OBJECTIVE: Mitochondrial proteostasis is critical for cellular function. The molecular chaperone HSP60 is essential for cell function and dysregulation of HSP60 expression has been implicated in cancer and diabetes. The few reported patients carrying HSP60 gene variants show neurodevelopmental delay and brain hypomyelination. Hsp60 interacts with more than 260 mitochondrial proteins but the mitochondrial proteins and functions affected by HSP60 deficiency are poorly characterized.
METHODS: We studied two model systems for HSP60 deficiency: (1) engineered HEK cells carrying an inducible dominant negative HSP60 mutant protein, (2) zebrafish HSP60 knockout larvae. Both systems were analyzed by RNASeq, proteomics, and targeted metabolomics, and several functional assays relevant for the respective model. In addition, skin fibroblasts from patients with disease-associated HSP60 variants were analyzed by proteomics.
RESULTS: We show that HSP60 deficiency leads to a differentially downregulated mitochondrial matrix proteome, transcriptional activation of stress responses, and dysregulated cholesterol biosynthesis. This leads to lipid accumulation in zebrafish knockout larvae.
CONCLUSIONS: Our data provide a compendium of the effects of HSP60 deficiency on the mitochondrial matrix proteome. We show that HSP60 is a master regulator and modulator of mitochondrial functions and metabolic pathways. HSP60 dysfunction also affects cellular metabolism and disrupts the integrated stress response. The effect on cholesterol synthesis explains the effect of HSP60 dysfunction on myelination observed in patients carrying genetic variants of HSP60.

Vesicular transport relies on multimeric trafficking complexes to capture cargo and drive vesicle budding and fusion. Faithful assembly of the trafficking complexes is essential to their functions but remains largely unexplored. Assembly of AP2 adaptor, a heterotetrameric protein complex regulating clathrin-mediated endocytosis, is assisted by the chaperone AAGAB. Here, we found that AAGAB initiates AP2 assembly by stabilizing its α and σ2 subunits, but the AAGAB:α:σ2 complex cannot recruit additional AP2 subunits. We identified CCDC32 as another chaperone regulating AP2 assembly. CCDC32 recognizes the AAGAB:α:σ2 complex, and its binding leads to the formation of an α:σ2:CCDC32 ternary complex. The α:σ2:CCDC32 complex serves as a template that sequentially recruits the µ2 and β2 subunits of AP2 to complete AP2 assembly, accompanied by CCDC32 release. The AP2-regulating function of CCDC32 is disrupted by a disease-causing mutation. These findings demonstrate that AP2 is assembled by a handover mechanism switching from AAGAB-based initiation complexes to CCDC32-based template complexes. A similar mechanism may govern the assembly of other trafficking complexes exhibiting the same configuration as AP2.

Prion variants are self-perpetuating conformers of a single protein that assemble into amyloid fibers and confer unique phenotypic states. Multiple prion variants can arise, particularly in response to changing environments, and interact within an organism. These interactions are often competitive, with one variant establishing phenotypic dominance over the others. This dominance has been linked to the competition for non-prion state protein, which must be converted to the prion state via a nucleated polymerization mechanism. However, the intrinsic rates of conversion, determined by the conformation of the variant, cannot explain prion variant dominance, suggesting a more complex interaction. Using the yeast prion system [PSI+ ], we have determined the mechanism of dominance of the [PSI+ ]Strong variant over the [PSI+ ]Weak variant in vivo. When mixed by mating, phenotypic dominance is established in zygotes, but the two variants persist and co-exist in the lineage descended from this cell. [PSI+ ]Strong propagons, the heritable unit, are amplified at the expense of [PSI+ ]Weak propagons, through the efficient conversion of soluble Sup35 protein, as revealed by fluorescence photobleaching experiments employing variant-specific mutants of Sup35. This competition, however, is highly sensitive to the fragmentation of [PSI+ ]Strong amyloid fibers, with even transient inhibition of the fragmentation catalyst Hsp104 promoting amplification of [PSI+ ]Weak propagons. Reducing the number of [PSI+ ]Strong propagons prior to mating, similarly promotes [PSI+ ]Weak amplification and conversion of soluble Sup35, indicating that template number and conversion efficiency combine to determine dominance. Thus, prion variant dominance is not an absolute hierarchy but rather an outcome arising from the dynamic interplay between unique protein conformations and their interactions with distinct cellular proteostatic niches.

Heat shock cognate protein 70 (Hsc70/HSPA8) belongs to the Hsp70 family of molecular chaperones. The fundamental functions of Hsp70 family molecular chaperones depend on ATP-dependent allosteric regulation of binding and release of hydrophobic polypeptide substrates. Hsc70 is also involved in various other cellular functions including selective pathways of protein degradation: chaperone-mediated autophagy (CMA) and endosomal microautophagy (eMI), in which Hsc70 recruits substrate proteins containing a KFERQ-like pentapeptide motif from the cytosol to lysosomes and late endosomes, respectively. However, whether the interaction between Hsc70 and the pentapeptide motif is direct or mediated by other molecules has remained unknown. In the present study, we introduced a photo-crosslinker near the KFERQ motif in a CMA/eMI model substrate and successfully detected its crosslinking with Hsc70, revealing the direct interaction between Hsc70 and the KFERQ motif for the first time. In addition, we demonstrated that the loss of the Hsc70 ATPase activity by the D10 N mutation appreciably reduced the crosslinking efficiency. Our present results suggested that the ATP allostery of Hsc70 is involved in the direct interaction of Hsc70 with the KFERQ-like pentapeptide.

