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Jadhav R, Mach RL, Mach-Aigner AR. Protein secretion and associated stress in industrially employed filamentous fungi. Appl Microbiol Biotechnol 2024; 108:92. [PMID: 38204136 PMCID: PMC10781871 DOI: 10.1007/s00253-023-12985-4] [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: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.
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Affiliation(s)
- Reshma Jadhav
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
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2
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Niemelä LRK, Koskela EV, Frey AD. Modification of the endoplasmic reticulum morphology enables improved recombinant antibody expression in Saccharomyces cerevisiae. J Biotechnol 2024; 387:1-11. [PMID: 38555020 DOI: 10.1016/j.jbiotec.2024.03.009] [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: 10/21/2023] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
The yeast Saccharomyces cerevisiae is a versatile cell factory used for manufacturing of a wide range of products, among them recombinant proteins. Protein folding is one of the rate-limiting processes and this shortcoming is often overcome by the expression of folding catalysts and chaperones in the endoplasmic reticulum (ER). In this work, we aimed to establish the impact of ER structure on cellular productivity. The reticulon proteins Rtn1p and Rtn2p, and Yop1p are membrane curvature inducing proteins that define the morphology of the ER and depletion of these proteins creates yeast cells with a higher ER sheet-to-tubule ratio. We created yeast strains with different combinations of deletions of Rtn1p, Rtn2p, and Yop1p coding genes in cells with a normal or expanded ER lumen. We identified strains that reached up to 2.2-fold higher antibody titres compared to the control strain. The expanded ER membrane reached by deletion of the lipid biosynthesis repressor OPI1 was essential for the increased productivity. The improved specific productivity was accompanied by an up to 2-fold enlarged ER surface area and a 1.5-fold increased cross-sectional cell area. Furthermore, the strains with enlarged ER displayed an attenuated unfolded protein response. These results underline the impact that ER structures have on productivity and support the notion that reprogramming subcellular structures belongs into the toolbox of synthetic biology.
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Affiliation(s)
- Laura R K Niemelä
- Aalto University, Department of Bioproducts and Biosystems, Espoo, Finland
| | - Essi V Koskela
- Aalto University, Department of Bioproducts and Biosystems, Espoo, Finland
| | - Alexander D Frey
- Aalto University, Department of Bioproducts and Biosystems, Espoo, Finland.
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3
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Zung N, Aravindan N, Boshnakovska A, Valenti R, Preminger N, Jonas F, Yaakov G, Willoughby MM, Homberg B, Keller J, Kupervaser M, Dezorella N, Dadosh T, Wolf SG, Itkin M, Malitsky S, Brandis A, Barkai N, Fernández-Busnadiego R, Reddi AR, Rehling P, Rapaport D, Schuldiner M. The molecular mechanism of on-demand sterol biosynthesis at organelle contact sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593285. [PMID: 38766039 PMCID: PMC11100823 DOI: 10.1101/2024.05.09.593285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Contact-sites are specialized zones of proximity between two organelles, essential for organelle communication and coordination. The formation of contacts between the Endoplasmic Reticulum (ER), and other organelles, relies on a unique membrane environment enriched in sterols. However, how these sterol-rich domains are formed and maintained had not been understood. We found that the yeast membrane protein Yet3, the homolog of human BAP31, is localized to multiple ER contact sites. We show that Yet3 interacts with all the enzymes of the post-squalene ergosterol biosynthesis pathway and recruits them to create sterol-rich domains. Increasing sterol levels at ER contacts causes its depletion from the plasma membrane leading to a compensatory reaction and altered cell metabolism. Our data shows that Yet3 provides on-demand sterols at contacts thus shaping organellar structure and function. A molecular understanding of this protein's functions gives new insights into the role of BAP31 in development and pathology.
