bims-proarb Biomed News
on Proteostasis in aging and regenerative biology
Issue of 2021–11–21
sixteen papers selected by
Rich Giadone, Harvard University
  1. Rescue of α-synuclein aggregation in Parkinson's patient neurons by synergistic enhancement of ER proteostasis and protein trafficking.
  2. Carrying Excess Baggage Can Slowdown Life: Protein Clearance Machineries That Go Awry During Aging and the Relevance of Maintaining Them.
  3. Autophagy and Aging: Roles in Skeletal Muscle, Eye, Brain and Hepatic Tissue.
  4. Mitochondrial chaperone in human health and diseases.
  5. Mapping protein carboxymethylation sites provides insights into their role in proteostasis and cell proliferation.
  6. Metabolically Activated Proteostasis Regulators Protect against Glutamate Toxicity by Activating NRF2.
  7. DA-9805 protects dopaminergic neurons from endoplasmic reticulum stress and inflammation.
  8. Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability.
  9. Brain-wide cellular mapping of acute stress-induced activation in male and female mice.
  10. Phosphorylation activates the yeast small heat shock protein Hsp26 by weakening domain contacts in the oligomer ensemble.
  11. Editorial: Ubiquitin Code: From Cell Biology to Translational Medicine.
  12. More Alzheimer's drugs head for FDA review: what scientists are watching.
  13. SIRT5 Represses Neurotrophic Pathways and Aβ Production in Alzheimer's Disease by Targeting Autophagy.
  14. Arginine and Arginine-Rich Peptides as Modulators of Protein Aggregation and Cytotoxicity Associated With Alzheimer's Disease.
  15. Structural insights into Ubr1-mediated N-degron polyubiquitination.
  16. A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics.
  1. Neuron. 2021 Nov 09. pii: S0896-6273(21)00862-X. [Epub ahead of print]
    Rescue of α-synuclein aggregation in Parkinson's patient neurons by synergistic enhancement of ER proteostasis and protein trafficking.
    Iva Stojkovska, Willayat Y Wani, Friederike Zunke, Nandkishore R Belur, Egor A Pavlenko, Nkatha Mwenda, Karan Sharma, Laetitia Francelle, Joseph R Mazzulli.
      Neurodegenerative disorders are characterized by a collapse in proteostasis, as shown by the accumulation of insoluble protein aggregates in the brain. Proteostasis involves a balance of protein synthesis, folding, trafficking, and degradation, but how aggregates perturb these pathways is unknown. Using Parkinson's disease (PD) patient midbrain cultures, we find that aggregated α-synuclein induces endoplasmic reticulum (ER) fragmentation and compromises ER protein folding capacity, leading to misfolding and aggregation of immature lysosomal β-glucocerebrosidase. Despite this, PD neurons fail to initiate the unfolded protein response, indicating perturbations in sensing or transducing protein misfolding signals in the ER. Small molecule enhancement of ER proteostasis machinery promotes β-glucocerebrosidase solubility, while simultaneous enhancement of trafficking improves ER morphology, lysosomal function, and reduces α-synuclein. Our studies suggest that aggregated α-synuclein perturbs the ability of neurons to respond to misfolded proteins in the ER, and that synergistic enhancement of multiple proteostasis branches may provide therapeutic benefit in PD.
    Keywords:  ER stress; Parkinson's disease; alpha-synuclein; beta-glucocerebrosidase; iPSC-derived midbrain dopaminergic neurons; lysosomal dysfunction; protein aggregation
    DOI:  https://doi.org/10.1016/j.neuron.2021.10.032
  2. Mol Neurobiol. 2021 Nov 18.
    Carrying Excess Baggage Can Slowdown Life: Protein Clearance Machineries That Go Awry During Aging and the Relevance of Maintaining Them.
    Arunabh Sarkar, Aamir Nazir.
