bims-proarb 2022-02-13 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–02–13
thirteen papers selected by
Rich Giadone, Harvard University

Chaperones directly and efficiently disperse stress-triggered biomolecular condensates.
Involvement of molecular chaperone in protein-misfolding brain diseases.
Perspective: Modulating the integrated stress response to slow aging and ameliorate age-related pathology.
Endoplasmic reticulum-mitochondria signaling in neurons and neurodegenerative diseases.
Proteasome activity modulates amyloid toxicity.
Two distinct classes of co-chaperones compete for the EEVD motif in heat shock protein 70 (Hsp70) to tune its chaperone activities.
The different autophagy degradation pathways and neurodegeneration.
Chaperones mainly suppress primary nucleation during formation of functional amyloid required for bacterial biofilm formation.
Molecular mechanisms of amyloid disaggregation.
Genetic and pharmacological inhibition of XBP1 protects against APAP hepatotoxicity through the activation of autophagy.
Autophagy and intracellular product degradation genes identified by systems biology analysis reduce aggregation of bispecific antibody in CHO cells.
Modeling the cellular fate of alpha-synuclein aggregates: A pathway to pathology.
Circadian control of heparan sulfate levels times phagocytosis of amyloid beta aggregates.

Mol Cell. 2022 Feb 08. pii: S1097-2765(22)00005-3. [Epub ahead of print]

Chaperones directly and efficiently disperse stress-triggered biomolecular condensates.

Haneul Yoo, Jared A M Bard, Evgeny V Pilipenko, D Allan Drummond.

  Stresses such as heat shock trigger the formation of protein aggregates and the induction of a disaggregation system composed of molecular chaperones. Recent work reveals that several cases of apparent heat-induced aggregation, long thought to be the result of toxic misfolding, instead reflect evolved, adaptive biomolecular condensation, with chaperone activity contributing to condensate regulation. Here we show that the yeast disaggregation system directly disperses heat-induced biomolecular condensates of endogenous poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used misfolded model substrate, firefly luciferase. Beyond its efficiency, heat-induced condensate dispersal differs from heat-induced aggregate dispersal in its molecular requirements and mechanistic behavior. Our work establishes a bona fide endogenous heat-induced substrate for long-studied heat shock proteins, isolates a specific example of chaperone regulation of condensates, and underscores needed expansion of the proteotoxic interpretation of the heat shock response to encompass adaptive, chaperone-mediated regulation.

Keywords:  biomolecular condensates; cell stress; disaggregation; heat shock; molecular chaperones; stress response

DOI:  https://doi.org/10.1016/j.molcel.2022.01.005
Biomed Pharmacother. 2022 Feb 08. pii: S0753-3322(22)00035-X. [Epub ahead of print]147 112647

Involvement of molecular chaperone in protein-misfolding brain diseases.

Nitu L Wankhede, Mayur B Kale, Aman B Upaganlawar, Brijesh G Taksande, Milind J Umekar, Tapan Behl, Ahmed A H Abdellatif, Prasanna Mohana Bhaskaran, Sudarshan Reddy Dachani, Aayush Sehgal, Sukhbir Singh, Neelam Sharma, Hafiz A Makeen, Mohammed Albratty, Hamed Ghaleb Dailah, Saurabh Bhatia, Ahmed Al-Harrasi, Simona Bungau.

  Protein misfolding causes aggregation and build-up in a variety of brain diseases. There are numeral molecules that are linked with the protein homeostasis mechanism. Molecular chaperones are one of such molecules that are responsible for protection against protein misfolded and aggregation-induced neurotoxicity. Many studies have explored the participation of molecular chaperones in Parkinson's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, and Huntington's diseases. In this review, we highlighted the constructive role of molecular chaperones in neurological diseases characterized by protein misfolding and aggregation and their capability to control aberrant protein interactions at an early stage thus successfully suppressing pathogenic cascades. A comprehensive understanding of the protein misfolding associated with brain diseases and the molecular basis of involvement of chaperone against aggregation-induced cellular stress might lead to the progress of new therapeutic intrusion-related to protein misfolding and aggregation.