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Nguyen HM, Hong UVT, Ruocco M, Dattolo E, Marín-Guirao L, Pernice M, Procaccini G. Thermo-priming triggers species-specific physiological and transcriptome responses in Mediterranean seagrasses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108614. [PMID: 38626655 DOI: 10.1016/j.plaphy.2024.108614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/18/2024]
Abstract
Heat-priming improves plants' tolerance to a recurring heat stress event. The underlying molecular mechanisms of heat-priming are largely unknown in seagrasses. Here, ad hoc mesocosm experiments were conducted with two Mediterranean seagrass species, Posidonia oceanica and Cymodocea nodosa. Plants were first exposed to heat-priming, followed by a heat-triggering event. A comprehensive assessment of plant stress response across different levels of biological organization was performed at the end of the triggering event. Morphological and physiological results showed an improved response of heat-primed P. oceanica plants while in C. nodosa both heat- and non-primed plants enhanced their growth rates at the end of the triggering event. As resulting from whole transcriptome sequencing, molecular functions related to several cellular compartments and processes were involved in the response to warming of non-primed plants, while the response of heat-primed plants involved a limited group of processes. Our results suggest that seagrasses acquire a primed state during the priming event, that eventually gives plants the ability to induce a more energy-effective response when the thermal stress event recurs. Different species may differ in their ability to perform an improved heat stress response after priming. This study provides pioneer molecular insights into the emerging topic of seagrass stress priming and may benefit future studies in the field.
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Affiliation(s)
- Hung Manh Nguyen
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Uyen V T Hong
- La Trobe University, AgriBio Building, Bundoora, 3086, VIC, Australia; Department of Plant Biotechnology & Biotransformation, University of Science, Vietnam National University, 700000, Ho Chi Minh City, Viet Nam
| | - Miriam Ruocco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Emanuela Dattolo
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy
| | - Lázaro Marín-Guirao
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; Oceanographic Center of Murcia, Seagrass Ecology Group, Spanish Institute of Oceanography (IEO-CSIC), C/Varadero, San Pedro del Pinatar, 30740, Murcia, Spain.
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, 2007, NSW, Australia
| | - Gabriele Procaccini
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy
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5
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Sonsalla G, Malpartida AB, Riedemann T, Gusic M, Rusha E, Bulli G, Najas S, Janjic A, Hersbach BA, Smialowski P, Drukker M, Enard W, Prehn JHM, Prokisch H, Götz M, Masserdotti G. Direct neuronal reprogramming of NDUFS4 patient cells identifies the unfolded protein response as a novel general reprogramming hurdle. Neuron 2024; 112:1117-1132.e9. [PMID: 38266647 PMCID: PMC10994141 DOI: 10.1016/j.neuron.2023.12.020] [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: 06/23/2022] [Revised: 10/12/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Mitochondria account for essential cellular pathways, from ATP production to nucleotide metabolism, and their deficits lead to neurological disorders and contribute to the onset of age-related diseases. Direct neuronal reprogramming aims at replacing neurons lost in such conditions, but very little is known about the impact of mitochondrial dysfunction on the direct reprogramming of human cells. Here, we explore the effects of mitochondrial dysfunction on the neuronal reprogramming of induced pluripotent stem cell (iPSC)-derived astrocytes carrying mutations in the NDUFS4 gene, important for Complex I and associated with Leigh syndrome. This led to the identification of the unfolded protein response as a major hurdle in the direct neuronal conversion of not only astrocytes and fibroblasts from patients but also control human astrocytes and fibroblasts. Its transient inhibition potently improves reprogramming by influencing the mitochondria-endoplasmic-reticulum-stress-mediated pathways. Taken together, disease modeling using patient cells unraveled novel general hurdles and ways to overcome these in human astrocyte-to-neuron reprogramming.
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Affiliation(s)
- Giovanna Sonsalla
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Graduate School of Systemic Neurosciences, BMC, LMU Munich, Planegg-Martinsried 82152 Germany
| | - Ana Belen Malpartida
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried 82152, Germany
| | - Therese Riedemann
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Ejona Rusha
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Giorgia Bulli
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Graduate School of Systemic Neurosciences, BMC, LMU Munich, Planegg-Martinsried 82152 Germany
| | - Sonia Najas
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Aleks Janjic
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Bob A Hersbach
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Graduate School of Systemic Neurosciences, BMC, LMU Munich, Planegg-Martinsried 82152 Germany
| | - Pawel Smialowski
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Biomedical Center Munich, Bioinformatic Core Facility, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Micha Drukker
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Gorlaeus Building, 2333 CC RA, Leiden, the Netherlands
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Jochen H M Prehn
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Excellence Cluster of Systems Neurology (SYNERGY), Munich, Germany.
| | - Giacomo Masserdotti
- Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany.
