bims-unfpre 2021-05-30 papers

bims-unfpre

Biomed News

on Unfolded protein response

Issue of 2021–05–30
eleven papers selected by
Susan Logue, University of Manitoba

A View of the Endoplasmic Reticulum Through the Calreticulin Lens.
Defects in Protein Folding and/or Quality Control Cause Protein Aggregation in the Endoplasmic Reticulum.
Endoplasmic Reticulum (ER) and ER-Phagy.
Transcription- and phosphorylation-dependent control of a functional interplay between XBP1s and PINK1 governs mitophagy and potentially impacts Parkinson disease pathophysiology.
Disruption of Endoplasmic Reticulum Proteostasis in Age-Related Nervous System Disorders.
Endoplasmic Reticulum Homeostasis and Stress Responses in Caenorhabditis elegans.
A novel XBP1 variant is highly enriched in cancer tissues and is specifically required for cancer cell survival.
Phosphorylation of Pal2 by the protein kinases Kin1 and Kin2 modulates HAC1 mRNA splicing in the unfolded protein response in yeast.
The XBP1-MARCH5-MFN2 axis confers ER stress resistance by coordinating mitochondrial fission and mitophagy in melanoma.
Detection of Unfolded Protein Response by Polymerase Chain Reaction.
In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.

Prog Mol Subcell Biol. 2021 ;59 1-11

A View of the Endoplasmic Reticulum Through the Calreticulin Lens.

Luis B Agellon, Marek Michalak.

  Calreticulin is well known as an ER-resident protein that serves as the major endoplasmic reticulum (ER) Ca2+ binding protein. This protein has been the major topic of discussion in an international workshop that has been meeting for a quarter of a century. In sharing information about this protein, the field also witnessed remarkable insights into the importance of the ER as an organelle and the role of ER Ca2+ in coordinating ER and cellular functions. Recent technological advances have helped to uncover the contributions of calreticulin in maintaining Ca2+ homeostasis in the ER and to unravel its involvement in a multitude of cellular processes as highlighted in this collection of articles. The continuing revelations of unexpected involvement of calreticulin and Ca2+ in many critical aspects of cellular function promises to further improve insights into the significance of this protein in the promotion of physiology as well as prevention of pathology.

Keywords:  Calcium homeostasis; Calreticulin; ER stress; Endoplasmic reticulum

DOI:  https://doi.org/10.1007/978-3-030-67696-4_1
Prog Mol Subcell Biol. 2021 ;59 115-143

Defects in Protein Folding and/or Quality Control Cause Protein Aggregation in the Endoplasmic Reticulum.

Juthakorn Poothong, Insook Jang, Randal J Kaufman.

  Protein aggregation is now a common hallmark of numerous human diseases, most of which involve cytosolic aggregates including Aβ (AD) and ⍺-synuclein (PD) in Alzheimer's disease and Parkinson's disease. However, it is also evident that protein aggregation can also occur in the lumen of the endoplasmic reticulum (ER) that leads to specific diseases due to loss of protein function or detrimental effects on the host cell, the former is inherited in a recessive manner where the latter are dominantly inherited. However, the mechanisms of protein aggregation, disaggregation and degradation in the ER are not well understood. Here we provide an overview of factors that cause protein aggregation in the ER and how the ER handles aggregated proteins. Protein aggregation in the ER can result from intrinsic properties of the protein (hydrophobic residues in the ER), oxidative stress or nutrient depletion. The ER has quality control mechanisms [chaperone functions, ER-associated protein degradation (ERAD) and autophagy] to ensure only correctly folded proteins exit the ER and enter the cis-Golgi compartment. Perturbation of protein folding in the ER activates the unfolded protein response (UPR) that evolved to increase ER protein folding capacity and efficiency and degrade misfolded proteins. Accumulation of misfolded proteins in the ER to a level that exceeds the ER-chaperone folding capacity is a major factor that exacerbates protein aggregation. The most significant ER resident protein that prevents protein aggregation in the ER is the heat shock protein 70 (HSP70) homologue, BiP/GRP78, which is a peptide-dependent ATPase that binds unfolded/misfolded proteins and releases them upon ATP binding. Since exogenous factors can also reduce protein misfolding and aggregation in the ER, such as chemical chaperones and antioxidants, these treatments have potential therapeutic benefit for ER protein aggregation-associated diseases.

