首页 > 最新文献

Biochemical Society transactions最新文献

英文 中文
Exploring the dynamics of messenger ribonucleoprotein-mediated translation repression. 探索信使核糖核蛋白介导的翻译抑制动态。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20231240
Julia Meyer, Marco Payr, Olivier Duss, Janosch Hennig

Translational control is crucial for well-balanced cellular function and viability of organisms. Different mechanisms have evolved to up- and down-regulate protein synthesis, including 3' untranslated region (UTR)-mediated translation repression. RNA binding proteins or microRNAs interact with regulatory sequence elements located in the 3' UTR and interfere most often with the rate-limiting initiation step of translation. Dysregulation of post-transcriptional gene expression leads to various kinds of diseases, emphasizing the significance of understanding the mechanisms of these processes. So far, only limited mechanistic details about kinetics and dynamics of translation regulation are understood. This mini-review focuses on 3' UTR-mediated translational regulation mechanisms and demonstrates the potential of using single-molecule fluorescence-microscopy for kinetic and dynamic studies of translation regulation in vivo and in vitro.

翻译控制对于平衡细胞功能和生物体的生存能力至关重要。蛋白质合成的上行和下行调节机制各不相同,其中包括 3' 非翻译区(UTR)介导的翻译抑制。RNA 结合蛋白或 microRNA 与位于 3' UTR 的调控序列元件相互作用,通常会干扰翻译的限速起始步骤。转录后基因表达失调会导致各种疾病,因此了解这些过程的机制意义重大。迄今为止,人们对翻译调控的动力学和动力学细节的了解还很有限。这篇微型综述重点介绍 3' UTR 介导的翻译调控机制,并展示了利用单分子荧光显微镜对体内和体外翻译调控的动力学和动态研究的潜力。
{"title":"Exploring the dynamics of messenger ribonucleoprotein-mediated translation repression.","authors":"Julia Meyer, Marco Payr, Olivier Duss, Janosch Hennig","doi":"10.1042/BST20231240","DOIUrl":"10.1042/BST20231240","url":null,"abstract":"<p><p>Translational control is crucial for well-balanced cellular function and viability of organisms. Different mechanisms have evolved to up- and down-regulate protein synthesis, including 3' untranslated region (UTR)-mediated translation repression. RNA binding proteins or microRNAs interact with regulatory sequence elements located in the 3' UTR and interfere most often with the rate-limiting initiation step of translation. Dysregulation of post-transcriptional gene expression leads to various kinds of diseases, emphasizing the significance of understanding the mechanisms of these processes. So far, only limited mechanistic details about kinetics and dynamics of translation regulation are understood. This mini-review focuses on 3' UTR-mediated translational regulation mechanisms and demonstrates the potential of using single-molecule fluorescence-microscopy for kinetic and dynamic studies of translation regulation in vivo and in vitro.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2267-2279"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142725336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 emerging role of Rab proteins in osteoclast organelle biogenesis and function. Rab蛋白在破骨细胞细胞器生物发生和功能中的新作用。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20240519
Shiou-Ling Lu, Takeshi Noda

Rab GTPase proteins have been extensively studied for their roles in regulating vesicle and organelle dynamics. Among the ∼60 subtypes in mammalian cells, several Rabs have been reported to play crucial roles in osteoclast biogenesis and function. In this review, we aim to provide an update on recently described Rab GTPases, Rab11, Rab32, Rab44, and Rab38, as well as Rab7, Rab3D and Rab27A in osteoclast formation and function.

兔GTPase蛋白因其在调节囊泡和细胞器动力学中的作用而被广泛研究。在哺乳动物细胞的约60种亚型中,有几种Rabs在破骨细胞的生物发生和功能中起着至关重要的作用。在这篇综述中,我们旨在提供最近描述的Rab11、Rab32、Rab44和Rab38以及Rab7、Rab3D和Rab27A在破骨细胞形成和功能中的最新进展。
{"title":"The emerging role of Rab proteins in osteoclast organelle biogenesis and function.","authors":"Shiou-Ling Lu, Takeshi Noda","doi":"10.1042/BST20240519","DOIUrl":"10.1042/BST20240519","url":null,"abstract":"<p><p>Rab GTPase proteins have been extensively studied for their roles in regulating vesicle and organelle dynamics. Among the ∼60 subtypes in mammalian cells, several Rabs have been reported to play crucial roles in osteoclast biogenesis and function. In this review, we aim to provide an update on recently described Rab GTPases, Rab11, Rab32, Rab44, and Rab38, as well as Rab7, Rab3D and Rab27A in osteoclast formation and function.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2469-2475"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Quaternary arrangements of membrane proteins: an aquaporin case. 膜蛋白的四级排列:水蒸发蛋白案例。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20241630
Maria Hrmova