      Cellular homeostasis is maintained by rapid and systematic cleansing of aberrant and aggregated proteins within cells. Neurodegenerative diseases (NDs) especially Parkinson's and Alzheimer's disease are known to be associated with multiple factors, most important being impaired clearance of aggregates, resulting in the accumulation of specific aggregated protein in the brain. Protein quality control (PQC) of proteostasis network comprises proteolytic machineries and chaperones along with their regulators to ensure precise operation and maintenance of proteostasis. Such regulatory factors coordinate among each other multiple functional aspects related to proteins, including their synthesis, folding, transport, and degradation. During aging due to inevitable endogenous and external stresses, sustaining a proteome balance is a challenging task. Such stresses decline the capacity of the proteostasis network compromising the proteome integrity, affecting the fundamental physiological processes including reproductive fitness of the organism. This review focuses on highlighting proteome-wide changes during aging and the strategies for proteostasis improvements. The possibility of augmenting the proteostasis network either via genetic or pharmacological interventions may be a promising strategy towards delaying age-associated pathological consequences due to proteome disbalance, thus promoting healthy aging and prolonged longevity.
    Keywords:  Aging; Neurodegenerative diseases; Protein quality control; Proteostasis
    DOI:  https://doi.org/10.1007/s12035-021-02640-2
  3. Front Cell Dev Biol. 2021 ;9 752962
    Autophagy and Aging: Roles in Skeletal Muscle, Eye, Brain and Hepatic Tissue.
    Ping Li, Yuanzheng Ma, Chengwei Yu, Shoutong Wu, Kai Wang, Hongyang Yi, Weizheng Liang.
      Autophagy is an evolutionary conserved degradative process contributing to cytoplasm quality control, metabolic recycling and cell defense. Aging is a universal phenomenon characterized by the progressive accumulation of impaired molecular and reduced turnover of cellular components. Recent evidence suggests a unique role for autophagy in aging and age-related disease. Indeed, autophagic activity declines with age and enhanced autophagy may prevent the progression of many age-related diseases and prolong life span. All tissues experience changes during aging, while the role of autophagy in different tissues varies. This review summarizes the links between autophagy and aging in the whole organism and discusses the physiological and pathological roles of autophagy in the aging process in tissues such as skeletal muscle, eye, brain, and liver.
    Keywords:  age-related diseases; aging; autophagy; brain; eye; liver; skeletal muscle
    DOI:  https://doi.org/10.3389/fcell.2021.752962
  4. Free Radic Biol Med. 2021 Nov 12. pii: S0891-5849(21)00812-1. [Epub ahead of print]
    Mitochondrial chaperone in human health and diseases.
    Tyler Bahr, Joshua Katuri, Ting Liang, Yidong Bai.
      Molecular chaperones are a family of proteins that maintain cellular protein homeostasis through non-covalent peptide folding and quality control mechanisms. The chaperone proteins found within mitochondria play significant protective roles in mitochondrial biogenesis, quality control, and stress response mechanisms. Defective mitochondrial chaperones have been implicated in aging, neurodegeneration, and cancer. In this review, we focus on the two most prominent mitochondrial chaperones: mtHsp60 and mtHsp70. These proteins demonstrate different cellular localization patterns, interact with different targets, and have different functional activities. We discuss the structure and function of these prominent mitochondrial chaperone proteins and give an update on newly discovered regulatory mechanisms and disease implications.
    Keywords:  Mitochondrial chaperone; Mitochondrial homeostasis; Stressresponse; mtHsp60; mtHsp70
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.11.015
  5. Nat Commun. 2021 Nov 18. 12(1): 6743
    Mapping protein carboxymethylation sites provides insights into their role in proteostasis and cell proliferation.
    Simone Di Sanzo, Katrin Spengler, Anja Leheis, Joanna M Kirkpatrick, Theresa L Rändler, Tim Baldensperger, Therese Dau, Christian Henning, Luca Parca, Christian Marx, Zhao-Qi Wang, Marcus A Glomb, Alessandro Ori, Regine Heller.