Keywords:  Amyloid; BiP/GRP78; CANX/CALR; CFTR; Clotting factor VIII; Proinsulin; UPR

DOI:  https://doi.org/10.1007/978-3-030-67696-4_6
Prog Mol Subcell Biol. 2021 ;59 99-114

Endoplasmic Reticulum (ER) and ER-Phagy.

Marisa Loi, Alessandro Marazza, Maurizio Molinari.

  The endoplasmic reticulum (ER) is a biosynthetic organelle in eukaryotic cells. Its capacity to produce proteins, lipids and oligosaccharides responds to physiologic and pathologic demand. The transcriptional and translational unfolded protein response (UPR) programs increase ER size and activity. In contrast, ER-phagy programs in all their flavors select ER subdomains for lysosomal clearance. These programs are activated by nutrient deprivation, accumulation of excess ER (recov-ER-phagy), production of misfolded proteins that cannot be degraded by ER-associated degradation and that are removed from cells by the so-called ER-to-lysosome-associated degradation (ERLAD). Selection of ER subdomains to be cleared from cells relies on ER-phagy receptors, a class of membrane-bound proteins displaying cytosolic domains that engage the cytosolic ubiquitin-like protein LC3. Mechanistically, ER clearance proceeds via macro-ER-phagy, micro-ER-phagy and LC3-regulated vesicular delivery.

Keywords:  Autophagy; ER-phagy receptors; ERLAD; Endoplasmic reticulum; LC3; Macro-ER-phagy and micro-ER-phagy; Vesicular transport

DOI:  https://doi.org/10.1007/978-3-030-67696-4_5
Autophagy. 2021 May 24. 1-23

Transcription- and phosphorylation-dependent control of a functional interplay between XBP1s and PINK1 governs mitophagy and potentially impacts Parkinson disease pathophysiology.

Wejdane El Manaa, Eric Duplan, Thomas Goiran, Inger Lauritzen, Loan Vaillant Beuchot, Sandra Lacas-Gervais, Vanessa Alexandra Morais, Han You, Ling Qi, Mario Salazar, Umut Ozcan, Mounia Chami, Frédéric Checler, Cristine Alves da Costa.

  Parkinson disease (PD)-affected brains show consistent endoplasmic reticulum (ER) stress and mitophagic dysfunctions. The mechanisms underlying these perturbations and how they are directly linked remain a matter of questions. XBP1 is a transcription factor activated upon ER stress after unconventional splicing by the nuclease ERN1/IREα thereby yielding XBP1s, whereas PINK1 is a kinase considered as the sensor of mitochondrial physiology and a master gatekeeper of mitophagy process. We showed that XBP1s transactivates PINK1 in human cells, primary cultured neurons and mice brain, and triggered a pro-mitophagic phenotype that was fully dependent of endogenous PINK1. We also unraveled a PINK1-dependent phosphorylation of XBP1s that conditioned its nuclear localization and thereby, governed its transcriptional activity. PINK1-induced XBP1s phosphorylation occurred at residues reminiscent of, and correlated to, those phosphorylated in substantia nigra of sporadic PD-affected brains. Overall, our study delineated a functional loop between XBP1s and PINK1 governing mitophagy that was disrupted in PD condition.Abbreviations: 6OHDA: 6-hydroxydopamine; baf: bafilomycin A1; BECN1: beclin 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CCCP: carbonyl cyanide chlorophenylhydrazone; COX8A: cytochrome c oxidase subunit 8A; DDIT3/CHOP: DNA damage inducible transcript 3; EGFP: enhanced green fluorescent protein; ER: endoplasmic reticulum; ERN1/IRE1α: endoplasmic reticulum to nucleus signaling 1; FACS: fluorescence-activated cell sorting; HSPD1/HSP60: heat shock protein family D (Hsp60) member 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFN2: mitofusin 2; OPTN: optineurin; PD: Parkinson disease; PINK1: PTEN-induced kinase 1; PCR: polymerase chain reaction:; PRKN: parkin RBR E3 ubiquitin protein ligase; XBP1s [p-S61A]: XBP1s phosphorylated at serine 61; XBP1s [p-T48A]: XBP1s phosphorylated at threonine 48; shRNA: short hairpin RNA, SQSTM1/p62: sequestosome 1; TIMM23: translocase of inner mitochondrial membrane 23; TM: tunicamycin; TMRM: tetramethyl rhodamine methylester; TOMM20: translocase of outer mitochondrial membrane 20; Toy: toyocamycin; TP: thapsigargin; UB: ubiquitin; UB (S65): ubiquitin phosphorylated at serine 65; UPR: unfolded protein response, XBP1: X-box binding protein 1; XBP1s: spliced X-box binding protein 1.

