ER Stress-Sensor Proteins and ER-Mitochondrial Crosstalk—Signaling Beyond (ER) Stress Response

Recent studies undoubtedly show the importance of inter organellar connections to maintain cellular homeostasis. In normal physiological conditions or in the presence of cellular and environmental stress, each organelle responds alone or in coordination to maintain cellular function. The Endoplasmic reticulum (ER) and mitochondria are two important organelles with very specialized structural and functional properties. These two organelles are physically connected through very specialized proteins in the region called the mitochondria-associated ER membrane (MAM). The molecular foundation of this relationship is complex and involves not only ion homeostasis through the shuttling of calcium but also many structural and apoptotic proteins. IRE1alpha and PERK are known for their canonical function as an ER stress sensor controlling unfolded protein response during ER stress. The presence of these transmembrane proteins at the MAM indicates its potential involvement in other biological functions beyond ER stress signaling. Many recent studies have now focused on the non-canonical function of these sensors. In this review, we will focus on ER mitochondrial interdependence with special emphasis on the non-canonical role of ER stress sensors beyond ER stress

ER Stress-Sensor Proteins and ER-Mitochondrial Crosstalk—Signaling Beyond (ER) Stress Response

Recent studies undoubtedly show the importance of inter organellar connections to maintain cellular homeostasis. In normal physiological conditions or in the presence of cellular and environmental stress, each organelle responds alone or in coordination to maintain cellular function. The Endoplasmic reticulum (ER) and mitochondria are two important organelles with very specialized structural and functional properties. These two organelles are physically connected through very specialized proteins in the region called the mitochondria-associated ER membrane (MAM). The molecular foundation of this relationship is complex and involves not only ion homeostasis through the shuttling of calcium but also many structural and apoptotic proteins. IRE1alpha and PERK are known for their canonical function as an ER stress sensor controlling unfolded protein response during ER stress. The presence of these transmembrane proteins at the MAM indicates its potential involvement in other biological functions beyond ER stress signaling. Many recent studies have now focused on the non-canonical function of these sensors. In this review, we will focus on ER mitochondrial interdependence with special emphasis on the non-canonical role of ER stress sensors beyond ER stress

Impact of ER Stress and ER-Mitochondrial Crosstalk in Huntington’s Disease

Accumulation of misfolded proteins is a common phenomenon of several neurodegenerative diseases. The misfolding of proteins due to abnormal polyglutamine (PolyQ) expansions are linked to the development of PolyQ diseases including Huntington’s disease (HD). Though the genetic basis of PolyQ repeats in HD remains prominent, the primary molecular basis mediated by PolyQ toxicity remains elusive. Accumulation of misfolded proteins in the ER or disruption of ER homeostasis causes ER stress and activates an evolutionarily conserved pathway called Unfolded protein response (UPR). Protein homeostasis disruption at organelle level involving UPR or ER stress response pathways are found to be linked to HD. Due to dynamic intricate connections between ER and mitochondria, proteins at ER-mitochondria contact sites (mitochondria associated ER membranes or MAMs) play a significant role in HD development. The current review aims at highlighting the most updated information about different UPR pathways and their involvement in HD disease progression. Moreover, the role of MAMs in HD progression has also been discussed. In the end, the review has focused on the therapeutic interventions responsible for ameliorating diseased states via modulating either ER stress response proteins or modulating the expression of ER-mitochondrial contact proteins

Chemical chaperones reverse early suppression of regulatory circuits during Unfolded Protein Response in B cells from Common Variable Immunodeficiency patients

Rare B cell samples from two CVID patients (P1 and P2) and a healthy donor (C) were used in controlled experiments analyzing the early UPR with and without the presence of chemical chaperones. As ER stressors we used Thapsigargin (Tg) and Tunicamycin (Tm). As exogenous chaperones we used DMSO, PBA, and TUDCA. For quantification of specific transcripts of interest we used a high-throughput platform based on TaqMan technology (Applied Biosystems TaqMan OpenArray Real-Time PCR System). Samples containing 3 x 10e5 EBV-B cells that received treatments with ER stressors and/or chemical chaperones for 0, 1, 2, 3, or 4 hr. Purified RNA was quali- and quantified by spectrometry in a Nanodrop and by fluorimetry in a Qubit, respectively. cDNA was generated using 300 ng of total RNA, and amplified in triplicate reactions for quantification of specific transcripts using a QuantStudio 12K Flex Real-Time PCR System. TaqMan OpenArray primers were custom-made by Thermo Fisher Scientific. Genes access numbers can be found in Supplementary Table 2 of the respective publication. Target DCq values were normalized against Gapdh DCq levels. Replicates were averaged and filtered for SE < 0.5 for removal of low-abundance measurements. A ratio of Treated / Untreated was calculated, log2-transformed, and a T-test was applied. Only those ratios whose SE were < 0.5 and that were significantly different (p ≤ 0.05) from untreated controls in at least two time-points were considered relevant. Regulatory circuits were built using BioTapestry 7.1 software. Networks show only those elements assayed in this study. Inputs and outputs of indicated genes are color coded according to their upstream origin (yellow for ATF6, red for PERK, blue for IRE1a, and green for sXBP1). Orange lines indicate those elements whose expression depends on inputs from both ATF6 and PERK pathways. Linkages substantiated by cis-regulatory data are indicated by diamonds colored according to strength of the experimental evidence: blue diamonds for expression studies using gain/loss of function, pink diamonds for binding affinity assays, and orange diamonds for promoter analysis in vivo. A green bar represents post-transcriptional modification of Xbp1 mRNA. A yellow bar represents post-translational modification of ATF6 protein. # (OR) and & (AND) are Boolean rules governing input elements in specific promoters. Bold gene = active expression. Bold gene + thick line = upregulated expression compared to untreated control. Grey gene + grey line = downregulated expression compared to untreated control. For visualization of each patient’s experimental regulatory network, refer to Supplementary Movies (A-G) for average [CVID patients minus healthy control], (H-N) for healthy control, (O-U) for patient P1, and (V-Y) for patient P2