Integral polytopic α-helical membrane transporters and aquaporins move and distribute various molecules and dispose of or compartmentalize harmful elements that gather in living cells. The view shaped nearly 25 years ago states that integrating these proteins into cellular membranes can be considered a two-stage process, with hydrophobic core folding into α-helices across membranes to form functional entities (Popot and Engelman, 1990; Biochemistry29, 4031-4037). Since then, a large body of evidence cemented the roles of structural properties of membrane proteins and bilayer solvent components in forming functional assemblies. This mini-review updates our understanding of multifaced factors, which underlie transporters integration and oligomerization, focusing on water-permeating aquaporins. This work also elaborates on how individual monomers of bacterial and mammalian aquaporin tetramers, interact with each other, and how tetramers form contacts with lipids after being embedded in lipid bilayers of known composition, which mimics bacterial and mammalian membranes. Although this mini-review describes findings acquired using current methods, the view is open to how to extend this knowledge through, e.g. single-molecule-based and in situ cryogenic-electron tomography techniques. These and other methods could unravel the sources of entropy for membrane protein assemblies and pathways underlying integration, folding, oligomerization and quaternary structure formation with binding partners. We could expect that these exceedingly interdisciplinary approaches will form the basis for creating optimized transport systems, which could inspire bioengineering to develop a sustainable and healthy society.

整体多面体α-螺旋膜转运蛋白和水通道蛋白移动和分布各种分子,并处理或分隔聚集在活细胞中的有害元素。近25年前形成的观点认为,将这些蛋白质整合到细胞膜上可以被认为是一个两阶段的过程,疏水核心折叠成跨越膜的α-螺旋,形成功能实体(Popot和Engelman, 1990;Biochemistry29, 4031 - 4037)。从那时起,大量的证据巩固了膜蛋白的结构特性和双层溶剂组分在形成功能组装中的作用。这篇综述更新了我们对多重因素的理解,这些因素是转运体整合和寡聚的基础,重点是渗透水通道蛋白。这项工作还详细阐述了细菌和哺乳动物水通道蛋白四聚体的单个单体如何相互作用,以及四聚体在嵌入已知成分的脂质双层后如何与脂质形成接触,这模仿了细菌和哺乳动物的膜。虽然这篇小型综述描述了使用当前方法获得的发现,但对如何通过单分子和原位低温电子断层扫描技术扩展这一知识持开放态度。这些方法和其他方法可以揭示膜蛋白组装的熵源,以及与结合伙伴整合、折叠、寡聚化和四级结构形成的途径。我们可以期待,这些跨学科的方法将为创造优化的交通系统奠定基础,这可能会激发生物工程来发展一个可持续和健康的社会。
{"title":"Quaternary arrangements of membrane proteins: an aquaporin case.","authors":"Maria Hrmova","doi":"10.1042/BST20241630","DOIUrl":"10.1042/BST20241630","url":null,"abstract":"<p><p>Integral polytopic α-helical membrane transporters and aquaporins move and distribute various molecules and dispose of or compartmentalize harmful elements that gather in living cells. The view shaped nearly 25 years ago states that integrating these proteins into cellular membranes can be considered a two-stage process, with hydrophobic core folding into α-helices across membranes to form functional entities (Popot and Engelman, 1990; Biochemistry29, 4031-4037). Since then, a large body of evidence cemented the roles of structural properties of membrane proteins and bilayer solvent components in forming functional assemblies. This mini-review updates our understanding of multifaced factors, which underlie transporters integration and oligomerization, focusing on water-permeating aquaporins. This work also elaborates on how individual monomers of bacterial and mammalian aquaporin tetramers, interact with each other, and how tetramers form contacts with lipids after being embedded in lipid bilayers of known composition, which mimics bacterial and mammalian membranes. Although this mini-review describes findings acquired using current methods, the view is open to how to extend this knowledge through, e.g. single-molecule-based and in situ cryogenic-electron tomography techniques. These and other methods could unravel the sources of entropy for membrane protein assemblies and pathways underlying integration, folding, oligomerization and quaternary structure formation with binding partners. We could expect that these exceedingly interdisciplinary approaches will form the basis for creating optimized transport systems, which could inspire bioengineering to develop a sustainable and healthy society.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2557-2568"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Regulatory dynamics of arginine metabolism in Staphylococcus aureus. 金黄色葡萄球菌精氨酸代谢的调控动力学。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20240710
Itidal Reslane, Gabrielle F Watson, Luke D Handke, Paul D Fey

