bims-proarb 2022-09-18 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–09–18
seven papers selected by
Rich Giadone, Harvard University

The disturbance of protein synthesis/degradation homeostasis is a common trait of age-related neurodegenerative disorders.
Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates.
A systems biological analysis of the ATF4-GADD34-CHOP regulatory triangle upon endoplasmic reticulum stress.
The C. elegans Observatory: High-throughput exploration of behavioral aging.
Lipids uniquely alter secondary structure and toxicity of lysozyme aggregates.
Toward high-throughput oligomer detection and classification for early-stage aggregation of amyloidogenic protein.
Mesenchymal stem cells derived from patients with premature aging syndromes display hallmarks of physiological aging.

Adv Protein Chem Struct Biol. 2022 ;pii: S1876-1623(22)00050-5. [Epub ahead of print]132 49-87

The disturbance of protein synthesis/degradation homeostasis is a common trait of age-related neurodegenerative disorders.

Fabio Di Domenico, Chiara Lanzillotta.

  Protein homeostasis or "proteostasis" represent the process that regulates the balance of the intracellular functional and "healthy" proteins. Proteostasis is fundamental to preserve physiological metabolic processes in the cell and it allow to respond to any given stimulus as the expression of components of the proteostasis network is customized according to the proteomic demands of different cellular environments. In conditions that promote unfolding/misfolding of proteins chaperones act as signaling molecules inducing extreme measures to either fix the problem or destroy unfolded proteins. When the chaperone machinery fails under pathological insults unfolded proteins induce the endoplasmic reticulum (ER) stress activating the unfolded protein response (UPR) machinery. The activation of the UPR restores ER proteostasis primarily through the transcriptional remodeling of ER protein folding, trafficking, and degradation pathways, such as the ubiquitin proteasome system (UPS). If these mechanisms do not manage to clear the aberrant proteins, proteasome overload and become defective, and misfolded proteins may form aggregates thus extending the UPR mechanism. These aggregates are then attempted to be cleared by macroautophagy. Impaired proteostasis promote the accumulation of misfolded proteins that exacerbate the damage to chaperones, surveillance systems and/or degradative activities. Remarkably, the removal of toxic misfolded proteins is critical for all cells, but it is especially significant in neurons since these cannot be readily replaced. In neurons, the maintenance of efficient proteostasis is essential to healthy aging since the dysregulation of the proteostasis network can lead to neurodegenerative disease. Each of these brain pathologies is characterized by the repeated misfolding of one of more peculiar proteins, which evade both the protein folding machinery and cellular degradation mechanisms and begins to form aggregates that nucleate out into large fibrillar aggregates. In this chapter we describe the mechanisms, associated with faulty proteostasis, that promote the formation of protein aggregates, amyloid fibrils, intracellular, and extracellular inclusions in the most common nondegenerative disorders also referred to as protein misfolding disorders.

Keywords:  Alzheimer's disease; Amyotrophic lateral sclerosis; Autophagy; Chaperones; Parkinson's disease; Proteostasis; Ubiquitin proteasome system; Unfolded protein response

DOI:  https://doi.org/10.1016/bs.apcsb.2022.05.008
J Biol Chem. 2022 Sep 09. pii: S0021-9258(22)00919-X. [Epub ahead of print] 102476

Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates.

Kara L Schneider, Doryaneh Ahmadpour, Katharina S Keuenhof, Anna-Maria Eisele-Bürger, Lisa Larsson Berglund, Frederik Eisele, Roja Babazadeh, Johanna L Höög, Thomas Nyström, Per O Widlund.

  The accumulation of misfolded proteins is a hallmark of aging and many neurodegenerative diseases, making it important to understand how the cellular machinery recognizes and processes such proteins. A key question in this respect is whether misfolded proteins are handled in a similar way regardless of their genetic origin. To approach this question, we compared how three different misfolded proteins, guk1-7, gus1-3 and pro3-1, are handled by the cell. We show that all three are non-toxic, even though highly overexpressed, highlighting their usefulness in analyzing the cellular response to misfolding in the absence of severe stress. We found significant differences between the aggregation and disaggregation behavior of the misfolded proteins. Specifically, gus1-3 formed some aggregates that did not efficiently recruit the protein disaggregase Hsp104 and did not co-localize with the other misfolded reporter proteins. Strikingly, while all three misfolded proteins generally co-aggregated and co-localized to specific sites in the cell, disaggregation was notably different; the rate of aggregate clearance of pro3-1 was faster than that of the other misfolded proteins, and its clearance rate was not hindered when pro3-1 co-localized with a slowly resolved misfolded protein. Finally, we observed using super-resolution light microscopy as well as immunogold labeling electron microscopy both showed an even distribution of the different misfolded proteins within an inclusion, suggesting that misfolding characteristics and remodeling, rather than spatial compartmentalization, allows for differential clearance of these misfolding reporters residing in the same inclusion. Taken together, our results highlight how properties of misfolded proteins can significantly affect processing.

