP-dependent chromatin remodeling.","authors":"James T Kadonaga","doi":"10.1016/bs.enz.2023.03.002","DOIUrl":"10.1016/bs.enz.2023.03.002","url":null,"abstract":"<p><p>Nucleosomes are intrinsically immobile, and thus, ATP-dependent chromatin remodeling factors are needed to alter nucleosomes to facilitate DNA-directed processes such as transcription. More generally, chromatin remodeling factors mediate chromatin dynamics, which encompasses nucleosome assembly, movement, and disruption as well as histone exchange. Here, I present selected thoughts and perspectives on the past, present, and future of these fascinating ATP-driven motor proteins.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"53 ","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10552720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41169574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex. SIN3复合物代谢和表观遗传学调控之间的串扰协调。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-07-28 DOI: 10.1016/bs.enz.2023.06.001
Imad Soukar, Anjalie Amarasinghe, Lori A Pile
{"title":"Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex.","authors":"Imad Soukar,&nbsp;Anjalie Amarasinghe,&nbsp;Lori A Pile","doi":"10.1016/bs.enz.2023.06.001","DOIUrl":"https://doi.org/10.1016/bs.enz.2023.06.001","url":null,"abstract":"<p><p>Post-translational modifications of histone proteins control the expression of genes. Metabolites from central and one-carbon metabolism act as donor moieties to modify histones and regulate gene expression. Thus, histone modification and gene regulation are connected to the metabolite status of the cell. Histone modifiers, such as the SIN3 complex, regulate genes involved in proliferation and metabolism. The SIN3 complex contains a histone deacetylase and a histone demethylase, which regulate the chromatin landscape and gene expression. In this chapter, we review the cross-talk between metabolic pathways that produce donor moieties, and epigenetic complexes regulating proliferation and metabolic genes. This cross-talk between gene regulation and metabolism is tightly controlled, and disruption of this cross-talk leads to metabolic diseases. We discuss promising therapeutics that directly regulate histone modifiers, and can affect the metabolic status of the cell, alleviating some metabolic diseases.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"53 ","pages":"33-68"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41168895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Helicases required for nucleotide excision repair: structure, function and mechanism. 核苷酸切除修复所需的螺旋酶：结构、功能和机制。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-06-03 DOI: 10.1016/bs.enz.2023.05.002
Feng He, Marco Bravo, Li Fan
{"title":"Helicases required for nucleotide excision repair: structure, function and mechanism.","authors":"Feng He, Marco Bravo, Li Fan","doi":"10.1016/bs.enz.2023.05.002","DOIUrl":"10.1016/bs.enz.2023.05.002","url":null,"abstract":"<p><p>Nucleotide excision repair (NER) is a major DNA repair pathway conserved from bacteria to humans. Various DNA helicases, a group of enzymes capable of separating DNA duplex into two strands through ATP binding and hydrolysis, are required by NER to unwind the DNA duplex around the lesion to create a repair bubble and for damage verification and removal. In prokaryotes, UvrB helicase is required for repair bubble formation and damage verification, while UvrD helicase is responsible for the removal of the excised damage containing single-strand (ss) DNA fragment. In addition, UvrD facilitates transcription-coupled repair (TCR) by backtracking RNA polymerase stalled at the lesion. In eukaryotes, two helicases XPB and XPD from the transcription factor TFIIH complex fulfill the helicase requirements of NER. Interestingly, homologs of all these four helicases UvrB, UvrD, XPB, and XPD have been identified in archaea. This review summarizes our current understanding about the structure, function, and mechanism of these four helicases.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"54 ","pages":"273-304"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72015662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulatory miRNAs in cancer cell recovery from therapy exposure and its implications as a novel therapeutic strategy for preventing disease recurrence. 癌症细胞从治疗暴露中恢复的调节性miRNA及其作为预防疾病复发的新治疗策略的意义。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-08-30 DOI: 10.1016/bs.enz.2023.07.007
Joseph Landry, Kathryn Shows, Akash Jagdeesh, Aashka Shah, Mihir Pokhriyal, Vasily Yakovlev
{"title":"Regulatory miRNAs in cancer cell recovery from therapy exposure and its implications as a novel therapeutic strategy for preventing disease recurrence.","authors":"Joseph Landry, Kathryn Shows, Akash Jagdeesh, Aashka Shah, Mihir Pokhriyal, Vasily Yakovlev","doi":"10.1016/bs.enz.2023.07.007","DOIUrl":"10.1016/bs.enz.2023.07.007","url":null,"abstract":"<p><p>The desired outcome of cancer therapies is the eradication of disease. This can be achieved when therapy exposure leads to therapy-induced cancer cell death as the dominant outcome. Theoretically, a permanent therapy-induced growth arrest could also contribute to a complete response, which has the potential to lead to remission. However, preclinical models have shown that therapy-induced growth arrest is not always durable, as recovering cancer cell populations can contribute to the recurrence of cancer. Significant research efforts have been expended to develop strategies focusing on the prevention of recurrence. Recovery of cells from therapy exposure can occur as a result of several cell stress adaptations. These include cytoprotective autophagy, cellular quiescence, a reversable form of senescence, and the suppression of apoptosis and necroptosis. It is well documented that microRNAs regulate the response of cancer cells to anti-cancer therapies, making targeting microRNAs therapeutically a viable strategy to sensitization and the prevention of recovery. We propose that the use of microRNA-targeting therapies in prolonged sequence, that is, a significant period after initial therapy exposure, could reduce toxicity from the standard combination strategy, and could exploit new epigenetic states essential for cancer cells to recover from therapy exposure. In a step toward supporting this strategy, we survey the available scientific literature to identify microRNAs which could be targeted in sequence to eliminate residual cancer cell populations that were arrested as a result of therapy exposure. It is our hope that by successfully identifying microRNAs which could be targeted in sequence we can prevent disease recurrence.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"53 ","pages":"113-196"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12790109/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41132747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Five decades of metalloenzymology. 50年的金属酶学。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-03-30 DOI: 10.1016/bs.enz.2023.03.001
