bims-proarb 2022-03-20 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–03–20
eightteen papers selected by
Rich Giadone, Harvard University

The Unfolded Protein Responses in Health, Aging, and Neurodegeneration: Recent Advances and Future Considerations.
Activation of the UPR sensor ATF6α is regulated by its redox-dependent dimerization and ER retention by ERp18.
Cryptic elements of the heat-shock response.
Minocycline treatment improves proteostasis during Drosophila aging via autophagy mediated by FOXO and Hsp70.
Endoplasmic reticulum-unfolded protein response pathway modulates the cellular response to mitochondrial proteotoxic stress.
Hsp104 N-terminal Domain Interaction with Substrates Plays a Regulatory Role in Protein Disaggregation.
The effect of gestational age on mitochondrial properties of the mouse placenta.
Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells.
The needs of a synapse-How local organelles serve synaptic proteostasis.
Insights on Human Small Heat Shock Proteins and Their Alterations in Diseases.
Organelle dysfunction upon asrij depletion causes aging-like changes in mouse hematopoietic stem cells.
Aging impact on amyloid precursor protein neuronal trafficking.
Inhibition of unfolded protein response prevents post-anesthesia neuronal hyperactivity and synapse loss in aged mice.
A trio of ubiquitin ligases sequentially drives ubiquitylation and autophagic degradation of dysfunctional yeast proteasomes.
Editorial: Amyloid-Membrane Interactions in Protein Misfolding Disorders: From Basic Mechanisms to Therapy.
Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers.
Single-molecule fluorescence imaging and deep learning reveal highly heterogeneous aggregation of amyloid-β 42.
Clusterin in Alzheimer's disease: An amyloidogenic inhibitor of amyloid formation?

Front Mol Neurosci. 2022 ;15 831116

The Unfolded Protein Responses in Health, Aging, and Neurodegeneration: Recent Advances and Future Considerations.

Andrew P K Wodrich, Andrew W Scott, Arvind Kumar Shukla, Brent T Harris, Edward Giniger.

  Aging and age-related neurodegeneration are both associated with the accumulation of unfolded and abnormally folded proteins, highlighting the importance of protein homeostasis (termed proteostasis) in maintaining organismal health. To this end, two cellular compartments with essential protein folding functions, the endoplasmic reticulum (ER) and the mitochondria, are equipped with unique protein stress responses, known as the ER unfolded protein response (UPR ER ) and the mitochondrial UPR (UPR mt ), respectively. These organellar UPRs play roles in shaping the cellular responses to proteostatic stress that occurs in aging and age-related neurodegeneration. The loss of adaptive UPR ER and UPR mt signaling potency with age contributes to a feed-forward cycle of increasing protein stress and cellular dysfunction. Likewise, UPR ER and UPR mt signaling is often altered in age-related neurodegenerative diseases; however, whether these changes counteract or contribute to the disease pathology appears to be context dependent. Intriguingly, altering organellar UPR signaling in animal models can reduce the pathological consequences of aging and neurodegeneration which has prompted clinical investigations of UPR signaling modulators as therapeutics. Here, we review the physiology of both the UPR ER and the UPR mt , discuss how UPR ER and UPR mt signaling changes in the context of aging and neurodegeneration, and highlight therapeutic strategies targeting the UPR ER and UPR mt that may improve human health.

Keywords:  aging; endoplasmic reticulum unfolded protein response; mitochondrial unfolded protein response (UPRmt); neurodegeneration; unfolded protein response (UPR)

DOI:  https://doi.org/10.3389/fnmol.2022.831116
Proc Natl Acad Sci U S A. 2022 Mar 22. 119(12): e2122657119

Activation of the UPR sensor ATF6α is regulated by its redox-dependent dimerization and ER retention by ERp18.

Ojore Benedict Valentine Oka, Arvin Shedrach Pierre, Marie Anne Pringle, Wanida Tungkum, Zhenbo Cao, Bethany Fleming, Neil John Bulleid.

  SignificanceMembrane and secretory proteins are synthesized in the endoplasmic reticulum (ER). Perturbations to ER function disrupts protein folding, causing misfolded proteins to accumulate, a condition known as ER stress. Cells adapt to stress by activating the unfolded protein response (UPR), which ultimately restores proteostasis. A key player in the UPR response is ATF6α, which requires release from ER retention and modulation of its redox status during activation. Here, we report that ER stress promotes formation of a specific ATF6α dimer, which is preferentially trafficked to the Golgi for processing. We show that ERp18 regulates ATF6α by mitigating its dimerization and trafficking to the Golgi and identify redox-dependent oligomerization of ATF6α as a key mechanism regulating its function during the UPR.