Keywords:  Mitophagy; PINK1; Parkinson disease; XBP1; phosphorylation; transcription; unfolded protein response

DOI:  https://doi.org/10.1080/15548627.2021.1917129
Prog Mol Subcell Biol. 2021 ;59 239-278

Disruption of Endoplasmic Reticulum Proteostasis in Age-Related Nervous System Disorders.

Danilo B Medinas, Younis Hazari, Claudio Hetz.

  Endoplasmic reticulum (ER) stress is a prominent cellular alteration of diseases impacting the nervous system that are associated to the accumulation of misfolded and aggregated protein species during aging. The unfolded protein response (UPR) is the main pathway mediating adaptation to ER stress, but it can also trigger deleterious cascades of inflammation and cell death leading to cell dysfunction and neurodegeneration. Genetic and pharmacological studies in experimental models shed light into molecular pathways possibly contributing to ER stress and the UPR activation in human neuropathies. Most of experimental models are, however, based on the overexpression of mutant proteins causing familial forms of these diseases or the administration of neurotoxins that induce pathology in young animals. Whether the mechanisms uncovered in these models are relevant for the etiology of the vast majority of age-related sporadic forms of neurodegenerative diseases is an open question. Here, we provide a systematic analysis of the current evidence linking ER stress to human pathology and the main mechanisms elucidated in experimental models. Furthermore, we highlight the recent association of metabolic syndrome to increased risk to undergo neurodegeneration, where ER stress arises as a common denominator in the pathogenic crosstalk between peripheral organs and the nervous system.

Keywords:  Aging; ER stress; Metabolic syndrome; Neurodegenerative diseases; Protein misfolding

DOI:  https://doi.org/10.1007/978-3-030-67696-4_12
Prog Mol Subcell Biol. 2021 ;59 279-303

Endoplasmic Reticulum Homeostasis and Stress Responses in Caenorhabditis elegans.

Sun-Kyung Lee.

  The unfolded protein response (UPR) is an evolutionarily conserved adaptive regulatory pathway that alleviates protein-folding defects in the endoplasmic reticulum (ER). Physiological demands, environmental perturbations and pathological conditions can cause accumulation of unfolded proteins in the ER and the stress signal is transmitted to the nucleus to turn on a series of genes to respond the challenge. In metazoan, the UPR pathways consisted of IRE1/XBP1, PEK-1 and ATF6, which function in parallel and downstream transcriptional activation triggers the proteostasis networks consisting of molecular chaperones, protein degradation machinery and other stress response pathways ((Labbadia J, Morimoto RI, F1000Prime Rep 6:7, 2014); (Shen X, Ellis RE, Lee K, Annu Rev Biochem 28:893-903, 2014)). The integrated responses act on to resolve the ER stress by increasing protein folding capacity, attenuating ER-loading translation, activating ER-associated proteasomal degradation (ERAD), and regulating IRE1-dependent decay of mRNA (RIDD). Therefore, the effective UPR to internal and external causes is linked to the multiple pathophysiological conditions such as aging, immunity, and neurodegenerative diseases. Recent development in the research of the UPR includes cell-nonautonomous features of the UPR, interplay between the UPR and other stress response pathways, unconventional UPR inducers, and noncanonical UPR independent of the three major branches, originated from multiple cellular and molecular machineries in addition to ER. Caenorhabditis elegans model system has critically contributed to these unprecedented aspects of the ER UPR and broadens the possible therapeutic targets to treat the ER-stress associated human disorders and time-dependent physiological deterioration of aging.