      Posttranslational mechanisms play a key role in modifying the abundance and function of cellular proteins. Among these, modification by advanced glycation end products has been shown to accumulate during aging and age-associated diseases but specific protein targets and functional consequences remain largely unexplored. Here, we devise a proteomic strategy to identify sites of carboxymethyllysine modification, one of the most abundant advanced glycation end products. We identify over 1000 sites of protein carboxymethylation in mouse and primary human cells treated with the glycating agent glyoxal. By using quantitative proteomics, we find that protein glycation triggers a proteotoxic response and indirectly affects the protein degradation machinery. In primary endothelial cells, we show that glyoxal induces cell cycle perturbation and that carboxymethyllysine modification reduces acetylation of tubulins and impairs microtubule dynamics. Our data demonstrate the relevance of carboxymethyllysine modification for cellular function and pinpoint specific protein networks that might become compromised during aging.
    DOI:  https://doi.org/10.1038/s41467-021-26982-6
  6. ACS Chem Biol. 2021 Nov 19.
    Metabolically Activated Proteostasis Regulators Protect against Glutamate Toxicity by Activating NRF2.
    Jessica D Rosarda, Kelsey R Baron, Kayla Nutsch, Gabriel M Kline, Caroline Stanton, Jeffery W Kelly, Michael J Bollong, R Luke Wiseman.
      The extracellular accumulation of glutamate is a pathologic hallmark of numerous neurodegenerative diseases including ischemic stroke and Alzheimer's disease. At high extracellular concentrations, glutamate causes neuronal damage by promoting oxidative stress, which can lead to cellular death. This has led to significant interest in developing pharmacologic approaches to mitigate the oxidative toxicity caused by high levels of glutamate. Here, we show that the small molecule proteostasis regulator AA147 protects against glutamate-induced cell death in a neuronal-derived cell culture model. While originally developed as an activator of the activating transcription factor 6 (ATF6) arm of the unfolded protein response, this AA147-dependent protection against glutamate toxicity is primarily mediated through activation of the NRF2-regulated oxidative stress response. We demonstrate that AA147 activates NRF2 selectively in neuronal-derived cells through a mechanism involving metabolic activation to a reactive electrophile and covalent modification of KEAP1─a mechanism analogous to that involved in the AA147-dependent activation of ATF6. These results define the potential for AA147 to protect against glutamate-induced oxidative toxicity and highlight the potential for metabolically activated proteostasis regulators like AA147 to activate both protective ATF6 and NRF2 stress-responsive signaling pathways to mitigate oxidative damage associated with diverse neurologic diseases.
    DOI:  https://doi.org/10.1021/acschembio.1c00810
  7. Biomed Pharmacother. 2021 Nov 11. pii: S0753-3322(21)01175-6. [Epub ahead of print]145 112389
    DA-9805 protects dopaminergic neurons from endoplasmic reticulum stress and inflammation.
    Sora Kang, Ying Piao, Young Cheol Kang, Suyeol Lim, Youngmi Kim Pak.
      Parkinson's disease (PD) is a multifactorial neurodegenerative disease with damages to mitochondria and endoplasmic reticulum (ER), followed by neuroinflammation. We previously reported that a triple herbal extract DA-9805 in experimental PD toxin-models had neuroprotective effects by alleviating mitochondrial damage and oxidative stress. In the present study, we investigated whether DA-9805 could suppress ER stress and neuroinflammation in vitro and/or in vivo. Pre-treatment with DA-9805 (1 μg/ml) attenuated upregulation of glucose-regulated protein 78 (GRP78), C/EBP homologous protein (CHOP) and cleaved caspase-3 in SH-SY5Y neuroblastoma cells treated with thapsigargin (1 µg/ml) or tunicamycin (2 µg/ml). In addition, DA-9805 prevented the production of IL-1β, IL-6, TNF-α and nitric oxide through inhibition of NF-κB activation in BV2 microglial cells stimulated with lipopolysaccharides (LPS). Intraperitoneal injection of LPS (10 mg/kg) into mice can induce acute neuroinflammation and dopaminergic neuronal cell death. Oral administration of DA-9805 (10 or 30 mg/kg/day for 3 days before LPS injection) prevented loss of dopaminergic neurons and activation of microglia and astrocytes in the substantia nigra in LPS-injected mouse models. Taken together, these results indicate that DA-9805 can effectively prevent ER stress and neuroinflammation, suggesting that DA-9805 is a multitargeting and disease-modifying therapeutic candidate for PD.