Heat stress due to global warming adversely affects plant physiology and metabolism, significantly reducing agricultural productivity. Plants have evolved various adaptive mechanisms to cope with such stresses, involving a range of heat stress-responsive proteins. This study investigates the molecular functions and structural changes of OsTDX (Oryza sativa TPR repeat-containing thioredoxin) in rice under heat stress, focusing on its roles as a disulfide reductase and molecular chaperone. OsTDX, sharing a 52 % overall amino acid identity with AtTDX, predominantly forms high molecular weight (HMW) complexes under heat stress conditions. Functional assays revealed that OsTDX exhibited increased disulfide reductase activity in a dose-dependent manner and significantly enhanced holdase chaperone activity, particularly under specific heat stress conditions (60 °C). The structural shift from low molecular weight (LMW) to HMW forms was accompanied by increased hydrophobicity, as indicated by bis-ANS fluorescence intensity measurements. In conclusion, OsTDX exhibits dual functions as a disulfide reductase and a holdase chaperone, with its chaperone activity significantly enhanced under heat stress through structural changes to HMW complexes. These findings contribute to understand the molecular mechanisms of heat tolerance in rice and highlight the potential role of OsTDX in the development of heat-tolerant crops to address crop yield declines due to global warming.

Many RNA binding proteins (RBPs) contain low-complexity domains (LCDs) with prion-like compositions. These long intrinsically disordered regions regulate their solubility, contributing to their physiological roles in RNA processing and organization. However, this also makes these RBPs prone to pathological misfolding and aggregation that are characteristic of neurodegenerative diseases. For example, TAR DNA-binding protein 43 (TDP-43) forms pathological aggregates associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). While molecular chaperones are well-known suppressors of these aberrant events, we recently reported that highly disordered, hydrophilic and charged heat-resistant obscure (Hero) proteins may have similar effects. Specifically, Hero proteins can maintain the activity of other proteins from denaturing conditions in vitro, while their overexpression can suppress cellular aggregation and toxicity associated with aggregation-prone proteins. However, it is unclear how these protective effects are achieved. Here, we utilized single-molecule FRET to monitor the conformations of the aggregation-prone prion-like LCD of TDP-43. While we observed high conformational heterogeneity in wild-type LCD, the ALS-associated mutation A315T promoted collapsed conformations. In contrast, an Hsp40 chaperone, DNAJA2, and a Hero protein, Hero11 stabilized extended states of the LCD, consistent with their ability to suppress the aggregation of TDP-43. Our results link single-molecule effects on conformation to macro effects on bulk aggregation, where a Hero protein, like a chaperone, can maintain the conformational integrity of a client protein to prevent its aggregation.

Introduction: Medical associations and medicolegal bodies are urging for increased chaperone use by physicians during intimate physical examinations in clinical practice (such as breast or pelvic examinations). However, widespread chaperone use is limited by factors such as staff availability and financial considerations. Presently, there is a scarcity of information available regarding the cost of hiring a dedicated chaperone. This study investigates the cost of hiring a chaperone and its financial implications for a physician\'s clinical practice. Materials and Methods: Using data from the Government of Canada website, the range of salary rates for clinic staff who can act as a chaperone in Canada was analyzed. The cost of hiring a chaperone was estimated to be in the range between the cost of hiring a minimum-wage worker and a nurse (the highest-paid hired medical office staff). Obstetrics and Gynecology as well as Plastic Surgery urban community practices were consulted regarding the costs of operating a clinic. Results: The approximate annual income for a minimum-wage worker in Canada is $29,250 CAD. Registered nurses earn on average $72,783.75 CAD per year. The cost of operating a private clinic practice with one staff member in Canada is on average $102,500 CAD per year. Thus, hiring an additional full-time chaperone could increase clinic expenses by approximately 49% per year, bringing the clinic cost to approximately $153,517 CAD per year. For part-time employment, the annual cost of hiring a chaperone is approximately $10,203 CAD for each day/week of employment. Conclusion: In terms of financial considerations, hiring a chaperone can increase clinic expenses by approximately one-and-a-half times. The findings of this study provide an important reference for physicians and may assist with the decision to employ chaperones in clinical practice.
Introduction: Les associations médiales et les institutions médico-légales encouragent fortement le recours à un chaperon lors d’examen physique intime par des médecins en pratique clinique (dans le cas, par exemple, d’examen pelvien ou mammaire). Cependant, le recours généralisé à un chaperon est limité par des facteurs tels que la disponibilité du personnel et des considérations financières. On ne dispose actuellement que de peu d’information sur le coût de l’embauche d’un chaperon dédié. Cette étude porte sur le coût d’un tel recrutement et sur ses implications financières pour la pratique clinique d’un médecin. Matériels et Méthodes: Utilisant des données d’un site Web du gouvernement du Canada, nous avons analysé l’éventail des salaires du personnel d’une clinique pouvant servir de chaperon au Canada. Le coût du recrutement d’un chaperon a été évalué comme se situant entre celui d’une embauche au salaire minimum et celui d’une infirmière (l’emploi le mieux payé parmi le personnel médical d’une clinique). Les cliniques communautaires urbaines d’obstétrique et de gynécologie, ainsi que les cliniques de chirurgie plastique ont été consultées pour ce qui concerne les coûts de fonctionnement des cliniques. Résultats: Le revenu annuel moyen approximatif d’un travailleur au salaire minimum au Canada est de 29 250 dollars canadiens. Les infirmières autorisées gagnent en moyenne 72 783,75 dollars canadiens par an. Le coût de fonctionnement d’une clinique privée ne comptant qu’un(e) employé(e) au Canada est en moyenne de 102 500 dollars canadiens par an. Par conséquent, l’embauche d’un chaperon à temps plein augmenterait les dépenses de la clinique d’environ 49 % par an, soit un total approximatif de 153 517 dollars canadiens par an. Dans le cas d’une embauche à temps partiel, le coût annuel d’un chaperon serait d’environ 10 203 dollars canadiens pour chaque jour/semaine d’emploi. Conclusion: En termes de considérations financières, l’embauche d’un chaperon peut multiplier les dépenses de la clinique par 1,5. Les constatations de cette étude fournissent une référence importante aux médecins et peut les aider dans leur décision d’embaucher des chaperons en pratique clinique.

