bims-proarb 2022-11-13 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–11–13
eleven papers selected by
Rich Giadone, Harvard University

Differential contributions of the proteasome, autophagy, and chaperones to the clearance of arsenite-induced protein aggregates in yeast.
The Proteostasis Network: A Global Therapeutic Target for Neuroprotection after Spinal Cord Injury.
Lessons Learned from Two Decades of Modeling the Heat-Shock Response.
Modulating autophagy and mitophagy as a promising therapeutic approach in neurodegenerative disorders.
Integration of O-GlcNAc into Stress Response Pathways.
Dynamic SILAC to Determine Protein Turnover in Neurons and Glia.
Small molecules that enhance mitophagy to delay aging and neurodegeneration.
RNA methyltransferase NSun2 deficiency promotes neurodegeneration through epitranscriptomic regulation of tau phosphorylation.
Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models.
Human Induced Pluripotent Stem Cell Phenotyping and Preclinical Modeling of Familial Parkinson's Disease.
Integration of ER protein quality control mechanisms defines β-cell function and ER architecture.

J Biol Chem. 2022 Nov 07. pii: S0021-9258(22)01123-1. [Epub ahead of print] 102680

Differential contributions of the proteasome, autophagy, and chaperones to the clearance of arsenite-induced protein aggregates in yeast.

Sansan Hua, Agnieszka Kłosowska, Joana I Rodrigues, Gabriel Petelski, Lidia A Esquembre, Emma Lorentzon, Lars F Olsen, Krzysztof Liberek, Markus J Tamás.

  The poisonous metalloid arsenite induces widespread misfolding and aggregation of nascent proteins in vivo, and this mode of toxic action might underlie its suspected role in the pathology of certain protein misfolding diseases. Evolutionarily conserved protein quality-control systems protect cells against arsenite-mediated proteotoxicity and herein, we systematically assessed the contribution of the ubiquitin-proteasome system, the autophagy-vacuole pathway, and chaperone-mediated disaggregation to the clearance of arsenite-induced protein aggregates in Saccharomyces cerevisiae. We show that the ubiquitin-proteasome system is the main pathway that clears aggregates formed during arsenite stress and that cells depend on this pathway for optimal growth. The autophagy-vacuole pathway and chaperone-mediated disaggregation both contribute to clearance, but their roles appear less prominent than the ubiquitin-proteasome system. Our in vitro assays with purified components of the yeast disaggregating machinery demonstrated that chaperone binding to aggregates formed in the presence of arsenite is impaired. Hsp104 and Hsp70 chaperone activity was unaffected by arsenite, suggesting that this metalloid influences aggregate structure, making them less accessible for chaperone-mediated disaggregation. We further show that the defect in chaperone-mediated refolding of a model protein was abrogated in a cysteine-free version of the substrate, suggesting that arsenite directly modifies cysteines in non-native target proteins. In conclusion, our study sheds novel light on the differential contributions of protein quality-control systems to aggregate clearance and cell proliferation, and extends our understanding of how these systems operate during arsenite stress.

Keywords:  Hsp104; Hsp70; arsenite; protein aggregation; protein degradation; ubiquitin proteasome pathway

DOI:  https://doi.org/10.1016/j.jbc.2022.102680
Cells. 2022 Oct 22. pii: 3339. [Epub ahead of print]11(21):

The Proteostasis Network: A Global Therapeutic Target for Neuroprotection after Spinal Cord Injury.

Scott R Whittemore, Sujata Saraswat Ohri, Michael D Forston, George Z Wei, Michal Hetman.

  Proteostasis (protein homeostasis) is critical for cellular as well as organismal survival. It is strictly regulated by multiple conserved pathways including the ubiquitin-proteasome system, autophagy, the heat shock response, the integrated stress response, and the unfolded protein response. These overlapping proteostasis maintenance modules respond to various forms of cellular stress as well as organismal injury. While proteostasis restoration and ultimately organism survival is the main evolutionary driver of such a regulation, unresolved disruption of proteostasis may engage pro-apoptotic mediators of those pathways to eliminate defective cells. In this review, we discuss proteostasis contributions to the pathogenesis of traumatic spinal cord injury (SCI). Most published reports focused on the role of proteostasis networks in acute/sub-acute tissue damage post-SCI. Those reports reveal a complex picture with cell type- and/or proteostasis mediator-specific effects on loss of neurons and/or glia that often translate into the corresponding modulation of functional recovery. Effects of proteostasis networks on such phenomena as neuro-repair, post-injury plasticity, as well as systemic manifestations of SCI including dysregulation of the immune system, metabolism or cardiovascular function are currently understudied. However, as potential interventions that target the proteostasis networks are expected to impact many cell types across multiple organ systems that are compromised after SCI, such therapies could produce beneficial effects across the wide spectrum of highly variable human SCI.