    Keywords:  ER stress; Herbal medicine; Mitochondria; Neuroinflammation; Parkinson’s disease
    DOI:  https://doi.org/10.1016/j.biopha.2021.112389
  8. J Am Chem Soc. 2021 Nov 17.
    Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability.
    Nirnay Samanta, Sara S Ribeiro, Mailin Becker, Emeline Laborie, Roland Pollak, Stepan Timr, Fabio Sterpone, Simon Ebbinghaus.
      Stress granules (SGs) are among the most studied membraneless organelles that form upon heat stress (HS) to sequester unfolded, misfolded, or aggregated protein, supporting protein quality control (PQC) clearance. The folding states that are primarily associated with SGs, as well as the function of the phase separated environment in adjusting the energy landscapes, remain unknown. Here, we investigate the association of superoxide dismutase 1 (SOD1) proteins with different folding stabilities and aggregation propensities with condensates in cells, in vitro and by simulation. We find that irrespective of aggregation the folding stability determines the association of SOD1 with SGs in cells. In vitro and in silico experiments however suggest that the increased flexibility of the unfolded state constitutes only a minor driving force to associate with the dynamic biomolecular network of the condensate. Specific protein-protein interactions in the cytoplasm in comparison to SGs determine the partitioning of folding states between the respective phases during HS.
    DOI:  https://doi.org/10.1021/jacs.1c09589
  9. FASEB J. 2021 Dec;35(12): e22041
    Brain-wide cellular mapping of acute stress-induced activation in male and female mice.
    Woonhee Kim, ChiHye Chung.
      Mood disorders are more prevalent and often reported to be more severe in women; however, little is known about the underlying mechanisms of this sexual prevalence. To gain insight into the functional differences in female brains in response to stress, we systemically compared brain activation in male and female C57BL/6N mice after acute stress exposure. We measured c-Fos expression levels in 18 brain areas related to stress responses after a 3-h long restraint stress and found that activation was sexually dimorphic in several brain areas, including the nucleus accumbens, ventral tegmental area, nucleus reuniens, and medial part of the lateral habenula. Moreover, stress-activated a substantial number of cells in the medial prefrontal cortex, amygdala, and lateral part of the lateral habenula; however, the levels of activation were comparable in males and females, suggesting that the core stress responding machineries are largely shared. Pearson correlation analysis revealed several interesting connections between the analyzed areas that are implicated in stress responses and depression. Overall, stress strengthened intra-circuitries in the hippocampus, amygdala, and prefrontal cortex in female mice, whereas more longer-range connections were highlighted in stressed male mice. Our study provides a highly valuable neuroanatomical framework for investigating the circuit mechanism underlying the higher vulnerability to depression in women.
    Keywords:  c-Fos; depression; female; immobilization stress; sex specificity
    DOI:  https://doi.org/10.1096/fj.202101287R
  10. Nat Commun. 2021 Nov 18. 12(1): 6697
    Phosphorylation activates the yeast small heat shock protein Hsp26 by weakening domain contacts in the oligomer ensemble.
    Moritz Mühlhofer, Carsten Peters, Thomas Kriehuber, Marina Kreuzeder, Pamina Kazman, Natalia Rodina, Bernd Reif, Martin Haslbeck, Sevil Weinkauf, Johannes Buchner.