Staphylococcus aureus is a highly significant pathogen with several well studied and defined virulence factors. However, the metabolic pathways that are required to facilitate infection are not well described. Previous data have documented that S. aureus requires glucose catabolism during initial stages of infection. Therefore, certain nutrients whose biosynthetic pathway is under carbon catabolite repression and CcpA, including arginine, must be acquired from the host. However, even though S. aureus encodes pathways to synthesize arginine, biosynthesis of arginine is repressed even in the absence of glucose. Why is S. aureus a functional arginine auxotroph? This review discusses recently described regulatory mechanisms that are linked to repression of arginine biosynthesis using either proline or glutamate as substrates. In addition, recent studies are discussed that shed insight into the ultimate mechanisms linking arginine auxotrophy and infection persistence.

金黄色葡萄球菌是一种非常重要的病原体,有几个已被充分研究和确定的毒力因子。然而,促进感染所需的代谢途径尚未得到很好的描述。以前的数据已经证明金黄色葡萄球菌在感染的初始阶段需要葡萄糖分解代谢。因此,某些生物合成途径受到碳分解代谢物和CcpA抑制的营养物质,包括精氨酸,必须从宿主获得。然而,即使金黄色葡萄球菌编码合成精氨酸的途径,即使在没有葡萄糖的情况下,精氨酸的生物合成也会受到抑制。为什么金黄色葡萄球菌是功能性精氨酸营养不良菌?这篇综述讨论了最近描述的以脯氨酸或谷氨酸为底物抑制精氨酸生物合成的调控机制。此外,本文还讨论了最近的研究,揭示了精氨酸萎缩和感染持续之间的最终机制。
{"title":"Regulatory dynamics of arginine metabolism in Staphylococcus aureus.","authors":"Itidal Reslane, Gabrielle F Watson, Luke D Handke, Paul D Fey","doi":"10.1042/BST20240710","DOIUrl":"10.1042/BST20240710","url":null,"abstract":"<p><p>Staphylococcus aureus is a highly significant pathogen with several well studied and defined virulence factors. However, the metabolic pathways that are required to facilitate infection are not well described. Previous data have documented that S. aureus requires glucose catabolism during initial stages of infection. Therefore, certain nutrients whose biosynthetic pathway is under carbon catabolite repression and CcpA, including arginine, must be acquired from the host. However, even though S. aureus encodes pathways to synthesize arginine, biosynthesis of arginine is repressed even in the absence of glucose. Why is S. aureus a functional arginine auxotroph? This review discusses recently described regulatory mechanisms that are linked to repression of arginine biosynthesis using either proline or glutamate as substrates. In addition, recent studies are discussed that shed insight into the ultimate mechanisms linking arginine auxotrophy and infection persistence.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2513-2523"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Advances in utilizing reverse micelles to investigate membrane proteins. 利用反向胶束研究膜蛋白的进展。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20240830
Sara H Walters, Aaron S Birchfield, Brian Fuglestad

Reverse micelles (RMs) have emerged as useful tools for the study of membrane associated proteins. With a nanoscale water core surrounded by surfactant and solubilized in a non-polar solvent, RMs stand apart as a unique membrane model. While RMs have been utilized as tools to investigate the physical properties of membranes and their associated water, RMs also effectively house membrane associated proteins for a variety of studies. High-resolution protein NMR revealed a need for development of improved RM formulations, which greatly enhanced the use of RMs for aqueous proteins. Protein-optimized RM formulations enabled encapsulation of challenging membrane associated protein types, including lipidated proteins, transmembrane proteins, and peripheral membrane proteins. Improvements in biological accuracy of RMs using phospholipid-based surfactants has advanced their utility as a membrane mimetic even further, better matching the chemistry of the most common cellular membrane lipids. Natural lipid extracts may also be used to construct RMs and house proteins, resulting in a membrane model that better represents the complexity of biological membranes. Recent applications in high-resolution investigations of protein-membrane interactions and inhibitor design of membrane associated proteins have demonstrated the usefulness of these systems in addressing this difficult category of protein. Further developments of RMs as membrane models will enhance the breadth of investigations facilitated by these systems and will enhance their use in biophysical, structural, and drug discovery pursuits of membrane associated proteins. In this review, we present the development of RMs as membrane models and their application to structural and biophysical study of membrane proteins.