Keywords:  ER stress; cell death; neurons; neuroprotection; neurotrauma; oligodendrocytes; proteostasis; spinal cord injury; white matter

DOI:  https://doi.org/10.3390/cells11213339
Biomolecules. 2022 Nov 07. pii: 1645. [Epub ahead of print]12(11):

Lessons Learned from Two Decades of Modeling the Heat-Shock Response.

Ayush Ranawade, Rati Sharma, Erel Levine.

  The Heat Shock Response (HSR) is a highly conserved genetic system charged with protecting the proteome in a wide range of organisms and species. Experiments since the early 1980s have elucidated key elements in these pathways and revealed a canonical mode of regulation, which relies on a titration feedback. This system has been subject to substantial modeling work, addressing questions about resilience, design and control. The compact core regulatory circuit, as well as its apparent conservation, make this system an ideal 'hydrogen atom' model for the regulation of stress response. Here we take a broad view of the models of the HSR, focusing on the different questions asked and the approaches taken. After 20 years of modeling work, we ask what lessons had been learned that would have been hard to discover without mathematical models. We find that while existing models lay strong foundations, many important questions that can benefit from quantitative modeling are still awaiting investigation.

Keywords:  differential equations; heat shock factor; heat shock proteins; heat shock response; mathematical modelling; sensitivity analysis

DOI:  https://doi.org/10.3390/biom12111645
Life Sci. 2022 Nov 04. pii: S0024-3205(22)00853-0. [Epub ahead of print] 121153

Modulating autophagy and mitophagy as a promising therapeutic approach in neurodegenerative disorders.

Jayapriya Mishra, Gurjit Kaur Bhatti, Abhishek Sehrawat, Charan Singh, Arti Singh, Arubala P Reddy, P Hemachandra Reddy, Jasvinder Singh Bhatti.

  The high prevalence of neurodegenerative diseases has become a major public health challenge and is associated with a tremendous burden on individuals, society and federal governments worldwide. Protein misfolding and aggregation are the major pathological hallmarks of several neurodegenerative disorders. The cells have evolved several regulatory mechanisms to deal with aberrant protein folding, namely the classical ubiquitin pathway, where ubiquitination of protein aggregates marks their degradation via lysosome and the novel autophagy or mitophagy pathways. Autophagy is a catabolic process in eukaryotic cells that allows the lysosome to recycle the cell's own contents, such as organelles and proteins, known as autophagic cargo. Their most significant role is to keep cells alive in distressed situations. Mitophagy is also crucial for reducing abnormal protein aggregation and increasing organelle clearance and partly accounts for maintaining cellular homeostasis. Furthermore, substantial data indicate that any disruption in these homeostatic mechanisms leads to the emergence of several age-associated metabolic and neurodegenerative diseases. So, targeting autophagy and mitophagy might be a potential therapeutic strategy for a variety of health conditions.

Keywords:  Aggregation; Autophagic cargo; Autophagy; Functional foods; Homeostasis; Misfolding; Mitophagy; Neurodegenerative disorders

DOI:  https://doi.org/10.1016/j.lfs.2022.121153
Cells. 2022 Nov 05. pii: 3509. [Epub ahead of print]11(21):

Integration of O-GlcNAc into Stress Response Pathways.

Kamau M M Fahie, Kyriakos N Papanicolaou, Natasha E Zachara.

  The modification of nuclear, mitochondrial, and cytosolic proteins by O-linked βN-acetylglucosamine (O-GlcNAc) has emerged as a dynamic and essential post-translational modification of mammalian proteins. O-GlcNAc is cycled on and off over 5000 proteins in response to diverse stimuli impacting protein function and, in turn, epigenetics and transcription, translation and proteostasis, metabolism, cell structure, and signal transduction. Environmental and physiological injury lead to complex changes in O-GlcNAcylation that impact cell and tissue survival in models of heat shock, osmotic stress, oxidative stress, and hypoxia/reoxygenation injury, as well as ischemic reperfusion injury. Numerous mechanisms that appear to underpin O-GlcNAc-mediated survival include changes in chaperone levels, impacts on the unfolded protein response and integrated stress response, improvements in mitochondrial function, and reduced protein aggregation. Here, we discuss the points at which O-GlcNAc is integrated into the cellular stress response, focusing on the roles it plays in the cardiovascular system and in neurodegeneration.

