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Rajakumar T, Hossain MA, Stopka SA, Micoogullari Y, Ang J, Agar NYR, Hanna J. Dysregulation of ceramide metabolism causes phytoceramide-dependent induction of the unfolded protein response. Mol Biol Cell 2024; 35:ar117. [PMID: 39024283 DOI: 10.1091/mbc.e24-03-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
The unfolded protein response (UPR) detects and mitigates the harmful effects of dysregulated endoplasmic reticulum (ER) function. The UPR has been best characterized as a protein quality control response, and the sole UPR sensor in yeast, Ire1, is known to detect misfolded ER proteins. However, recent work suggests the UPR can also sense diverse defects within the ER membrane, including increased fatty acid saturation and altered phospholipid abundance. These and other lipid-related stimuli have been referred to as lipid bilayer stress and may be sensed independently through Ire1's transmembrane domain. Here, we show that the loss of Isc1, a phospholipase that catabolizes complex ceramides, causes UPR induction, even in the absence of exogenous stress. A series of chemical and genetic approaches identified a requirement for very long-chain fatty acid (VLCFA)-containing phytoceramides for UPR induction. In parallel, comprehensive lipidomics analyses identified large increases in the abundance of specific VLCFA-containing phytoceramides in the isc1Δ mutant. We failed to identify evidence of an accompanying defect in protein quality control or ER-associated protein degradation. These results extend our understanding of lipid bilayer stress in the UPR and provide a foundation for mechanistic investigation of this fascinating intersection between ceramide metabolism, membrane homeostasis, and the UPR.
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Affiliation(s)
- Tamayanthi Rajakumar
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Md Amin Hossain
- Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Sylwia A Stopka
- Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Yagmur Micoogullari
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Jessie Ang
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Nathalie Y R Agar
- Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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2
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Ernst R, Renne MF, Jain A, von der Malsburg A. Endoplasmic Reticulum Membrane Homeostasis and the Unfolded Protein Response. Cold Spring Harb Perspect Biol 2024; 16:a041400. [PMID: 38253414 PMCID: PMC11293554 DOI: 10.1101/cshperspect.a041400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The endoplasmic reticulum (ER) is the key organelle for membrane biogenesis. Most lipids are synthesized in the ER, and most membrane proteins are first inserted into the ER membrane before they are transported to their target organelle. The composition and properties of the ER membrane must be carefully controlled to provide a suitable environment for the insertion and folding of membrane proteins. The unfolded protein response (UPR) is a powerful signaling pathway that balances protein and lipid production in the ER. Here, we summarize our current knowledge of how aberrant compositions of the ER membrane, referred to as lipid bilayer stress, trigger the UPR.
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Affiliation(s)
- Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Mike F Renne
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Aamna Jain
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Alexander von der Malsburg
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
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3
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Kettel P, Karagöz GE. Endoplasmic reticulum: Monitoring and maintaining protein and membrane homeostasis in the endoplasmic reticulum by the unfolded protein response. Int J Biochem Cell Biol 2024; 172:106598. [PMID: 38768891 DOI: 10.1016/j.biocel.2024.106598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
The endoplasmic reticulum (ER) regulates essential cellular processes, including protein folding, lipid synthesis, and calcium homeostasis. The ER homeostasis is maintained by a conserved set of signaling cascades called the Unfolded Protein Response (UPR). How the UPR senses perturbations in ER homeostasis has been the subject of active research for decades. In metazoans, the UPR consists of three ER-membrane embedded sensors: IRE1, PERK and ATF6. These sensors detect the accumulation of misfolded proteins in the ER lumen and adjust protein folding capacity according to cellular needs. Early work revealed that the ER-resident chaperone BiP binds to all three UPR sensors in higher eukaryotes and BiP binding was suggested to regulate their activity. More recent data have shown that in higher eukaryotes the interaction of the UPR sensors with a complex network of chaperones and misfolded proteins modulates their activation and deactivation dynamics. Furthermore, emerging evidence suggests that the UPR monitors ER membrane integrity beyond protein folding defects. However, the mechanistic and structural basis of UPR activation by proteotoxic and lipid bilayer stress in higher eukaryotes remains only partially understood. Here, we review the current understanding of novel protein interaction networks and the contribution of the lipid membrane environment to UPR activation.
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Affiliation(s)
- Paulina Kettel
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Medical University of Vienna, Vienna, Austria.
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4
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Białek W, Hryniewicz-Jankowska A, Czechowicz P, Sławski J, Collawn JF, Czogalla A, Bartoszewski R. The lipid side of unfolded protein response. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159515. [PMID: 38844203 DOI: 10.1016/j.bbalip.2024.159515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/16/2024] [Accepted: 05/31/2024] [Indexed: 06/12/2024]
Abstract
Although our current knowledge of the molecular crosstalk between the ER stress, the unfolded protein response (UPR), and lipid homeostasis remains limited, there is increasing evidence that dysregulation of either protein or lipid homeostasis profoundly affects the other. Most research regarding UPR signaling in human diseases has focused on the causes and consequences of disrupted protein folding. The UPR itself consists of very complex pathways that function to not only maintain protein homeostasis, but just as importantly, modulate lipid biogenesis to allow the ER to adjust and promote cell survival. Lipid dysregulation is known to activate many aspects of the UPR, but the complexity of this crosstalk remains a major research barrier. ER lipid disequilibrium and lipotoxicity are known to be important contributors to numerous human pathologies, including insulin resistance, liver disease, cardiovascular diseases, neurodegenerative diseases, and cancer. Despite their medical significance and continuous research, however, the molecular mechanisms that modulate lipid synthesis during ER stress conditions, and their impact on cell fate decisions, remain poorly understood. Here we summarize the current view on crosstalk and connections between altered lipid metabolism, ER stress, and the UPR.
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Affiliation(s)
- Wojciech Białek
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | | | - Paulina Czechowicz
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Jakub Sławski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA
| | - Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Rafał Bartoszewski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland.
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5
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Igal RA. Death and the desaturase: implication of Stearoyl-CoA desaturase-1 in the mechanisms of cell stress, apoptosis, and ferroptosis. Biochimie 2024:S0300-9084(24)00125-1. [PMID: 38823621 DOI: 10.1016/j.biochi.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/05/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Growth and proliferation of normal and cancerous cells necessitate a finely-tuned regulation of lipid metabolic pathways to ensure the timely supply of structural, energetic, and signaling lipid molecules. The synthesis and remodeling of lipids containing fatty acids with an appropriate carbon length and insaturation level are required for supporting each phase of the mechanisms of cell replication and survival. Mammalian Stearoyl-CoA desaturases (SCD), particularly SCD1, play a crucial role in modulating the fatty acid composition of cellular lipids, converting saturated fatty acids (SFA) into monounsaturated fatty acids (MUFA) in the endoplasmic reticulum (ER). Extensive research has elucidated in great detail the participation of SCD1 in the molecular mechanisms that govern cell replication in normal and cancer cells. More recently, investigations have shed new light on the functional and regulatory role of the Δ9-desaturase in the processes of cell stress and cell death. This review will examine the latest findings on the involvement of SCD1 in the molecular pathways of cell survival, particularly on the mechanisms of ER stress and autophagy, as well in apoptotic and non-apoptotic cell death.