      Hsp26 is a small heat shock protein (sHsp) from S. cerevisiae. Its chaperone activity is activated by oligomer dissociation at heat shock temperatures. Hsp26 contains 9 phosphorylation sites in different structural elements. Our analysis of phospho-mimetic mutations shows that phosphorylation activates Hsp26 at permissive temperatures. The cryo-EM structure of the Hsp26 40mer revealed contacts between the conserved core domain of Hsp26 and the so-called thermosensor domain in the N-terminal part of the protein, which are targeted by phosphorylation. Furthermore, several phosphorylation sites in the C-terminal extension, which link subunits within the oligomer, are sensitive to the introduction of negative charges. In all cases, the intrinsic inhibition of chaperone activity is relieved and the N-terminal domain becomes accessible for substrate protein binding. The weakening of domain interactions within and between subunits by phosphorylation to activate the chaperone activity in response to proteotoxic stresses independent of heat stress could be a general regulation principle of sHsps.
    DOI:  https://doi.org/10.1038/s41467-021-27036-7
  11. Front Cell Dev Biol. 2021 ;9 791967
    Editorial: Ubiquitin Code: From Cell Biology to Translational Medicine.
    Cui Hua Liu, Yu Rao, Daming Gao, Lixin Wan, Lingqiang Zhang.
      
    Keywords:  PROTAC technology; deubiquitination; disease; ubiquitin code; ubiquitination
    DOI:  https://doi.org/10.3389/fcell.2021.791967
  12. Nature. 2021 Nov 15.
    More Alzheimer's drugs head for FDA review: what scientists are watching.
    Asher Mullard.
      
    Keywords:  Alzheimer's disease; Drug discovery; Neurodegeneration; Policy
    DOI:  https://doi.org/10.1038/d41586-021-03410-9
  13. ACS Chem Neurosci. 2021 Nov 17.
    SIRT5 Represses Neurotrophic Pathways and Aβ Production in Alzheimer's Disease by Targeting Autophagy.
    Shanshan Wu, Yafen Wei, Jingxin Li, Yan Bai, Ping Yin, Shun Wang.
      Alzheimer's disease (AD) is the most prevalent neurodegenerative disease in elderly individuals and characterized by impaired cognition and accumulation of β-amyloid (Aβ). Activating autophagy to clear Aβ is a plausible approach for AD treatment. The levels of Aβ and autophagy signaling factors in APP695/PS1-dE9 transgenic (APP/PS1) mice were detected by immuno histological analysis, real-time PCR, and the western blotting assay. The progression of AD was determined by Aβ levels, activated neurons (MAP2+), and microglia (Iba-1+). The learning ability was measured using a Morris water maze. Reactive oxygen species (ROS) production, malondialdehyde (MDA) levels, and mitochondrial superoxide dismutase (SOD) activity were checked to determine oxidative stress. AD mice exhibited impaired autophagy and a decreased level of SIRT5. SIRT5 overexpression promoted autophagy, manifested by elevated Becn1 and ratio of LC3b-II/I, as well as suppressed oxidative stress. The SIRT5-ameliorated neuron damage was correlated with suppressed activation of microglia and astrocytes. Elevated SIRT5 expression decreased the inflammation in AD brains and neurons. Inhibition of autophagy abolished the protective role of SIRT5 in neurons during AD. Our findings suggested that SIRT5 overexpression could ameliorate the progression of AD both in vitro and in vivo through activating autophagy. We presented ectopic expression of SIRT5 as a promising therapeutic approach for AD.
    Keywords:  Alzheimer’s disease; SIRT5; autophagy; oxidative stress
    DOI:  https://doi.org/10.1021/acschemneuro.1c00468
  14. Front Mol Neurosci. 2021 ;14 759729
    Arginine and Arginine-Rich Peptides as Modulators of Protein Aggregation and Cytotoxicity Associated With Alzheimer's Disease.