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6
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Wang G, Zhao H, Zou J, Liang W, Zhao Z, Li D. Role of BcSfb3, the subunit of COPII vesicles, in fungal development and pathogenicity, ER-phagy and autophagy in the gray mold fungus Botrytis cinerea. Int J Biol Macromol 2024; 263:130379. [PMID: 38403214 DOI: 10.1016/j.ijbiomac.2024.130379] [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: 01/03/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Cytoplasmic coat protein complex II (COPII) plays a multifunctional role in the transport of newly synthesized proteins, autophagosome formation, and endoplasmic reticulum (ER)-ER-phagy. However, the molecular mechanisms of the COPII subunit in ER-phagy in plant pathogens remain unknown. Here, we identified the subunit of COPII vesicles (BcSfb3) and explored the importance of BcSfb3 in Botrytis cinerea. BcSfb3 deletion affected vegetative growth, conidiation, conidial morphology, and plasma membrane integrity. We confirmed that the increase in infectious hyphal growth was delayed in the ΔBcSfb3 mutant, reducing its pathogenicity in the host plant. Furthermore, the ΔBcSfb3 mutant was sensitive to ER stress, which caused massive ER expansion and induced the formation of ER whorls that were taken up into the vacuole. Further examination demonstrated that BcSfb3 deletion caused ER stress initiated by unfolded protein response, and which led to the promotion of ER-phagy and autophagy that participate in sclerotia formation. In conclusion, these results demonstrate that BcSfb3 plays an important role in fungal development, pathogenesis, ER-phagy and autophagy in B. cinerea.
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Affiliation(s)
- Guanbo Wang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, China
| | - Haonan Zhao
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, China
| | - Jian Zou
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, China
| | - Wenxing Liang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, China
| | - Zhijian Zhao
- Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming 650203, China.
| | - Delong Li
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, China; Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China.
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7
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Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R. MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress. EMBO J 2024; 43:1653-1685. [PMID: 38491296 PMCID: PMC11021466 DOI: 10.1038/s44318-024-00063-y] [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: 09/14/2022] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
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Affiliation(s)
- John Reinhard
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Leonhard Starke
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | | | - Per Haberkant
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | | | - Frank Stein
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | - Ofir Klein
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Charlotte Berhorst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Heike Stumpf
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - James P Sáenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Jochen Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | - Maya Schuldiner
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Robert Ernst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany.
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany.
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8
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Nickerson KW, Gutzmann DJ, Boone CHT, Pathirana RU, Atkin AL. Physiological adventures in Candida albicans: farnesol and ubiquinones. Microbiol Mol Biol Rev 2024; 88:e0008122. [PMID: 38436263 PMCID: PMC10966945 DOI: 10.1128/mmbr.00081-22] [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] [Indexed: 03/05/2024] Open
Abstract
SUMMARYFarnesol was first identified as a quorum-sensing molecule, which blocked the yeast to hyphal transition in Candida albicans, 22 years ago. However, its interactions with Candida biology are surprisingly complex. Exogenous (secreted or supplied) farnesol can also act as a virulence factor during pathogenesis and as a fungicidal agent triggering apoptosis in other competing fungi. Farnesol synthesis is turned off both during anaerobic growth and in opaque cells. Distinctly different cellular responses are observed as exogenous farnesol levels are increased from 0.1 to 100 µM. Reported changes include altered morphology, stress response, pathogenicity, antibiotic sensitivity/resistance, and even cell lysis. Throughout, there has been a dearth of mechanisms associated with these observations, in part due to the absence of accurate measurement of intracellular farnesol levels (Fi). This obstacle has recently been overcome, and the above phenomena can now be viewed in terms of changing Fi levels and the percentage of farnesol secreted. Critically, two aspects of isoprenoid metabolism present in higher organisms are absent in C. albicans and likely in other yeasts. These are pathways for farnesol salvage (converting farnesol to farnesyl pyrophosphate) and farnesylcysteine cleavage, a necessary step in the turnover of farnesylated proteins. Together, these developments suggest a unifying model, whereby high, threshold levels of Fi regulate which target proteins are farnesylated or the extent to which they are farnesylated. Thus, we suggest that the diversity of cellular responses to farnesol reflects the diversity of the proteins that are or are not farnesylated.