Keywords:  Alzheimer’s disease (AD); Amyotrophic lateral sclerosis (ALS); Huntington’s disease (HD); Molecular chaperone; Parkinson’s disease (PD); Protein misfolding and aggregation

DOI:  https://doi.org/10.1016/j.biopha.2022.112647
Nat Aging. 2021 Sep;1(9): 760-768

Perspective: Modulating the integrated stress response to slow aging and ameliorate age-related pathology.

Maxime J Derisbourg, Matías D Hartman, Martin S Denzel.

Healthy aging requires the coordination of numerous stress signaling pathways that converge on the protein homeostasis network. The Integrated Stress Response (ISR) is activated by diverse stimuli, leading to phosphorylation of the eukaryotic translation initiation factor elF2 in its α-subunit. Under replete conditions, elF2 orchestrates 5' cap-dependent mRNA translation and is thus responsible for general protein synthesis. elF2α phosphorylation, the key event of the ISR, reduces global mRNA translation while enhancing the expression of a signature set of stress response genes. Despite the critical role of protein quality control in healthy aging and in numerous longevity pathways, the role of the ISR in longevity remains largely unexplored. ISR activity increases with age, suggesting a potential link with the aging process. Although decreased protein biosynthesis, which occurs during ISR activation, have been linked to lifespan extension, recent data show that lifespan is limited by the ISR as its inhibition extends survival in nematodes and enhances cognitive function in aged mice. Here we survey how aging affects the ISR, the role of the ISR in modulating aging, and pharmacological interventions to tune the ISR. Finally, we will explore the ISR as a plausible target for clinical interventions in aging and age-related disease.

DOI: https://doi.org/10.1038/s43587-021-00112-9
J Cell Sci. 2022 Feb 01. pii: jcs248534. [Epub ahead of print]135(3):

Endoplasmic reticulum-mitochondria signaling in neurons and neurodegenerative diseases.

Andrea Markovinovic, Jenny Greig, Sandra María Martín-Guerrero, Shaakir Salam, Sebastien Paillusson.

  Recent advances have revealed common pathological changes in neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis with related frontotemporal dementia (ALS/FTD). Many of these changes can be linked to alterations in endoplasmic reticulum (ER)-mitochondria signaling, including dysregulation of Ca2+ signaling, autophagy, lipid metabolism, ATP production, axonal transport, ER stress responses and synaptic dysfunction. ER-mitochondria signaling involves specialized regions of ER, called mitochondria-associated membranes (MAMs). Owing to their role in neurodegenerative processes, MAMs have gained attention as they appear to be associated with all the major neurodegenerative diseases. Furthermore, their specific role within neuronal maintenance is being revealed as mutant genes linked to major neurodegenerative diseases have been associated with damage to these specialized contacts. Several studies have now demonstrated that these specialized contacts regulate neuronal health and synaptic transmission, and that MAMs are damaged in patients with neurodegenerative diseases. This Review will focus on the role of MAMs and ER-mitochondria signaling within neurons and how damage of the ER-mitochondria axis leads to a disruption of vital processes causing eventual neurodegeneration.

Keywords:  Endoplasmic reticulum; MAMs; Mitochondria; Neurodegenerative diseases; Neurons; Tethers

DOI:  https://doi.org/10.1242/jcs.248534
FEMS Yeast Res. 2022 Feb 12. pii: foac004. [Epub ahead of print]

Proteasome activity modulates amyloid toxicity.

John Galvin, Elizabeth Curran, Francisco Arteaga, Alicia Goossens, Nicki Aubuchon-Endsley, Michael A McMurray, Jeffrey Moore, Kirk C Hansen, Heidi J Chial, Huntington Potter, Jeffrey L Brodsky, Christina M Coughlan.

