bims-unfpre 2022-05-08 papers

Issue of 2022‒05‒08
five papers selected by
Susan Logue
University of Manitoba

Nat Commun. 2022 May 06. 13(1): 2493

Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer.

Aitor Almanza, Katarzyna Mnich, Arnaud Blomme, Claire M Robinson, Giovanny Rodriguez-Blanco, Sylwia Kierszniowska, Eoghan P McGrath, Matthieu Le Gallo, Eleftherios Pilalis, Johannes V Swinnen, Aristotelis Chatziioannou, Eric Chevet, Adrienne M Gorman, Afshin Samali.

IRE1α is constitutively active in several cancers and can contribute to cancer progression. Activated IRE1α cleaves XBP1 mRNA, a key step in production of the transcription factor XBP1s. In addition, IRE1α cleaves select mRNAs through regulated IRE1α-dependent decay (RIDD). Accumulating evidence implicates IRE1α in the regulation of lipid metabolism. However, the roles of XBP1s and RIDD in this process remain ill-defined. In this study, transcriptome and lipidome profiling of triple negative breast cancer cells subjected to pharmacological inhibition of IRE1α reveals changes in lipid metabolism genes associated with accumulation of triacylglycerols (TAGs). We identify DGAT2 mRNA, encoding the rate-limiting enzyme in TAG biosynthesis, as a RIDD target. Inhibition of IRE1α, leads to DGAT2-dependent accumulation of TAGs in lipid droplets and sensitizes cells to nutritional stress, which is rescued by treatment with the DGAT2 inhibitor PF-06424439. Our results highlight the importance of IRE1α RIDD activity in reprograming cellular lipid metabolism.

DOI: https://doi.org/10.1038/s41467-022-30159-0

Nat Commun. 2022 May 06. 13(1): 2501

Stress-induced protein disaggregation in the endoplasmic reticulum catalysed by BiP.

Eduardo Pinho Melo, Tasuku Konno, Ilaria Farace, Mosab Ali Awadelkareem, Lise R Skov, Fernando Teodoro, Teresa P Sancho, Adrienne W Paton, James C Paton, Matthew Fares, Pedro M R Paulo, Xin Zhang, Edward Avezov.

Protein synthesis is supported by cellular machineries that ensure polypeptides fold to their native conformation, whilst eliminating misfolded, aggregation prone species. Protein aggregation underlies pathologies including neurodegeneration. Aggregates' formation is antagonised by molecular chaperones, with cytoplasmic machinery resolving insoluble protein aggregates. However, it is unknown whether an analogous disaggregation system exists in the Endoplasmic Reticulum (ER) where ~30% of the proteome is synthesised. Here we show that the ER of a variety of mammalian cell types, including neurons, is endowed with the capability to resolve protein aggregates under stress. Utilising a purpose-developed protein aggregation probing system with a sub-organellar resolution, we observe steady-state aggregate accumulation in the ER. Pharmacological induction of ER stress does not augment aggregates, but rather stimulate their clearance within hours. We show that this dissagregation activity is catalysed by the stress-responsive ER molecular chaperone - BiP. This work reveals a hitherto unknow, non-redundant strand of the proteostasis-restorative ER stress response.

DOI: https://doi.org/10.1038/s41467-022-30238-2

RSC Adv. 2020 May 20. 10(33): 19720-19729

Deciphering the selectivity of inhibitor MKC9989 towards residue K907 in IRE1α; a multiscale in silico approach.

Sayyed Jalil Mahdizadeh, Antonio Carlesso, Leif A Eriksson.

The selectivity of the ligand MKC9989, as inhibitor of the Inositol-Requiring Enzyme 1α (IRE1α) transmembrane kinase/ribonuclease protein, towards the residue K907 in the context of Schiff base formation, has been investigated by employing an array of in silico techniques including Multi-Conformation Continuum Electrostatics (MCCE) simulations, Quantum Mechanics/Molecular Mechanics (QM/MM) calculations, covalent docking, and Molecular Dynamics (MD) simulations. According to the MCCE results, K907 displays the lowest pK a value among all 23 lysine residues in IRE1α. The MMCE simulations also indicate a critical interaction between K907 and D885 within the hydrophobic pocket which increases significantly at low protein dielectric constants. The QM/MM calculations reveal a spontaneous proton transfer from K907 to D885, consistent with the low pK a value of K907. A Potential Energy Surface (PES) scan confirms the lack of energy barrier and transition state associated with this proton transfer reaction. Covalent docking and MD simulations verify that the protein pocket containing K907 can effectively stabilize the inhibitor by strong π-π and hydrogen bonding interactions. In addition, Radial Distribution Function (RDF) analysis shows that the imine group formed in the chemical reaction between MKC9989 and K907 is inaccessible to water molecules and thus the probability of imine hydrolysis is almost zero. The results of the current study explain the high selectivity of the MKC9989 inhibitor towards the K907 residue of IRE1α.

