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Ubiquitin system mutations in neurological diseases 神经系统疾病中的泛素系统突变。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-01 DOI: 10.1016/j.tibs.2024.06.011
Neuronal ubiquitin balance impacts the fate of countless cellular proteins, and its disruption is associated with various neurological disorders. The ubiquitin system is critical for proper neuronal cell state transitions and the clearance of misfolded or aggregated proteins that threaten cellular integrity. This article reviews the state of and recent advancements in our understanding of the disruptions to components of the ubiquitin system, in particular E3 ligases and deubiquitylases, in neurodevelopmental and neurodegenerative diseases. Specific focus is on enzymes with recent progress in their characterization, including identifying enzyme-substrate pairs, the use of stem cell and animal models, and the development of therapeutics for ubiquitin-related diseases.
神经元泛素平衡影响着无数细胞蛋白质的命运,泛素平衡的破坏与各种神经系统疾病有关。泛素系统对神经元细胞的正常状态转换以及清除威胁细胞完整性的错误折叠或聚集蛋白至关重要。这篇文章回顾了我们对泛素系统(尤其是 E3 连接酶和去泛素化酶)成分在神经发育和神经退行性疾病中的破坏的认识现状和最新进展。具体重点是最近在酶表征方面取得进展的酶,包括确定酶-底物配对、干细胞和动物模型的使用,以及泛素相关疾病疗法的开发。
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引用次数: 0
Liquid–liquid phase separation in presynaptic nerve terminals 突触前神经末梢的液-液相分离
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-01 DOI: 10.1016/j.tibs.2024.07.005
The presynaptic nerve terminal is crucial for transmitting signals to the adjacent cell. To fulfill this role, specific proteins with distinct functions are concentrated in spatially confined areas within the nerve terminals. A recent concept termed liquid–liquid phase separation (LLPS) has provided new insights into how this process may occur. In this review, we aim to summarize the LLPS of proteins in different parts of the presynaptic nerve terminals, including synaptic vesicle (SV) clusters, the active zone (AZ), and the endocytic zone, with an additional focus on neurodegenerative diseases (NDDs), where the functional relevance of these properties is explored. Last, we propose new perspectives and future directions for the role of LLPS in presynaptic nerve terminals.
突触前神经末梢是向邻近细胞传递信号的关键。为了发挥这一作用,具有不同功能的特定蛋白质会集中在神经末梢内空间受限的区域。最近一种被称为液-液相分离(LLPS)的概念为这一过程如何发生提供了新的见解。在这篇综述中,我们旨在总结突触前神经末梢不同部位蛋白质的液液相分离现象,包括突触小泡(SV)簇、活性区(AZ)和内细胞区,并重点关注神经退行性疾病(NDDs),探讨这些特性的功能相关性。最后,我们就 LLPS 在突触前神经末梢中的作用提出了新的观点和未来方向。
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引用次数: 0
Beyond simple tails: poly(A) tail-mediated RNA epigenetic regulation 超越简单的尾巴:多聚(A)尾介导的 RNA 表观遗传调控。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-01 DOI: 10.1016/j.tibs.2024.06.013
The poly(A) tail is an essential structural component of mRNA required for the latter’s stability and translation. Recent technologies have enabled transcriptome-wide profiling of the length and composition of poly(A) tails, shedding light on their overlooked regulatory capacities. Notably, poly(A) tails contain not only adenine but also uracil, cytosine, and guanine residues. These findings strongly suggest that poly(A) tails could encode a wealth of regulatory information, similar to known reversible RNA chemical modifications. This review aims to succinctly summarize our current knowledge on the composition, dynamics, and regulatory functions of RNA poly(A) tails. Given their capacity to carry rich regulatory information beyond the genetic code, we propose the concept of ‘poly(A) tail epigenetic information’ as a new layer of RNA epigenetic regulation.
多聚(A)尾是 mRNA 的重要结构成分,是后者稳定和翻译所必需的。最近的技术实现了对整个转录组的多聚(A)尾的长度和组成的分析,从而揭示了它们被忽视的调控能力。值得注意的是,聚(A)尾不仅含有腺嘌呤,还含有尿嘧啶、胞嘧啶和鸟嘌呤残基。这些发现有力地表明,多聚(A)尾可能编码丰富的调控信息,类似于已知的可逆 RNA 化学修饰。本综述旨在简明扼要地总结我们目前对 RNA 聚(A)尾的组成、动态和调控功能的了解。鉴于 RNA 多聚(A)尾能够携带遗传密码之外的丰富调控信息,我们提出了 "多聚(A)尾表观遗传信息 "的概念,作为 RNA 表观遗传调控的一个新层次。
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引用次数: 0
UPS-dependent strategies of protein quality control degradation 依赖 UPS 的蛋白质质量控制降解策略。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-01 DOI: 10.1016/j.tibs.2024.06.006
The degradation of damaged proteins is critical for tissue integrity and organismal health because damaged proteins have a high propensity to form aggregates. E3 ubiquitin ligases are key regulators of protein quality control (PQC) and mediate the selective degradation of damaged proteins, a process termed ‘PQC degradation’ (PQCD). The degradation signals (degrons) that trigger PQCD are based on hydrophobic sites that are normally buried within the native protein structure. However, an open question is how PQCD-specialized E3 ligases distinguish between transiently misfolded proteins, which can be efficiently refolded, and permanently damaged proteins, which must be degraded. While significant progress has been made in characterizing degradation determinants, understanding the key regulatory signals of cellular and organismal PQCD pathways remains a challenge.
由于受损蛋白质极易形成聚集体,因此降解受损蛋白质对组织完整性和生物体健康至关重要。E3 泛素连接酶是蛋白质质量控制(PQC)的关键调控因子,介导受损蛋白质的选择性降解,这一过程被称为 "PQC 降解"(PQCD)。触发 PQCD 的降解信号(degrons)基于通常埋藏在原生蛋白质结构中的疏水位点。然而,一个悬而未决的问题是,PQCD 专化的 E3 连接酶如何区分瞬时错误折叠的蛋白质(可以有效地重新折叠)和永久受损的蛋白质(必须降解)。虽然在降解决定因素的特征描述方面取得了重大进展,但了解细胞和生物体 PQCD 途径的关键调控信号仍然是一项挑战。
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引用次数: 0
Enzoology: understanding enzyme interactions and epistasis in the cell 酶学:了解细胞中的酶相互作用和表观遗传。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-01 DOI: 10.1016/j.tibs.2024.07.002
Recent work from Nguyen et al. unveils massively parallel measurements of epistatic interactions between two enzymes, dihydrofolate reductase and thymidylate synthase, in their natural cellular context. Almost 3000 mutations of DHFR in three TYMS backgrounds reveal a complex interaction network. The authors capture much of this complexity using a simple model.
Nguyen 等人的最新研究揭示了在自然细胞背景下,对二氢叶酸还原酶和胸腺嘧啶合成酶这两种酶之间的表观相互作用的大规模并行测量。三种 TYMS 背景中近 3000 个 DHFR 突变揭示了复杂的相互作用网络。作者用一个简单的模型捕捉到了这种复杂性的大部分。
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引用次数: 0
Structural diversity of the CE-clan proteases in bacteria to disarm host ubiquitin defenses. 细菌中解除宿主泛素防御的 CE 族蛋白酶的结构多样性。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-28 DOI: 10.1016/j.tibs.2024.09.001
Lucía Sánchez-Alba, Helena Borràs-Gas, Ge Huang, Nathalia Varejão, David Reverter

