bims-proarb 2022-07-24 papers

Issue of 2022–07–24
eight papers selected by
Rich Giadone, Harvard University

Mol Cell. 2022 Jul 12. pii: S1097-2765(22)00607-4. [Epub ahead of print]

Sequence grammar underlying the unfolding and phase separation of globular proteins.

Kiersten M Ruff, Yoon Hee Choi, Dezerae Cox, Angelique R Ormsby, Yoochan Myung, David B Ascher, Sheena E Radford, Rohit V Pappu, Danny M Hatters.

Aberrant phase separation of globular proteins is associated with many diseases. Here, we use a model protein system to understand how the unfolded states of globular proteins drive phase separation and the formation of unfolded protein deposits (UPODs). We find that for UPODs to form, the concentrations of unfolded molecules must be above a threshold value. Additionally, unfolded molecules must possess appropriate sequence grammars to drive phase separation. While UPODs recruit molecular chaperones, their compositional profiles are also influenced by synergistic physicochemical interactions governed by the sequence grammars of unfolded proteins and cellular proteins. Overall, the driving forces for phase separation and the compositional profiles of UPODs are governed by the sequence grammars of unfolded proteins. Our studies highlight the need for uncovering the sequence grammars of unfolded proteins that drive UPOD formation and cause gain-of-function interactions whereby proteins are aberrantly recruited into UPODs.

Keywords: Cry2; SOD1; TRiC; barnase; chaperonin-containing T-complex; molecular condensate; protein deposit; protein folding; protein misfolding; protein quality control; proteostasis; superoxide dismutase 1

DOI: https://doi.org/10.1016/j.molcel.2022.06.024

MicroPubl Biol. 2022 ;2022

Human PERK rescues unfolded protein response-deficient yeast cells.

Wei Sheng Yap, Guillaume Thibault.

Protein folding and quality control is tightly regulated at the endoplasmic reticulum (ER), and its disruption is associated with many diseases. In eukaryotes, the accumulation of unfolded protein in the ER is sensed by the three sensors, IRE1, PERK, and ATF6 to activate the unfolded protein response (UPR) to restore ER homeostasis. However, uncoupling the sensing of each sensor and their respective downstream pathways has been challenging as the absence of one is compensated by the remaining two sensors. Here, we report a fully functional human PERK (hPERK) chimeric protein expressed in Saccharomyces cerevisiae that could be used for high throughput screen to identify new PERK inhibitory or activating compounds as well as to characterize the PERK stress sensing mechanisms.

DOI: https://doi.org/10.17912/micropub.biology.000592

Front Aging Neurosci. 2022 ;14 921573

Patient-Derived Fibroblasts With Presenilin-1 Mutations, That Model Aspects of Alzheimer's Disease Pathology, Constitute a Potential Object for Early Diagnosis.

Gustavo Lopez-Toledo, Maria-Del-Carmen Silva-Lucero, Jorge Herrera-Díaz, David-Erasmo García, José-Antonio Arias-Montaño, Maria-Del-Carmen Cardenas-Aguayo.

Alzheimer's disease (AD), a neurodegenerative disorder that can occur in middle or old age, is characterized by memory loss, a continuous decline in thinking, behavioral and social skills that affect the ability of an individual to function independently. It is divided into sporadic and familial subtypes. Early-onset familial AD (FAD) is linked to mutations in genes coding for the amyloid-β protein precursor (AβPP), presenilin 1 (PS1), and presenilin 2 (PS2), which lead to alterations in AβPP processing, generation of the Amyloid-β peptide and hyperphosphorylation of tau protein. Identification of early biomarkers for AD diagnosis represents a challenge, and it has been suggested that molecular changes in neurodegenerative pathways identified in the brain of AD patients can be detected in peripheral non-neural cells derived from familial or sporadic AD patients. In the present study, we determined the protein expression, the proteomic and in silico characterization of skin fibroblasts from FAD patients with PS1 mutations (M146L or A246E) or from healthy individuals. Our results shown that fibroblasts from AD patients had increased expression of the autophagy markers LC3II, LAMP2 and Cathepsin D, a significant increase in total GSK3, phosphorylated ERK1/2 (Thr202/Tyr204) and phosphorylated tau (Thr231, Ser396, and Ser404), but no difference in the phosphorylation of Akt (Ser473) or the α (Ser21) and β (Ser9) GSK3 isoforms, highlighting the relevant role of abnormal protein post-translational modifications in age-related neurodegenerative diseases, such as AD. Both 2-DE gels and mass spectrometry showed significant differences in the expression of the signaling pathways associated with protein folding and the autophagic pathway mediated by chaperones with the expression of HSPA5, HSPE1, HSPD1, HSP90AA1, and HSPE1 and reticular stress in the FAD samples. Furthermore, expression of the heat shock proteins HSP90 and HSP70 was significantly higher in the cells from AD patients as confirmed by Western blot. Taken together our results indicate that fibroblasts from patients with FAD-PS1 present alterations in signaling pathways related to cellular stress, autophagy, lysosomes, and tau phosphorylation. Fibroblasts can therefore be useful in modeling pathways related to neurodegeneration, as well as for the identification of early AD biomarkers.