Keywords:  ATF6; ER stress; proteostasis; unfolded protein response

DOI:  https://doi.org/10.1073/pnas.2122657119
Nat Struct Mol Biol. 2022 Mar;29(3): 189

Cryptic elements of the heat-shock response.

Beth Moorefield.

DOI: https://doi.org/10.1038/s41594-022-00752-4
Biomed Pharmacother. 2022 Mar 11. pii: S0753-3322(22)00191-3. [Epub ahead of print]149 112803

Minocycline treatment improves proteostasis during Drosophila aging via autophagy mediated by FOXO and Hsp70.

Jin Ju Lim, Seogang Hyun.

  Minocycline is a semi-synthetic tetracycline derivative antibiotic that has been examined for its non-antibiotic properties, such as anti-inflammatory, tumor-suppressive, and neuroprotective effects. In this study, we found that feeding minocycline to Drosophila improves proteostasis during organismal aging. Poly-ubiquitinated protein aggregates increase in the flight muscles as flies age, which are reduced in response to minocycline feeding. Minocycline feeding increases the expression of several autophagy genes and the activity of the autophagy/lysosomal pathway in Drosophila muscles. Interestingly, mutant flies lacking either FOXO or Hsp70 showed increased levels of poly-ubiquitinated protein aggregates with reduced autophagy/lysosomal activity, which was not reversed by minocycline feeding. Our findings suggest that minocycline may improve proteostasis in aging tissues via FOXO-Hsp70 axis, which highlights the multifaceted effects of minocycline as a therapeutic agent in age-associated features.

Keywords:  Drosophila; Drug-repurposing; Minocycline; Muscle aging; Proteostasis

DOI:  https://doi.org/10.1016/j.biopha.2022.112803
Cell Stress Chaperones. 2022 Mar 16.

Endoplasmic reticulum-unfolded protein response pathway modulates the cellular response to mitochondrial proteotoxic stress.

Rajasri Sarkar, Kannan Boosi Narayana Rao, Mainak Pratim Jha, Koyeli Mapa.

  Mitochondria and endoplasmic reticulum (ER) remain closely tethered by contact sites to maintain unhindered biosynthetic, metabolic, and signalling functions. Apart from its constituent proteins, contact sites localize ER-unfolded protein response (UPR) sensors like Ire1 and PERK, indicating the importance of ER-mitochondria communication during stress. In the mitochondrial sub-compartment-specific proteotoxic model of yeast, Saccharomyces cerevisiae, we show that an intact ER-UPR pathway is important in stress tolerance of mitochondrial intermembrane space (IMS) proteotoxic stress, while disrupting the pathway is beneficial during matrix stress. Deletion of IRE1 and HAC1 leads to accumulation of misfolding-prone proteins in mitochondrial IMS indicating the importance of intact ER-UPR pathway in enduring mitochondrial IMS proteotoxic stresses. Although localized proteotoxic stress within mitochondrial IMS does not induce ER-UPR, its artificial activation helps cells to better withstand the IMS proteotoxicity. Furthermore, overexpression of individual components of ER-mitochondria contact sites is found to be beneficial for general mitochondrial proteotoxic stress, in an Ire1-Hac1-independent manner.

Keywords:  ER stress; ER-mitochondria contact sites; Mito-UPR; Protein homeostasis; Proteotoxic stress; Unfolded protein response

DOI:  https://doi.org/10.1007/s12192-022-01264-2
FEBS J. 2022 Mar 19.

Hsp104 N-terminal Domain Interaction with Substrates Plays a Regulatory Role in Protein Disaggregation.

Anna Harari, Guy Zoltsman, Tal Levin, Rina Rosenzweig.