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Affiliation(s)
| | - Daniel J. Gutzmann
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Cory H. T. Boone
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Ruvini U. Pathirana
- Department of Biology and Chemistry, Texas A&M International University, Laredo, Texas, USA
| | - Audrey L. Atkin
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
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9
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Müller R, König A, Groth S, Zarnowski R, Visser C, Handrianz T, Maufrais C, Krüger T, Himmel M, Lee S, Priest EL, Yildirim D, Richardson JP, Blango MG, Bougnoux ME, Kniemeyer O, d'Enfert C, Brakhage AA, Andes DR, Trümper V, Nehls C, Kasper L, Mogavero S, Gutsmann T, Naglik JR, Allert S, Hube B. Secretion of the fungal toxin candidalysin is dependent on conserved precursor peptide sequences. Nat Microbiol 2024; 9:669-683. [PMID: 38388771 DOI: 10.1038/s41564-024-01606-z] [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] [Received: 11/22/2022] [Accepted: 01/12/2024] [Indexed: 02/24/2024]
Abstract
The opportunistic fungal pathogen Candida albicans damages host cells via its peptide toxin, candidalysin. Before secretion, candidalysin is embedded in a precursor protein, Ece1, which consists of a signal peptide, the precursor of candidalysin and seven non-candidalysin Ece1 peptides (NCEPs), and is found to be conserved in clinical isolates. Here we show that the Ece1 polyprotein does not resemble the usual precursor structure of peptide toxins. C. albicans cells are not susceptible to their own toxin, and single NCEPs adjacent to candidalysin are sufficient to prevent host cell toxicity. Using a series of Ece1 mutants, mass spectrometry and anti-candidalysin nanobodies, we show that NCEPs play a role in intracellular Ece1 folding and candidalysin secretion. Removal of single NCEPs or modifications of peptide sequences cause an unfolded protein response (UPR), which in turn inhibits hypha formation and pathogenicity in vitro. Our data indicate that the Ece1 precursor is not required to block premature pore-forming toxicity, but rather to prevent intracellular auto-aggregation of candidalysin sequences.
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Affiliation(s)
- Rita Müller
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Annika König
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Sabrina Groth
- Division of Biophysics, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Robert Zarnowski
- Department of Medicine, Section of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA
| | - Corissa Visser
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Tom Handrianz
- Division of Biophysics, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Maximilian Himmel
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Sejeong Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Emily L Priest
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Deniz Yildirim
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Jonathan P Richardson
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Matthew G Blango
- RNA Biology of Fungal Infections, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Marie-Elisabeth Bougnoux
- Institut Pasteur, Université Paris Cité, Unité Biologie et Pathogénicité Fongiques, Paris, France
- Unité de Parasitologie-Mycologie, Service de Microbiologie Clinique, Hôpital Necker-Enfants-Malades, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Christophe d'Enfert
- Institut Pasteur, Université Paris Cité, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Axel A Brakhage
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - David R Andes
- Department of Medicine, Section of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA
| | - Verena Trümper
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Christian Nehls
- Division of Biophysics, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Kiel, Germany
| | - Lydia Kasper
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Selene Mogavero
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Thomas Gutsmann
- Division of Biophysics, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Kiel, Germany
| | - Julian R Naglik
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Stefanie Allert
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany.
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany.