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Affiliation(s)
- R Ariel Igal
- Institute of Human Nutrition and Department of Pediatrics, Columbia University Irving Medical Center, New York City, New York.
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6
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Cullen JK, Yap PY, Ferguson B, Bruce ZC, Koyama M, Handoko H, Hendrawan K, Simmons JL, Brooks KM, Johns J, Wilson ES, de Souza MMA, Broit N, Stewart P, Shelley D, McMahon T, Ogbourne SM, Nguyen TH, Lim YC, Pagani A, Appendino G, Gordon VA, Reddell PW, Boyle GM, Parsons PG. Tigilanol tiglate is an oncolytic small molecule that induces immunogenic cell death and enhances the response of both target and non-injected tumors to immune checkpoint blockade. J Immunother Cancer 2024; 12:e006602. [PMID: 38658031 PMCID: PMC11043783 DOI: 10.1136/jitc-2022-006602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Tigilanol tiglate (TT) is a protein kinase C (PKC)/C1 domain activator currently being developed as an intralesional agent for the treatment of various (sub)cutaneous malignancies. Previous work has shown that intratumoral (I.T.) injection of TT causes vascular disruption with concomitant tumor ablation in several preclinical models of cancer, in addition to various (sub)cutaneous tumors presenting in the veterinary clinic. TT has completed Phase I dose escalation trials, with some patients showing signs of abscopal effects. However, the exact molecular details underpinning its mechanism of action (MoA), together with its immunotherapeutic potential in oncology remain unclear. METHODS A combination of microscopy, luciferase assays, immunofluorescence, immunoblotting, subcellular fractionation, intracellular ATP assays, phagocytosis assays and mixed lymphocyte reactions were used to probe the MoA of TT in vitro. In vivo studies with TT used MM649 xenograft, CT-26 and immune checkpoint inhibitor refractory B16-F10-OVA tumor bearing mice, the latter with or without anti-programmed cell death 1 (PD-1)/anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) mAb treatment. The effect of TT at injected and non-injected tumors was also assessed. RESULTS Here, we show that TT induces the death of endothelial and cancer cells at therapeutically relevant concentrations via a caspase/gasdermin E-dependent pyroptopic pathway. At therapeutic doses, our data demonstrate that TT acts as a lipotoxin, binding to and promoting mitochondrial/endoplasmic reticulum (ER) dysfunction (leading to unfolded protein responsemt/ER upregulation) with subsequent ATP depletion, organelle swelling, caspase activation, gasdermin E cleavage and induction of terminal necrosis. Consistent with binding to ER membranes, we found that TT treatment promoted activation of the integrated stress response together with the release/externalization of damage-associated molecular patterns (HMGB1, ATP, calreticulin) from cancer cells in vitro and in vivo, characteristics indicative of immunogenic cell death (ICD). Confirmation of ICD in vivo was obtained through vaccination and rechallenge experiments using CT-26 colon carcinoma tumor bearing mice. Furthermore, TT also reduced tumor volume, induced immune cell infiltration, as well as improved survival in B16-F10-OVA tumor bearing mice when combined with immune checkpoint blockade. CONCLUSIONS These data demonstrate that TT is an oncolytic small molecule with multiple targets and confirms that cell death induced by this compound has the potential to augment antitumor responses to immunotherapy.
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Affiliation(s)
- Jason K Cullen
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- The University of Queensland, Brisbane, Queensland, Australia
- QBiotics Group Limited, Brisbane, Queensland, Australia
| | - Pei-Yi Yap
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Blake Ferguson
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Zara C Bruce
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Motoko Koyama
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Herlina Handoko
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kevin Hendrawan
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jacinta L Simmons
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- The University of Queensland, Brisbane, Queensland, Australia
| | - Kelly M Brooks
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jenny Johns
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Emily S Wilson
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | - Natasa Broit
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Praphaporn Stewart
- University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Daniel Shelley
- University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Tracey McMahon
- University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Steven M Ogbourne
- QBiotics Group Limited, Brisbane, Queensland, Australia
- University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Tam Hong Nguyen
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yi Chieh Lim
- Danish Cancer Society Research Centre, Copenhagen DK, Denmark
| | - Alberto Pagani
- Dipartimento di Scienze del Farmaco, Università Degli Studi del Piemonte Orientale, Novara, Italy
| | - Giovanni Appendino
- Dipartimento di Scienze del Farmaco, Università Degli Studi del Piemonte Orientale, Novara, Italy
| | | | | | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- The University of Queensland, Brisbane, Queensland, Australia
| | - Peter G Parsons
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- QBiotics Group Limited, Brisbane, Queensland, Australia
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7
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Pierre AS, Gavriel N, Guilbard M, Ogier-Denis E, Chevet E, Delom F, Igbaria A. Modulation of Protein Disulfide Isomerase Functions by Localization: The Example of the Anterior Gradient Family. Antioxid Redox Signal 2024. [PMID: 38411504 DOI: 10.1089/ars.2024.0561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Significance: Oxidative folding within the endoplasmic reticulum (ER) introduces disulfide bonds into nascent polypeptides, ensuring proteins' stability and proper functioning. Consequently, this process is critical for maintaining proteome integrity and overall health. The productive folding of thousands of secretory proteins requires stringent quality control measures, such as the unfolded protein response (UPR) and ER-Associated Degradation (ERAD), which contribute significantly to maintaining ER homeostasis. ER-localized protein disulfide isomerases (PDIs) play an essential role in each of these processes, thereby contributing to various aspects of ER homeostasis, including maintaining redox balance, proper protein folding, and signaling from the ER to the nucleus. Recent Advances: Over the years, there have been increasing reports of the (re)localization of PDI family members and other ER-localized proteins to various compartments. A prime example is the anterior gradient (AGR) family of PDI proteins, which have been reported to relocate to the cytosol or the extracellular environment, acquiring gain of functions that intersect with various cellular signaling pathways. Critical Issues: Here, we summarize the functions of PDIs and their gain or loss of functions in non-ER locations. We will focus on the activity, localization, and function of the AGR proteins: AGR1, AGR2, and AGR3. Future Directions: Targeting PDIs in general and AGRs in particular is a promising strategy in different human diseases. Thus, there is a need for innovative strategies and tools aimed at targeting PDIs; those strategies should integrate the specific localization and newly acquired functions of these PDIs rather than solely focusing on their canonical roles.