  Hsp104 protein disaggregases are powerful molecular machines that harness the energy derived from ATP binding and hydrolysis to disaggregate a wide range of protein aggregates and amyloids, as well as to assist in yeast prion propagation. Little is known, however, about how Hsp104 chaperones recognize such a diversity of substrates, or indeed the contribution of the substrate-binding N-terminal domain (NTD) to Hsp104 function. Herein we present a Nuclear Magnetic Resonance (NMR) spectroscopy study which structurally characterizes the Hsp104 NTD-substrate interaction. We show that the NTD includes a substrate-binding groove that specifically recognizes exposed hydrophobic stretches in unfolded, misfolded, amyloid, and prion substrates of Hsp104. In addition, we find that the NTD itself has chaperoning activities which help to protect the exposed hydrophobic regions of its substrates from further misfolding and aggregation, thereby priming them for threading through the Hsp104 central channel. We further demonstrate that mutations to this substrate binding groove abolish Hsp104 activation by client proteins and keep the chaperone in a partially inhibited state. The Hsp104 variant with these mutations also exhibited significantly reduced disaggregation activity and cell survival at extreme temperatures. Together, our findings provide both a detailed characterization of the NTD-substrate complex and insight into the functional regulatory role of the N-terminal domain in protein disaggregation and yeast thermotolerance.

Keywords:  Hsp104; Molecular chaperones; NMR spectroscopy; protein disaggregation

DOI:  https://doi.org/10.1111/febs.16441
Reprod Fertil. 2022 Jan 01. 3(1): 19-29

The effect of gestational age on mitochondrial properties of the mouse placenta.

Lucy A Bartho, Joshua J Fisher, Sarah L Walton, Anthony V Perkins, James S M Cuffe.

  Mitochondria are organelles within the cell that generate energy, which is essential to the developing placenta. As the placenta approaches term, organelles such as mitochondria and the endoplasmic reticulum adapt to cellular stressors (e.g. oxidative stress and fluctuations in oxygen concentration) which are likely to result in the progressive decline of tissue function, known as placental ageing. This ageing phenotype may induce cellular senescence, a process whereby the cell is no longer proliferating, yet remains metabolically active. Mitochondria, endoplasmic reticulum and senescent processes are still poorly understood in the developing placenta. Therefore, a rodent ontogeny model was used to measure genes and proteins involved in mitochondrial biogenesis, antioxidant function, electron transport chain, mitophagy, dynamics and unfolded protein response in the placenta. CD-1 mouse placental samples were collected at embryonic day (E)12.5, E14.5, E16.5 and E18.5 of pregnancy for gene and protein analysis via qPCR, protein assays and Western blotting. Mitochondrial content, SDHB (complex II) and MFN2 (mitochondrial fusion) proteins were all increased throughout pregnancy, while citrate synthase activity/mitochondrial content, Tfam, Sirt3, Mfn1, TOMM20 (mitochondrial biogenesis and dynamics); Tp53(senescence); Eif2ak3, Eif4g1(endoplasmic reticulum stress);NDUFB8, UQCRC2, ATP5A (electron transport chain sub-complexes) were decreased at E18.5, compared to E12.5. Overall, mitochondria undergo changes in response to gestational progression and pathways associated with cellular ageing to facilitate adaptions in a healthy pregnancy. This data holds great promise that mitochondrial markers across pregnancy may help to establish when a placenta is ageing inappropriately.
Lay summary: Human pregnancy lasts approximately 266 days. If a baby is born early, organs may be poorly formed but if pregnancy continues past this time, stillbirth risk is increased. Gestational duration is regulated by the placenta. As the placenta approaches the end of pregnancy, it displays properties similar to tissues from aged individuals. However, it is unknown how this placental ageing contributes to pregnancy duration. This study characterised normal placental ageing by measuring properties of mitochondria in healthy placentas collected at four different gestational ages ranging from 7 days before birth to 1 day before birth of the 19-day mouse pregnancy. We found that mitochondrial number increased per cell but that a marker of mitochondrial function was reduced. Proteins that control mitochondrial number, morphology and function also changed over time. This work lays the platform to understand how placental ageing contributes to adverse pregnancy outcomes related to altered pregnancy duration.

Keywords:  ageing; endoplasmic reticulum; mitochondria; placenta; senescence

DOI:  https://doi.org/10.1530/RAF-21-0064
Clin Transl Med. 2022 Mar;12(3): e759

Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells.

Maria Georgiou, Chunbo Yang, Robert Atkinson, Kuan-Ting Pan, Adriana Buskin, Marina Moya Molina, Joseph Collin, Jumana Al-Aama, Franziska Goertler, Sebastian E J Ludwig, Tracey Davey, Reinhard Lührmann, Sushma Nagaraja-Grellscheid, Colin A Johnson, Robin Ali, Lyle Armstrong, Viktor Korolchuk, Henning Urlaub, Sina Mozaffari-Jovin, Majlinda Lako.