Keywords:  O-GlcNAc; chaperone; glycosylation; stress

DOI:  https://doi.org/10.3390/cells11213509
Methods Mol Biol. 2023 ;2603 1-17

Dynamic SILAC to Determine Protein Turnover in Neurons and Glia.

Aline R Dörrbaum, Erin M Schuman, Julian D Langer.

  Cellular protein turnover-the net result of protein synthesis and degradation-is crucial to maintain protein homeostasis and cellular function under steady-state conditions and to enable cells to remodel their proteomes upon a perturbation. In brain cells, proteins are continuously turned over at different rates depending on various factors including cell type, subcellular localization, cellular environment, and neuronal activity. Here we describe a workflow for the analysis of protein synthesis, degradation, and turnover in primary cultured rat neurons and glia using dynamic/pulsed SILAC and mass spectrometry.

Keywords:  Dynamic SILAC; Glia; Mass spectrometry; Neurons; Protein degradation; Protein synthesis; Protein turnover; SILAC

DOI:  https://doi.org/10.1007/978-1-0716-2863-8_1
J Cardiovasc Aging. 2022 Oct;pii: 45. [Epub ahead of print]2(4):

Small molecules that enhance mitophagy to delay aging and neurodegeneration.

Gerald W Dorn.

DOI: https://doi.org/10.20517/jca.2022.36
Acta Neuropathol. 2022 Nov 10.

RNA methyltransferase NSun2 deficiency promotes neurodegeneration through epitranscriptomic regulation of tau phosphorylation.

Yoon A Kim, Tohid Siddiqui, Jennifer Blaze, Mehmet Ilyas Cosacak, Tristan Winters, Atul Kumar, Ellen Tein, Andrew A Sproul, Andrew F Teich, Francesca Bartolini, Schahram Akbarian, Caghan Kizil, Gunnar Hargus, Ismael Santa-Maria.

  Epitranscriptomic regulation adds a layer of post-transcriptional control to brain function during development and adulthood. The identification of RNA-modifying enzymes has opened the possibility of investigating the role epitranscriptomic changes play in the disease process. NOP2/Sun RNA methyltransferase 2 (NSun2) is one of the few known brain-enriched methyltransferases able to methylate mammalian non-coding RNAs. NSun2 loss of function due to autosomal-recessive mutations has been associated with neurological abnormalities in humans. Here, we show NSun2 is expressed in adult human neurons in the hippocampal formation and prefrontal cortex. Strikingly, we unravel decreased NSun2 protein expression and an increased ratio of pTau/NSun2 in the brains of patients with Alzheimer's disease (AD) as demonstrated by Western blotting and immunostaining, respectively. In a well-established Drosophila melanogaster model of tau-induced toxicity, reduction of NSun2 exacerbated tau toxicity, while overexpression of NSun2 partially abrogated the toxic effects. Conditional ablation of NSun2 in the mouse brain promoted a decrease in the miR-125b m6A levels and tau hyperphosphorylation. Utilizing human induced pluripotent stem cell (iPSC)-derived neuronal cultures, we confirmed NSun2 deficiency results in tau hyperphosphorylation. We also found that neuronal NSun2 levels decrease in response to amyloid-beta oligomers (AβO). Notably, AβO-induced tau phosphorylation and cell toxicity in human neurons could be rescued by overexpression of NSun2. Altogether, these results indicate that neuronal NSun2 deficiency promotes dysregulation of miR-125b and tau phosphorylation in AD and highlights a novel avenue for therapeutic targeting.

Keywords:  Alzheimer’s disease; Methylation; MicroRNA; NSun2; Neurodegeneration; Tau phosphorylation

DOI:  https://doi.org/10.1007/s00401-022-02511-7
Int J Mol Sci. 2022 Nov 03. pii: 13428. [Epub ahead of print]23(21):

Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models.

Igor Sedov, Diliara Khaibrakhmanova.