Keywords: autophagy; familial Alzheimer’s disease (FAD); fibroblasts; neurodegeneration; post-translational modifications (PTM); presenilin; proteomics; stress

DOI: https://doi.org/10.3389/fnagi.2022.921573

Sci Signal. 2022 Jul 05. 15(741): eabm7524

Balancing energy and protein homeostasis at ER-mitochondria contact sites.

Amado Carreras-Sureda, Guido Kroemer, Julio Cesar Cardenas, Claudio Hetz.

The endoplasmic reticulum (ER) is the largest organelle of the cell and participates in multiple essential functions, including the production of secretory proteins, lipid synthesis, and calcium storage. Sustaining proteostasis requires an intimate coupling with energy production. Mitochondrial respiration evolved to be functionally connected to ER physiology through a physical interface between both organelles known as mitochondria-associated membranes. This quasi-synaptic structure acts as a signaling hub that tunes the function of both organelles in a bidirectional manner and controls proteostasis, cell death pathways, and mitochondrial bioenergetics. Here, we discuss the main signaling mechanisms governing interorganellar communication and their putative role in diseases including cancer and neurodegeneration.

DOI: https://doi.org/10.1126/scisignal.abm7524

Front Physiol. 2022 ;13 959570

Editorial: Protein Phase Separation and Aggregation in (Patho)Physiology of Neurons.

Dragomir Milovanovic, Silvio O Rizzoli.

Keywords: AMPA and NMDA-type receptors; TDP43; alpha-synuclein; neurodegenerative diseases; neuron; phase separation; synapse; synaptic vesicles

DOI: https://doi.org/10.3389/fphys.2022.959570

Acta Pharm Sin B. 2022 Apr;12(4): 1688-1706

Pharmacological modulation of autophagy for Alzheimer's disease therapy: Opportunities and obstacles.

Zhiqiang Deng, Yu Dong, Xiaoting Zhou, Jia-Hong Lu, Zhenyu Yue.

Alzheimer's disease (AD) is a prevalent and deleterious neurodegenerative disorder characterized by an irreversible and progressive impairment of cognitive abilities as well as the formation of amyloid β (Aβ) plaques and neurofibrillary tangles (NFTs) in the brain. By far, the precise mechanisms of AD are not fully understood and no interventions are available to effectively slow down progression of the disease. Autophagy is a conserved degradation pathway that is crucial to maintain cellular homeostasis by targeting damaged organelles, pathogens, and disease-prone protein aggregates to lysosome for degradation. Emerging evidence suggests dysfunctional autophagy clearance pathway as a potential cellular mechanism underlying the pathogenesis of AD in affected neurons. Here we summarize the current evidence for autophagy dysfunction in the pathophysiology of AD and discuss the role of autophagy in the regulation of AD-related protein degradation and neuroinflammation in neurons and glial cells. Finally, we review the autophagy modulators reported in the treatment of AD models and discuss the obstacles and opportunities for potential clinical application of the novel autophagy activators for AD therapy.

Keywords: Alzheimer's disease; Autophagy; Autophagy modulators; Genetic modulation; LC3-associated phagocytosis; Microglial autophagy; Neuroinflammation; Neuronal autophagy

DOI: https://doi.org/10.1016/j.apsb.2021.12.009

Front Mol Neurosci. 2022 ;15 966139

Editorial: Blood Biomarkers of Neurodegenerative Diseases.

Thomas K Karikari, Nicholas J Ashton, Henrik Zetterberg, Kaj Blennow.

Keywords: Alzheimer's disease; amyloid; blood biomarker; neurofilament; tau

DOI: https://doi.org/10.3389/fnmol.2022.966139

Proc Natl Acad Sci U S A. 2022 Aug 16. 119(33): e2207200119

Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins.

Jianhua Zhao, Suraj Makhija, Chenyu Zhou, Hanxiao Zhang, YongQiang Wang, Monita Muralidharan, Bo Huang, Yifan Cheng.

The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αβ-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4β engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.

Keywords: CRISPR-Cas9; endogenous protein tagging; proteasome; single-particle cryo-EM

DOI: https://doi.org/10.1073/pnas.2207200119