Ubiquitin (Ub) and ubiquitin-like (UbL) modifications are critical regulators of multiple cellular processes in eukaryotes. These modifications are dynamically controlled by proteases that balance conjugation and deconjugation. In eukaryotes, these proteases include deubiquitinases (DUBs), mostly belonging to the CA-clan of cysteine proteases, and ubiquitin-like proteases (ULPs), belonging to the CE-clan proteases. Intriguingly, infectious bacteria exploit the CE-clan protease fold to generate deubiquitinating activities to disarm the immune system and degradation defenses of the host during infection. In this review, we explore the substrate preferences encoded within the CE-clan proteases and the structural determinants in the protease fold behind its selectivity, in particular those from infectious bacteria and viruses. Understanding this protease family provides crucial insights into the molecular mechanisms underlying infection and transmission of pathogenic organisms.

泛素(Ub)和类泛素(UbL)修饰是真核生物多种细胞过程的关键调节因子。这些修饰受蛋白酶的动态控制,蛋白酶可平衡共轭和解共轭作用。在真核生物中,这些蛋白酶包括主要属于半胱氨酸蛋白酶 CA 族的去泛素酶(DUBs)和属于 CE 族蛋白酶的类泛素蛋白酶(ULPs)。耐人寻味的是,感染性细菌利用 CE 族蛋白酶折叠产生去泛素化活性,从而在感染期间解除宿主免疫系统和降解防御系统的武装。在这篇综述中,我们探讨了 CE 族蛋白酶编码的底物偏好以及蛋白酶折叠结构决定因素在其选择性背后的作用,特别是那些来自传染性细菌和病毒的蛋白酶。了解这一蛋白酶家族有助于深入了解病原体感染和传播的分子机制。
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引用次数: 0
Catchers of folding gone awry: a tale of small heat shock proteins. 折叠出错的捕手:小型热休克蛋白的故事。
IF 13.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-12 DOI: 10.1016/j.tibs.2024.08.003
Carsten Peters,Martin Haslbeck,Johannes Buchner
Small heat shock proteins (sHsps) are an important part of the cellular system maintaining protein homeostasis under physiological and stress conditions. As molecular chaperones, they form complexes with different non-native proteins in an ATP-independent manner. Many sHsps populate ensembles of energetically similar but different-sized oligomers. Regulation of chaperone activity occurs by changing the equilibrium of these ensembles. This makes sHsps a versatile and adaptive system for trapping non-native proteins in complexes, allowing recycling with the help of ATP-dependent chaperones. In this review, we discuss progress in our understanding of the structural principles of sHsp oligomers and their functional principles, as well as their roles in aging and eye lens transparency.
小热休克蛋白(sHsps)是在生理和应激条件下维持蛋白质平衡的细胞系统的重要组成部分。作为分子伴侣,它们以不依赖 ATP 的方式与不同的非本源蛋白质形成复合物。许多 sHsps 形成了能量相似但大小不同的寡聚体组合。通过改变这些组合体的平衡来调节伴侣活性。这使得 sHsps 成为一种多功能的适应性系统,可将非本地蛋白质困在复合物中,并在 ATP 依赖性伴侣的帮助下进行回收。在这篇综述中,我们将讨论对 sHsp 寡聚体结构原理及其功能原理的理解进展,以及它们在衰老和眼睛晶状体透明度中的作用。
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引用次数: 0
The expanding landscape of canonical and non-canonical protein phosphorylation. 规范和非规范蛋白质磷酸化的不断扩展。
IF 13.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-11 DOI: 10.1016/j.tibs.2024.08.004
Thibault Houles,Sang-Oh Yoon,Philippe P Roux
