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Annual review of biochemistry最新文献

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The Design and Application of DNA-Editing Enzymes as Base Editors. 作为碱基编辑器的 DNA 编辑酶的设计与应用。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-04-05 DOI: 10.1146/annurev-biochem-052521-013938
Kartik L Rallapalli, Alexis C Komor
{"title":"The Design and Application of DNA-Editing Enzymes as Base Editors.","authors":"Kartik L Rallapalli, Alexis C Komor","doi":"10.1146/annurev-biochem-052521-013938","DOIUrl":"10.1146/annurev-biochem-052521-013938","url":null,"abstract":"<p><p>DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"43-79"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10330504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9756297","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
The Inseparable Relationship Between Cholesterol and Hedgehog Signaling. 胆固醇与刺猬信号之间密不可分的关系
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-03-31 DOI: 10.1146/annurev-biochem-052521-040313
Christian Siebold, Rajat Rohatgi
{"title":"The Inseparable Relationship Between Cholesterol and Hedgehog Signaling.","authors":"Christian Siebold, Rajat Rohatgi","doi":"10.1146/annurev-biochem-052521-040313","DOIUrl":"10.1146/annurev-biochem-052521-040313","url":null,"abstract":"<p><p>Ligands of the Hedgehog (HH) pathway are paracrine signaling molecules that coordinate tissue development in metazoans. A remarkable feature of HH signaling is the repeated use of cholesterol in steps spanning ligand biogenesis, secretion, dispersal, and reception on target cells. A cholesterol molecule covalently attached to HH ligands is used as a molecular baton by transfer proteins to guide their secretion, spread, and reception. On target cells, a signaling circuit composed of a cholesterol transporter and sensor regulates transmission of HH signals across the plasma membrane to the cytoplasm. The repeated use of cholesterol in signaling supports the view that the HH pathway likely evolved by coopting ancient systems to regulate the abundance or organization of sterol-like lipids in membranes.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"273-298"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10330520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9769873","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
The Activation Mechanism of the Insulin Receptor: A Structural Perspective. 胰岛素受体的激活机制:一个结构视角。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-052521-033250
Eunhee Choi, Xiao-Chen Bai
{"title":"The Activation Mechanism of the Insulin Receptor: A Structural Perspective.","authors":"Eunhee Choi,&nbsp;Xiao-Chen Bai","doi":"10.1146/annurev-biochem-052521-033250","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-033250","url":null,"abstract":"<p><p>The insulin receptor (IR) is a type II receptor tyrosine kinase that plays essential roles in metabolism, growth, and proliferation. Dysregulation of IR signaling is linked to many human diseases, such as diabetes and cancers. The resolution revolution in cryo-electron microscopy has led to the determination of several structures of IR with different numbers of bound insulin molecules in recent years, which have tremendously improved our understanding of how IR is activated by insulin. Here, we review the insulin-induced activation mechanism of IR, including (<i>a</i>) the detailed binding modes and functions of insulin at site 1 and site 2 and (<i>b</i>) the insulin-induced structural transitions that are required for IR activation. We highlight several other key aspects of the activation and regulation of IR signaling and discuss the remaining gaps in our understanding of the IR activation mechanism and potential avenues of future research.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"247-272"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10398885/pdf/nihms-1919378.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9929688","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: 6
The Proteins of mRNA Modification: Writers, Readers, and Erasers. mRNA修饰的蛋白质:写入器，读取器和擦除器。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-052521-035330
Mathieu N Flamand, Matthew Tegowski, Kate D Meyer
{"title":"The Proteins of mRNA Modification: Writers, Readers, and Erasers.","authors":"Mathieu N Flamand,&nbsp;Matthew Tegowski,&nbsp;Kate D Meyer","doi":"10.1146/annurev-biochem-052521-035330","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-035330","url":null,"abstract":"<p><p>Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A). We first describe the discovery of the key enzymes that deposit and remove m<sup>6</sup>A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m<sup>6</sup>A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"145-173"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443600/pdf/nihms-1922506.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10042992","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: 14
Polyamines in Parkinson's Disease: Balancing Between Neurotoxicity and Neuroprotection. 帕金森病中的多胺:神经毒性和神经保护之间的平衡。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-071322-021330