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Affiliation(s)
- Arvin S Pierre
- INSERM U1242, University of Rennes, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Noa Gavriel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Marianne Guilbard
- ARTiSt Group, Univ. Bordeaux, INSERM U1312, Institut Bergonié, Bordeaux, France
- Thabor Therapeutics, Paris, France
| | - Eric Ogier-Denis
- INSERM U1242, University of Rennes, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Frederic Delom
- ARTiSt Group, Univ. Bordeaux, INSERM U1312, Institut Bergonié, Bordeaux, France
| | - Aeid Igbaria
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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8
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Le Goupil S, Laprade H, Aubry M, Chevet E. Exploring the IRE1 interactome: From canonical signaling functions to unexpected roles. J Biol Chem 2024; 300:107169. [PMID: 38494075 PMCID: PMC11007444 DOI: 10.1016/j.jbc.2024.107169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024] Open
Abstract
The unfolded protein response is a mechanism aiming at restoring endoplasmic reticulum (ER) homeostasis and is likely involved in other adaptive pathways. The unfolded protein response is transduced by three proteins acting as sensors and triggering downstream signaling pathways. Among them, inositol-requiring enzyme 1 alpha (IRE1α) (referred to as IRE1 hereafter), an endoplasmic reticulum-resident type I transmembrane protein, exerts its function through both kinase and endoribonuclease activities, resulting in both X-box binding protein 1 mRNA splicing and RNA degradation (regulated ire1 dependent decay). An increasing number of studies have reported protein-protein interactions as regulators of these signaling mechanisms, and additionally, driving other noncanonical functions. In this review, we deliver evolutive and structural insights on IRE1 and further describe how this protein interaction network (interactome) regulates IRE1 signaling abilities or mediates other cellular processes through catalytic-independent mechanisms. Moreover, we focus on newly discovered targets of IRE1 kinase activity and discuss potentially novel IRE1 functions based on the nature of the interactome, thereby identifying new fields to explore regarding this protein's biological roles.
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Affiliation(s)
- Simon Le Goupil
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France.
| | - Hadrien Laprade
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France
| | - Marc Aubry
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France
| | - Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France
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9
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Köberlin MS, Fan Y, Liu C, Chung M, Pinto AFM, Jackson PK, Saghatelian A, Meyer T. A fast-acting lipid checkpoint in G1 prevents mitotic defects. Nat Commun 2024; 15:2441. [PMID: 38499565 PMCID: PMC10948896 DOI: 10.1038/s41467-024-46696-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
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Affiliation(s)
- Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94111, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
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10
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Jang W, Haucke V. ER remodeling via lipid metabolism. Trends Cell Biol 2024:S0962-8924(24)00023-0. [PMID: 38395735 DOI: 10.1016/j.tcb.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Unlike most other organelles found in multiple copies, the endoplasmic reticulum (ER) is a unique singular organelle within eukaryotic cells. Despite its continuous membrane structure, encompassing more than half of the cellular endomembrane system, the ER is subdivided into specialized sub-compartments, including morphological, membrane contact site (MCS), and de novo organelle biogenesis domains. In this review, we discuss recent emerging evidence indicating that, in response to nutrient stress, cells undergo a reorganization of these sub-compartmental ER domains through two main mechanisms: non-destructive remodeling of morphological ER domains via regulation of MCS and organelle hitchhiking, and destructive remodeling of specialized domains by ER-phagy. We further highlight and propose a critical role of membrane lipid metabolism in this ER remodeling during starvation.
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Affiliation(s)
- Wonyul Jang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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11
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Has C, Das SL. The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation. J Membr Biol 2023; 256:343-372. [PMID: 37650909 DOI: 10.1007/s00232-023-00289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.
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Affiliation(s)
- Chandra Has
- Department of Chemical Engineering, GSFC University, Vadodara, 391750, Gujarat, India.
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology, Palakkad, 678623, Kerala, India
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12
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Terry AR, Nogueira V, Rho H, Ramakrishnan G, Li J, Kang S, Pathmasiri KC, Bhat SA, Jiang L, Kuchay S, Cologna SM, Hay N. CD36 maintains lipid homeostasis via selective uptake of monounsaturated fatty acids during matrix detachment and tumor progression. Cell Metab 2023; 35:2060-2076.e9. [PMID: 37852255 DOI: 10.1016/j.cmet.2023.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 04/11/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023]
Abstract
A high-fat diet (HFD) promotes metastasis through increased uptake of saturated fatty acids (SFAs). The fatty acid transporter CD36 has been implicated in this process, but a detailed understanding of CD36 function is lacking. During matrix detachment, endoplasmic reticulum (ER) stress reduces SCD1 protein, resulting in increased lipid saturation. Subsequently, CD36 is induced in a p38- and AMPK-dependent manner to promote preferential uptake of monounsaturated fatty acids (MUFAs), thereby maintaining a balance between SFAs and MUFAs. In attached cells, CD36 palmitoylation is required for MUFA uptake and protection from palmitate-induced lipotoxicity. In breast cancer mouse models, CD36-deficiency induced ER stress while diminishing the pro-metastatic effect of HFD, and only a palmitoylation-proficient CD36 rescued this effect. Finally, AMPK-deficient tumors have reduced CD36 expression and are metastatically impaired, but ectopic CD36 expression restores their metastatic potential. Our results suggest that, rather than facilitating HFD-driven tumorigenesis, CD36 plays a supportive role by preventing SFA-induced lipotoxicity.
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Affiliation(s)
- Alexander R Terry
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Veronique Nogueira
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hyunsoo Rho
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Gopalakrishnan Ramakrishnan
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jing Li
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Soeun Kang
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Koralege C Pathmasiri
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sameer Ahmed Bhat
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Liping Jiang
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Shafi Kuchay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Stephanie M Cologna
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nissim Hay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA; Research and Development Section, Jesse Brown VA Medical Center, Chicago, IL 60612, USA.
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13
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Ruiz M, Devkota R, Kaper D, Ruhanen H, Busayavalasa K, Radović U, Henricsson M, Käkelä R, Borén J, Pilon M. AdipoR2 recruits protein interactors to promote fatty acid elongation and membrane fluidity. J Biol Chem 2023:104799. [PMID: 37164154 DOI: 10.1016/j.jbc.2023.104799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/12/2023] Open
Abstract
The human AdipoR2 and its C. elegans homolog PAQR-2 are multi-pass plasma membrane proteins that protect cells against membrane rigidification. However, how AdipoR2 promotes membrane fluidity mechanistically is not clear. Using 13C-labelled fatty acids, we show that AdipoR2 can promote the elongation and incorporation of membrane-fluidizing polyunsaturated fatty acids into phospholipids. To elucidate the molecular basis of these activities, we performed immunoprecipitations of tagged AdipoR2 and PAQR-2 expressed in HEK293 cells or whole C. elegans, respectively, and identified co-immunoprecipitated proteins using mass spectroscopy. We found that several of the evolutionarily conserved AdipoR2/PAQR-2 interactors are important for fatty acid elongation and incorporation into phospholipids. We experimentally verified some of these interactions, namely with the dehydratase HACD3 that is essential for the third of four steps in long-chain fatty acid elongation, and ACSL4 that is important for activation of unsaturated fatty acids and their channeling into phospholipids. We conclude that AdipoR2 and PAQR-2 can recruit protein interactors to promote the production and incorporation of unsaturated fatty acids into phospholipids.