反胶束(RMs)已成为研究膜相关蛋白质的有用工具。反胶束的纳米级水核被表面活性剂包围,并溶解在非极性溶剂中,是一种独特的膜模型。RMs 被用作研究膜及其相关水的物理性质的工具,同时 RMs 还能有效地容纳膜相关蛋白质,用于各种研究。高分辨率蛋白质 NMR 揭示了开发改良 RM 配方的需求,这大大提高了 RM 在水性蛋白质方面的应用。蛋白质优化的 RM 配方能够封装具有挑战性的膜相关蛋白质类型,包括脂化蛋白质、跨膜蛋白质和外周膜蛋白质。使用磷脂基表面活性剂的 RM 在生物准确性方面的改进进一步提高了其作为膜模拟物的效用,使其与最常见的细胞膜脂质的化学性质更加匹配。天然脂质提取物也可用于构建 RM 和容纳蛋白质,从而使膜模型更好地代表生物膜的复杂性。最近在蛋白质-膜相互作用的高分辨率研究和膜相关蛋白质的抑制剂设计中的应用,证明了这些系统在处理这类困难蛋白质方面的有用性。作为膜模型的 RM 的进一步发展将提高这些系统所能促进的研究的广度,并将加强它们在膜相关蛋白的生物物理、结构和药物发现方面的应用。在这篇综述中,我们介绍了作为膜模型的 RM 的发展及其在膜蛋白结构和生物物理研究中的应用。
{"title":"Advances in utilizing reverse micelles to investigate membrane proteins.","authors":"Sara H Walters, Aaron S Birchfield, Brian Fuglestad","doi":"10.1042/BST20240830","DOIUrl":"10.1042/BST20240830","url":null,"abstract":"<p><p>Reverse micelles (RMs) have emerged as useful tools for the study of membrane associated proteins. With a nanoscale water core surrounded by surfactant and solubilized in a non-polar solvent, RMs stand apart as a unique membrane model. While RMs have been utilized as tools to investigate the physical properties of membranes and their associated water, RMs also effectively house membrane associated proteins for a variety of studies. High-resolution protein NMR revealed a need for development of improved RM formulations, which greatly enhanced the use of RMs for aqueous proteins. Protein-optimized RM formulations enabled encapsulation of challenging membrane associated protein types, including lipidated proteins, transmembrane proteins, and peripheral membrane proteins. Improvements in biological accuracy of RMs using phospholipid-based surfactants has advanced their utility as a membrane mimetic even further, better matching the chemistry of the most common cellular membrane lipids. Natural lipid extracts may also be used to construct RMs and house proteins, resulting in a membrane model that better represents the complexity of biological membranes. Recent applications in high-resolution investigations of protein-membrane interactions and inhibitor design of membrane associated proteins have demonstrated the usefulness of these systems in addressing this difficult category of protein. Further developments of RMs as membrane models will enhance the breadth of investigations facilitated by these systems and will enhance their use in biophysical, structural, and drug discovery pursuits of membrane associated proteins. In this review, we present the development of RMs as membrane models and their application to structural and biophysical study of membrane proteins.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2499-2511"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
A closer look at the role of deubiquitinating enzymes in the Hypoxia Inducible Factor pathway. 仔细研究去泛素化酶在缺氧诱导因子途径中的作用。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20230861
Tekle Pauzaite, James A Nathan

Hypoxia Inducible transcription Factors (HIFs) are central to the metazoan oxygen-sensing response. Under low oxygen conditions (hypoxia), HIFs are stabilised and govern an adaptive transcriptional programme to cope with prolonged oxygen starvation. However, when oxygen is present, HIFs are continuously degraded by the proteasome in a process involving prolyl hydroxylation and subsequent ubiquitination by the Von Hippel Lindau (VHL) E3 ligase. The essential nature of VHL in the HIF response is well established but the role of other enzymes involved in ubiquitination is less clear. Deubiquitinating enzymes (DUBs) counteract ubiquitination and provide an important regulatory aspect to many signalling pathways involving ubiquitination. In this review, we look at the complex network of ubiquitination and deubiquitination in controlling HIF signalling in normal and low oxygen tensions. We discuss the relative importance of DUBs in opposing VHL, and explore roles of DUBs more broadly in hypoxia, in both VHL and HIF independent contexts. We also consider the catalytic and non-catalytic roles of DUBs, and elaborate on the potential benefits and challenges of inhibiting these enzymes for therapeutic use.