   INTRODUCTION: Mutations in pre-mRNA processing factor 31 (PRPF31), a core protein of the spliceosomal tri-snRNP complex, cause autosomal-dominant retinitis pigmentosa (adRP). It has remained an enigma why mutations in ubiquitously expressed tri-snRNP proteins result in retina-specific disorders, and so far, the underlying mechanism of splicing factors-related RP is poorly understood.
METHODS: We used the induced pluripotent stem cell (iPSC) technology to generate retinal organoids and RPE models from four patients with severe and very severe PRPF31-adRP, unaffected individuals and a CRISPR/Cas9 isogenic control.
RESULTS: To fully assess the impacts of PRPF31 mutations, quantitative proteomics analyses of retinal organoids and RPE cells were carried out showing RNA splicing, autophagy and lysosome, unfolded protein response (UPR) and visual cycle-related pathways to be significantly affected. Strikingly, the patient-derived RPE and retinal cells were characterised by the presence of large amounts of cytoplasmic aggregates containing the mutant PRPF31 and misfolded, ubiquitin-conjugated proteins including key visual cycle and other RP-linked tri-snRNP proteins, which accumulated progressively with time. The mutant PRPF31 variant was not incorporated into splicing complexes, but reduction of PRPF31 wild-type levels led to tri-snRNP assembly defects in Cajal bodies of PRPF31 patient retinal cells, altered morphology of nuclear speckles and reduced formation of active spliceosomes giving rise to global splicing dysregulation. Moreover, the impaired waste disposal mechanisms further exacerbated aggregate formation, and targeting these by activating the autophagy pathway using Rapamycin reduced cytoplasmic aggregates, leading to improved cell survival.
CONCLUSIONS: Our data demonstrate that it is the progressive aggregate accumulation that overburdens the waste disposal machinery rather than direct PRPF31-initiated mis-splicing, and thus relieving the RPE cells from insoluble cytoplasmic aggregates presents a novel therapeutic strategy that can be combined with gene therapy studies to fully restore RPE and retinal cell function in PRPF31-adRP patients.

Keywords:  PRPF31; RPE; UPR; aggregate formation; autophagy; human pluripotent stem cells; proteasome; retinal organoids; retinitis pigmentosa; tri-snRNP assembly defects

DOI:  https://doi.org/10.1002/ctm2.759
EMBO J. 2022 Mar 14. e110057

The needs of a synapse-How local organelles serve synaptic proteostasis.

Katarzyna M Grochowska, Maria Andres-Alonso, Anna Karpova, Michael R Kreutz.

  Synaptic function crucially relies on the constant supply and removal of neuronal membranes. The morphological complexity of neurons poses a significant challenge for neuronal protein transport since the machineries for protein synthesis and degradation are mainly localized in the cell soma. In response to this unique challenge, local micro-secretory systems have evolved that are adapted to the requirements of neuronal membrane protein proteostasis. However, our knowledge of how neuronal proteins are synthesized, trafficked to membranes, and eventually replaced and degraded remains scarce. Here, we review recent insights into membrane trafficking at synaptic sites and into the contribution of local organelles and micro-secretory pathways to synaptic function. We describe the role of endoplasmic reticulum specializations in neurons, Golgi-related organelles, and protein complexes like retromer in the synthesis and trafficking of synaptic transmembrane proteins. We discuss the contribution of autophagy and of proteasome-mediated and endo-lysosomal degradation to presynaptic proteostasis and synaptic function, as well as nondegradative roles of autophagosomes and lysosomes in signaling and synapse remodeling. We conclude that the complexity of neuronal cyto-architecture necessitates long-distance protein transport that combines degradation with signaling functions.

Keywords:  Golgi satellites; autophagy; lysosomes; secretory trafficking

DOI:  https://doi.org/10.15252/embj.2021110057
Front Mol Biosci. 2022 ;9 842149

Insights on Human Small Heat Shock Proteins and Their Alterations in Diseases.

B Tedesco, R Cristofani, V Ferrari, M Cozzi, P Rusmini, E Casarotto, M Chierichetti, F Mina, M Galbiati, M Piccolella, V Crippa, A Poletti.

