Pre-emptive Quality Control of a Misfolded Membrane Protein by Ribosome-Driven Effects

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Restricted access: spatial sequestration of damaged proteins during stress and aging

The accumulation of damaged and aggregated proteins is a hallmark of aging and increased proteotoxic stress. To limit the toxicity of damaged and aggregated proteins and to ensure that the damage is not inherited by succeeding cell generations, a system of spatial quality control operates to sequester damaged/aggregated proteins into inclusions at specific protective sites. Such spatial sequestration and asymmetric segregation of damaged proteins have emerged as key processes required for cellular rejuvenation. In this review, we summarize findings on the nature of the different quality control sites identified in yeast, on genetic determinants required for spatial quality control, and on how aggregates are recognized depending on the stress generating them. We also briefly compare the yeast system to spatial quality control in other organisms. The data accumulated demonstrate that spatial quality control involves factors beyond the canonical quality control factors, such as chaperones and proteases, and opens up new venues in approaching how proteotoxicity might be mitigated, or delayed, upon aging.     

线粒体蛋白质组及蛋白质量控制

线粒体是哺乳动物细胞内重要细胞器,不仅通过氧化磷酸化产生ATP为细胞提供能量,也参与调节钙离子稳态、活性氧(reactive oxygen species,ROS)的产生、细胞应激反应和细胞死亡等过程,其功能障碍不仅导致多种人类疾病的发生,而且也能降低动物卵母细胞质量和早期胚胎发育能力。大量证据表明,线粒体的功能依赖于线粒体蛋白质组完整性和稳态。基于此,该文综述了线粒体蛋白组、线粒体蛋白转运,聚焦蛋白酶、分子伴侣、线粒体囊泡、线粒体自噬和线粒体未折叠蛋白反应在帮助正确的蛋白质折叠,去除错误折叠或聚集的蛋白质和清除功能失调的线粒体方面的作用,为调控线粒体蛋白质量,从而维持线粒体健康、降低疾病发生提供理论依据。     

核糖体相关质量控制与核糖体自噬研究进展

细胞中蛋白质处于不断合成和降解的动态更新过程中,其稳态与细胞功能密切相关。细胞中存在多种蛋白质质量控制（protein quality control,PQC）机制来监测蛋白质合成和降解过程的异常,以确保蛋白质组的完整性和细胞适应性。核糖体是细胞内数量最多的细胞器,系细胞内蛋白质合成的主要场所。现已明确,核糖体相关质量控制（ribosome-associated quality control,RQC）与核糖体自噬能通过溶酶体依赖和非依赖途径调节细胞内核糖体数量及功能以维持蛋白质稳态,从而增强细胞在应激状态下的适应能力。RQC失调、核糖体自噬障碍则参与多种疾病的发生及发展过程,靶向RQC和核糖体自噬可能成为防治多种疾病的有效手段。本综述聚焦核糖体相关的PQC途径,并进一步讨论了它们在蛋白质稳态维持中的重要地位及其在人类疾病发生发展中的潜在作用。     

Chaperone function and mechanism of small heat-shock proteins

Small heat-shock proteins （sHSPs） are ubiquitous ATP-independent molecular chaperones that play crucial roles in protein quality control in cells. They are able to prevent the aggregation and/or inactivation of various non-native sub- strate proteins and assist the refolding of these substrates independently or under the help of other ATP-dependent chaperones. Substrate recognition and binding by sHSPs are essential for their chaperone functions. This review focuses on what natural substrate proteins an sHSP pro- tects and how it binds the substrates in cells under fluctuat- ing conditions. It appears that sHSPs of prokaryotes, although being able to bind a wide range of cellular pro- teins, preferentially protect certain classes of functional proteins, such as translation-related proteins and metabolic enzymes, which may well explain why they could increase the resistance of host cells against various stresses. Mechanistically, the sHSPs of prokaryotes appear to possess numerous multi-type substrate-binding residues and are able to hierarchically activate these residues in a temperature-dependent manner, and thus act as tempera- ture-regulated chaperones. The mechanism of hierarchical activation of substrate-binding residues is also discussed regarding its implication for eukaryotic sHSPs.     

Yeast prions are useful for studying protein chaperones and protein quality control

Abstract

Protein chaperones help proteins adopt and maintain native conformations and play vital roles in cellular processes where proteins are partially folded. They comprise a major part of the cellular protein quality control system that protects the integrity of the proteome. Many disorders are caused when proteins misfold despite this protection. Yeast prions are fibrous amyloid aggregates of misfolded proteins. The normal action of chaperones on yeast prions breaks the fibers into pieces, which results in prion replication. Because this process is necessary for propagation of yeast prions, even small differences in activity of many chaperones noticeably affect prion phenotypes. Several other factors involved in protein processing also influence formation, propagation or elimination of prions in yeast. Thus, in much the same way that the dependency of viruses on cellular functions has allowed us to learn much about cell biology, the dependency of yeast prions on chaperones presents a unique and sensitive way to monitor the functions and interactions of many components of the cell's protein quality control system. Our recent work illustrates the utility of this system for identifying and defining chaperone machinery interactions.     