Protein phosphorylation is a crucial regulatory mechanism in cell signaling, acting as a molecular switch that modulates protein function. Catalyzed by protein kinases and reversed by phosphoprotein phosphatases, it is essential in both normal physiological and pathological states. Recent advances have uncovered a vast and intricate landscape of protein phosphorylation that include histidine phosphorylation and more unconventional events, such as pyrophosphorylation and polyphosphorylation. Many questions remain about the true size of the phosphoproteome and, more importantly, its site-specific functional relevance. The involvement of unconventional actors such as pseudokinases and pseudophosphatases adds further complexity to be resolved. This review explores recent discoveries and ongoing challenges, highlighting the need for continued research to fully elucidate the roles and regulation of protein phosphorylation.
蛋白质磷酸化是细胞信号传导过程中的重要调节机制,是调节蛋白质功能的分子开关。它由蛋白激酶催化,由磷蛋白磷酸酶逆转,在正常生理和病理状态下都至关重要。最近的研究进展揭示了蛋白质磷酸化错综复杂的巨大格局,其中包括组氨酸磷酸化和更多非常规事件,如焦磷酸化和多磷酸化。关于磷酸化蛋白质组的真正规模,更重要的是其特定位点的功能相关性,仍存在许多问题。假激酶和假磷酸酶等非常规参与者的参与进一步增加了有待解决的复杂性。这篇综述探讨了最近的发现和正在面临的挑战,强调了继续研究以全面阐明蛋白质磷酸化的作用和调控的必要性。
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引用次数: 0
The Leishmania ribosome: more than passive mRNA translating machinery 利什曼原虫核糖体:不只是被动的 mRNA 翻译机器。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.tibs.2024.06.008

While the central dogma of molecular biology describes how genetic information flows, gene expression is also affected by epigenetic and epitranscriptomic processes. A recent report by Rajan et al. demonstrates how pseudouridylation of a Leishmania ribosomal rRNA affects the expression of particular proteins: an example of epitranslatomic control.

虽然分子生物学的核心原理是描述遗传信息如何流动,但基因表达也受到表观遗传和表观转录组过程的影响。Rajan 等人最近的一份报告展示了利什曼病核糖体 rRNA 的假苷酸化如何影响特定蛋白质的表达:这是表转录组控制的一个例子。
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引用次数: 0
Migrasome biogenesis: when biochemistry meets biophysics on membranes 移行体的生物发生:当生物化学与生物物理学在膜上相遇。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.tibs.2024.06.004

Migrasomes, newly identified organelles, play crucial roles in intercellular communication, contributing to organ development and angiogenesis. These vesicles, forming on retraction fibers of migrating cells, showcase a sophisticated architecture. Recent research reveals that migrasome biogenesis is a complicated and highly regulated process. This review summarizes the mechanisms governing migrasome formation, proposing a model in which biogenesis is understood through the lens of membrane microdomain assembly. It underscores the critical interplay between biochemistry and biophysics. The biogenesis unfolds in three distinct stages: nucleation, maturation, and expansion, each characterized by unique morphological, biochemical, and biophysical features. We also explore the broader implications of migrasome research in membrane biology and outline key unanswered questions that represent important directions for future investigation.

移行体是新发现的细胞器,在细胞间通信中发挥着至关重要的作用,有助于器官发育和血管生成。这些囊泡形成于迁移细胞的回缩纤维上,显示出复杂的结构。最新研究发现,迁移体的生物发生是一个复杂而高度调控的过程。本综述总结了迁移小体的形成机制,提出了一个通过膜微域组装来理解生物生成的模型。它强调了生物化学和生物物理学之间的重要相互作用。生物发生分为三个不同的阶段:成核、成熟和扩展,每个阶段都具有独特的形态学、生物化学和生物物理学特征。我们还探讨了迁移体研究对膜生物学的广泛影响,并概述了代表未来研究重要方向的关键未解之谜。
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引用次数: 0
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Trends in Biochemical Sciences
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