  The family of the human small Heat Shock Proteins (HSPBs) consists of ten members of chaperones (HSPB1-HSPB10), characterized by a low molecular weight and capable of dimerization and oligomerization forming large homo- or hetero-complexes. All HSPBs possess a highly conserved centrally located α-crystallin domain and poorly conserved N- and C-terminal domains. The main feature of HSPBs is to exert cytoprotective functions by preserving proteostasis, assuring the structural maintenance of the cytoskeleton and acting in response to cellular stresses and apoptosis. HSPBs take part in cell homeostasis by acting as holdases, which is the ability to interact with a substrate preventing its aggregation. In addition, HSPBs cooperate in substrates refolding driven by other chaperones or, alternatively, promote substrate routing to degradation. Notably, while some HSPBs are ubiquitously expressed, others show peculiar tissue-specific expression. Cardiac muscle, skeletal muscle and neurons show high expression levels for a wide variety of HSPBs. Indeed, most of the mutations identified in HSPBs are associated to cardiomyopathies, myopathies, and motor neuropathies. Instead, mutations in HSPB4 and HSPB5, which are also expressed in lens, have been associated with cataract. Mutations of HSPBs family members encompass base substitutions, insertions, and deletions, resulting in single amino acid substitutions or in the generation of truncated or elongated proteins. This review will provide an updated overview of disease-related mutations in HSPBs focusing on the structural and biochemical effects of mutations and their functional consequences.

Keywords:  HSPBs; aggregation; muscle disease; neuropathy; proteostasis

DOI:  https://doi.org/10.3389/fmolb.2022.842149
Aging Cell. 2022 Mar 15. e13570

Organelle dysfunction upon asrij depletion causes aging-like changes in mouse hematopoietic stem cells.

Saloni Sinha, Alice Sinha, Prathamesh Dongre, Kajal Kamat, Maneesha S Inamdar.

  Aging of the blood system is characterized by increased hematopoietic stem cells (HSCs) and myeloid-biased differentiation leading to higher propensity for hematological malignancies. Unraveling cell-intrinsic mechanisms regulating HSC aging could aid reversal or slowing of aging. Asrij/OCIAD1 is an evolutionarily conserved regulator of hematopoiesis and governs mitochondrial, endosomal, and proteasomal function in mammalian stem cells. Asrij deletion in mice causes loss of HSC quiescence, myeloid skewing, reduced p53 and increased DNA damage, features attributed to aged HSCs. Mechanistically, Asrij controls p53 ubiquitination and degradation and AKT/STAT5 activation. Asrij localizes to endosomes and mitochondria. As decline in organelle structure and function are common hallmarks of aging, we asked whether Asrij regulates organelle function in aged HSCs. We find that chronologically aged wild-type (WT) HSCs had reduced Asrij levels. Expectedly, young asrij KO mice had reduced AcH4K16 levels; however, transcriptome analysis of KO HSCs showed a modest overlap of gene expression with aged WT HSCs. Further, analysis of organelle structure and function in asrij KO mice revealed significant changes, namely damaged mitochondria, elevated ROS; impaired endosomal trafficking seen by increased cleaved Notch1, reduced Rab5; and reduced 26S proteasome activity. Pharmacological correction of mitochondrial and proteasome activity in asrij KO mice restored HSC and myeloid cell frequencies. Furthermore, lysophosphatidic acid-induced Asrij upregulation in aged WT mice rescued mitochondrial and proteasome activity and restored HSC frequency. Our results highlight a new role for Asrij in preventing HSC aging by regulating organelle homeostasis and will help decipher organelle dynamics in HSC longevity.

Keywords:  Asrij/OCIAD1; HSC; aging; endosome; homeostasis; mitochondria; organelle; proteasome

DOI:  https://doi.org/10.1111/acel.13570
Curr Opin Neurobiol. 2022 Mar 15. pii: S0959-4388(22)00016-2. [Epub ahead of print]73 102524

Aging impact on amyloid precursor protein neuronal trafficking.

Tatiana Burrinha, Guimas Almeida Cláudia.

Neurons live a lifetime. Neuronal aging may increase the risk of Alzheimer's disease. How does neuronal membrane trafficking maintain synapse function during aging? In the normal aged brain, intraneuronal beta-amyloid (Aβ) accumulates without Alzheimer's disease mutations or risk variants. However, do changes with neuronal aging potentiate Aβ accumulation? We reviewed the membrane trafficking of the amyloid precursor protein in neurons and highlighted its importance in Aβ production. Importantly, we reviewed the evidence supporting the impact of aging on neuronal membrane trafficking, APP processing, and consequently Aβ production. Dissecting the molecular regulators of APP trafficking during neuronal aging is required to identify strategies to delay synaptic decline and protect from Alzheimer's disease.