Keywords:  Aging; Caenorhabditis elegans; ER homeostasis; Proteostasis; Unfolded protein response

DOI:  https://doi.org/10.1007/978-3-030-67696-4_13
Biochem Biophys Res Commun. 2021 May 23. pii: S0006-291X(21)00809-3. [Epub ahead of print]562 69-75

A novel XBP1 variant is highly enriched in cancer tissues and is specifically required for cancer cell survival.

Yongwang Zhong, Wenjing Yan, Jingjing Ruan, Mike Fang, Rena G Lapidus, Shaojun Du, Shengyun Fang.

  XBP1 is a basic leucine zipper (bZIP) transcription factor and a key mediator of the endoplasmic reticulum (ER) stress-activated unfolded protein response (UPR). XBP1-mediated transcription facilitates cell adaptation to ER stress and also promotes tumor progression, while suppressing anti-tumor immunity. Here we report a novel XBP1 variant, namely XBP1 variant 1 (XBP1v1, Xv1 for short), that is specifically required for survival of cancer cells. Xv1 contains a cryptic first exon that is conserved only in humans and great apes. Comparing to XBP1, Xv1 encodes a protein with a different N-terminal sequence containing 25 amino acids. Analysis of RNAseq database reveals that Xv1 is broadly expressed across cancer types but almost none in normal tissues. Elevated Xv1 expression is associated with poor survival of patients with several types of cancer. Knockdown of Xv1 induces death of multiple cancer cell lines but has little effect on non-cancerous cells in vitro. Moreover, knockdown of Xv1 also inhibits growth of a xenograft breast tumor in mice. Together, our results indicate that Xv1 is essential for survival of cancer cells.

Keywords:  Cancer cell survival; XBP1; XBP1v1; Xv1

DOI:  https://doi.org/10.1016/j.bbrc.2021.05.038
Sci Signal. 2021 May 25. pii: eaaz4401. [Epub ahead of print]14(684):

Phosphorylation of Pal2 by the protein kinases Kin1 and Kin2 modulates HAC1 mRNA splicing in the unfolded protein response in yeast.

Chandrima Ghosh, Jagadeesh Kumar Uppala, Leena Sathe, Charlotte I Hammond, Ashish Anshu, P Raj Pokkuluri, Benjamin E Turk, Madhusudan Dey.

During cellular stress in the budding yeast Saccharomyces cerevisiae, an endoplasmic reticulum (ER)-resident dual kinase and RNase Ire1 splices an intron from HAC1 mRNA in the cytosol, thereby releasing its translational block. Hac1 protein then activates an adaptive cellular stress response called the unfolded protein response (UPR) that maintains ER homeostasis. The polarity-inducing protein kinases Kin1 and Kin2 contribute to HAC1 mRNA processing. Here, we showed that an RNA-protein complex that included the endocytic proteins Pal1 and Pal2 mediated HAC1 mRNA splicing downstream of Kin1 and Kin2. We found that Pal1 and Pal2 bound to the 3' untranslated region (3'UTR) of HAC1 mRNA, and a yeast strain lacking both Pal1 and Pal2 was deficient in HAC1 mRNA processing. We also showed that Kin1 and Kin2 directly phosphorylated Pal2, and that a nonphosphorylatable Pal2 mutant could not rescue the UPR defect in a pal1Δ pal2Δ strain. Thus, our work uncovers a Kin1/2-Pal2 signaling pathway that coordinates HAC1 mRNA processing and ER homeostasis.

DOI: https://doi.org/10.1126/scisignal.aaz4401
J Invest Dermatol. 2021 May 25. pii: S0022-202X(21)01243-4. [Epub ahead of print]

The XBP1-MARCH5-MFN2 axis confers ER stress resistance by coordinating mitochondrial fission and mitophagy in melanoma.