DOI: https://doi.org/10.1039/d0ra01895c

J Biol Chem. 2022 Apr 29. pii: S0021-9258(22)00437-9. [Epub ahead of print] 101997

Phosphorylation at Ser724 of the ER stress sensor IRE1α governs its activation state and limits ER stress-induced hepatosteatosis.

Yang Li, Shijia Huang, Jingsi Wang, Jianli Dai, Jie Cai, Shuai Yan, Zhiliang Huang, Shengqi He, Ping Wang, Jianmiao Liu, Yong Liu.

Inositol-requiring enzyme 1 (IRE1) is an evolutionarily conserved sensor of endoplasmic reticulum (ER) stress and mediates a key branch of the unfolded protein response (UPR) in eukaryotic cells. It is an ER-resident transmembrane protein that possesses Ser/Thr protein kinase and endoribonuclease (RNase) activities in its cytoplasmic region. IRE1 is activated through dimerization/oligomerization and autophosphorylation at multiple sites, acting through its RNase activity to restore the functional capacity of the ER. However, it remains poorly defined in vivo how the autophosphorylation events of endogenous IRE1 govern its dynamic activation and functional output. Here we generated a mouse model harboring a S724A knock-in mutation (Ern1S724A/S724A) and investigated the importance of phosphorylation at Ser724 located within the kinase activation loop of murine IRE1α. We found that in mouse embryonic fibroblast (MEF) cells as well as in primary hepatocytes, S724A mutation resulted in markedly reduced rate of IRE1α autophosphorylation in parallel with blunted activation of its RNase activity to catalyze Xbp1 mRNA splicing. Furthermore, ablation of IRE1α phosphorylation at Ser724 exacerbated ER stress-induced hepatic steatosis in Tunicamycin-treated Ern1S724A/S724A mice. This was accompanied by significantly decreased production of XBP1s protein but increased CHOP protein levels in the liver, along with suppressed expression of key metabolic regulators of fatty acid β-oxidation and lipid secretion. These results demonstrate a critical role of phosphorylation at Ser724 of IRE1α in dynamically controlling its kinase activity, and thus its autophosphorylation state, which is coupled to the activation of its RNase activity in counteracting hepatic steatosis under ER stress conditions.

Keywords: ER stress; Hepatic steatosis; IRE1α; RIDD; Xbp1; autophosphorylation

DOI: https://doi.org/10.1016/j.jbc.2022.101997

Hepatology. 2022 May 06.

Endoplasmic Reticulum Stress in Liver Diseases.

Amir Ajoolabady, Neil Kaplowitz, Cynthia Lebeaupin, Guido Kroemer, Randal J Kaufman, Harmeet Malhi, Jun Ren.

The endoplasmic reticulum (ER) is an intracellular organelle that fosters the correct folding of linear polypeptides and proteins, a process tightly governed by the ER-resident enzymes and chaperones. Failure to shape the proper 3-dimensional architecture of proteins culminates in the accumulation of misfolded or unfolded proteins within the ER, disturbs ER homeostasis, and leads to canonically defined ER stress. Recent studies have elucidated that cellular perturbations, such as lipotoxicity, can also lead to ER stress. In response to ER stress, the unfolded protein response (UPR) is activated to reestablish ER homeostasis ("adaptive UPR") or conversely, to provoke cell death when ER stress is overwhelmed and sustained ("maladaptive UPR"). It is well documented that ER stress contributes to the onset and progression of multiple hepatic pathologies including non-alcoholic fatty liver disease (NAFLD), alcoholic liver disease (ALD), viral hepatitis, liver ischemia, drug toxicity, and liver cancers. Here, we review key studies dealing with the emerging role of ER stress and the UPR in the pathophysiology of liver diseases from cellular, murine, and human models. Specifically, we will summarize current available knowledge on pharmacological and non-pharmacological interventions that may be employed to target maladaptive UPR for the treatment of non-malignant liver diseases.

Keywords: ER stress; Liver cancer; Liver disease; Liver toxicity; Liver viral infections; UPR

DOI: https://doi.org/10.1002/hep.32562