缺氧诱导转录因子(HIFs)是元类动物氧感应反应的核心。在低氧条件下(缺氧),HIFs 保持稳定,并支配着一种适应性转录程序,以应对长时间的缺氧。然而,当氧气存在时,HIFs 会被蛋白酶体持续降解,降解过程涉及脯氨酰羟基化,随后被 Von Hippel Lindau(VHL)E3 连接酶泛素化。VHL 在 HIF 反应中的重要作用已得到证实,但参与泛素化的其他酶的作用却不太清楚。去泛素化酶(DUBs)可抵消泛素化作用,并为许多涉及泛素化的信号通路提供重要的调节作用。在这篇综述中,我们探讨了泛素化和去泛素化在正常和低氧条件下控制 HIF 信号传导的复杂网络。我们讨论了 DUBs 在对抗 VHL 时的相对重要性,并探讨了 DUBs 在 VHL 和独立于 HIF 的低氧环境中的更广泛作用。我们还考虑了 DUBs 的催化和非催化作用,并阐述了抑制这些酶用于治疗的潜在益处和挑战。
{"title":"A closer look at the role of deubiquitinating enzymes in the Hypoxia Inducible Factor pathway.","authors":"Tekle Pauzaite, James A Nathan","doi":"10.1042/BST20230861","DOIUrl":"10.1042/BST20230861","url":null,"abstract":"<p><p>Hypoxia Inducible transcription Factors (HIFs) are central to the metazoan oxygen-sensing response. Under low oxygen conditions (hypoxia), HIFs are stabilised and govern an adaptive transcriptional programme to cope with prolonged oxygen starvation. However, when oxygen is present, HIFs are continuously degraded by the proteasome in a process involving prolyl hydroxylation and subsequent ubiquitination by the Von Hippel Lindau (VHL) E3 ligase. The essential nature of VHL in the HIF response is well established but the role of other enzymes involved in ubiquitination is less clear. Deubiquitinating enzymes (DUBs) counteract ubiquitination and provide an important regulatory aspect to many signalling pathways involving ubiquitination. In this review, we look at the complex network of ubiquitination and deubiquitination in controlling HIF signalling in normal and low oxygen tensions. We discuss the relative importance of DUBs in opposing VHL, and explore roles of DUBs more broadly in hypoxia, in both VHL and HIF independent contexts. We also consider the catalytic and non-catalytic roles of DUBs, and elaborate on the potential benefits and challenges of inhibiting these enzymes for therapeutic use.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2253-2265"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Beyond expectations: the development and biological activity of cytokinin oxidase/dehydrogenase inhibitors. 超越期望:细胞分裂素氧化酶/脱氢酶抑制剂的开发和生物活性。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20231561
Jaroslav Nisler

Cytokinins are one of the main groups of plant hormones that regulate growth and development of plants. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that rapidly and irreversibly degrades cytokinins and thus directly affects their concentration and physiological effect. Genetically modified plants with reduced CKX activity in the shoot, i.e. with a higher concentration of cytokinins, showed e.g. increased tolerance to drought stress, formed larger inflorescences and had higher grain yield. For these reasons, chemical compounds capable of inhibiting the CKX activity (CKX inhibitors) were sought. First, they were identified among strong synthetic cytokinins, but their inhibitory activity was low. The trend has been to develop potent CKX inhibitors with minimal intrinsic cytokinin activity in the hope of avoiding the negative effect of cytokinins on root growth. Cloning CKX, production of key recombinant enzymes from Arabidopsis (AtCKX2) and maize (ZmCKX1 and ZmCKX4a), development of screening bioassays and progress in X-ray crystallography and synthetic organic chemistry led to extensive progress in the development of these compounds. Currently, the most suitable CKX inhibitors are seeking their application in research and the commercial sphere in two main areas - plant tissue cultures and agriculture. The key milestones that preceded it are summarized in this review.