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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10
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Liu Z, Wang G, Sheng C, Zheng Y, Tang D, Zhang Y, Hou X, Yao M, Zong Q, Zhou Z. Intracellular Protein Adsorption Behavior and Biological Effects of Polystyrene Nanoplastics in THP-1 Cells. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2652-2661. [PMID: 38294362 DOI: 10.1021/acs.est.3c05493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Micro(nano)plastics (MNPs) are emerging pollutants that can adsorb pollutants in the environment and biological molecules and ultimately affect human health. However, the aspects of adsorption of intracellular proteins onto MNPs and its biological effects in cells have not been investigated to date. The present study revealed that 100 nm polystyrene nanoplastics (NPs) could be internalized by THP-1 cells and specifically adsorbed intracellular proteins. In total, 773 proteins adsorbed onto NPs with high reliability were identified using the proteomics approach and analyzed via bioinformatics to predict the route and distribution of NPs following cellular internalization. The representative proteins identified via the Kyoto Encyclopedia of Genes and Genomes pathway analysis were further investigated to characterize protein adsorption onto NPs and its biological effects. The analysis revealed that NPs affect glycolysis through pyruvate kinase M (PKM) adsorption, trigger the unfolded protein response through the adsorption of ribophorin 1 (RPN1) and heat shock 70 protein 8 (HSPA8), and are chiefly internalized into cells through clathrin-mediated endocytosis with concomitant clathrin heavy chain (CLTC) adsorption. Therefore, this work provides new insights and research strategies for the study of the biological effects caused by NPs.
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Affiliation(s)
- Zijia Liu
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Guozhen Wang
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100124, China
| | - Chao Sheng
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yuchen Zheng
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Duo Tang
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yuchen Zhang
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Xiaonan Hou
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Mengfei Yao
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Qi Zong
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Zhixiang Zhou
- Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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11
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Ahlstedt BA, Ganji R, Mukkavalli S, Paulo JA, Gygi SP, Raman M. UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation. EMBO Rep 2024; 25:672-703. [PMID: 38177917 PMCID: PMC10897191 DOI: 10.1038/s44319-023-00027-z] [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: 03/03/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
ER protein homeostasis (proteostasis) is essential for proper folding and maturation of proteins in the secretory pathway. Loss of ER proteostasis can lead to the accumulation of misfolded or aberrant proteins in the ER and triggers the unfolded protein response (UPR). In this study, we find that the p97 adaptor UBXN1 is an important negative regulator of the UPR. Loss of UBXN1 sensitizes cells to ER stress and activates the UPR. This leads to widespread upregulation of the ER stress transcriptional program. Using comparative, quantitative proteomics we show that deletion of UBXN1 results in a significant enrichment of proteins involved in ER-quality control processes including those involved in protein folding and import. Notably, we find that loss of UBXN1 does not perturb p97-dependent ER-associated degradation (ERAD). Our studies indicate that loss of UBXN1 increases translation in both resting and ER-stressed cells. Surprisingly, this process is independent of p97 function. Taken together, our studies have identified a new role for UBXN1 in repressing translation and maintaining ER proteostasis in a p97 independent manner.
