bims-proarb 2022-06-26 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–06–26
twelve papers selected by
Rich Giadone, Harvard University

A biosensor of protein foldedness identifies increased "holdase" activity of chaperones in the nucleus following increased cytosolic protein aggregation.
Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers.
Neuronal Rubicon Represses Extracellular APP/Amyloid β Deposition in Alzheimer's Disease.
HLH-1 Modulates Muscle Proteostasis During Caenorhabditis elegans Larval Development.
Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1α.
Chaperone-Mediated Autophagy and Its Implications for Neurodegeneration and Cancer.
Ketamine-induced neurotoxicity is mediated through endoplasmic reticulum stress in vitro in STHdhQ7/Q7 cells.
Dynamic regulation of ribosome levels and translation during development.
How ubiquitous is aging in vertebrates?
Lipids Reverse Supramolecular Chirality and Reduce Toxicity of Amyloid Fibrils.
Unraveling protein dynamics to understand the brain - the next molecular frontier.
Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis.

J Biol Chem. 2022 Jun 17. pii: S0021-9258(22)00600-7. [Epub ahead of print] 102158

A biosensor of protein foldedness identifies increased "holdase" activity of chaperones in the nucleus following increased cytosolic protein aggregation.

Candice B Raeburn, Angelique R Ormsby, Dezerae Cox, Chloe A Gerak, Christian Makhoul, Nagaraj S Moily, Simon Ebbinghaus, Alex Dickson, Gawain McColl, Danny M Hatters.

  Chaperones and other quality control machinery guard proteins from inappropriate aggregation, which is a hallmark of neurodegenerative diseases. However, how the systems that regulate the 'foldedness' of the proteome remain buffered under stress conditions and in different cellular compartments remains incompletely understood. In this study, we applied a FRET-based strategy to explore how well quality control machinery protects against the misfolding and aggregation of "bait" biosensor proteins, made from the prokaryotic ribonuclease barnase, in the nucleus and cytosol of HEK293T cells. We found those barnase biosensors prone to misfolding, were less engaged by quality control machinery and more prone to inappropriate aggregation in the nucleus as compared to the cytosol, and that these effects could be regulated by chaperone Hsp70-related machinery. Furthermore, aggregation of mutant huntingtin exon 1 protein (Httex1) in the cytosol appeared to outcompete and thus prevented the engagement of quality control machinery with the biosensor in the cytosol. This effect correlated with reduced levels of DNAJB1 and HSPA1A chaperones in the cell outside those sequestered to the aggregates, particularly in the nucleus. Unexpectedly, we found Httex1 aggregation also increased the apparent engagement of the barnase biosensor with quality control machinery in the nucleus suggesting an independent implementation of 'holdase' activity of chaperones other than DNAJB1 and HSPA1A. Collectively these results suggest that proteostasis stress can trigger a rebalancing of chaperone abundance in different subcellular compartments through a dynamic network involving different chaperone-client interactions.

Keywords:  Hsp40; Hsp70; chaperone DnaJ (DnaJ); chaperone DnaK (DnaK); flow cytometry; fluorescence resonance energy transfer (FRET); protein aggregation; protein folding; protein quality control; proteostasis

DOI:  https://doi.org/10.1016/j.jbc.2022.102158
Elife. 2022 Jun 22. pii: e74342. [Epub ahead of print]11

Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers.

Vladislav Belyy, Iratxe Zuazo-Gaztelu, Andrew Alamban, Avi Ashkenazi, Peter Walter.

  Protein folding homeostasis in the endoplasmic reticulum (ER) is regulated by a signaling network, termed the unfolded protein response (UPR). Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident kinase/RNase that mediates signal transmission in the most evolutionarily conserved branch of the UPR. Dimerization and/or higher-order oligomerization of IRE1 are thought to be important for its activation mechanism, yet the actual oligomeric states of inactive, active, and attenuated mammalian IRE1 complexes remain unknown. We developed an automated two-color single-molecule tracking approach to dissect the oligomerization of tagged endogenous human IRE1 in live cells. In contrast to previous models, our data indicate that IRE1 exists as a constitutive homodimer at baseline and assembles into small oligomers upon ER stress. We demonstrate that the formation of inactive dimers and stress-dependent oligomers is fully governed by IRE1's lumenal domain. Phosphorylation of IRE1's kinase domain occurs more slowly than oligomerization and is retained after oligomers disassemble back into dimers. Our findings suggest that assembly of IRE1 dimers into larger oligomers specifically enables trans-autophosphorylation, which in turn drives IRE1's RNase activity.