Yeast prions are useful for studying protein chaperones and protein quality control

Protein chaperones help proteins adopt and maintain native conformations and play vital roles in cellular processes where proteins are partially folded. They comprise a major part of the cellular protein quality control system that protects the integrity of the proteome. Many disorders are caused when proteins misfold despite this protection. Yeast prions are fibrous amyloid aggregates of misfolded proteins. The normal action of chaperones on yeast prions breaks the fibers into pieces, which results in prion replication. Because this process is necessary for propagation of yeast prions, even small differences in activity of many chaperones noticeably affect prion phenotypes. Several other factors involved in protein processing also influence formation, propagation or elimination of prions in yeast. Thus, in much the same way that the dependency of viruses on cellular functions has allowed us to learn much about cell biology, the dependency of yeast prions on chaperones presents a unique and sensitive way to monitor the functions and interactions of many components of the cell''s protein quality control system. Our recent work illustrates the utility of this system for identifying and defining chaperone machinery interactions.     

Protein misfolding, aggregation, and degradation in disease

Pathologies associated with protein misfolding have been observed in neurodegenerative diseases such as Alzheimer’s disease, metabolic diseases like phenylketonuria, and diseases affecting structural proteins like collagen or keratin. Misfolding of mutant proteins in these and many other diseases may result in premature degradation, formation of toxic aggregates, or incorporation of toxic conformations into structures. We review common traits of these diverse diseases under the unifying view of protein misfolding. The molecular pathogenesis is discussed in the context of protein quality control systems consisting of molecular chaperones and intracellular proteases that assist the folding and supervise the maintenance of the folded structure. Furthermore, genetic and environmental factors that may modify the severity of these diseases are underscored. The present article represents a partly revised and updated version of chapter 1 published earlier in volume 232 of the series Methods in Molecular Biology (Walker, J. M., ed., Humana Press, Totowa, NJ), Protein Misfolding and Disease: Principles and Protocols (Bross, P. & Gregersen, N., eds.), pp. 3–16 (2003).     

C-terminal extension of phaseolin with a short methionine-rich sequence can inhibit trimerisation and result in high instability

In an attempt to increase the content in essential amino acids methionine and tryptophan of the trimeric storage protein phaseolin, we fused a Met- and Trp-rich sequence to the C-terminus of a phaseolin variant lacking its vacuolar sorting signal, with the aim to target the protein for secretion and accumulation into the apoplast. The fate of the mutant protein, denominated Y3, was studied in transiently transfected tobacco protoplasts. We report that the presence of the additional sequence causes structural defects which inhibit trimerization and lead to partial aggregation of Y3. The protein interacts with the ER chaperone BiP prior to being degraded very rapidly, in a process that does not require vesicular transport from the ER. The rate of degradation of Y3 is higher than that observed for another assembly defective mutant of phaseolin, 360, which remains monomeric and does not aggregate. This indicates that the plant ER quality control machinery can dispose of defective proteins with different kinetics and perhaps mechanisms, depending on the nature of their defect.     

Atp23 biogenesis reveals a chaperone‐like folding activity of Mia40 in the IMS of mitochondria

Mia40 is a recently identified oxidoreductase in the intermembrane space (IMS) of mitochondria that mediates protein import in an oxidation‐dependent reaction. Substrates of Mia40 that were identified so far are of simple structure and receive one or two disulphide bonds. Here we identified the protease Atp23 as a novel substrate of Mia40. Atp23 contains ten cysteine residues which are oxidized during several rounds of interaction with Mia40. In contrast to other Mia40 substrates, oxidation of Atp23 is not essential for its import; an Atp23 variant in which all ten cysteine residues were replaced by serine residues still accumulates in mitochondria in a Mia40‐dependent manner. In vitro Mia40 can mediate the folding of wild‐type Atp23 and prevents its aggregation. In these reactions, the hydrophobic substrate‐binding pocket of Mia40 was found to be essential for its chaperone‐like activity. Thus, Mia40 plays a much broader role in import and folding of polypeptides than previously expected and can serve as folding factor for proteins with complex disulphide patterns as well as for cysteine‐free polypeptides.     