  Alzheimer's Disease (AD) is responsible for 60-80% of identified cases of dementia. While the generation and accumulation of amyloid precursor protein (APP) fragments is accepted as a key step in AD pathogenesis, the precise role of these fragments remains poorly understood. To overcome this deficit, we induced the expression of the soluble C-terminal fragment of APP (C99), the rate limiting peptide for the generation of amyloid fragments, in yeast that contain thermosensitive mutations in genes encoding proteasome subunits. Our previous work with this system demonstrated that these proteasome-deficient yeast cells, expressing C99 when proteasome activity was blunted, generated amyloid fragments similar to those observed in AD patients. We now report the phenotypic repercussions of inducing C99 expression in proteasome-deficient cells. We show increased levels of protein aggregation, cellular stress and chaperone expression, electron-dense accumulations in the nuclear envelope/ER, abnormal DNA condensation, and an induction of apoptosis. Taken together, these findings suggest that the generation of C99 and its associated fragments in yeast cells with compromised proteasomal activity result in phenotypes that may be relevant to the neuropathological processes observed in AD patients. These data also suggest that this yeast model should be useful for testing therapeutics that target AD-associated amyloid, since it allows for the assessment of the reversal of the perturbed cellular physiology observed when degradation pathways are dysfunctional.

Keywords:  Alzheimer's Disease; Amyloid Precursor Protein (APP); Aβ; C99; Proteostasis; Yeast

DOI:  https://doi.org/10.1093/femsyr/foac004
J Biol Chem. 2022 Feb 08. pii: S0021-9258(22)00137-5. [Epub ahead of print] 101697

Two distinct classes of co-chaperones compete for the EEVD motif in heat shock protein 70 (Hsp70) to tune its chaperone activities.

Oleta T Johnson, Cory M Nadel, Emma C Carroll, Taylor Arhar, Jason E Gestwicki.

  Chaperones of the heat shock protein 70 (Hsp70) family engage in protein-protein interactions (PPIs) with many co-chaperones to modulate their functions. One "hotspot" for co-chaperone binding is the EEVD motif, found at the extreme C-terminus of cytoplasmic Hsp70s. This motif is known to bind tetratricopeptide repeat (TPR) domain co-chaperones, such as the E3 ubiquitin ligase CHIP. In addition, the EEVD motif also interacts with a structurally distinct domain that is present in Class B J-domain proteins (JDPs), such as DnaJB4. These observations suggest that CHIP and DnaJB4 might compete for binding to Hsp70's EEVD motif; however, the molecular determinants of such competition are not clear. Using a collection of EEVD-derived peptides, including mutations and truncations, we explored which residues are critical for binding to both CHIP and DnaJB4 in parallel. These results revealed that some features, such as the C-terminal carboxylate, are important for both interactions. However, CHIP and DnaJB4 also had unique preferences, especially at the isoleucine position immediately adjacent to the EEVD. Finally, we show that competition between these co-chaperones is important in vitro, as DnaJB4 limits the ubiquitination activity of the Hsp70-CHIP complex, while CHIP suppresses the client re-folding activity of the Hsp70-DnaJB4 complex. Together, these data suggest that the EEVD motif has evolved to support diverse PPIs, such that competition between co-chaperones may help guide whether Hsp70-bound proteins are folded or degraded.

Keywords:  J-domain protein; fluorescence polarization; molecular chaperone; peptide-protein interaction; protein folding; protein-protein interaction; tetratricopeptide repeat; ubiquitination

DOI:  https://doi.org/10.1016/j.jbc.2022.101697
Neuron. 2022 Jan 31. pii: S0896-6273(22)00056-3. [Epub ahead of print]

The different autophagy degradation pathways and neurodegeneration.

Angeleen Fleming, Mathieu Bourdenx, Motoki Fujimaki, Cansu Karabiyik, Gregory J Krause, Ana Lopez, Adrián Martín-Segura, Claudia Puri, Aurora Scrivo, John Skidmore, Sung Min Son, Eleanna Stamatakou, Lidia Wrobel, Ye Zhu, Ana Maria Cuervo, David C Rubinsztein.