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Affiliation(s)
- Brittany A Ahlstedt
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
- ALPCA diagnostics, Salem, NH, USA
| | - Rakesh Ganji
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Sirisha Mukkavalli
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
- Dana Farber Cancer Research Institute, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology Harvard Medical School, Boston, MA, USA
| | - Steve P Gygi
- Department of Cell Biology Harvard Medical School, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
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12
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Porter A, Vorndran HE, Marciszyn A, Mutchler SM, Subramanya AR, Kleyman TR, Hendershot LM, Brodsky JL, Buck TM. Excess dietary sodium partially restores salt and water homeostasis caused by loss of the endoplasmic reticulum molecular chaperone, GRP170, in the mouse nephron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.13.575426. [PMID: 38260467 PMCID: PMC10802592 DOI: 10.1101/2024.01.13.575426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The maintenance of fluid and electrolyte homeostasis by the kidney requires proper folding and trafficking of ion channels and transporters in kidney epithelia. Each of these processes requires a specific subset of a diverse class of proteins termed molecular chaperones. One such chaperone is GRP170, which is an Hsp70-like, endoplasmic reticulum (ER)-localized chaperone that plays roles in protein quality control and protein folding in the ER. We previously determined that loss of GRP170 in the mouse nephron leads to hypovolemia, electrolyte imbalance, and rapid weight loss. In addition, GRP170-deficient mice develop an AKI-like phenotype, typified by tubular injury, elevation of clinical kidney injury markers, and induction of the unfolded protein response (UPR). By using an inducible GRP170 knockout cellular model, we confirmed that GRP170 depletion induces the UPR, triggers an apoptotic response, and disrupts protein homeostasis. Based on these data, we hypothesized that UPR induction underlies hyponatremia and volume depletion in rodents, but that these and other phenotypes might be rectified by supplementation with high salt. To test this hypothesis, control and GRP170 tubule-specific knockout mice were provided with a diet containing 8% sodium chloride. We discovered that sodium supplementation improved electrolyte imbalance and reduced clinical kidney injury markers, but was unable to restore weight or tubule integrity. These results are consistent with UPR induction contributing to the kidney injury phenotype in the nephron-specific GR170 knockout model, and that the role of GRP170 in kidney epithelia is essential to both maintain electrolyte balance and cellular protein homeostasis.
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Affiliation(s)
- Aidan Porter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
- Division of Pediatric Nephrology, University of Pittsburgh, Pittsburgh, PA
| | - Hannah E. Vorndran
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Allison Marciszyn
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Stephanie M. Mutchler
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Arohan R. Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA
| | - Thomas R. Kleyman
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA
| | - Linda M. Hendershot
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 30105
| | - Jeffrey L. Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Teresa M. Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
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13
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Ko DK, Brandizzi F. Multi-omics Resources for Understanding Gene Regulation in Response to ER Stress in Plants. Methods Mol Biol 2024; 2772:261-272. [PMID: 38411820 DOI: 10.1007/978-1-0716-3710-4_19] [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] [Indexed: 02/28/2024]
Abstract
Proteotoxic stress of the endoplasmic reticulum (ER) is a potentially lethal condition that ensues when the biosynthetic capacity of the ER is overwhelmed. A sophisticated and largely conserved signaling, known as the unfolded protein response (UPR), is designed to monitor and alleviate ER stress. In plants, the emerging picture of gene regulation by the UPR now appears to be more complex than ever before, requiring multi-omics-enabled network-level approaches to be untangled. In the past decade, with an increasing access and decreasing costs of next-generation sequencing (NGS) and high-throughput protein-DNA interaction (PDI) screening technologies, multitudes of global molecular measurements, known as omics, have been generated and analyzed by the research community to investigate the complex gene regulation of plant UPR. In this chapter, we present a comprehensive catalog of omics resources at different molecular levels (transcriptomes, protein-DNA interactomes, and networks) along with the introduction of key concepts in experimental and computational tools in data generation and analyses. This chapter will serve as a starting point for both experimentalists and bioinformaticians to explore diverse omics datasets for their biological questions in the plant UPR, with likely applications also in other species for conserved mechanisms.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