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Affiliation(s)
- Mario Ruiz
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ranjan Devkota
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Delaney Kaper
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Hanna Ruhanen
- Helsinki University Lipidomics Unit, Helsinki Institute of Life Science, Biocenter Finland, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kiran Busayavalasa
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Uroš Radović
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Marcus Henricsson
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Reijo Käkelä
- Helsinki University Lipidomics Unit, Helsinki Institute of Life Science, Biocenter Finland, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jan Borén
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pilon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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14
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Celik C, Lee SYT, Yap WS, Thibault G. Endoplasmic reticulum stress and lipids in health and diseases. Prog Lipid Res 2023; 89:101198. [PMID: 36379317 DOI: 10.1016/j.plipres.2022.101198] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/14/2022]
Abstract
The endoplasmic reticulum (ER) is a complex and dynamic organelle that regulates many cellular pathways, including protein synthesis, protein quality control, and lipid synthesis. When one or multiple ER roles are dysregulated and saturated, the ER enters a stress state, which, in turn, activates the highly conserved unfolded protein response (UPR). By sensing the accumulation of unfolded proteins or lipid bilayer stress (LBS) at the ER, the UPR triggers pathways to restore ER homeostasis and eventually induces apoptosis if the stress remains unresolved. In recent years, it has emerged that the UPR works intimately with other cellular pathways to maintain lipid homeostasis at the ER, and so does at cellular levels. Lipid distribution, along with lipid anabolism and catabolism, are tightly regulated, in part, by the ER. Dysfunctional and overwhelmed lipid-related pathways, independently or in combination with ER stress, can have reciprocal effects on other cellular functions, contributing to the development of diseases. In this review, we summarize the current understanding of the UPR in response to proteotoxic stress and LBS and the breadth of the functions mitigated by the UPR in different tissues and in the context of diseases.
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Affiliation(s)
- Cenk Celik
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Wei Sheng Yap
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Guillaume Thibault
- School of Biological Sciences, Nanyang Technological University, Singapore; Mechanobiology Institute, National University of Singapore, Singapore; Institute of Molecular and Cell Biology, A*STAR, Singapore.
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15
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Nakatani Y, Shimokawa N, Urano Y, Noguchi N, Takagi M. Suppression of Amyloid-β Adsorption on Endoplasmic Reticulum Stress-Mimicking Membranes by α-Tocopherol and α-Tocotrienol. J Phys Chem Lett 2022; 13:11955-11960. [PMID: 36534445 PMCID: PMC9806826 DOI: 10.1021/acs.jpclett.2c03098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Two forms of hydrophobic vitamin E (VE), α-tocopherol (Toc) and α-tocotrienol (Toc3), have been proposed to be effective against Alzheimer's disease (AD), the etiology of which is thought to involve endoplasmic reticulum (ER) stress. However, previous studies reported conflicting effects of Toc and Toc3 on the risk of AD. We prepared liposomes mimicking the phase separation of the ER membrane (solid-ordered/liquid-disordered phase separation) and studied how VE can influence the interaction between amyloid-β (Aβ) and the ER membrane. We found that Toc could inhibit the formation of the solid-ordered phase more significantly than Toc3. Furthermore, Aβ protofibril adsorption on ER stress-mimicking membranes was more strongly suppressed by Toc compared with Toc3. Therefore, we concluded that VE can relieve ER stress by destabilizing the solid-ordered phase of the ER membrane and subsequently reducing the amount of Aβ adsorbed on the membrane. Moreover, Toc exerted a stronger effect than Toc3.
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Affiliation(s)
- Yusuke Nakatani
- School
of Materials Science, Japan Advanced Institute
of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Naofumi Shimokawa
- School
of Materials Science, Japan Advanced Institute
of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Yasuomi Urano
- Department
of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Noriko Noguchi
- Department
of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Masahiro Takagi
- School
of Materials Science, Japan Advanced Institute
of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- (M.T.)
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16
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Luo Y, Jiao Q, Chen Y. Targeting endoplasmic reticulum stress-the responder to lipotoxicity and modulator of non-alcoholic fatty liver diseases. Expert Opin Ther Targets 2022; 26:1073-1085. [PMID: 36657744 DOI: 10.1080/14728222.2022.2170780] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Endoplasmic reticulum (ER) stress occurs with aberrant lipid accumulation and resultant adverse effects and widely exists in nonalcoholic fatty liver disease (NAFLD). It triggers the unfolded protein response (UPR) to restore ER homeostasis and actively participates in NAFLD pathological processes, including hepatic steatosis, inflammation, hepatocyte death, and fibrosis. Such acknowledges drive the discovery of novel NAFLD biomarker and therapeutic targets and the development of ER-stress targeted NAFLD drugs. AREAS COVERED This article discusses and updates the role of ER stress and UPR in NAFLD, the underlying action mechanism, and especially their full participation in NAFLD pathophysiology. It characterizes key molecular targets useful for the prevention and treatment of NAFLD and highlights the recent ER stress-targeted therapeutic strategies for NAFLD. EXPERT OPINION Targeting ER Stress is a valuable and promising strategy for NAFLD treatment, but its smooth translation into clinical application still requires better clarification of the different UPR patterns in diverse NAFLD physiological states. Further understanding of the distinct effects of these various patterns on NAFLD, the thresholds deciding their final impacts, and their actions via non-liver tissues and cells would be of great help to develop a precise and effective therapy for NAFLD. [Figure: see text].
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Affiliation(s)
- Yu Luo
- School of Pharmaceutical Science, University of South China, Hengyang, Hunan, China
| | - Qiangqiang Jiao
- School of Pharmaceutical Science, University of South China, Hengyang, Hunan, China
| | - Yuping Chen
- School of Pharmaceutical Science, University of South China, Hengyang, Hunan, China.,Institute of Pharmacy & Pharmacology, University of South China, Hengyang, Hunan, China
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17
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Brahma R, Raghuraman H. Measuring Membrane Penetration Depths and Conformational Changes in Membrane Peptides and Proteins. J Membr Biol 2022; 255:469-483. [PMID: 35274157 DOI: 10.1007/s00232-022-00224-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
The structural organization and dynamic nature of the biomembrane components are important determinants for numerous cellular functions. Particularly, membrane proteins are critically important for various physiological functions and are important drug targets. The mechanistic insights on the complex functionality of membrane lipids and proteins can be elucidated by understanding the interplay between structure and dynamics. In this regard, membrane penetration depth represents an important parameter to obtain the precise depth of membrane-embedded molecules that often define the conformation and topology of membrane probes and proteins. In this review, we discuss about the widely used fluorescence quenching-based methods (parallax method, distribution analysis, and dual-quencher analysis) to accurately determine the membrane penetration depths of fluorescent probes that are either membrane-embedded or attached to lipids and proteins. Further, we also discuss a relatively novel fluorescence quenching method that utilizes tryptophan residue as the quencher, namely the tryptophan-induced quenching, which is sensitive to monitor small-scale conformational changes (short distances of < 15 Å) and useful in mapping distances in proteins. We have provided numerous examples for the benefit of readers to appreciate the importance and applicability of these simple yet powerful methods to study membrane proteins.