The term autophagy encompasses different pathways that route cytoplasmic material to lysosomes for degradation and includes macroautophagy, chaperone-mediated autophagy, and microautophagy. Since these pathways are crucial for degradation of aggregate-prone proteins and dysfunctional organelles such as mitochondria, they help to maintain cellular homeostasis. As post-mitotic neurons cannot dilute unwanted protein and organelle accumulation by cell division, the nervous system is particularly dependent on autophagic pathways. This dependence may be a vulnerability as people age and these processes become less effective in the brain. Here, we will review how the different autophagic pathways may protect against neurodegeneration, giving examples of both polygenic and monogenic diseases. We have considered how autophagy may have roles in normal CNS functions and the relationships between these degradative pathways and different types of programmed cell death. Finally, we will provide an overview of recently described strategies for upregulating autophagic pathways for therapeutic purposes.

DOI: https://doi.org/10.1016/j.neuron.2022.01.017
Chem Sci. 2022 Jan 05. 13(2): 536-553

Chaperones mainly suppress primary nucleation during formation of functional amyloid required for bacterial biofilm formation.

Madhu Nagaraj, Zahra Najarzadeh, Jonathan Pansieri, Henrik Biverstål, Greta Musteikyte, Vytautas Smirnovas, Steve Matthews, Cecilia Emanuelsson, Janne Johansson, Joel N Buxbaum, Ludmilla Morozova-Roche, Daniel E Otzen.

Unlike misfolding in neurodegenerative diseases, aggregation of functional amyloids involved in bacterial biofilm, e.g. CsgA (E. coli) and FapC (Pseudomonas), is carefully regulated. However, it is unclear whether functional aggregation is inhibited by chaperones targeting pathological misfolding and if so by what mechanism. Here we analyze how four entirely different human chaperones or protein modulators (transthyretin, S100A9, Bri2 BRICHOS and DNAJB6) and bacterial CsgC affect CsgA and FapC fibrillation. CsgA is more susceptible to inhibition than FapC and the chaperones vary considerably in the efficiency of their inhibition. However, mechanistic analysis reveals that all predominantly target primary nucleation rather than elongation or secondary nucleation, while stoichiometric considerations suggest that DNAJB6 and CsgC target nuclei rather than monomers. Inhibition efficiency broadly scales with the chaperones' affinity for monomeric CsgA and FapC. The chaperones tend to target the most aggregation-prone regions of CsgA, but do not display such tendencies towards the more complex FapC sequence. Importantly, the most efficient inhibitors (Bri2 BRICHOS and DNAJB6) significantly reduce bacterial biofilm formation. This commonality of chaperone action may reflect the simplicity of functional amyloid formation, driven largely by primary nucleation, as well as the ability of non-bacterial chaperones to deploy their proteostatic capacities across biological kingdoms.

DOI: https://doi.org/10.1039/d1sc05790a
J Adv Res. 2022 Feb;36 113-132

Molecular mechanisms of amyloid disaggregation.

Kimberly Jia Yi Low, Anandalakshmi Venkatraman, Jodhbir S Mehta, Konstantin Pervushin.