DOI: https://doi.org/10.1016/j.conb.2022.102524
Aging Cell. 2022 Mar 17. e13592

Inhibition of unfolded protein response prevents post-anesthesia neuronal hyperactivity and synapse loss in aged mice.

Kai Chen, Qiuping Hu, Riya Gupta, Jessie Stephens, Zhongcong Xie, Guang Yang.

  Delirium is the most common postoperative complication in older patients after prolonged anesthesia and surgery and is associated with accelerated cognitive decline and dementia. The neuronal pathogenesis of postoperative delirium is largely unknown. The unfolded protein response (UPR) is an adaptive reaction of cells to perturbations in endoplasmic reticulum function. Dysregulation of UPR has been implicated in a variety of diseases including Alzheimer's disease and related dementias. However, whether UPR plays a role in anesthesia-induced cognitive impairment remains unexplored. By performing in vivo calcium imaging in the mouse frontal cortex, we showed that exposure of aged mice to the inhalational anesthetic sevoflurane for 2 hours resulted in a marked elevation of neuronal activity during recovery, which lasted for at least 24 hours after the end of exposure. Concomitantly, sevoflurane anesthesia caused a prolonged increase in phosphorylation of PERK and eIF2α, the markers of UPR activation. Genetic deletion or pharmacological inhibition of PERK prevented neuronal hyperactivity and memory impairment induced by sevoflurane. Moreover, we showed that PERK suppression also reversed various molecular and synaptic changes induced by sevoflurane anesthesia, including alterations of synaptic NMDA receptors, tau protein phosphorylation, and dendritic spine loss. Together, these findings suggest that sevoflurane anesthesia causes abnormal UPR in the aged brain, which contributes to neuronal hyperactivity, synapse loss and cognitive decline in aged mice.

Keywords:  delirium; dendritic spine; neuronal activity; sevoflurane; synapse; unfolded protein response

DOI:  https://doi.org/10.1111/acel.13592
Cell Rep. 2022 Mar 15. pii: S2211-1247(22)00276-5. [Epub ahead of print]38(11): 110535

A trio of ubiquitin ligases sequentially drives ubiquitylation and autophagic degradation of dysfunctional yeast proteasomes.

Richard S Marshall, Richard D Vierstra.

  As central effectors of ubiquitin (Ub)-mediated proteolysis, proteasomes are regulated at multiple levels, including degradation of unwanted or dysfunctional particles via autophagy (termed proteaphagy). In yeast, inactive proteasomes are exported from the nucleus, sequestered into cytoplasmic aggresomes via the Hsp42 chaperone, extensively ubiquitylated, and then tethered to the expanding phagophore by the autophagy receptor Cue5. Here, we demonstrate the need for ubiquitylation driven by the trio of Ub ligases (E3s), San1, Rsp5, and Hul5, which together with their corresponding E2s work sequentially to promote nuclear export and Cue5 recognition. Whereas San1 functions prior to nuclear export, Rsp5 and Hul5 likely decorate aggresome-localized proteasomes in concert. Ultimately, topologically complex Ub chain(s) containing both K48 and K63 Ub-Ub linkages are assembled, mainly on the regulatory particle, to generate autophagy-competent substrates. Because San1, Rsp5, Hul5, Hsp42, and Cue5 also participate in general proteostasis, proteaphagy likely engages a fundamental mechanism for eliminating inactive/misfolded proteins.

Keywords:  CP: Molecular Biology; aggresome; autophagy; core protease; proteaphagy; proteasome; regulatory particle; ubiquitin; ubiquitin ligase; yeast

DOI:  https://doi.org/10.1016/j.celrep.2022.110535
Front Cell Dev Biol. 2022 ;10 870791

Editorial: Amyloid-Membrane Interactions in Protein Misfolding Disorders: From Basic Mechanisms to Therapy.

Neville Vassallo, Céline Galvagnion, Eva Y Chi.



Keywords:  SOD1; aggregation inhibitors; amyloid-β; hIAPP; lipid membrane; protein aggregation; tau; α-synuclein

DOI:  https://doi.org/10.3389/fcell.2022.870791
Nat Commun. 2022 Mar 15. 13(1): 1351

Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers.