Keywords:  IRE1; UPR; cell biology; endoplasmic reticulum; human; molecular biophysics; single-molecule; stress signaling; structural biology

DOI:  https://doi.org/10.7554/eLife.74342
Cells. 2022 Jun 07. pii: 1860. [Epub ahead of print]11(12):

Neuronal Rubicon Represses Extracellular APP/Amyloid β Deposition in Alzheimer's Disease.

Sandra Espinoza, Felipe Grunenwald, Wileidy Gomez, Felipe García, Lorena Abarzúa-Catalan, Sebastián Oyarce-Pezoa, Maria Fernanda Hernandez, Bastián I Cortés, Markus Uhrig, Daniela P Ponce, Claudia Durán-Aniotz, Claudio Hetz, Carol D SanMartín, Victor H Cornejo, Fernando Ezquer, Valentina Parra, Maria Isabel Behrens, Patricio A Manque, Diego Rojas-Rivera, René L Vidal, Ute Woehlbier, Melissa Nassif.

  Alzheimer's disease (AD) is the most prevalent age-associated neurodegenerative disease. A decrease in autophagy during aging contributes to brain disorders by accumulating potentially toxic substrates in neurons. Rubicon is a well-established inhibitor of autophagy in all cells. However, Rubicon participates in different pathways depending on cell type, and little information is currently available on neuronal Rubicon's role in the AD context. Here, we investigated the cell-specific expression of Rubicon in postmortem brain samples from AD patients and 5xFAD mice and its impact on amyloid β burden in vivo and neuroblastoma cells. Further, we assessed Rubicon levels in human-induced pluripotent stem cells (hiPSCs), derived from early-to-moderate AD and in postmortem samples from severe AD patients. We found increased Rubicon levels in AD-hiPSCs and postmortem samples and a notable Rubicon localization in neurons. In AD transgenic mice lacking Rubicon, we observed intensified amyloid β burden in the hippocampus and decreased Pacer and p62 levels. In APP-expressing neuroblastoma cells, increased APP/amyloid β secretion in the medium was found when Rubicon was absent, which was not observed in cells depleted of Atg5, essential for autophagy, or Rab27a, required for exosome secretion. Our results propose an uncharacterized role of Rubicon on APP/amyloid β homeostasis, in which neuronal Rubicon is a repressor of APP/amyloid β secretion, defining a new way to target AD and other similar diseases therapeutically.

Keywords:  APP; Alzheimer’s disease; KIAA0226; KIAA0226L; Pacer; RUBCN; Rubicon; autophagy

DOI:  https://doi.org/10.3390/cells11121860
Front Cell Dev Biol. 2022 ;10 920569

HLH-1 Modulates Muscle Proteostasis During Caenorhabditis elegans Larval Development.

Khairun Nisaa, Anat Ben-Zvi.

  Muscle proteostasis is shaped by the myogenic transcription factor MyoD which regulates the expression of chaperones during muscle differentiation. Whether MyoD can also modulate chaperone expression in terminally differentiated muscle cells remains open. Here we utilized a temperature-sensitive (ts) conditional knockdown nonsense mutation in MyoD ortholog in C. elegans, HLH-1, to ask whether MyoD plays a role in maintaining muscle proteostasis post myogenesis. We showed that hlh-1 is expressed during larval development and that hlh-1 knockdown at the first, second, or third larval stages resulted in severe defects in motility and muscle organization. Motility defects and myofilament organization were rescued when the clearance of hlh-1(ts) mRNA was inhibited, and hlh-1 mRNA levels were restored. Moreover, hlh-1 knockdown modulated the expression of chaperones with putative HLH-1 binding sites in their promoters, supporting HLH-1 role in muscle maintenance during larval development. Finally, mild disruption of hlh-1 expression during development resulted in earlier dysregulation of muscle maintenance and function during adulthood. We propose that the differentiation transcription factor, HLH-1, contributes to muscle maintenance and regulates cell-specific chaperone expression post differentiation. HLH-1 may thus impact muscle proteostasis and potentially the onset and manifestation of sarcopenia.