  Inhibition of fibril formation is considered a possible treatment strategy for amyloid-related diseases. Understanding the molecular nature of inhibitor action is crucial for the design of drug candidates. In the present review, we describe the common kinetic models of fibril formation and classify known inhibitors by the mechanism of their interactions with the aggregating protein and its oligomers. This mechanism determines the step or steps of the aggregation process that become inhibited and the observed changes in kinetics and equilibrium of fibril formation. The results of numerous studies indicate that possible approaches to antiamyloid inhibitor discovery include the search for the strong binders of protein monomers, cappers blocking the ends of the growing fibril, or the species absorbing on the surface of oligomers preventing nucleation. Strongly binding inhibitors stabilizing the native state can be promising for the structured proteins while designing the drug candidates targeting disordered proteins is challenging.

Keywords:  Alzheimer’s disease; amyloid fibrils; drug discovery; fibril formation inhibitors; kinetic models; protein aggregation kinetics; protein misfolding; protein–ligand interactions; protein–protein interactions

DOI:  https://doi.org/10.3390/ijms232113428
Genes (Basel). 2022 Oct 25. pii: 1937. [Epub ahead of print]13(11):

Human Induced Pluripotent Stem Cell Phenotyping and Preclinical Modeling of Familial Parkinson's Disease.

Jeffrey Kim, Etienne W Daadi, Thomas Oh, Elyas S Daadi, Marcel M Daadi.

  Parkinson's disease (PD) is primarily idiopathic and a highly heterogenous neurodegenerative disease with patients experiencing a wide array of motor and non-motor symptoms. A major challenge for understanding susceptibility to PD is to determine the genetic and environmental factors that influence the mechanisms underlying the variations in disease-associated traits. The pathological hallmark of PD is the degeneration of dopaminergic neurons in the substantia nigra pars compacta region of the brain and post-mortem Lewy pathology, which leads to the loss of projecting axons innervating the striatum and to impaired motor and cognitive functions. While the cause of PD is still largely unknown, genome-wide association studies provide evidence that numerous polymorphic variants in various genes contribute to sporadic PD, and 10 to 15% of all cases are linked to some form of hereditary mutations, either autosomal dominant or recessive. Among the most common mutations observed in PD patients are in the genes LRRK2, SNCA, GBA1, PINK1, PRKN, and PARK7/DJ-1. In this review, we cover these PD-related mutations, the use of induced pluripotent stem cells as a disease in a dish model, and genetic animal models to better understand the diversity in the pathogenesis and long-term outcomes seen in PD patients.

Keywords:  Parkinson’s disease; brain organoids; genetic basis for pathophysiology; in vitro models of familial Parkinson’s disease; induced pluripotent stem cells; personalized medicine

DOI:  https://doi.org/10.3390/genes13111937
J Clin Invest. 2022 Nov 08. pii: e163584. [Epub ahead of print]

Integration of ER protein quality control mechanisms defines β-cell function and ER architecture.

Neha Shrestha, Mauricio Torres, Jason Zhang, You Lu, Leena Haataja, Rachel B Reinert, Jeffrey Knupp, Yu-Jie Chen, Gunes Parlakgul, Ana Paula Arruda, Billy Tsai, Peter Arvan, Ling Qi.

  Three principal ER quality-control mechanisms, namely, unfolded protein response (UPR), ER-associated degradation (ERAD) and ER-phagy are each important for the maintenance of ER homeostasis, yet how they are integrated to regulate ER homeostasis and organellar architecture in vivo is largely unclear. Here we report intricate crosstalk among the three pathways, centered around the SEL1L-HRD1 protein complex of ERAD, in the regulation of organellar organization in β-cells. SEL1L-HRD1 ERAD deficiency in β-cells triggers activation of autophagy via IRE1α [an endogenous ERAD substrate]. In the absence of functional SEL1L-HRD1 ERAD, proinsulin is retained in the ER as high molecular weight conformers, which are subsequently cleared via ER-phagy. A combined loss of both SEL1L and autophagy in β-cells leads to diabetes in mice shortly after weaning, with premature death by ~11 weeks of age, associated with marked ER retention of proinsulin and β-cell loss. Using focus-ion beam scanning electron microscopy (FIB-SEM) powered by deep-learning automated image segmentation and 3D reconstruction, our data demonstrate a profound organellar restructuring with a massive expansion of ER volume and network in β-cells lacking both SEL1L and autophagy. These data reveal at an unprecedented detail the intimate crosstalk among the three ER quality-control mechanisms in the dynamic regulation of organellar architecture and β-cell function.

Keywords:  Autophagy; Cell Biology; Diabetes; Metabolism; Protein misfolding

DOI:  https://doi.org/10.1172/JCI163584