Keywords:  Saccharomyces cerevisiae; chaperone; heat shock; protein aggregation; protein misfolding; proteostasis; spatial protein quality control; yeast

DOI:  https://doi.org/10.1016/j.jbc.2022.102476
FEBS Open Bio. 2022 Sep 13.

A systems biological analysis of the ATF4-GADD34-CHOP regulatory triangle upon endoplasmic reticulum stress.

Margita Márton, Gábor Bánhegyi, Norbert Gyöngyösi, Eszter Éva Kálmán, Aladár Pettkó-Szandtner, Krisztina Káldi, Orsolya Kapuy.

  Endoplasmic reticulum stress-dependent accumulation of incorrectly folded proteins leads to activation of the unfolded protein response. The role of the UPR is to avoid cell damage and restore the homeostatic state by autophagy; however, excessive ER stress results in apoptosis. Here, we investigated the ER stress-dependent feedback loops inside one of the UPR branches by focusing on PERK-induced ATF4 and its two targets, called CHOP and GADD34. Our goal was to qualitatively describe the dynamic behaviour of the system by exploring the key regulatory motifs using both molecular and theoretical biological techniques. Using the HEK293T cell line as a model system, we confirmed that the life-or-death decision is strictly regulated. We investigated the dynamic characteristics of the crucial elements of the PERK pathway at both the RNA and protein level upon tolerable and excessive levels of ER stress. Of particular note, inhibition of GADD34 or CHOP resulted in various phenotypes upon high levels of ER stress. Our computer simulations suggest the existence of two new feedback loops inside the UPR. First, GADD34 seems to have a positive effect on ATF4 activity, while CHOP inhibits it. We claim that these newly described feedback loops ensure the fine-tuning of the ATF4-dependent stress response mechanism of the cell.

Keywords:  ATF4-GADD34-CHOP; PERK pathway; endoplasmic reticulum stress; feedback loop; systems biology; unfolded protein response

DOI:  https://doi.org/10.1002/2211-5463.13484
Front Aging. 2022 ;3 932656

The C. elegans Observatory: High-throughput exploration of behavioral aging.

Rex A Kerr, Antoine E Roux, Jérôme Goudeau, Cynthia Kenyon.

  Organisms undergo a variety of characteristic changes as they age, suggesting a substantial commonality in the mechanistic basis of aging. Experiments in model organisms have revealed a variety of cellular systems that impact lifespan, but technical challenges have prevented a comprehensive evaluation of how these components impact the trajectory of aging, and many components likely remain undiscovered. To facilitate the deeper exploration of aging trajectories at a sufficient scale to enable primary screening, we have created the Caenorhabditis elegans Observatory, an automated system for monitoring the behavior of group-housed C. elegans throughout their lifespans. One Observatory consists of a set of computers running custom software to control an incubator containing custom imaging and motion-control hardware. In its standard configuration, the Observatory cycles through trays of standard 6 cm plates, running four assays per day on up to 576 plates per incubator. High-speed image processing captures a range of behavioral metrics, including movement speed and stimulus-induced turning, and a data processing pipeline continuously computes summary statistics. The Observatory software includes a web interface that allows the user to input metadata and view graphs of the trajectory of behavioral aging as the experiment unfolds. Compared to the manual use of a plate-based C. elegans tracker, the Observatory reduces the effort required by close to two orders of magnitude. Within the Observatory, reducing the function of known lifespan genes with RNA interference (RNAi) gives the expected phenotypic changes, including extended motility in daf-2(RNAi) and progeria in hsf-1(RNAi). Lifespans scored manually from worms raised in conventional conditions match those scored from images captured by the Observatory. We have used the Observatory for a small candidate-gene screen and identified an extended youthful vigor phenotype for tank-1(RNAi) and a progeric phenotype for cdc-42(RNAi). By utilizing the Observatory, it is now feasible to conduct whole-genome screens for an aging-trajectory phenotype, thus greatly increasing our ability to discover and analyze new components of the aging program.

Keywords:  C. elegans; aging; automation; behavior; lifespan

DOI:  https://doi.org/10.3389/fragi.2022.932656
FASEB J. 2022 10;36(10): e22543

Lipids uniquely alter secondary structure and toxicity of lysozyme aggregates.

Mikhail Matveyenka, Kiryl Zhaliazka, Stanislav Rizevsky, Dmitry Kurouski.

  Abrupt aggregation of misfolded proteins is a hallmark of the large group of amyloid pathologies that include diabetes type 2, Alzheimer and Parkinson's diseases. Protein aggregation yields oligomers and fibrils, β-sheet-rich structures that exert cell toxicity. Microscopic examination of amyloid deposits reveals the presence of lipids membranes, which suggests that lipids can be involved in the process of pathogenic protein assembly. In this study, we show that lipids can uniquely alter the aggregation rates of lysozyme, a protein that is associated with systemic amyloidosis. Specifically, cardiolipin (CL), ceramide (CER), and sphingomyelin (SM) accelerate, phosphatidylcholine (PC) strongly inhibits, whereas phosphatidylserine (PS) has no effect on the rate of protein aggregation. Furthermore, lipids uniquely alter the secondary structure of lysozyme aggregates. Furthermore, we found that lysozyme aggregates grown in the presence of CL, CER, SM, PS, and CL:PC mixtures exert significantly lower production of reactive oxygen species and mitochondrial dysfunction compared to lysozyme:PC aggregates and lysozyme fibrils grown in the lipid-free environment. These findings suggest that a change in the lipid composition of cell membranes, which is taken place upon neurodegeneration, may trigger the formation of toxic protein species that otherwise would not be formed.