Keywords:  Caenorhabditis elegans (c. elegans); MyoD; chaperone; development; hlh-1; myosin; proteostasis

DOI:  https://doi.org/10.3389/fcell.2022.920569
Elife. 2022 Jun 22. pii: e75580. [Epub ahead of print]11

Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1α.

Silvia Gómez-Puerta, Roberto Ferrero, Tobias Hochstoeger, Ivan Zubiri, Jeffrey Chao, Tomás Aragón, Franka Voigt.

  Endoplasmic reticulum (ER) to nucleus homeostatic signaling, known as the unfolded protein response (UPR), relies on the non-canonical splicing of XBP1 mRNA. The molecular switch that initiates splicing is the oligomerization of the ER stress sensor and UPR endonuclease IRE1α (inositol-requiring enzyme 1 alpha). While IRE1α can form large clusters that have been proposed to function as XBP1 processing centers on the ER, the actual oligomeric state of active IRE1α complexes as well as the targeting mechanism that recruits XBP1 to IRE1α oligomers remains unknown. Here, we have developed a single-molecule imaging approach to monitor the recruitment of individual XBP1 transcripts to the ER surface. Using this methodology, we confirmed that stable ER association of unspliced XBP1 mRNA is established through HR2 (hydrophobic region 2)-dependent targeting and relies on active translation. In addition, we show that IRE1α-catalyzed splicing mobilizes XBP1 mRNA from the ER membrane in response to ER stress. Surprisingly, we find that XBP1 transcripts are not recruited into large IRE1α clusters, which are only observed upon overexpression of fluorescently tagged IRE1α during ER stress. Our findings support a model where ribosome-engaged, immobilized XBP1 mRNA is processed by small IRE1α assemblies that could be dynamically recruited for processing of mRNA transcripts on the ER.

Keywords:  ER; IRE1; XBP1; cell biology; human; imaging; single-molecule; unfolded protein response

DOI:  https://doi.org/10.7554/eLife.75580
Int J Gen Med. 2022 ;15 5635-5649

Chaperone-Mediated Autophagy and Its Implications for Neurodegeneration and Cancer.

Masresha Ahmed Assaye, Solomon T Gizaw.

  Proteostasis, also known as protein homeostasis, is critical for cell survival. Autophagy is a cellular process that degrades and recycles damaged or long-lived proteins, misfolded proteins, and damaged or abnormal organelles in order to preserve homeostasis. Among the three forms of autophagy, chaperone-mediated autophagy (CMA) is distinct from macroautophagy and microautophagy; it does not require the formation of vacuoles and only degrades selected individual proteins. CMA helps to maintain cellular homeostasis by regulating protein quality, bioenergetics, and substrate-associated cellular processes at the right moment. This pathway's dysfunction has been linked to several diseases and disorders. Neurodegenerative diseases and cancer have received the most attention. In various neurodegenerative disorders, especially in their later stages, CMA activity declines. CMA has been shown to act as a tumor suppressor in cancer by destroying specific tumor promoters. Once a tumor has grown, it also helps tumor survival and the metastatic cascade. The presence of changes in CMA in these diseases disorders raises the idea of targeting CMA to restore cellular homeostasis as a potential therapeutic method. Manipulation of CMA activity may be effective therapeutic strategies for treating these diseases. Therefore, in this paper; we introduce the basic processes, regulatory mechanisms, and physiological functions of CMA; evidences supporting the role of impaired CMA function in neurodegeneration and cancer; and the potential of how targeting CMA could be a promising therapeutic method for the two diseases.