Huina Wang, Xiuli Yi, Sen Guo, Sijia Wang, Jinyuan Ma, Tao Zhao, Qiong Shi, Yangzi Tian, Hao Wang, Lintao Jia, Tianwen Gao, Chunying Li, Weinan Guo.

  Melanoma cells are relatively resistant to ER stress, which contributes to tumor progression under stressful conditions and renders tolerance to ER stress-inducing therapeutic agents. Mitochondria are tightly interconnected with ER. However, whether mitochondria play a role in regulating ER stress resistance in melanoma remains elusive. Herein, we reported that the XBP1-MARCH5-MFN2 axis conferred ER stress resistance by coordinating mitochondrial fission and mitophagy in melanoma. Our integrative bioinformatics first revealed that the down-regulation of mitochondrial genes was highly correlated with UPR activation in melanoma. Then we proved that mitochondrial fission and mitophagy were prominently induced to contribute to ER stress resistance both in vitro and in vivo by maintaining mitochondrial function. Mechanistically, the activation of IRE1α/ATF6-XBP1 branches of UPR promoted the transcription of E3 ligase MARCH5 to facilitate the ubiquitination and degradation of MFN2, which thereby triggered mitochondrial fission and mitophagy under ER stress. Together, our findings demonstrate a regulatory axis that links mitochondrial fission and mitophagy to the resistance to ER stress. Targeting mitochondrial quality control machinery can be exploited as an approach to reinforce the efficacy of ER stress-inducing agents against cancer.

Keywords:  ER stress; MFN2; melanoma; mitochondrial fission; mitophagy

DOI:  https://doi.org/10.1016/j.jid.2021.03.031
Methods Mol Biol. 2021 ;2255 13-20

Detection of Unfolded Protein Response by Polymerase Chain Reaction.

Alexander Paridon, Alexandra Fox, Ayesha B Alvero.

  The unfolded protein response is a cellular adaptive mechanism localized in the endoplasmic reticulum. It involves three phases: the detection of increased presence of unfolded proteins as a result of cellular stressors; the execution of an adaptive cascade of events aimed at the enhancement of proper protein folding and degradation of improperly folded proteins; and finally, when stress is not alleviated, the execution of programmed cell death. The main effectors of the UPR are transcription factors involved in the upregulation of either chaperone proteins or proapoptotic proteins. Two of these transcription factors are CHOP and the spliced variant of XBP-1 (XBP1s). In this chapter, we describe a quantitative PCR method to detect the upregulation of CHOP and XBP1s mRNA during Tunicamycin-induced UPR.

Keywords:  BiP; CHOP; RT-PCR; Real-time PCR; Spliced XBP1; UPR

DOI:  https://doi.org/10.1007/978-1-0716-1162-3_2
Nat Metab. 2021 May;3(5): 682-700

In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.

Jérémie Charbord, Lipeng Ren, Rohit B Sharma, Anna Johansson, Rasmus Ågren, Lianhe Chu, Dominika Tworus, Nadja Schulz, Pierre Charbord, Andrew F Stewart, Peng Wang, Laura C Alonso, Olov Andersson.

It is known that β cell proliferation expands the β cell mass during development and under certain hyperglycemic conditions in the adult, a process that may be used for β cell regeneration in diabetes. Here, through a new high-throughput screen using a luminescence ubiquitination-based cell cycle indicator (LUCCI) in zebrafish, we identify HG-9-91-01 as a driver of proliferation and confirm this effect in mouse and human β cells. HG-9-91-01 is an inhibitor of salt-inducible kinases (SIKs), and overexpression of Sik1 specifically in β cells blocks the effect of HG-9-91-01 on β cell proliferation. Single-cell transcriptomic analyses of mouse β cells demonstrate that HG-9-91-01 induces a wave of activating transcription factor (ATF)6-dependent unfolded protein response (UPR) before cell cycle entry. Importantly, the UPR wave is not associated with an increase in insulin expression. Additional mechanistic studies indicate that HG-9-91-01 induces multiple signalling effectors downstream of SIK inhibition, including CRTC1, CRTC2, ATF6, IRE1 and mTOR, which integrate to collectively drive β cell proliferation.

DOI: https://doi.org/10.1038/s42255-021-00391-x