Stephanie Vrijsen, Marine Houdou, Ana Cascalho, Jan Eggermont, Peter Vangheluwe
{"title":"Polyamines in Parkinson's Disease: Balancing Between Neurotoxicity and Neuroprotection.","authors":"Stephanie Vrijsen,&nbsp;Marine Houdou,&nbsp;Ana Cascalho,&nbsp;Jan Eggermont,&nbsp;Peter Vangheluwe","doi":"10.1146/annurev-biochem-071322-021330","DOIUrl":"https://doi.org/10.1146/annurev-biochem-071322-021330","url":null,"abstract":"<p><p>The polyamines putrescine, spermidine, and spermine are abundant polycations of vital importance in mammalian cells. Their cellular levels are tightly regulated by degradation and synthesis, as well as by uptake and export. Here, we discuss the delicate balance between the neuroprotective and neurotoxic effects of polyamines in the context of Parkinson's disease (PD). Polyamine levels decline with aging and are altered in patients with PD, whereas recent mechanistic studies on ATP13A2 (PARK9) demonstrated a driving role of a disturbed polyamine homeostasis in PD. Polyamines affect pathways in PD pathogenesis, such as α-synuclein aggregation, and influence PD-related processes like autophagy, heavy metal toxicity, oxidative stress, neuroinflammation, and lysosomal/mitochondrial dysfunction. We formulate outstanding research questions regarding the role of polyamines in PD, their potential as PD biomarkers, and possible therapeutic strategies for PD targeting polyamine homeostasis.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"435-464"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662523","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: 4
Translation and mRNA Stability Control. 翻译和 mRNA 稳定性控制
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-03-31 DOI: 10.1146/annurev-biochem-052621-091808
Qiushuang Wu, Ariel A Bazzini
{"title":"Translation and mRNA Stability Control.","authors":"Qiushuang Wu, Ariel A Bazzini","doi":"10.1146/annurev-biochem-052621-091808","DOIUrl":"10.1146/annurev-biochem-052621-091808","url":null,"abstract":"<p><p>Messenger RNA (mRNA) stability and translational efficiency are two crucial aspects of the post-transcriptional process that profoundly impact protein production in a cell. While it is widely known that ribosomes produce proteins, studies during the past decade have surprisingly revealed that ribosomes also control mRNA stability in a codon-dependent manner, a process referred to as codon optimality. Therefore, codons, the three-nucleotide words read by the ribosome, have a potent effect on mRNA stability and provide cis<i>-</i>regulatory information that extends beyond the amino acids they encode. While the codon optimality molecular mechanism is still unclear, the translation elongation rate appears to trigger mRNA decay. Thus, transfer RNAs emerge as potential master gene regulators affecting mRNA stability. Furthermore, while few factors related to codon optimality have been identified in yeast, the orthologous genes in vertebrates do not necessary share the same functions. Here, we discuss codon optimality findings and gene regulation layers related to codon composition in different eukaryotic species.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"227-245"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9668847","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
Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. 通过核糖体动力学管理稳态染色质景观
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 Epub Date: 2022-03-18 DOI: 10.1146/annurev-biochem-032620-104508
Kami Ahmad, Steven Henikoff, Srinivas Ramachandran
{"title":"Managing the Steady State Chromatin Landscape by Nucleosome Dynamics.","authors":"Kami Ahmad, Steven Henikoff, Srinivas Ramachandran","doi":"10.1146/annurev-biochem-032620-104508","DOIUrl":"10.1146/annurev-biochem-032620-104508","url":null,"abstract":"<p><p>Gene regulation arises out of dynamic competition between nucleosomes, transcription factors, and other chromatin proteins for the opportunity to bind genomic DNA. The timescales of nucleosome assembly and binding of factors to DNA determine the outcomes of this competition at any given locus. Here, we review how these properties of chromatin proteins and the interplay between the dynamics of different factors are critical for gene regulation. We discuss how molecular structures of large chromatin-associated complexes, kinetic measurements, and high resolution mapping of protein-DNA complexes in vivo set the boundary conditions for chromatin dynamics, leading to models of how the steady state behaviors of regulatory elements arise.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"183-195"},"PeriodicalIF":12.1,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10277172/pdf/nihms-1814593.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10019043","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
The Life of SARS-CoV-2 Inside Cells: Replication-Transcription Complex Assembly and Function. SARS-CoV-2在细胞内的生命:复制-转录复合体的组装和功能
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-052521-115653
Zhiyong Lou, Zihe Rao