Keywords:  AFM-IR; ROS; amyloid aggregates; lipids; lysozyme; toxicity

DOI:  https://doi.org/10.1096/fj.202200841R
Front Chem. 2022 ;10 967882

Toward high-throughput oligomer detection and classification for early-stage aggregation of amyloidogenic protein.

Bogachan Tahirbegi, Alastair J Magness, Maria Elena Piersimoni, Xiangyu Teng, James Hooper, Yuan Guo, Thomas Knöpfel, Keith R Willison, David R Klug, Liming Ying.

  Aggregation kinetics of proteins and peptides have been studied extensively due to their significance in many human diseases, including neurodegenerative disorders, and the roles they play in some key physiological processes. However, most of these studies have been performed as bulk measurements using Thioflavin T or other fluorescence turn-on reagents as indicators of fibrillization. Such techniques are highly successful in making inferences about the nucleation and growth mechanism of fibrils, yet cannot directly measure assembly reactions at low protein concentrations which is the case for amyloid-β (Aβ) peptide under physiological conditions. In particular, the evolution from monomer to low-order oligomer in early stages of aggregation cannot be detected. Single-molecule methods allow direct access to such fundamental information. We developed a high-throughput protocol for single-molecule photobleaching experiments using an automated fluorescence microscope. Stepwise photobleaching analysis of the time profiles of individual foci allowed us to determine stoichiometry of protein oligomers and probe protein aggregation kinetics. Furthermore, we investigated the potential application of supervised machine learning with support vector machines (SVMs) as well as multilayer perceptron (MLP) artificial neural networks to classify bleaching traces into stoichiometric categories based on an ensemble of measurable quantities derivable from individual traces. Both SVM and MLP models achieved a comparable accuracy of more than 80% against simulated traces up to 19-mer, although MLP offered considerable speed advantages, thus making it suitable for application to high-throughput experimental data. We used our high-throughput method to study the aggregation of Aβ40 in the presence of metal ions and the aggregation of α-synuclein in the presence of gold nanoparticles.

Keywords:  amyloid-β; artificial neural network; fluorescence imaging; machine learning; neurodegenerative disease; protein aggregation; single-molecule photobleaching; α-synuclein

DOI:  https://doi.org/10.3389/fchem.2022.967882
Life Sci Alliance. 2022 Dec;pii: e202201501. [Epub ahead of print]5(12):

Mesenchymal stem cells derived from patients with premature aging syndromes display hallmarks of physiological aging.

Jean Philippe Trani, Raphaël Chevalier, Leslie Caron, Claire El Yazidi, Natacha Broucqsault, Léa Toury, Morgane Thomas, Karima Annab, Bernard Binetruy, Annachiara De Sandre-Giovannoli, Nicolas Levy, Frédérique Magdinier, Jérôme D Robin.

Progeroid syndromes are rare genetic diseases with most of autosomal dominant transmission, the prevalence of which is less than 1/10,000,000. These syndromes caused by mutations in the LMNA gene encoding A-type lamins belong to a group of disorders called laminopathies. Lamins are implicated in the architecture and function of the nucleus and chromatin. Patients affected with progeroid laminopathies display accelerated aging of mesenchymal stem cells (MSCs)-derived tissues associated with nuclear morphological abnormalities. To identify pathways altered in progeroid patients' MSCs, we used induced pluripotent stem cells (hiPSCs) from patients affected with classical Hutchinson-Gilford progeria syndrome (HGPS, c.1824C>T-p.G608G), HGPS-like syndrome (HGPS-L; c.1868C>G-p.T623S) associated with farnesylated prelamin A accumulation, or atypical progeroid syndromes (APS; homozygous c.1583C> T-p.T528M; heterozygous c.1762T>C-p.C588R; compound heterozygous c.1583C>T and c.1619T>C-p.T528M and p.M540T) without progerin accumulation. By comparative analysis of the transcriptome and methylome of hiPSC-derived MSCs, we found that patient's MSCs display specific DNA methylation patterns and modulated transcription at early stages of differentiation. We further explored selected biological processes deregulated in the presence of LMNA variants and confirmed alterations of age-related pathways during MSC differentiation. In particular, we report the presence of an altered mitochondrial pattern; an increased response to double-strand DNA damage; and telomere erosion in HGPS, HGPS-L, and APS MSCs, suggesting converging pathways, independent of progerin accumulation, but a distinct DNA methylation profile in HGPS and HGPS-L compared with APS cells.

DOI: https://doi.org/10.26508/lsa.202201501