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Affiliation(s)
- Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF, Bidhannagar, Kolkata, 700 064, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF, Bidhannagar, Kolkata, 700 064, India.
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18
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Zhang P, Konja D, Zhang Y, Xu A, Lee IK, Jeon JH, Bashiri G, Mitra A, Wang Y. Clusterin is involved in mediating the metabolic function of adipose SIRT1. iScience 2022; 25:103709. [PMID: 35072003 PMCID: PMC8762396 DOI: 10.1016/j.isci.2021.103709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/17/2021] [Accepted: 12/24/2021] [Indexed: 02/06/2023] Open
Abstract
SIRT1 is a metabolic sensor regulating energy homeostasis. The present study revealed that mice with selective overexpression of human SIRT1 in adipose tissue (Adipo-SIRT1) were protected from high-fat diet (HFD)-induced metabolic abnormalities. Adipose SIRT1 was enriched at mitochondria-ER contacts (MERCs) to trigger mitohormesis and unfolded protein response (UPRmt), in turn preventing ER stress. As a downstream target of UPRmt, clusterin was significantly upregulated and acted together with SIRT1 to regulate the protein and lipid compositions at MERCs of adipose tissue. In mice lacking clusterin, HFD-induced metabolic abnormalities were significantly enhanced and could not be prevented by overexpression of SIRT1 in adipose tissue. Treatment with ER stress inhibitors restored adipose SIRT1-mediated beneficial effects on systemic energy metabolism. In summary, adipose SIRT1 facilitated the dynamic interactions and communications between mitochondria and ER, via MERCs, in turn triggering a mild mitochondrial stress to instigate the defense responses against dietary obesity-induced metabolic dysfunctions.
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Affiliation(s)
- Pengcheng Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Daniels Konja
- The State Key Laboratory of Pharmaceutical Biotechnology, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Yiwei Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Aimin Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Department of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - In-Kyu Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University Hospital, Daegu41944, South Korea
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu41404, South Korea
| | - Jae-Han Jeon
- Department of Internal Medicine, School of Medicine, Kyungpook National University Hospital, Daegu41944, South Korea
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu41404, South Korea
| | - Ghader Bashiri
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Alok Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Yu Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
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19
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The Unfolded Protein Response as a Guardian of the Secretory Pathway. Cells 2021; 10:cells10112965. [PMID: 34831188 PMCID: PMC8616143 DOI: 10.3390/cells10112965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is the major site of membrane biogenesis in most eukaryotic cells. As the entry point to the secretory pathway, it handles more than 10,000 different secretory and membrane proteins. The insertion of proteins into the membrane, their folding, and ER exit are affected by the lipid composition of the ER membrane and its collective membrane stiffness. The ER is also a hotspot of lipid biosynthesis including sterols, glycerophospholipids, ceramides and neural storage lipids. The unfolded protein response (UPR) bears an evolutionary conserved, dual sensitivity to both protein-folding imbalances in the ER lumen and aberrant compositions of the ER membrane, referred to as lipid bilayer stress (LBS). Through transcriptional and non-transcriptional mechanisms, the UPR upregulates the protein folding capacity of the ER and balances the production of proteins and lipids to maintain a functional secretory pathway. In this review, we discuss how UPR transducers sense unfolded proteins and LBS with a particular focus on their role as guardians of the secretory pathway.
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20
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Väth K, Mattes C, Reinhard J, Covino R, Stumpf H, Hummer G, Ernst R. Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. J Cell Biol 2021; 220:212449. [PMID: 34196665 PMCID: PMC8256922 DOI: 10.1083/jcb.202011078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
The ER is a key organelle of membrane biogenesis and crucial for the folding of both membrane and secretory proteins. Sensors of the unfolded protein response (UPR) monitor the unfolded protein load in the ER and convey effector functions for maintaining ER homeostasis. Aberrant compositions of the ER membrane, referred to as lipid bilayer stress, are equally potent activators of the UPR. How the distinct signals from lipid bilayer stress and unfolded proteins are processed by the conserved UPR transducer Ire1 remains unknown. Here, we have generated a functional, cysteine-less variant of Ire1 and performed systematic cysteine cross-linking experiments in native membranes to establish its transmembrane architecture in signaling-active clusters. We show that the transmembrane helices of two neighboring Ire1 molecules adopt an X-shaped configuration independent of the primary cause for ER stress. This suggests that different forms of stress converge in a common, signaling-active transmembrane architecture of Ire1.
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Affiliation(s)
- Kristina Väth
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,Preclinical Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,Preclinical Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - John Reinhard
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,Preclinical Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Roberto Covino
- Frankfurt Institute of Advanced Sciences, Goethe-University, Frankfurt, Germany
| | - Heike Stumpf
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,Preclinical Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute of Biophysics, Goethe-University, Frankfurt, Germany
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,Preclinical Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
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21
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Zhemkov V, Ditlev JA, Lee WR, Wilson M, Liou J, Rosen MK, Bezprozvanny I. The role of sigma 1 receptor in organization of endoplasmic reticulum signaling microdomains. eLife 2021; 10:e65192. [PMID: 33973848 PMCID: PMC8112866 DOI: 10.7554/elife.65192] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Sigma 1 receptor (S1R) is a 223-amino-acid-long transmembrane endoplasmic reticulum (ER) protein. S1R modulates activity of multiple effector proteins and is a well-established drug target. However, signaling functions of S1R in cells are poorly understood. Here, we test the hypothesis that biological activity of S1R in cells can be explained by its ability to interact with cholesterol and to form cholesterol-enriched microdomains in the ER membrane. By performing experiments in reduced reconstitution systems, we demonstrate direct effects of cholesterol on S1R clustering. We identify a novel cholesterol-binding motif in the transmembrane region of human S1R. Mutations of this motif impair association of recombinant S1R with cholesterol beads, affect S1R clustering in vitro and disrupt S1R subcellular localization. We demonstrate that S1R-induced membrane microdomains have increased local membrane thickness and that increased local cholesterol concentration and/or membrane thickness in these microdomains can modulate signaling of inositol-requiring enzyme 1α in the ER. Further, S1R agonists cause disruption of S1R clusters, suggesting that biological activity of S1R agonists is linked to remodeling of ER membrane microdomains. Our results provide novel insights into S1R-mediated signaling mechanisms in cells.