{"title":"The Life of SARS-CoV-2 Inside Cells: Replication-Transcription Complex Assembly and Function.","authors":"Zhiyong Lou,&nbsp;Zihe Rao","doi":"10.1146/annurev-biochem-052521-115653","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-115653","url":null,"abstract":"<p><p>The persistence of the coronavirus disease 2019 (COVID-19) pandemic has resulted in increasingly disruptive impacts, and it has become the most devastating challenge to global health in a century. The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges the currently available therapeutics for clinical application. Nonstructural proteins (also known as replicase proteins) with versatile biological functions play central roles in viral replication and transcription inside the host cells, and they are the most conserved target proteins among the SARS-CoV-2 variants. Specifically, they constitute the replication-transcription complexes (RTCs) dominating the synthesis of viral RNA. Knowledge of themolecular mechanisms of nonstructural proteins and their assembly into RTCs will benefit the development of antivirals targeting them against existing or potentially emerging variants. In this review, we summarize current knowledge of the structures and functions of coronavirus nonstructural proteins as well as the assembly and functions of RTCs in the life cycle of the virus.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"381-401"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40150642","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: 6
Structure and Mechanism of the Lipid Flippase MurJ. 脂质翻转酶murp的结构与机制
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-040320-105145
Alvin C Y Kuk, Aili Hao, Seok-Yong Lee
{"title":"Structure and Mechanism of the Lipid Flippase MurJ.","authors":"Alvin C Y Kuk,&nbsp;Aili Hao,&nbsp;Seok-Yong Lee","doi":"10.1146/annurev-biochem-040320-105145","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-105145","url":null,"abstract":"<p><p>Biosynthesis of many important polysaccharides (including peptidoglycan, lipopolysaccharide, and <i>N</i>-linked glycans) necessitates the transport of lipid-linked oligosaccharides (LLO) across membranes from their cytosolic site of synthesis to their sites of utilization. Much of our current understanding of LLO transport comes from genetic, biochemical, and structural studies of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) superfamily protein MurJ, which flips the peptidoglycan precursor lipid II. MurJ plays a pivotal role in bacterial cell wall synthesis and is an emerging antibiotic target. Here, we review the mechanism of LLO flipping by MurJ, including the structural basis for lipid II flipping and ion coupling. We then discuss inhibition of MurJ by antibacterials, including humimycins and the phage M lysis protein, as well as how studies on MurJ could provide insight into other flippases, both within and beyond the MOP superfamily.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"705-729"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108830/pdf/nihms-1871783.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9701467","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: 6
Structural Mimicry in Microbial and Antimicrobial Amyloids. 微生物和抗微生物淀粉样蛋白的结构拟态。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-032620-105157
Nimrod Golan, Yizhaq Engelberg, Meytal Landau
{"title":"Structural Mimicry in Microbial and Antimicrobial Amyloids.","authors":"Nimrod Golan,&nbsp;Yizhaq Engelberg,&nbsp;Meytal Landau","doi":"10.1146/annurev-biochem-032620-105157","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-105157","url":null,"abstract":"<p><p>The remarkable variety of microbial species of human pathogens and microbiomes generates significant quantities of secreted amyloids, which are structured protein fibrils that serve diverse functions related to virulence and interactions with the host. Human amyloids are associated largely with fatal neurodegenerative and systemic aggregation diseases, and current research has put forward the hypothesis that the interspecies amyloid interactome has physiological and pathological significance. Moreover, functional and molecular-level connections between antimicrobial activity and amyloid structures suggest a neuroimmune role for amyloids that are otherwise known to be pathological. Compared to the extensive structural information that has been accumulated for human amyloids, high-resolution structures of microbial and antimicrobial amyloids are only emerging. These recent structures reveal both similarities and surprising departures from the typical amyloid motif, in accordance with their diverse activities, and advance the discovery of novel antivirulence and antimicrobial agents. In addition, the structural information has led researchers to postulate that amyloidogenic sequences are natural targets for structural mimicry, for instance in host-microbe interactions. Microbial amyloid research could ultimately be used to fight aggressive infections and possibly processes leading to autoimmune and neurodegenerative diseases.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"403-422"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40150641","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: 1
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