   Introduction: Protein aggregation and deposition of uniformly arranged amyloid fibrils in the form of plaques or amorphous aggregates is characteristic of amyloid diseases. The accumulation and deposition of proteins result in toxicity and cause deleterious effects on affected individuals known as amyloidosis. There are about fifty different proteins and peptides involved in amyloidosis including neurodegenerative diseases and diseases affecting vital organs. Despite the strenuous effort to find a suitable treatment option for these amyloid disorders, very few compounds had made it to unsuccessful clinical trials. It has become a compelling challenge to understand and manage amyloidosis with the increased life expectancy and ageing population.
Objective: While most of the currently available literature and knowledge base focus on the amyloid inhibitory mechanism as a treatment option, it is equally important to organize and understand amyloid disaggregation strategies. Disaggregation strategies are important and crucial as they are present innately functional in many living systems and dissolution of preformed amyloids may provide a direct benefit in many pathological conditions. In this review, we have compiled the known amyloid disaggregation mechanism, interactions, and possibilities of using disaggregases as a treatment option for amyloidosis.
Methods: We have provided the structural details using protein-ligand docking models to visualize the interaction between these disaggregases with amyloid fibrils and their respective proposed amyloid disaggregation mechanisms.
Results: After reviewing and comparing the different amyloid disaggregase systems and their proposed mechanisms, we presented two different hypotheses for ATP independent disaggregases using L-PGDS as a model.
Conclusion: Finally, we have highlighted the importance of understanding the underlying disaggregation mechanisms used by these chaperones and organic compounds before the implementation of these disaggregases as a potential treatment option for amyloidosis.

Keywords:  Amyloids; Chaperones; Disaggregation; Protein aggregation; Protein folding and misfolding

DOI:  https://doi.org/10.1016/j.jare.2021.05.007
Cell Death Dis. 2022 Feb 10. 13(2): 143

Genetic and pharmacological inhibition of XBP1 protects against APAP hepatotoxicity through the activation of autophagy.

Hui Ye, Chaobo Chen, Hanghang Wu, Kang Zheng, Beatriz Martín-Adrados, Esther Caparros, Rubén Francés, Leonard J Nelson, Manuel Gómez Del Moral, Iris Asensio, Javier Vaquero, Rafael Bañares, Matías A Ávila, Raúl J Andrade, M Isabel Lucena, Maria Luz Martínez-Chantar, Helen L Reeves, Steven Masson, Richard S Blumberg, Jordi Gracia-Sancho, Yulia A Nevzorova, Eduardo Martínez-Naves, Francisco Javier Cubero.

Acetaminophen (APAP) hepatotoxicity induces endoplasmic reticulum (ER) stress which triggers the unfolded protein response (UPR) in hepatocytes. However, the mechanisms underlying ER stress remain poorly understood, thus reducing the options for exploring new pharmacological therapies for patients with hyperacute liver injury. Eight-to-twelve-week-old C57BL/6J Xbp1-floxed (Xbp1f/f) and hepatocyte-specific knockout Xbp1 mice (Xbp1∆hepa) were challenged with either high dose APAP [500 mg/kg] and sacrificed at early (1-2 h) and late (24 h) stages of hepatotoxicity. Histopathological examination of livers, immunofluorescence and immunohistochemistry, Western blot, real time (RT)-qPCR studies and transmission electron microscopy (TEM) were performed. Pharmacological inhibition of XBP1 using pre-treatment with STF-083010 [STF, 75 mg/kg] and autophagy induction with Rapamycin [RAPA, 8 mg/kg] or blockade with Chloroquine [CQ, 60 mg/kg] was also undertaken in vivo. Cytoplasmic expression of XBP1 coincided with severity of human and murine hyperacute liver injury. Transcriptional and translational activation of the UPR and sustained activation of JNK1/2 were major events in APAP hepatotoxicity, both in a human hepatocytic cell line and in a preclinical model. Xbp1∆hepa livers showed decreased UPR and JNK1/2 activation but enhanced autophagy in response to high dose APAP. Additionally, blockade of XBP1 splicing by STF, mitigated APAP-induced liver injury and without non-specific off-target effects (e.g., CYP2E1 activity). Furthermore, enhanced autophagy might be responsible for modulating CYP2E1 activity in Xbp1∆hepa animals. Genetic and pharmacological inhibition of Xbp1 specifically in hepatocytes ameliorated APAP-induced liver injury by enhancing autophagy and decreasing CYP2E1 expression. These findings provide the basis for the therapeutic restoration of ER stress and/or induction of autophagy in patients with hyperacute liver injury.