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Affiliation(s)
- Vladimir Zhemkov
- Department of Physiology, UT Southwestern Medical Center at DallasDallasUnited States
| | - Jonathon A Ditlev
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center at DallasDallasUnited States
| | - Wan-Ru Lee
- Department of Physiology, UT Southwestern Medical Center at DallasDallasUnited States
| | - Mikaela Wilson
- Department of Physiology, UT Southwestern Medical Center at DallasDallasUnited States
| | - Jen Liou
- Department of Physiology, UT Southwestern Medical Center at DallasDallasUnited States
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center at DallasDallasUnited States
| | - Ilya Bezprozvanny
- Department of Physiology, UT Southwestern Medical Center at DallasDallasUnited States
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg State Polytechnic UniversitySt. PetersburgRussian Federation
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22
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Gong Y, Yang J, Wei S, Yang R, Gao L, Shao S, Zhao J. Lipotoxicity suppresses the synthesis of growth hormone in pituitary somatotrophs via endoplasmic reticulum stress. J Cell Mol Med 2021; 25:5250-5259. [PMID: 33943005 PMCID: PMC8178284 DOI: 10.1111/jcmm.16532] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/04/2021] [Accepted: 03/20/2021] [Indexed: 02/06/2023] Open
Abstract
Lipotoxicity has been shown to cause dysfunction of many organs and tissues. However, it is unclear whether lipotoxicity is harmful to the somatotrophs, a kind of cell that synthesize growth hormone (GH) in the pituitary. In this study, we performed an epidemiological study, serum levels of triglyceride (TG) and GH showed a negative correlation, even after adjustment for potential confounders. In an animal study, male Sprague‐Dawley rats were fed a high‐fat diet (HFD) or a control diet for 28 weeks. HFD rats showed impaired GH synthesis, resulting in a decrease in circulating GH levels. The expression of pituitary Pit‐1, a key transcription factor of GH, was inhibited. We found that the inositol‐requiring enzyme 1α (IRE1α) pathway of endoplasmic reticulum (ER) stress was triggered in HFD rat pituitary glands and palmitic acid‐treated GH3 cells, respectively. On the contrary, applying 4‐phenyl butyric acid (4‐PBA) to alleviate ER stress or 4µ8c to specifically block the IRE1α pathway attenuated the impairment of both Pit‐1 and GH expression. In conclusion, we demonstrated that lipotoxicity directly inhibits the synthesis of GH, probably by reducing Pit‐1 expression. The IRE1α signaling pathway of ER stress may play an important role in this process.
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Affiliation(s)
- Ying Gong
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, China
| | - Jianmei Yang
- Department of Pediatric Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shuoshuo Wei
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, China
| | - Rui Yang
- Experimental Animal Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ling Gao
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, China.,Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shanshan Shao
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, China.,Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jiajun Zhao
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, China.,Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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23
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Mela A, Momany M. Septins coordinate cell wall integrity and lipid metabolism in a sphingolipid-dependent process. J Cell Sci 2021; 135:256543. [PMID: 33912961 DOI: 10.1242/jcs.258336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/31/2020] [Indexed: 01/09/2023] Open
Abstract
Septins colocalize with membrane sterol-rich regions and facilitate recruitment of cell wall synthases during wall remodeling. We show that null mutants missing an Aspergillus nidulans core septin present in hexamers and octamers (ΔaspAcdc11, ΔaspBcdc3 or ΔaspCcdc12) are sensitive to multiple cell wall-disturbing agents that activate the cell wall integrity MAPK pathway. The null mutant missing the octamer-exclusive core septin (ΔaspDcdc10) showed similar sensitivity, but only to a single cell wall-disturbing agent and the null mutant missing the noncore septin (ΔaspE) showed only very mild sensitivity to a different single agent. Core septin mutants showed changes in wall polysaccharide composition and chitin synthase localization. Mutants missing any of the five septins resisted ergosterol-disrupting agents. Hexamer mutants showed increased sensitivity to sphingolipid-disrupting agents. Core septins mislocalized after treatment with sphingolipid-disrupting agents, but not after ergosterol-disrupting agents. Our data suggest that the core septins are involved in cell wall integrity signaling, that all five septins are involved in monitoring ergosterol metabolism, that the hexamer septins are required for sphingolipid metabolism and that septins require sphingolipids to coordinate the cell wall integrity response.
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Affiliation(s)
- Alexander Mela
- Fungal Biology Group and Plant Biology Department, University of Georgia, 2502 Miller Plant Science Building, Athens, GA 30602, USA
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, 2502 Miller Plant Science Building, Athens, GA 30602, USA
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24
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The Structure, Activation and Signaling of IRE1 and Its Role in Determining Cell Fate. Biomedicines 2021; 9:biomedicines9020156. [PMID: 33562589 PMCID: PMC7914947 DOI: 10.3390/biomedicines9020156] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
Inositol-requiring enzyme type 1 (IRE1) is a serine/threonine kinase acting as one of three branches of the Unfolded Protein Response (UPR) signaling pathway, which is activated upon endoplasmic reticulum (ER) stress conditions. It is known to be capable of inducing both pro-survival and pro-apoptotic cellular responses, which are strictly related to numerous human pathologies. Among others, IRE1 activity has been confirmed to be increased in cancer, neurodegeneration, inflammatory and metabolic disorders, which are associated with an accumulation of misfolded proteins within ER lumen and the resulting ER stress conditions. Emerging evidence suggests that genetic or pharmacological modulation of IRE1 may have a significant impact on cell viability, and thus may be a promising step forward towards development of novel therapeutic strategies. In this review, we extensively describe the structural analysis of IRE1 molecule, the molecular dynamics associated with IRE1 activation, and interconnection between it and the other branches of the UPR with regard to its potential use as a therapeutic target. Detailed knowledge of the molecular characteristics of the IRE1 protein and its activation may allow the design of specific kinase or RNase modulators that may act as drug candidates.
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25
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Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS. Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. eLife 2020; 9:e62611. [PMID: 33236988 PMCID: PMC7785296 DOI: 10.7554/elife.62611] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.