Keywords:  autophagy; cancer; chaperone; chaperone-mediated autophagy; lysosome; neurodegeneration; therapy

DOI:  https://doi.org/10.2147/IJGM.S368364
Neurotoxicology. 2022 Jun 18. pii: S0161-813X(22)00095-X. [Epub ahead of print]

Ketamine-induced neurotoxicity is mediated through endoplasmic reticulum stress in vitro in STHdhQ7/Q7 cells.

Nicolette Rigg, Fahed Abu-Hijleh, Vidhi Patel, Ram K Mishra.

  Ketamine has traditionally been used as a dissociative anesthetic agent and more recently as a treatment for treatment-resistant depression. However, there is growing concern over the increased use of ketamine in recreational and therapeutic settings due to the potential neurotoxic effects. Recent studies have demonstrated that ketamine is cytotoxic in several cell types, such as fibroblasts, hepatocytes, uroepithelial cells, and adult induced pluripotent stem cells (iPSCs). Ketamine has been shown to dysregulate calcium signalling, increase reactive oxygen species (ROS) production, and impair mitochondrial function, ultimately leading to apoptosis. However, it is unclear whether endoplasmic reticulum (ER) stress plays a role in ketamine associated neurotoxicity in striatal neurons. Disruption to ER homeostasis can initiate ER-mediated cell death, which has been implicated in several neurodegenerative diseases. Thus, the purpose of this study was to determine whether ketamine's neurotoxic effects involve an ER stress-dependent pathway and to elucidate the underlying mechanisms involved in its neurotoxic effects. Mouse striatal cells were treated with various concentrations of ketamine (10μM, 100μM, 1mM) or DMEM for 9 to 72 hrs. Cell viability was assessed using the MTT assay, and changes in gene expression of ER stress markers were evaluated using RT-qPCR. MTT results revealed that 1mM ketamine decreased cell viability in striatal cells after 24hours of treatment. Gene expression studies complemented these findings such that ketamine upregulated pro-apoptotic ER stress markers, including X-box binding protein 1 (XBP1), activating transcription factor 4 (ATF4), and C/EBP homologous protein (CHOP) and downregulated pro-survival ER stress proteins such as GRP78, MANF and CDNF. Ketamine activated all three stress sensing pathways including PERK, IRE1, and ATF6. Taken together, our results show that ketamine-induced neurotoxicity is mediated through an ER stress-dependent apoptotic pathway.

Keywords:  Endoplasmic Reticulum (ER) Stress; Ketamine; Neurotoxicity; Unfolded Protein Response (UPR)

DOI:  https://doi.org/10.1016/j.neuro.2022.06.004
Semin Cell Dev Biol. 2022 Jun 18. pii: S1084-9521(22)00214-2. [Epub ahead of print]

Dynamic regulation of ribosome levels and translation during development.

Shane M Breznak, Noor M Kotb, Prashanth Rangan.

  The ability of ribosomes to translate mRNAs into proteins is the basis of all life. While ribosomes are essential for cell viability, reduction in levels of ribosomes can affect cell fate and developmental transitions in a tissue specific manner and can cause a plethora of related diseases called ribosomopathies. How dysregulated ribosomes homeostasis influences cell fate and developmental transitions is not fully understood. Model systems such as Drosophila and C. elegans oogenesis have been used to address these questions since defects in conserved steps in ribosome biogenesis result in stem cell differentiation and developmental defects. In this review, we first explore how ribosome levels affect stem cell differentiation. Second, we describe how ribosomal modifications and incorporation of ribosomal protein paralogs contribute to development. Third, we summarize how cells with perturbed ribosome biogenesis are sensed and eliminated during organismal growth.

Keywords:  Differentiation; Germline; Ribosome biogenesis; Stem cells; Translation

DOI:  https://doi.org/10.1016/j.semcdb.2022.06.004
Science. 2022 Jun 24. 376(6600): 1384-1385

How ubiquitous is aging in vertebrates?

Steven N Austad, Caleb E Finch.