DOI: https://doi.org/10.1038/s41419-022-04580-8
N Biotechnol. 2022 Feb 02. pii: S1871-6784(22)00010-3. [Epub ahead of print]68 68-76

Autophagy and intracellular product degradation genes identified by systems biology analysis reduce aggregation of bispecific antibody in CHO cells.

Mona Moradi Barzadd, Magnus Lundqvist, Claire Harris, Magdalena Malm, Anna-Luisa Volk, Niklas Thalén, Veronique Chotteau, Luigi Grassi, Andrew Smith, Marina Leal Abadi, Giulia Lambiase, Suzanne Gibson, Diane Hatton, Johan Rockberg.

  Aggregation of therapeutic bispecific antibodies negatively affects the yield, shelf-life, efficacy and safety of these products. Pairs of stable Chinese hamster ovary (CHO) cell lines produced two difficult-to-express bispecific antibodies with different levels of aggregated product (10-75% aggregate) in a miniaturised bioreactor system. Here, transcriptome analysis was used to interpret the biological causes for the aggregation and to identify strategies to improve product yield and quality. Differential expression- and gene set analysis revealed upregulated proteasomal degradation, unfolded protein response and autophagy processes to be correlated with reduced protein aggregation. Fourteen candidate genes with the potential to reduce aggregation were co-expressed in the stable clones for validation. Of these, HSP90B1, DDIT3, AKT1S1, and ATG16L1, were found to significantly lower aggregation in the stable producers and two (HSP90B1 and DNAJC3) increased titres of the anti-HER2 monoclonal antibody trastuzumab by 50% during transient expression. It is suggested that this approach could be of general use for defining aggregation bottlenecks in CHO cells.

Keywords:  Aggregation; Autophagy; Bispecific antibody; CHO cells; ER stress; System biology

DOI:  https://doi.org/10.1016/j.nbt.2022.01.010
Curr Opin Neurobiol. 2022 Feb 04. pii: S0959-4388(22)00003-4. [Epub ahead of print]72 171-177

Modeling the cellular fate of alpha-synuclein aggregates: A pathway to pathology.

Nicholas P Marotta, Virginia M-Y Lee.

Parkinson's disease is a progressive neurodegenerative disorder that is characterized by pathological protein inclusions that form in the brains of patients, leading to neuron loss and the observed clinical symptoms. These inclusions, containing aggregates of the protein α-Synuclein, spread throughout the brain as the disease progresses. This spreading follows patterns that inform our understanding of the disease. One way to further our understanding of disease progression is to model the discrete steps from when a cell first encounters an aggregate to when those aggregates propagate to new cells. This review will serve to highlight the recent progress made in the effort to better understand the mechanistic steps that determine how this propagation happens at the cellular level.

DOI: https://doi.org/10.1016/j.conb.2022.01.003
PLoS Genet. 2022 Feb;18(2): e1009994

Circadian control of heparan sulfate levels times phagocytosis of amyloid beta aggregates.

Gretchen T Clark, Yanlei Yu, Cooper A Urban, Guo Fu, Chunyu Wang, Fuming Zhang, Robert J Linhardt, Jennifer M Hurley.

Alzheimer's Disease (AD) is a neuroinflammatory disease characterized partly by the inability to clear, and subsequent build-up, of amyloid-beta (Aβ). AD has a bi-directional relationship with circadian disruption (CD) with sleep disturbances starting years before disease onset. However, the molecular mechanism underlying the relationship of CD and AD has not been elucidated. Myeloid-based phagocytosis, a key component in the metabolism of Aβ, is circadianly-regulated, presenting a potential link between CD and AD. In this work, we revealed that the phagocytosis of Aβ42 undergoes a daily circadian oscillation. We found the circadian timing of global heparan sulfate proteoglycan (HSPG) biosynthesis was the molecular timer for the clock-controlled phagocytosis of Aβ and that both HSPG binding and aggregation may play a role in this oscillation. These data highlight that circadian regulation in immune cells may play a role in the intricate relationship between the circadian clock and AD.

DOI: https://doi.org/10.1371/journal.pgen.1009994