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14
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Karamali N, Mahmoudi Z, Roghani SA, Assar S, Pournazari M, Soufivand P, Karaji AG, Rezaiemanesh A. Overexpression of Synoviolin and miR-125a-5p, miR-19b-3p in peripheral blood of rheumatoid arthritis patients after treatment with conventional DMARDs and methylprednisolone. Clin Rheumatol 2024; 43:147-157. [PMID: 38049563 DOI: 10.1007/s10067-023-06808-0] [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: 04/11/2023] [Revised: 10/02/2023] [Accepted: 10/31/2023] [Indexed: 12/06/2023]
Abstract
PURPOSE SYVN1 is an endoplasmic reticulum (ER)-resident E3 ubiquitin ligase that has an essential function along with SEL1L in rheumatoid arthritis (RA) pathogenesis. This study aimed to investigate the changes in the expression of peripheral blood ncRNAs and SYVN1-SEL1L affected by DMARDs treatment. METHODS Twenty-five newly diagnosed RA patients were randomly assigned to receive conventional DMARDs (csDMARDs) and methylprednisolone for six months. The peripheral blood gene expression of SYVN1 and SEL1L and possible regulatory axes, NEAT1, miR-125a-5p, and miR-19b-3p, were evaluated before and after qRT-PCR. We also compared differences between the patients and healthy controls (HCs), and statistical analyses were performed to determine the correlation between ncRNAs with SYVN1-SEL1L and the clinical parameters of RA. RESULTS Expression of NEAT1 (P = 0.0001), miR-19b-3p (P = 0.007), miR-125a-5p (P = 0.005), and SYVN1 (P = 0.036) was significantly increased in newly diagnosed patients compared to HCs; also, miR-125a-5p, miR-19b-3p, and SYVN1 were significantly overexpressed after treatment (P = 0.001, P = 0.001, and P = 0.005, respectively). NEAT1 was positively correlated with SYVN1, and miR-125a-5p had a negative correlation with anti-cyclic citrullinated peptides. The ROC curve analysis showed the potential role of selected ncRNAs in RA pathogenesis. CONCLUSION The results indicate the ineffectiveness of the csDMARDs in reducing SYVN1 expression. The difference in expression of ncRNAs might be useful markers for monitoring disease activity and determining therapeutic responses in RA patients. Key Points • The expression of NEAT1 is significantly upregulated in RA patients compared to HC subjects. • miR-19b-3p, miR-125a-5p, and SYVN1 are significantly upregulated in RA patients compared to HC subjects. • The expression of miR-19b-3p and miR-125a-5p is significantly increased in RA patients after treatment with DMARDs and methylprednisolone. • NEAT1 is positively correlated with SYVN1.
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Affiliation(s)
- Negin Karamali
- Student Research Committee, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Mahmoudi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Askar Roghani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shirin Assar
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehran Pournazari
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parviz Soufivand
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Gorgin Karaji
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Daneshgah Street, Shahid Shiroudi Boulevard, Kermanshah, 6714869914, Iran
| | - Alireza Rezaiemanesh
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Daneshgah Street, Shahid Shiroudi Boulevard, Kermanshah, 6714869914, Iran.
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15
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Kim G, Lee J, Ha J, Kang I, Choe W. Endoplasmic Reticulum Stress and Its Impact on Adipogenesis: Molecular Mechanisms Implicated. Nutrients 2023; 15:5082. [PMID: 38140341 PMCID: PMC10745682 DOI: 10.3390/nu15245082] [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: 10/28/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Endoplasmic reticulum (ER) stress plays a pivotal role in adipogenesis, which encompasses the differentiation of adipocytes and lipid accumulation. Sustained ER stress has the potential to disrupt the signaling of the unfolded protein response (UPR), thereby influencing adipogenesis. This comprehensive review illuminates the molecular mechanisms that underpin the interplay between ER stress and adipogenesis. We delve into the dysregulation of UPR pathways, namely, IRE1-XBP1, PERK and ATF6 in relation to adipocyte differentiation, lipid metabolism, and tissue inflammation. Moreover, we scrutinize how ER stress impacts key adipogenic transcription factors such as proliferator-activated receptor γ (PPARγ) and CCAAT-enhancer-binding proteins (C/EBPs) along with their interaction with other signaling pathways. The cellular ramifications include alterations in lipid metabolism, dysregulation of adipokines, and aged adipose tissue inflammation. We also discuss the potential roles the molecular chaperones cyclophilin A and cyclophilin B play in adipogenesis. By shedding light on the intricate relationship between ER stress and adipogenesis, this review paves the way for devising innovative therapeutic interventions.
