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Annual review of biochemistry最新文献

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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
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
Sensory TRP Channels in Three Dimensions. 三维感官 TRP 通道
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 Epub Date: 2022-03-14 DOI: 10.1146/annurev-biochem-032620-105738
Melinda M Diver, John V Lin King, David Julius, Yifan Cheng
{"title":"Sensory TRP Channels in Three Dimensions.","authors":"Melinda M Diver, John V Lin King, David Julius, Yifan Cheng","doi":"10.1146/annurev-biochem-032620-105738","DOIUrl":"10.1146/annurev-biochem-032620-105738","url":null,"abstract":"<p><p>Transient receptor potential (TRP) ion channels are sophisticated signaling machines that detect a wide variety of environmental and physiological signals. Every cell in the body expresses one or more members of the extended TRP channel family, which consists of over 30 subtypes, each likely possessing distinct pharmacological, biophysical, and/or structural attributes. While the function of some TRP subtypes remains enigmatic, those involved in sensory signaling are perhaps best characterized and have served as models for understanding how these excitatory ion channels serve as polymodal signal integrators. With the recent resolution revolution in cryo-electron microscopy, these and other TRP channel subtypes are now yielding their secrets to detailed atomic analysis, which is beginning to reveal structural underpinnings of stimulus detection and gating, ion permeation, and allosteric mechanisms governing signal integration. These insights are providing a framework for designing and evaluating modality-specific pharmacological agents for treating sensory and other TRP channel-associated disorders.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"629-649"},"PeriodicalIF":12.1,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9233036/pdf/nihms-1809634.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9702300","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 Purinosome: A Case Study for a Mammalian Metabolon. 嘌呤酶:哺乳动物代谢物的案例研究。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-032620-105728
Anthony M Pedley, Vidhi Pareek, Stephen J Benkovic
{"title":"The Purinosome: A Case Study for a Mammalian Metabolon.","authors":"Anthony M Pedley,&nbsp;Vidhi Pareek,&nbsp;Stephen J Benkovic","doi":"10.1146/annurev-biochem-032620-105728","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-105728","url":null,"abstract":"<p><p>Over the past fifteen years, we have unveiled a new mechanism by which cells achieve greater efficiency in de novo purine biosynthesis. This mechanism relies on the compartmentalization of de novo purine biosynthetic enzymes into a dynamic complex called the purinosome. In this review, we highlight our current understanding of the purinosome with emphasis on its biophysical properties and function and on the cellular mechanisms that regulate its assembly. We propose a model for functional purinosomes in which they consist of at least ten enzymes that localize near mitochondria and carry out de novo purine biosynthesis by metabolic channeling. We conclude by discussing challenges and opportunities associated with studying the purinosome and analogous metabolons.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"89-106"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531488/pdf/nihms-1837650.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9701464","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: 15
Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. 更好，更快，更便宜:冷冻电子显微镜的最新进展。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-032620-110705
Eugene Y D Chua, Joshua H Mendez, Micah Rapp, Serban L Ilca, Yong Zi Tan, Kashyap Maruthi, Huihui Kuang, Christina M Zimanyi, Anchi Cheng, Edward T Eng, Alex J Noble, Clinton S Potter, Bridget Carragher
{"title":"Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy.","authors":"Eugene Y D Chua,&nbsp;Joshua H Mendez,&nbsp;Micah Rapp,&nbsp;Serban L Ilca,&nbsp;Yong Zi Tan,&nbsp;Kashyap Maruthi,&nbsp;Huihui Kuang,&nbsp;Christina M Zimanyi,&nbsp;Anchi Cheng,&nbsp;Edward T Eng,&nbsp;Alex J Noble,&nbsp;Clinton S Potter,&nbsp;Bridget Carragher","doi":"10.1146/annurev-biochem-032620-110705","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-110705","url":null,"abstract":"<p><p>Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"1-32"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10393189/pdf/nihms-1916146.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10286487","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: 19
Encapsulins. 密封剂。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-040320-102858
Tobias W Giessen
{"title":"Encapsulins.","authors":"Tobias W Giessen","doi":"10.1146/annurev-biochem-040320-102858","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-102858","url":null,"abstract":"<p><p>Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"353-380"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944552/pdf/nihms-1869567.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10750512","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
The Structural Dynamics of Translation. 翻译的结构动力学。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-071921-122857
Andrei A Korostelev
{"title":"The Structural Dynamics of Translation.","authors":"Andrei A Korostelev","doi":"10.1146/annurev-biochem-071921-122857","DOIUrl":"https://doi.org/10.1146/annurev-biochem-071921-122857","url":null,"abstract":"<p><p>Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"245-267"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10389292/pdf/nihms-1920330.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9890319","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: 13
Lipoproteins in the Central Nervous System: From Biology to Pathobiology. 中枢神经系统中的脂蛋白：从生物学到病理生物学
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-032620-104801
Ana-Caroline Raulin, Yuka A Martens, Guojun Bu
{"title":"Lipoproteins in the Central Nervous System: From Biology to Pathobiology.","authors":"Ana-Caroline Raulin, Yuka A Martens, Guojun Bu","doi":"10.1146/annurev-biochem-032620-104801","DOIUrl":"10.1146/annurev-biochem-032620-104801","url":null,"abstract":"<p><p>The brain, as one of the most lipid-rich organs, heavily relies on lipid transport and distribution to maintain homeostasis and neuronal function. Lipid transport mediated by lipoprotein particles, which are complex structures composed of apolipoproteins and lipids, has been thoroughly characterized in the periphery. Although lipoproteins in the central nervous system (CNS) were reported over half a century ago, the identification of <i>APOE4</i> as the strongest genetic risk factor for Alzheimer's disease has accelerated investigation of the biology and pathobiology of lipoproteins in the CNS. This review provides an overview of the different components of lipoprotein particles, in particular apolipoproteins, and their involvements in both physiological functions and pathological mechanisms in the CNS.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"731-759"},"PeriodicalIF":12.1,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9634960/pdf/nihms-1844218.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9743352","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
Kinetic Proofreading. 动能校对。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-04-01 DOI: 10.1146/annurev-biochem-040320-103630
Hinrich Boeger
{"title":"Kinetic Proofreading.","authors":"Hinrich Boeger","doi":"10.1146/annurev-biochem-040320-103630","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-103630","url":null,"abstract":"Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution-an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment-is shown to be widely employed by biological processes that transmit genetic and regulatory information. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42335189","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
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