Nikolaos Louros, Meine Ramakers, Emiel Michiels, Katerina Konstantoulea, Chiara Morelli, Teresa Garcia, Nele Moonen, Sam D'Haeyer, Vera Goossens, Dietmar Rudolf Thal, Dominique Audenaert, Frederic Rousseau, Joost Schymkowitz.

Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. While sequence homology seems to favour heterotypic amyloid interactions, we have no systematic understanding of the structural rules determining such interactions nor whether they inhibit or facilitate amyloid assembly. Using structure-based thermodynamic calculations and extensive experimental validation, we performed a comprehensive exploration of the defining role of sequence promiscuity in amyloid interactions. Using tau as a model system we demonstrate that proteins with local sequence homology to tau amyloid nucleating regions can modify fibril nucleation, morphology, assembly and spreading of aggregates in cultured cells. Depending on the type of mutation such interactions inhibit or promote aggregation in a manner that can be predicted from structure. We find that these heterotypic amyloid interactions can result in the subcellular mis-localisation of these proteins. Moreover, equilibrium studies indicate that the critical concentration of aggregation is altered by heterotypic interactions. Our findings suggest a structural mechanism by which the proteomic background can modulate the aggregation propensity of amyloidogenic proteins and we discuss how such sequence-specific proteostatic perturbations could contribute to the selective cellular susceptibility of amyloid disease progression.

DOI: https://doi.org/10.1038/s41467-022-28955-9
Proc Natl Acad Sci U S A. 2022 Mar 22. 119(12): e2116736119

Single-molecule fluorescence imaging and deep learning reveal highly heterogeneous aggregation of amyloid-β 42.

Fanjie Meng, Janghyun Yoo, Hoi Sung Chung.

  SignificanceThere are various diseases caused by protein aggregation such as Alzheimer's, Parkinson's, and Huntington's diseases. From the diversity in the fibril structure, aggregation is expected to occur via heterogeneous pathways. However, characterization of this heterogeneity is extremely difficult because it requires following individual fibril formation in a mixture from early oligomerization stages. In this work, we investigated aggregation of the 42-residue isoform of amyloid β (Aβ42) using single-molecule fluorescence imaging and deep learning. We could track the growth of individual fibrils, which allows for a quantitative description of heterogeneous fibril formation and discovery of a new fibril nucleation mechanism. Further characterization of heterogeneity involving Aβ42 will be important for better understanding the disease mechanism.

Keywords:  amyloid; deep neural network; fluorescence lifetime imaging; protein aggregation; single-molecule spectroscopy

DOI:  https://doi.org/10.1073/pnas.2116736119
Biochim Biophys Acta Mol Basis Dis. 2022 Mar 12. pii: S0925-4439(22)00047-3. [Epub ahead of print] 166384

Clusterin in Alzheimer's disease: An amyloidogenic inhibitor of amyloid formation?

Panagiotis M Spatharas, Georgia I Nasi, Paraskevi L Tsiolaki, Marilena K Theodoropoulou, Nikos C Papandreou, Andreas Hoenger, Ioannis P Trougakos, Vassiliki A Iconomidou.

  Clusterin is a heterodimeric glycoprotein (α- and β-chain), which has been described as an extracellular molecular chaperone. In humans, clusterin is an amyloid-associated protein, co-localizing with fibrillar deposits in several amyloidoses, including Alzheimer's disease. To clarify its potential implication in amyloid formation, we located aggregation-prone regions within the sequence of clusterin α-chain, via computational methods. We had peptide-analogues, which correspond to each of these regions, chemically synthesized and experimentally demonstrated that all of them can form amyloid-like fibrils. We also provide evidence that the same peptide-analogues can inhibit amyloid-β fibril formation, potentially making them appropriate drug candidates for Alzheimer's disease. At the same time, our findings hint that the respective aggregation-prone clusterin regions may be implicated in the molecular mechanism in which clusterin inhibits amyloid formation. Furthermore, we suggest that molecular chaperones with amyloidogenic properties might have a role in the regulation of amyloid formation, essentially acting as functional amyloids.

Keywords:  Aggregation-prone regions; Alzheimer's disease; Amyloid; Amyloid inhibitors; Amyloid-β; Clusterin

DOI:  https://doi.org/10.1016/j.bbadis.2022.166384