Robert P Hausinger
{"title":"Five decades of metalloenzymology.","authors":"Robert P Hausinger","doi":"10.1016/bs.enz.2023.03.001","DOIUrl":"10.1016/bs.enz.2023.03.001","url":null,"abstract":"<p><p>Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"54 ","pages":"71-105"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72015661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Preface. 前言
Enzymes Pub Date : 2023-01-01 DOI: 10.1016/S1874-6047(23)00025-2
David N Arnosti, Laurie S Kaguni
{"title":"Preface.","authors":"David N Arnosti,&nbsp;Laurie S Kaguni","doi":"10.1016/S1874-6047(23)00025-2","DOIUrl":"https://doi.org/10.1016/S1874-6047(23)00025-2","url":null,"abstract":"","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"53 ","pages":"xi-xii"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41152427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Soft repression and chromatin modification by conserved transcriptional corepressors. 保守转录辅压子的软抑制和染色质修饰。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-09-14 DOI: 10.1016/bs.enz.2023.08.001
David N Arnosti
{"title":"Soft repression and chromatin modification by conserved transcriptional corepressors.","authors":"David N Arnosti","doi":"10.1016/bs.enz.2023.08.001","DOIUrl":"https://doi.org/10.1016/bs.enz.2023.08.001","url":null,"abstract":"<p><p>Transcriptional regulation in eukaryotic cells involves the activity of multifarious DNA-binding transcription factors and recruited corepressor complexes. Together, these complexes interact with the core transcriptional machinery, chromatin, and nuclear environment to effect complex patterns of gene regulation. Much focus has been paid to the action of master regulatory switches that are key to developmental and environmental responses, as these genetic elements have important phenotypic effects. The regulation of widely-expressed metabolic control genes has been less well studied, particularly in cases in which physically-interacting repressors and corepressors have subtle influences on steady-state expression. This latter phenomenon, termed \"soft repression\" is a topic of increasing interest as genomic approaches provide ever more powerful tools to uncover the significance of this level of control. This review provides an oversight of classic and current approaches to the study of transcriptional repression in eukaryotic systems, with a specific focus on opportunities and challenges that lie ahead in the study of soft repression.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"53 ","pages":"69-96"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41151731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DNA replication machineries: Structural insights from crystallography and electron microscopy. DNA复制机制：结晶学和电子显微镜的结构见解。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-07-27 DOI: 10.1016/bs.enz.2023.07.004
Rebeca Bocanegra, María Ortíz-Rodríguez, Lyra Zumeta, Ismael Plaza-G A, Elías Faro, Borja Ibarra
{"title":"DNA replication machineries: Structural insights from crystallography and electron microscopy.","authors":"Rebeca Bocanegra, María Ortíz-Rodríguez, Lyra Zumeta, Ismael Plaza-G A, Elías Faro, Borja Ibarra","doi":"10.1016/bs.enz.2023.07.004","DOIUrl":"10.1016/bs.enz.2023.07.004","url":null,"abstract":"<p><p>Since the discovery of DNA as the genetic material, scientists have been investigating how the information contained in this biological polymer is transmitted from generation to generation. X-ray crystallography, and more recently, cryo-electron microscopy techniques have been instrumental in providing essential information about the structure, functions and interactions of the DNA and the protein machinery (replisome) responsible for its replication. In this chapter, we highlight several works that describe the structure and structure-function relationships of the core components of the prokaryotic and eukaryotic replisomes. We also discuss the most recent studies on the structural organization of full replisomes.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"54 ","pages":"249-271"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72015660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The mitochondrial respiratory chain. 线粒体呼吸链。
Enzymes Pub Date : 2023-01-01 Epub Date: 2023-05-26 DOI: 10.1016/bs.enz.2023.05.001
Mårten Wikström, Cristina Pecorilla, Vivek Sharma
{"title":"The mitochondrial respiratory chain.","authors":"Mårten Wikström, Cristina Pecorilla, Vivek Sharma","doi":"10.1016/bs.enz.2023.05.001","DOIUrl":"10.1016/bs.enz.2023.05.001","url":null,"abstract":"<p><p>We present a brief review of the mitochondrial respiratory chain with emphasis on complexes I, III and IV, which contribute to the generation of protonmotive force across the inner mitochondrial membrane, and drive the synthesis of ATP by the process called oxidative phosphorylation. The basic structural and functional details of these complexes are discussed. In addition, we briefly review the information on the so-called supercomplexes, aggregates of complexes I-IV, and summarize basic physiological aspects of cell respiration.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"54 ","pages":"15-36"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72015669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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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