细胞分裂素是调节植物生长和发育的主要植物激素类之一。细胞分裂素氧化酶/脱氢酶(CKX)是一种能快速、不可逆地降解细胞分裂素的酶,因此直接影响细胞分裂素的浓度和生理效应。转基因植物的嫩枝中 CKX 活性降低,即细胞分裂素浓度升高,表现出对干旱胁迫更强的耐受性,形成更大的花序,谷物产量更高。因此,人们开始寻找能够抑制 CKX 活性的化合物(CKX 抑制剂)。首先,在强合成细胞分裂素中发现了它们,但其抑制活性较低。目前的趋势是开发具有最小内在细胞分裂素活性的强效 CKX 抑制剂,希望避免细胞分裂素对根系生长的负面影响。克隆 CKX、从拟南芥(AtCKX2)和玉米(ZmCKX1 和 ZmCKX4a)中生产关键重组酶、开发筛选生物测定方法以及在 X 射线晶体学和合成有机化学方面取得进展,使得这些化合物的开发取得了广泛进展。目前,最合适的 CKX 抑制剂正在植物组织培养和农业两大领域的研究和商业领域寻求应用。本综述总结了之前的重要里程碑。
{"title":"Beyond expectations: the development and biological activity of cytokinin oxidase/dehydrogenase inhibitors.","authors":"Jaroslav Nisler","doi":"10.1042/BST20231561","DOIUrl":"10.1042/BST20231561","url":null,"abstract":"<p><p>Cytokinins are one of the main groups of plant hormones that regulate growth and development of plants. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that rapidly and irreversibly degrades cytokinins and thus directly affects their concentration and physiological effect. Genetically modified plants with reduced CKX activity in the shoot, i.e. with a higher concentration of cytokinins, showed e.g. increased tolerance to drought stress, formed larger inflorescences and had higher grain yield. For these reasons, chemical compounds capable of inhibiting the CKX activity (CKX inhibitors) were sought. First, they were identified among strong synthetic cytokinins, but their inhibitory activity was low. The trend has been to develop potent CKX inhibitors with minimal intrinsic cytokinin activity in the hope of avoiding the negative effect of cytokinins on root growth. Cloning CKX, production of key recombinant enzymes from Arabidopsis (AtCKX2) and maize (ZmCKX1 and ZmCKX4a), development of screening bioassays and progress in X-ray crystallography and synthetic organic chemistry led to extensive progress in the development of these compounds. Currently, the most suitable CKX inhibitors are seeking their application in research and the commercial sphere in two main areas - plant tissue cultures and agriculture. The key milestones that preceded it are summarized in this review.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2297-2306"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
The expanding roles of myonuclei in adult skeletal muscle health and function. 肌核在成人骨骼肌健康和功能中的作用不断扩大。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-19 DOI: 10.1042/BST20241637
Agnieszka K Borowik, Kevin A Murach, Benjamin F Miller

Skeletal muscle cells (myofibers) require multiple nuclei to support a cytoplasmic volume that is larger than other mononuclear cell types. It is dogmatic that mammalian resident myonuclei rely on stem cells (specifically satellite cells) for adding new DNA to muscle fibers to facilitate cytoplasmic expansion that occurs during muscle growth. In this review, we discuss the relationship between cell size and supporting genetic material. We present evidence that myonuclei may undergo DNA synthesis as a strategy to increase genetic material in myofibers independent from satellite cells. We then describe the details of our experiments that demonstrated that mammalian myonuclei can replicate DNA in vivo. Finally, we present our findings in the context of expanding knowledge about myonuclear heterogeneity, myonuclear mobility and shape. We also address why myonuclear replication is potentially important and provide future directions for remaining unknowns. Myonuclear DNA replication, coupled with new discoveries about myonuclear transcription, morphology, and behavior in response to stress, may provide opportunities to leverage previously unappreciated skeletal muscle biological processes for therapeutic targets that support muscle mass, function, and plasticity.

骨骼肌细胞(肌纤维)需要多个核来支持比其他单核细胞类型更大的细胞质体积。哺乳动物常驻肌核依赖干细胞(特别是卫星细胞)向肌纤维添加新的DNA,以促进肌肉生长过程中发生的细胞质扩张,这是教条的。本文就细胞大小与支持遗传物质的关系作一综述。我们提出的证据表明,肌核可能通过DNA合成来增加肌纤维中独立于卫星细胞的遗传物质。然后,我们描述了实验的细节,证明哺乳动物的肌核可以在体内复制DNA。最后,我们提出了我们的发现在扩大知识的背景下,我的核异质性,我的核流动性和形状。我们还解决了为什么我的核复制是潜在的重要,并提供了未来的方向,为剩余的未知数。肌核DNA复制,再加上对肌核转录、形态和应激反应行为的新发现,可能为利用以前未被重视的骨骼肌生物过程来支持肌肉质量、功能和可塑性的治疗靶点提供机会。
{"title":"The expanding roles of myonuclei in adult skeletal muscle health and function.","authors":"Agnieszka K Borowik, Kevin A Murach, Benjamin F Miller","doi":"10.1042/BST20241637","DOIUrl":"10.1042/BST20241637","url":null,"abstract":"<p><p>Skeletal muscle cells (myofibers) require multiple nuclei to support a cytoplasmic volume that is larger than other mononuclear cell types. It is dogmatic that mammalian resident myonuclei rely on stem cells (specifically satellite cells) for adding new DNA to muscle fibers to facilitate cytoplasmic expansion that occurs during muscle growth. In this review, we discuss the relationship between cell size and supporting genetic material. We present evidence that myonuclei may undergo DNA synthesis as a strategy to increase genetic material in myofibers independent from satellite cells. We then describe the details of our experiments that demonstrated that mammalian myonuclei can replicate DNA in vivo. Finally, we present our findings in the context of expanding knowledge about myonuclear heterogeneity, myonuclear mobility and shape. We also address why myonuclear replication is potentially important and provide future directions for remaining unknowns. Myonuclear DNA replication, coupled with new discoveries about myonuclear transcription, morphology, and behavior in response to stress, may provide opportunities to leverage previously unappreciated skeletal muscle biological processes for therapeutic targets that support muscle mass, function, and plasticity.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":"52 6","pages":"1-14"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Structural insights into the membrane-bound proteolytic machinery of bacterial protein quality control. 从结构上洞察细菌蛋白质质量控制的膜结合蛋白水解机制。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-30 DOI: 10.1042/BST20231250
Rya Ero, Zhu Qiao, Kwan Ann Tan, Yong-Gui Gao