    Somayra S A Mamsa, Bruno P Meloni.
      A substantial body of evidence indicates cationic, arginine-rich peptides (CARPs) are effective therapeutic compounds for a range of neurodegenerative pathologies, with beneficial effects including the reduction of excitotoxic cell death and mitochondrial dysfunction. CARPs, therefore, represent an emergent class of promising neurotherapeutics with multimodal mechanisms of action. Arginine itself is a known chaotrope, able to prevent misfolding and aggregation of proteins. The putative role of proteopathies in chronic neurodegenerative diseases such as Alzheimer's disease (AD) warrants investigation into whether CARPs could also prevent the aggregation and cytotoxicity of amyloidogenic proteins, particularly amyloid-beta and tau. While monomeric arginine is well-established as an inhibitor of protein aggregation in solution, no studies have comprehensively discussed the anti-aggregatory properties of arginine and CARPs on proteins associated with neurodegenerative disease. Here, we review the structural, physicochemical, and self-associative properties of arginine and the guanidinium moiety, to explore the mechanisms underlying the modulation of protein aggregation by monomeric and multimeric arginine molecules. Arginine-rich peptide-based inhibitors of amyloid-beta and tau aggregation are discussed, as well as further modulatory roles which could reduce proteopathic cytotoxicity, in the context of therapeutic development for AD.
    Keywords:  Alzheimer’s disease; aggregation; amyloid-beta (Aβ); arginine; peptides; tau & phospho-tau protein
    DOI:  https://doi.org/10.3389/fnmol.2021.759729
  15. Nature. 2021 Nov 17.
    Structural insights into Ubr1-mediated N-degron polyubiquitination.
    Man Pan, Qingyun Zheng, Tian Wang, Lujun Liang, Junxiong Mao, Chong Zuo, Ruichao Ding, Huasong Ai, Yuan Xie, Dong Si, Yuanyuan Yu, Lei Liu, Minglei Zhao.
      The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation1. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway2. How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here we developed chemical strategies to mimic the reaction intermediates of the first and second ubiquitin transfer steps, and determined the cryo-electron microscopy structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides, representing the initiation and elongation steps of ubiquitination. Key structural elements, including a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, were identified and characterized. These structures provide mechanistic insights into the initiation and elongation of ubiquitination catalysed by Ubr1.
    DOI:  https://doi.org/10.1038/s41586-021-04097-8
  16. Chem Sci. 2021 Oct 20. 12(40): 13530-13545
    A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics.
    Baishakhi Tikader, Samir K Maji, Sandip Kar.
      Amyloid formation is a generic property of many protein/polypeptide chains. A broad spectrum of proteins, despite having diversity in the inherent precursor sequence and heterogeneity present in the mechanism of aggregation produces a common cross β-spine structure that is often associated with several human diseases. However, a general modeling framework to interpret amyloid formation remains elusive. Herein, we propose a data-driven mathematical modeling approach that elucidates the most probable interaction network for the aggregation of a group of proteins (α-synuclein, Aβ42, Myb, and TTR proteins) by considering an ensemble set of network models, which include most of the mechanistic complexities and heterogeneities related to amyloidogenesis. The best-fitting model efficiently quantifies various timescales involved in the process of amyloidogenesis and explains the mechanistic basis of the monomer concentration dependency of amyloid-forming kinetics. Moreover, the present model reconciles several mutant studies and inhibitor experiments for the respective proteins, making experimentally feasible non-intuitive predictions, and provides further insights about how to fine-tune the various microscopic events related to amyloid formation kinetics. This might have an application to formulate better therapeutic measures in the future to counter unwanted amyloidogenesis. Importantly, the theoretical method used here is quite general and can be extended for any amyloid-forming protein.
    DOI:  https://doi.org/10.1039/d1sc03190b
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