Identification of molecular signatures defines the differential proteostasis response in induced spinal and cranial motor neurons

Summary: Amyotrophic lateral sclerosis damages proteostasis, affecting spinal and upper motor neurons earlier than a subset of cranial motor neurons. To aid disease understanding, we exposed induced cranial and spinal motor neurons (iCrMNs and iSpMNs) to proteotoxic stress, under which iCrMNs showed superior survival, quantifying the transcriptome and proteome for >8,200 genes at 0, 12, and 36 h. Two-thirds of the proteome showed cell-type differences. iSpMN-enriched proteins related to DNA/RNA metabolism, and iCrMN-enriched proteins acted in the endoplasmic reticulum (ER)/ER chaperone complex, tRNA aminoacylation, mitochondria, and the plasma/synaptic membrane, suggesting that iCrMNs expressed higher levels of proteins supporting proteostasis and neuronal function. When investigating the increased proteasome levels in iCrMNs, we showed that the activity of the 26S proteasome, but not of the 20S proteasome, was higher in iCrMNs than in iSpMNs, even after a stress-induced decrease. We identified Ublcp1 as an iCrMN-specific regulator of the nuclear 26S activity

Oxidative Homeostasis Regulates the Response to Reductive Endoplasmic Reticulum Stress through Translation Control

SummaryReductive stress leads to the loss of disulfide bond formation and induces the unfolded protein response of the endoplasmic reticulum (UPRER), necessary to regain proteostasis in the compartment. Here we show that peroxide accumulation during reductive stress attenuates UPRER amplitude by altering translation without any discernible effect on transcription. Through a comprehensive genetic screen in Saccharomyces cerevisiae, we identify modulators of reductive stress-induced UPRER and demonstrate that oxidative quality control (OQC) genes modulate this cellular response in the presence of chronic but not acute reductive stress. Using a combination of microarray and relative quantitative proteomics, we uncover a non-canonical translation attenuation mechanism that acts in a bipartite manner to selectively downregulate highly expressed proteins, decoupling the cell’s transcriptional and translational response during reductive ER stress. Finally, we demonstrate that PERK, a canonical translation attenuator in higher eukaryotes, helps in bypassing a ROS-dependent, non-canonical mode of translation attenuation

Complex changes in serum protein levels in COVID-19 convalescents

Abstract The COVID-19 pandemic, triggered by severe acute respiratory syndrome coronavirus 2, has affected millions of people worldwide. Much research has been dedicated to our understanding of COVID-19 disease heterogeneity and severity, but less is known about recovery associated changes. To address this gap in knowledge, we quantified the proteome from serum samples from 29 COVID-19 convalescents and 29 age-, race-, and sex-matched healthy controls. Samples were acquired within the first months of the pandemic. Many proteins from pathways known to change during acute COVID-19 illness, such as from the complement cascade, coagulation system, inflammation and adaptive immune system, had returned to levels seen in healthy controls. In comparison, we identified 22 and 15 proteins with significantly elevated and lowered levels, respectively, amongst COVID-19 convalescents compared to healthy controls. Some of the changes were similar to those observed for the acute phase of the disease, i.e. elevated levels of proteins from hemolysis, the adaptive immune systems, and inflammation. In contrast, some alterations opposed those in the acute phase, e.g. elevated levels of CETP and APOA1 which function in lipid/cholesterol metabolism, and decreased levels of proteins from the complement cascade (e.g. C1R, C1S, and VWF), the coagulation system (e.g. THBS1 and VWF), and the regulation of the actin cytoskeleton (e.g. PFN1 and CFL1) amongst COVID-19 convalescents. We speculate that some of these shifts might originate from a transient decrease in platelet counts upon recovery from the disease. Finally, we observed race-specific changes, e.g. with respect to immunoglobulins and proteins related to cholesterol metabolism

New proteomic signatures to distinguish between zika and dengue infections

10.1016/j.mcpro.2021.100052Molecular and Cellular Proteomics2010005