In bacteria and eukaryotic organelles of prokaryotic origin, ATP-dependent proteases are crucial for regulating protein quality control through substrate unfolding and degradation. Understanding the mechanism and regulation of this key cellular process could prove instrumental in developing therapeutic strategies. Very recently, cryo-electron microscopy structural studies have shed light on the functioning of AAA+ proteases, including membrane-bound proteolytic complexes. This review summarizes the structure and function relationship of bacterial AAA+ proteases, with a special focus on the sole membrane-bound AAA+ protease in Escherichia coli, FtsH. FtsH substrates include both soluble cytoplasmic and membrane-incorporated proteins, highlighting its intricate substrate recognition and processing mechanisms. Notably, 12 copies of regulatory HflK and HflC proteins, arranged in a cage-like structure embedded in the bacterial inner membrane, can encase up to 4 FtsH hexamers, thereby regulating their role in membrane protein quality control. FtsH represents an intriguing example, highlighting both its similarity to cytosolic AAA+ proteases with respect to overall architecture and oligomerization as well as its unique features, foremost its incorporation into a membrane-bound complex formed by HflK and HflC to mediate its function in protein quality control.

在细菌和原核生物的真核细胞器中,依赖 ATP 的蛋白酶对通过底物展开和降解来调节蛋白质质量控制至关重要。了解这一关键细胞过程的机制和调控方法有助于制定治疗策略。最近,冷冻电镜结构研究揭示了 AAA+蛋白酶的功能,包括膜结合蛋白水解复合物。本综述总结了细菌 AAA+ 蛋白酶的结构与功能关系,并特别关注大肠杆菌中唯一的膜结合型 AAA+ 蛋白酶 FtsH。FtsH 的底物包括可溶性细胞质蛋白和入膜蛋白,突出了其复杂的底物识别和处理机制。值得注意的是,12 个拷贝的调节性 HflK 和 HflC 蛋白排列在一个嵌入细菌内膜的笼状结构中,可包裹多达 4 个 FtsH 六聚体,从而调节它们在膜蛋白质量控制中的作用。FtsH 是一个耐人寻味的例子,既突出了它在整体结构和寡聚化方面与细胞质 AAA+ 蛋白酶的相似性,也突出了它的独特性,最重要的是它被纳入了由 HflK 和 HflC 形成的膜结合复合物,从而介导了它在蛋白质质量控制方面的功能。
{"title":"Structural insights into the membrane-bound proteolytic machinery of bacterial protein quality control.","authors":"Rya Ero, Zhu Qiao, Kwan Ann Tan, Yong-Gui Gao","doi":"10.1042/BST20231250","DOIUrl":"10.1042/BST20231250","url":null,"abstract":"<p><p>In bacteria and eukaryotic organelles of prokaryotic origin, ATP-dependent proteases are crucial for regulating protein quality control through substrate unfolding and degradation. Understanding the mechanism and regulation of this key cellular process could prove instrumental in developing therapeutic strategies. Very recently, cryo-electron microscopy structural studies have shed light on the functioning of AAA+ proteases, including membrane-bound proteolytic complexes. This review summarizes the structure and function relationship of bacterial AAA+ proteases, with a special focus on the sole membrane-bound AAA+ protease in Escherichia coli, FtsH. FtsH substrates include both soluble cytoplasmic and membrane-incorporated proteins, highlighting its intricate substrate recognition and processing mechanisms. Notably, 12 copies of regulatory HflK and HflC proteins, arranged in a cage-like structure embedded in the bacterial inner membrane, can encase up to 4 FtsH hexamers, thereby regulating their role in membrane protein quality control. FtsH represents an intriguing example, highlighting both its similarity to cytosolic AAA+ proteases with respect to overall architecture and oligomerization as well as its unique features, foremost its incorporation into a membrane-bound complex formed by HflK and HflC to mediate its function in protein quality control.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2077-2086"},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Understanding the role of ten-eleven translocation family proteins in kidney diseases. 了解十-十一转位家族蛋白在肾脏疾病中的作用。
IF 3.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-30 DOI: 10.1042/BST20240291
Yuelin Zhang, Jiahui Li, Li Tan, Jun Xue, Yujiang Geno Shi