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Affiliation(s)
- Lakshmi E Miller-Vedam
- Molecular, Cellular, and Computational Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Katerina D Popova
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Biomedical Sciences Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Nicole T Schirle Oakdale
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jessica L Bonnar
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jesuraj R Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Elizabeth A Boydston
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Matthew J Shurtleff
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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26
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Nath A, Oak A, Chen KY, Li I, Splichal RC, Portis J, Foster S, Walton SP, Chan C. Palmitate-Induced IRE1-XBP1-ZEB Signaling Represses Desmoplakin Expression and Promotes Cancer Cell Migration. Mol Cancer Res 2020; 19:240-248. [PMID: 33106375 DOI: 10.1158/1541-7786.mcr-19-0480] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 04/23/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022]
Abstract
Elevated uptake of saturated fatty acid palmitate is associated with metastatic progression of cancer cells; however, the precise signaling mechanism behind the phenomenon is unclear. The loss of cell adhesion proteins, such as desmoplakin (DSP), is a key driving event in the transformation of cancer cells to more aggressive phenotypes. Here, we investigated the mechanism by which palmitate induces the loss of DSP in liver and breast cancer cells. We propose that palmitate activates the IRE1-XBP1 branch of the endoplasmic reticulum (ER) stress pathway to upregulate the ZEB transcription factor, leading to transcriptional repression of DSP. Using liver and breast cancer cells treated with palmitate, we found loss of DSP leads to increased cell migration independent of E-cadherin. We report that the ZEB family of transcription factors function as direct transcriptional repressors of DSP. CRISPR-mediated knockdown of IRE1 confirmed that the transcription of ZEB, loss of DSP, and enhanced migration in the presence of palmitate is dependent on the IRE1-XBP1 pathway. In addition, by analyzing the somatic expression and copy number variation profiles of over 11,000 tumor samples, we corroborate our hypothesis and establish the clinical relevance of DSP loss via ZEB in human cancers. IMPLICATIONS: Provides mechanistic link on palmitate-induced activation of IRE1α to cancer cell migration.
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Affiliation(s)
- Aritro Nath
- Genetics Program, Michigan State University, East Lansing, Michigan
| | - Amrita Oak
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Kevin Y Chen
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Irene Li
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - R Chauncey Splichal
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Jason Portis
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Sean Foster
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Christina Chan
- Genetics Program, Michigan State University, East Lansing, Michigan. .,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
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27
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Xiao Y, Zeng B, Berner N, Frishman D, Langosch D, George Teese M. Experimental determination and data-driven prediction of homotypic transmembrane domain interfaces. Comput Struct Biotechnol J 2020; 18:3230-3242. [PMID: 33209210 PMCID: PMC7649602 DOI: 10.1016/j.csbj.2020.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/22/2022] Open
Abstract
Homotypic TMD interfaces identified by different techniques share strong similarities. The GxxxG motif is the feature most strongly associated with interfaces. Other features include conservation, polarity, coevolution, and depth in the membrane The role of each of each feature strongly depends on the individual protein. Machine-learning helps predict interfaces from evolutionary sequence data
Interactions between their transmembrane domains (TMDs) frequently support the assembly of single-pass membrane proteins to non-covalent complexes. Yet, the TMD-TMD interactome remains largely uncharted. With a view to predicting homotypic TMD-TMD interfaces from primary structure, we performed a systematic analysis of their physical and evolutionary properties. To this end, we generated a dataset of 50 self-interacting TMDs. This dataset contains interfaces of nine TMDs from bitopic human proteins (Ire1, Armcx6, Tie1, ATP1B1, PTPRO, PTPRU, PTPRG, DDR1, and Siglec7) that were experimentally identified here and combined with literature data. We show that interfacial residues of these homotypic TMD-TMD interfaces tend to be more conserved, coevolved and polar than non-interfacial residues. Further, we suggest for the first time that interface positions are deficient in β-branched residues, and likely to be located deep in the hydrophobic core of the membrane. Overrepresentation of the GxxxG motif at interfaces is strong, but that of (small)xxx(small) motifs is weak. The multiplicity of these features and the individual character of TMD-TMD interfaces, as uncovered here, prompted us to train a machine learning algorithm. The resulting prediction method, THOIPA (www.thoipa.org), excels in the prediction of key interface residues from evolutionary sequence data.
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Affiliation(s)
- Yao Xiao
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Bo Zeng
- Department of Bioinformatics, Wissenschaftszentrum, Weihenstephan, Maximus-von-Imhof-Forum 3, Freising 85354, Germany
| | - Nicola Berner
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum, Weihenstephan, Maximus-von-Imhof-Forum 3, Freising 85354, Germany.,Department of Bioinformatics, Peter the Great Saint Petersburg Polytechnic University, St. Petersburg 195251, Russian Federation
| | - Dieter Langosch
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Mark George Teese
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.,TNG Technology Consulting GmbH, Beta-Straße 13a, 85774 Unterföhring, Germany
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28
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Ho N, Yap WS, Xu J, Wu H, Koh JH, Goh WWB, George B, Chong SC, Taubert S, Thibault G. Stress sensor Ire1 deploys a divergent transcriptional program in response to lipid bilayer stress. J Cell Biol 2020; 219:e201909165. [PMID: 32349127 PMCID: PMC7337508 DOI: 10.1083/jcb.201909165] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/26/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane integrity at the endoplasmic reticulum (ER) is tightly regulated, and its disturbance is implicated in metabolic diseases. Using an engineered sensor that activates the unfolded protein response (UPR) exclusively when normal ER membrane lipid composition is compromised, we identified pathways beyond lipid metabolism that are necessary to maintain ER integrity in yeast and in C. elegans. To systematically validate yeast mutants that disrupt ER membrane homeostasis, we identified a lipid bilayer stress (LBS) sensor in the UPR transducer protein Ire1, located at the interface of the amphipathic and transmembrane helices. Furthermore, transcriptome and chromatin immunoprecipitation analyses pinpoint the UPR as a broad-spectrum compensatory response wherein LBS and proteotoxic stress deploy divergent transcriptional UPR programs. Together, these findings reveal the UPR program as the sum of two independent stress responses, an insight that could be exploited for future therapeutic intervention.
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Affiliation(s)
- Nurulain Ho
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Wei Sheng Yap
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jiaming Xu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Haoxi Wu
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jhee Hong Koh
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Wilson Wen Bin Goh
- Bio-Data Science and Education Research Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Bhawana George
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Shu Chen Chong
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Stefan Taubert
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Guillaume Thibault
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore
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29
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Whitehead TA, Banta S, Bentley WE, Betenbaugh MJ, Chan C, Clark DS, Hoesli CA, Jewett MC, Junker B, Koffas M, Kshirsagar R, Lewis A, Li CT, Maranas C, Terry Papoutsakis E, Prather KLJ, Schaffer S, Segatori L, Wheeldon I. The importance and future of biochemical engineering. Biotechnol Bioeng 2020; 117:2305-2318. [PMID: 32343367 DOI: 10.1002/bit.27364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 02/06/2023]
Abstract
Today's Biochemical Engineer may contribute to advances in a wide range of technical areas. The recent Biochemical and Molecular Engineering XXI conference focused on "The Next Generation of Biochemical and Molecular Engineering: The role of emerging technologies in tomorrow's products and processes". On the basis of topical discussions at this conference, this perspective synthesizes one vision on where investment in research areas is needed for biotechnology to continue contributing to some of the world's grand challenges.