Two new studies find little evidence of aging in some turtle species.

DOI: https://doi.org/10.1126/science.adc9442
FEBS J. 2022 Jun 23.

Lipids Reverse Supramolecular Chirality and Reduce Toxicity of Amyloid Fibrils.

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

  Abrupt aggregation of misfolded proteins is a hallmark of many medical pathologies including diabetes type 2, Alzheimer and Parkinson diseases. This results in formation of amyloid fibrils, protein aggregates with distinct supramolecular chirality. A growing body of evidence suggests that lipids can alter rates of protein aggregation. In this study, we investigated whether lipids could alter the supramolecular chirality of amyloid fibrils. We found that if present at the stage of protein aggregation, phospho- and sphingolipids uniquely reversed supramolecular chirality of insulin and lysozyme fibrils. Furthermore, amyloid fibrils with opposite supramolecular chirality exerted distinctly different cell toxicity. Specifically, insulin and lysozyme fibrils with reversed supramolecular chirality were less toxic to cells than the aggregates with normal supramolecular chirality. These findings point on the important role of lipids and supramolecular chirality of amyloid fibrils in the onset and progression of amyloid diseases.

Keywords:  Amyloid fibrils; VCD; insulin; lysozyme; supramolecular chirality; toxicity

DOI:  https://doi.org/10.1111/febs.16564
Mol Neurodegener. 2022 Jun 18. 17(1): 45

Unraveling protein dynamics to understand the brain - the next molecular frontier.

Kyle D Brewer, Sophia M Shi, Tony Wyss-Coray.

  The technological revolution to measure global gene expression at the single-cell level is currently transforming our knowledge of the brain and neurological diseases, leading from a basic understanding of genetic regulators and risk factors to one of more complex gene interactions and biological pathways. Looking ahead, our next challenge will be the reliable measurement and understanding of proteins. We describe in this review how to apply new, powerful methods of protein labeling, tracking, and detection. Recent developments of these methods now enable researchers to uncover protein mechanisms in vivo that may previously have only been hypothesized. These methods are also useful for discovering new biology because how proteins regulate systemic interactions is not well understood in most cases, such as how they travel through the bloodstream to distal targets or cross the blood-brain barrier. Genetic sequencing of DNA and RNA have enabled many great discoveries in the past 20 years, and now, the protein methods described here are creating a more complete picture of how cells to whole organisms function. It is likely that these developments will generate another transformation in biomedical research and our understanding of the brain and will ultimately allow for patient-specific medicine on a protein level.

Keywords:  Bioorthogonal labeling; Blood–brain barrier; Mass spectrometry; Plasma; Protein labeling; Protein tracking; Proteomics

DOI:  https://doi.org/10.1186/s13024-022-00546-8
iScience. 2022 Jun 17. 25(6): 104489

Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis.

Di Xiao, Marissa Caldow, Hani Jieun Kim, Ronnie Blazev, Rene Koopman, Deborah Manandi, Benjamin L Parker, Pengyi Yang.

  Myogenesis is governed by signaling networks that are tightly regulated in a time-dependent manner. Although different protein kinases have been identified, knowledge of the global signaling networks and their downstream substrates during myogenesis remains incomplete. Here, we map the myogenic differentiation of C2C12 cells using phosphoproteomics and proteomics. From these data, we infer global kinase activity and predict the substrates that are involved in myogenesis. We found that multiple mitogen-activated protein kinases (MAPKs) mark the initial wave of signaling cascades. Further phosphoproteomic and proteomic profiling with MAPK1/3 and MAPK8/9 specific inhibitions unveil their shared and distinctive roles in myogenesis. Lastly, we identified and validated the transcription factor nuclear factor 1 X-type (NFIX) as a novel MAPK1/3 substrate and demonstrated the functional impact of NFIX phosphorylation on myogenesis. Altogether, these data characterize the dynamics, interactions, and downstream control of kinase signaling networks during myogenesis on a global scale.

Keywords:  Developmental biology; cell biology; proteomics

DOI:  https://doi.org/10.1016/j.isci.2022.104489