Epigenetic mechanisms play a critical role in the pathogenesis of human diseases including kidney disorders. As the erasers of DNA methylation, Ten-eleven translocation (TET) family proteins can oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), thus leading to passive or active DNA demethylation. Similarly, TET family proteins can also catalyze the same reaction on RNA. In addition, TET family proteins can also regulate chromatin structure and gene expression in a catalytic activity-independent manner through recruiting the SIN3A/HDAC co-repressor complex. In 2012, we reported for the first time that the genomic 5-hydroxymethylcytosine level and the mRNA levels of Tet1 and Tet2 were significantly downregulated in murine kidneys upon ischemia and reperfusion injury. Since then, accumulating evidences have eventually established an indispensable role of TET family proteins in not only acute kidney injury but also chronic kidney disease. In this review, we summarize the upstream regulatory mechanisms and the pathophysiological role of TET family proteins in major types of kidney diseases and discuss their potential values in clinical diagnosis and treatment.

表观遗传机制在包括肾脏疾病在内的人类疾病的发病机制中起着至关重要的作用。作为 DNA 甲基化的侵蚀者,十-十一转位(TET)家族蛋白可将 5-甲基胞嘧啶(5mC)氧化为 5-羟甲基胞嘧啶(5hmC)、5-甲酰基胞嘧啶(5fC)和 5-羧基胞嘧啶(5caC),从而导致被动或主动的 DNA 去甲基化。同样,TET 家族蛋白也能催化 RNA 上的相同反应。此外,TET家族蛋白还能通过招募SIN3A/HDAC共抑制因子复合物,以一种与催化活性无关的方式调控染色质结构和基因表达。2012 年,我们首次报道了小鼠肾脏缺血再灌注损伤后,基因组中 5-羟甲基胞嘧啶水平以及 Tet1 和 Tet2 的 mRNA 水平显著下调。此后,越来越多的证据最终证实,TET 家族蛋白不仅在急性肾损伤中发挥着不可或缺的作用,而且在慢性肾脏疾病中也发挥着重要作用。在这篇综述中,我们总结了 TET 家族蛋白在主要类型肾脏疾病中的上游调控机制和病理生理作用,并讨论了它们在临床诊断和治疗中的潜在价值。
{"title":"Understanding the role of ten-eleven translocation family proteins in kidney diseases.","authors":"Yuelin Zhang, Jiahui Li, Li Tan, Jun Xue, Yujiang Geno Shi","doi":"10.1042/BST20240291","DOIUrl":"10.1042/BST20240291","url":null,"abstract":"<p><p>Epigenetic mechanisms play a critical role in the pathogenesis of human diseases including kidney disorders. As the erasers of DNA methylation, Ten-eleven translocation (TET) family proteins can oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), thus leading to passive or active DNA demethylation. Similarly, TET family proteins can also catalyze the same reaction on RNA. In addition, TET family proteins can also regulate chromatin structure and gene expression in a catalytic activity-independent manner through recruiting the SIN3A/HDAC co-repressor complex. In 2012, we reported for the first time that the genomic 5-hydroxymethylcytosine level and the mRNA levels of Tet1 and Tet2 were significantly downregulated in murine kidneys upon ischemia and reperfusion injury. Since then, accumulating evidences have eventually established an indispensable role of TET family proteins in not only acute kidney injury but also chronic kidney disease. In this review, we summarize the upstream regulatory mechanisms and the pathophysiological role of TET family proteins in major types of kidney diseases and discuss their potential values in clinical diagnosis and treatment.</p>","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2203-2214"},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
期刊
Biochemical Society transactions
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1