Salicylic Acid Signaling Controls the Maturation and Localization of the Arabiclopsis Defense Protein ACCELERATED CELL DEATH6

ACCELERATED CELL DEATH6 （ACD6） is a multipass membrane protein with an ankyrin domain that acts in a positive feedback loop with the defense signal salicylic acid （SA）. This study implemented biochemical approaches to infer changes in ACD6 complexes and localization. In addition to forming endoplasmic reticulum （ER）- and plasma membrane （PM）-Iocalized complexes, ACD6 forms soluble complexes, where it is bound to cytosolic HSP70, ubiquitinated, and degraded via the proteasome. Thus, ACD6 constitutively undergoes ER-associated degradation. During SA signaling, the soluble ACD6 pool decreases, whereas the PM pool increases. Similarly, ACD6-1, an activated version of ACD6 that induces SA, is present at low levels in the soluble fraction and high levels in the PM. However, ACD6 variants with amino acid substitutions in the ankyrin domain form aberrant, inactive complexes, are induced by a SA agonist, but show no PM localization. SA signaling also increases the PM pools of FLAGELLIN SENSING2 （FLS2） and BRI1-ASSOClATED RECEPTOR KINASE 1 （BAK1）. FLS2 forms complexes ACD6; both FLS2 and BAK1 require ACD6 for maximal accumulation at the PM in response to SA signaling. A plausible scenario is that SA increases the efficiency of productive folding and/or complex formation in the ER, such that ACD6, together with FLS2 and BAK1, reaches the cell surface to more effectively promote immune responses.     

Order through destruction: how ER‐associated protein degradation contributes to organelle homeostasis

The endoplasmic reticulum (ER) is a large, dynamic, and multifunctional organelle. ER protein homeostasis is essential for the coordination of its diverse functions and depends on ER‐associated protein degradation (ERAD). The latter process selects target proteins in the lumen and membrane of the ER, promotes their ubiquitination, and facilitates their delivery into the cytosol for degradation by the proteasome. Originally characterized for a role in the degradation of misfolded proteins and rate‐limiting enzymes of sterol biosynthesis, the many branches of ERAD now appear to control the levels of a wider range of substrates and influence more broadly the organization and functions of the ER, as well as its interactions with adjacent organelles. Here, we discuss recent mechanistic advances in our understanding of ERAD and of its consequences for the regulation of ER functions.     

Photochemical Isomerization of Leaf Aldehyde

Isopimpinellin, bergapten, xanthotoxin, kokusagine, evoxine and japonin were isolated and identified in the leaves of Orixa japonica (Rutaceae) as feeding inhibitors against Spodoptera litura F. (Noctuidae). Isopimpinellin exhibited the most potent activity among above substances at the feeding inhibitory test. The isolated evoxine was the optical antipode of the previously reported one.     

High capacity of the endoplasmic reticulum to prevent secretion and aggregation of amyloidogenic proteins

Protein aggregation is associated with neurodegeneration and various other pathologies. How specific cellular environments modulate the aggregation of disease proteins is not well understood. Here, we investigated how the endoplasmic reticulum (ER) quality control system handles β‐sheet proteins that were designed de novo to form amyloid‐like fibrils. While these proteins undergo toxic aggregation in the cytosol, we find that targeting them to the ER (ER‐β) strongly reduces their toxicity. ER‐β is retained within the ER in a soluble, polymeric state, despite reaching very high concentrations exceeding those of ER‐resident molecular chaperones. ER‐β is not removed by ER‐associated degradation (ERAD) but interferes with ERAD of other proteins. These findings demonstrate a remarkable capacity of the ER to prevent the formation of insoluble β‐aggregates and the secretion of potentially toxic protein species. Our results also suggest a generic mechanism by which proteins with exposed β‐sheet structure in the ER interfere with proteostasis.     

Flow cytometric quantification and characterization of intracellular protein aggregates in yeast

The sequestration of misfolded proteins into aggregates is an integral pathway of the protein quality control network that becomes particularly prominent during proteotoxic stress and in various pathologies. Methods for systematic analysis of cellular aggregate content are still largely limited to fluorescence microscopy and to separation by biochemical techniques. Here, we describe an alternative approach, using flow cytometric analysis, applied to protein aggregates released from their intracellular milieu by mild lysis of yeast cells. Protein aggregates were induced in yeast by heat shock or by chaperone deprivation and labeled using GFP- or mCherry-tagged quality control substrate proteins and chaperones. The fluorescence-labeled aggregate particles were distinguishable from cell debris by flow cytometry. The assay was used to quantify the number of fluorescent aggregates per μg of cell lysate protein and for monitoring changes in the cellular content and properties of aggregates, induced by stress. The results were normalized to the frequencies of fluorescent reporter expression in the cell population, allowing quantitative comparison. The assay also provided a quantitative measure of co-localization of aggregate components, such as chaperones and quality control substrates, within the same aggregate particle. This approach may be extended by fluorescence-activated sorting and isolation of various protein aggregates, including those harboring proteins associated with conformation disorders.