The toxicity of non-proteinogenic amino acids has been known for decades. Numerous reports describe their antimicrobial/anticancer potential. However, these molecules are often toxic to the host as well; thus, a synthetic lethality approach that reduces the dose of these toxins while maintaining toxicity can be beneficial. Here we investigate synthetic lethality between toxic amino acids, the retrograde pathway, and molecular chaperones. In Saccharomyces cerevisiae, mitochondrial retrograde (RTG) pathway activation induces transcription of RTG-target genes to replenish alpha-ketoglutarate and its downstream product glutamate; both metabolites are required for arginine and lysine biosynthesis. We previously reported that tolerance of canavanine, a toxic arginine derivative, requires an intact RTG pathway, and low-dose canavanine exposure reduces the expression of RTG-target genes. Here we show that only a few of the examined chaperone mutants are sensitive to sublethal doses of canavanine. To predict synthetic lethality potential between RTG-target genes and chaperones, we measured the expression of RTG-target genes in canavanine-sensitive and canavanine-tolerant chaperone mutants. Most RTG-target genes were induced in all chaperone mutants starved for arginine; the same trend was not observed under lysine starvation. Canavanine exposure under arginine starvation attenuated and even reversed RTG-target-gene expression in the tested chaperone mutants. Importantly, under nearly all tested genetic and pharmacological conditions, the expression of IDH1 and/or IDH2 was induced. In agreement, idh1 and idh2 mutants are sensitive to canavanine and thialysine and show synthetic growth inhibition with chaperone mutants. Overall, we show that inhibiting molecular chaperones, RTG-target genes, or both can sensitize cells to low doses of toxic amino acids.

Protein folding is crucial for achieving functional three-dimensional structures. However, the process is often hampered by aggregate formation, necessitating the presence of chaperones and quality control systems within the cell to maintain protein homeostasis. Despite a long history of folding studies involving the denaturation and subsequent refolding of translation-completed purified proteins, numerous facets of cotranslational folding, wherein nascent polypeptides are synthesized by ribosomes and folded during translation, remain unexplored. Cell-free protein synthesis (CFPS) systems are invaluable tools for studying cotranslational folding, offering a platform not only for elucidating mechanisms but also for large-scale analyses to identify aggregation-prone proteins. This review provides an overview of the extensive use of CFPS in folding studies to date. In particular, we discuss a comprehensive aggregation formation assay of thousands of Escherichia coli proteins conducted under chaperone-free conditions using a reconstituted translation system, along with its derived studies.

INTS11 and CPSF73 are metal-dependent endonucleases for Integrator and pre-mRNA 3\'-end processing, respectively. Here, we show that the INTS11 binding partner BRAT1/CG7044, a factor important for neuronal fitness, stabilizes INTS11 in the cytoplasm and is required for Integrator function in the nucleus. Loss of BRAT1 in neural organoids leads to transcriptomic disruption and precocious expression of neurogenesis-driving transcription factors. The structures of the human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes reveal that the conserved C terminus of BRAT1/CG7044 is captured in the active site of INTS11, with a cysteine residue directly coordinating the metal ions. Inspired by these observations, we find that UBE3D is a binding partner for CPSF73, and UBE3D likely also uses a conserved cysteine residue to directly coordinate the active site metal ions. Our studies have revealed binding partners for INTS11 and CPSF73 that behave like cytoplasmic chaperones with a conserved impact on the nuclear functions of these enzymes.