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Affiliation(s)
- Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California
| | - Corinne A Hoesli
- Department of Chemical Engineering & Department of Biological and Biomedical Engineering, McGill University, Montreal, Québec, Canada
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois
| | - Beth Junker
- BioProcess Advantage LLC, Middesex, New Jersey
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | | | | | - Chien-Ting Li
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - E Terry Papoutsakis
- Department of Chemical & Biomolecular Engineering & the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Laura Segatori
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, California
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30
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Wang K, Liu JQ, Zhong T, Liu XL, Zeng Y, Qiao X, Xie T, Chen Y, Gao YY, Tang B, Li J, Zhou J, Pang DW, Chen J, Chen C, Liang Y. Phase Separation and Cytotoxicity of Tau are Modulated by Protein Disulfide Isomerase and S-nitrosylation of this Molecular Chaperone. J Mol Biol 2020; 432:2141-2163. [PMID: 32087196 DOI: 10.1016/j.jmb.2020.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/21/2020] [Accepted: 02/11/2020] [Indexed: 12/26/2022]
Abstract
Cells have evolved molecular chaperones that modulate phase separation and misfolding of amyloidogenic proteins to prevent neurodegenerative diseases. Protein disulfide isomerase (PDI), mainly located at the endoplasmic reticulum and also present in the cytosol, acts as both an enzyme and a molecular chaperone. PDI is observed to be S-nitrosylated in the brain of Alzheimer's disease patients, but the mechanism has remained elusive. We herein report that both wild-type PDI and its quadruple cysteine mutant only having chaperone activity, significantly inhibit pathological phosphorylation and abnormal aggregation of Tau in cells, and significantly decrease the mitochondrial damage and Tau cytotoxicity resulting from Tau aberrant aggregation, highlighting the chaperone property of PDI. More importantly, we show that wild-type PDI is selectively recruited by liquid droplets of Tau, which significantly inhibits phase separation and stress granule formation of Tau, whereas S-nitrosylation of PDI abrogates the recruitment and inhibition. These findings demonstrate how phase separation of Tau is physiologically regulated by PDI and how S-nitrosylation of PDI, a perturbation in this regulation, leads to disease.
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Affiliation(s)
- Kan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jia-Qi Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tao Zhong
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiao-Ling Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yan Zeng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Xie
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuzhe Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying-Ying Gao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bo Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Jia Li
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun Zhou
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dai-Wen Pang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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31
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Makarova M, Peter M, Balogh G, Glatz A, MacRae JI, Lopez Mora N, Booth P, Makeyev E, Vigh L, Oliferenko S. Delineating the Rules for Structural Adaptation of Membrane-Associated Proteins to Evolutionary Changes in Membrane Lipidome. Curr Biol 2020; 30:367-380.e8. [PMID: 31956022 PMCID: PMC6997885 DOI: 10.1016/j.cub.2019.11.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/31/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023]
Abstract
Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that, unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual "asymmetrical" glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S.-japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments support the hypothesis that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.
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Affiliation(s)
- Maria Makarova
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Maria Peter
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Gabor Balogh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Attila Glatz
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - James I MacRae
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nestor Lopez Mora
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK
| | - Paula Booth
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK
| | - Eugene Makeyev
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Laszlo Vigh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, Guy's Campus, London SE1 1UL, UK.
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32
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Huang S, Xing Y, Liu Y. Emerging roles for the ER stress sensor IRE1α in metabolic regulation and disease. J Biol Chem 2019; 294:18726-18741. [PMID: 31666338 DOI: 10.1074/jbc.rev119.007036] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Inositol-requiring enzyme 1 (IRE1) is an endoplasmic reticulum (ER)-resident transmembrane protein that senses ER stress and is evolutionarily conserved from yeast to humans. IRE1 possesses both Ser/Thr protein kinase and endoribonuclease (RNase) activities within its cytoplasmic domain and is activated through autophosphorylation and dimerization/oligomerization. It mediates a critical arm of the unfolded protein response to manage ER stress provoked by lumenal overload of unfolded/misfolded proteins. Emerging lines of evidence have revealed that in mammals, IRE1α functions as a multifunctional signal transducer that responds to metabolic cues and nutrient stress conditions, exerting profound and broad effects on metabolic homeostasis. In this review, we cover recent advances in our understanding of how IRE1α integrates a variety of metabolic and stress signals and highlight its tissue-specific or context-dependent metabolic activities. We also discuss how dysregulation of this metabolic stress sensor during handling of excessive nutrients in cells contributes to the progression of obesity and metabolic disorders.
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Affiliation(s)
- Shijia Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yuying Xing
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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Medkour Y, Mohammad K, Arlia-Ciommo A, Svistkova V, Dakik P, Mitrofanova D, Rodriguez MEL, Junio JAB, Taifour T, Escudero P, Goltsios FF, Soodbakhsh S, Maalaoui H, Simard É, Titorenko VI. Mechanisms by which PE21, an extract from the white willow Salix alba, delays chronological aging in budding yeast. Oncotarget 2019; 10:5780-5816. [PMID: 31645900 PMCID: PMC6791382 DOI: 10.18632/oncotarget.27209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/27/2019] [Indexed: 01/05/2023] Open
Abstract
We have recently found that PE21, an extract from the white willow Salix alba, slows chronological aging and prolongs longevity of the yeast Saccharomyces cerevisiae more efficiently than any of the previously known pharmacological interventions. Here, we investigated mechanisms through which PE21 delays yeast chronological aging and extends yeast longevity. We show that PE21 causes a remodeling of lipid metabolism in chronologically aging yeast, thereby instigating changes in the concentrations of several lipid classes. We demonstrate that such changes in the cellular lipidome initiate three mechanisms of aging delay and longevity extension. The first mechanism through which PE21 slows aging and prolongs longevity consists in its ability to decrease the intracellular concentration of free fatty acids. This postpones an age-related onset of liponecrotic cell death promoted by excessive concentrations of free fatty acids. The second mechanism of aging delay and longevity extension by PE21 consists in its ability to decrease the concentrations of triacylglycerols and to increase the concentrations of glycerophospholipids within the endoplasmic reticulum membrane. This activates the unfolded protein response system in the endoplasmic reticulum, which then decelerates an age-related decline in protein and lipid homeostasis and slows down an aging-associated deterioration of cell resistance to stress. The third mechanisms underlying aging delay and longevity extension by PE21 consists in its ability to change lipid concentrations in the mitochondrial membranes. This alters certain catabolic and anabolic processes in mitochondria, thus amending the pattern of aging-associated changes in several key aspects of mitochondrial functionality.
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Affiliation(s)
- Younes Medkour
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | | | - Veronika Svistkova
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Pamela Dakik
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Darya Mitrofanova
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | | | | | - Tarek Taifour
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Paola Escudero
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Fani-Fay Goltsios
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sahar Soodbakhsh
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Hana Maalaoui
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Éric Simard
- Idunn Technologies Inc., Rosemere, Quebec J7A 4A5, Canada
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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