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Affiliation(s)
- Gyuhui Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jiyoon Lee
- Department of Biological Sciences, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30609, USA;
| | - Joohun Ha
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Insug Kang
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Wonchae Choe
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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16
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Hicks D, Giresh K, Wrischnik LA, Weiser DC. The PPP1R15 Family of eIF2-alpha Phosphatase Targeting Subunits (GADD34 and CReP). Int J Mol Sci 2023; 24:17321. [PMID: 38139150 PMCID: PMC10743859 DOI: 10.3390/ijms242417321] [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: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The vertebrate PPP1R15 family consists of the proteins GADD34 (growth arrest and DNA damage-inducible protein 34, the product of the PPP1R15A gene) and CReP (constitutive repressor of eIF2α phosphorylation, the product of the PPP1R15B gene), both of which function as targeting/regulatory subunits for protein phosphatase 1 (PP1) by regulating subcellular localization, modulating substrate specificity and assembling complexes with target proteins. The primary cellular function of these proteins is to facilitate the dephosphorylation of eukaryotic initiation factor 2-alpha (eIF2α) by PP1 during cell stress. In this review, we will provide a comprehensive overview of the cellular function, biochemistry and pharmacology of GADD34 and CReP, starting with a brief introduction of eIF2α phosphorylation via the integrated protein response (ISR). We discuss the roles GADD34 and CReP play as feedback inhibitors of the unfolded protein response (UPR) and highlight the critical function they serve as inhibitors of the PERK-dependent branch, which is particularly important since it can mediate cell survival or cell death, depending on how long the stressful stimuli lasts, and GADD34 and CReP play key roles in fine-tuning this cellular decision. We briefly discuss the roles of GADD34 and CReP homologs in model systems and then focus on what we have learned about their function from knockout mice and human patients, followed by a brief review of several diseases in which GADD34 and CReP have been implicated, including cancer, diabetes and especially neurodegenerative disease. Because of the potential importance of GADD34 and CReP in aspects of human health and disease, we will discuss several pharmacological inhibitors of GADD34 and/or CReP that show promise as treatments and the controversies as to their mechanism of action. This review will finish with a discussion of the biochemical properties of GADD34 and CReP, their regulation and the additional interacting partners that may provide insight into the roles these proteins may play in other cellular pathways. We will conclude with a brief outline of critical areas for future study.
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Affiliation(s)
- Danielle Hicks
- Department of Science, Mathematics and Engineering, Modesto Junior College, Modesto, CA 95350, USA
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Krithika Giresh
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Lisa A. Wrischnik
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Douglas C. Weiser
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
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17
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Shah A, Huck I, Duncan K, Gansemer ER, Liu K, Adajar RC, Apte U, Stamnes MA, Rutkowski DT. Interference with the HNF4-dependent gene regulatory network diminishes endoplasmic reticulum stress in hepatocytes. Hepatol Commun 2023; 7:e0278. [PMID: 37820274 PMCID: PMC10578741 DOI: 10.1097/hc9.0000000000000278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/08/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND In all eukaryotic cell types, the unfolded protein response (UPR) upregulates factors that promote protein folding and misfolded protein clearance to help alleviate endoplasmic reticulum (ER) stress. Yet, ER stress in the liver is uniquely accompanied by the suppression of metabolic genes, the coordination and purpose of which are largely unknown. METHODS Here, we combined in silico machine learning, in vivo liver-specific deletion of the master regulator of hepatocyte differentiation HNF4α, and in vitro manipulation of hepatocyte differentiation state to determine how the UPR regulates hepatocyte identity and toward what end. RESULTS Machine learning identified a cluster of correlated genes that were profoundly suppressed by persistent ER stress in the liver. These genes, which encode diverse functions including metabolism, coagulation, drug detoxification, and bile synthesis, are likely targets of the master regulator of hepatocyte differentiation HNF4α. The response of these genes to ER stress was phenocopied by liver-specific deletion of HNF4α. Strikingly, while deletion of HNF4α exacerbated liver injury in response to an ER stress challenge, it also diminished UPR activation and partially preserved ER ultrastructure, suggesting attenuated ER stress. Conversely, pharmacological maintenance of hepatocyte identity in vitro enhanced sensitivity to stress. CONCLUSIONS Together, our findings suggest that the UPR regulates hepatocyte identity through HNF4α to protect ER homeostasis even at the expense of liver function.
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Affiliation(s)
- Anit Shah
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Ian Huck
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, Kansas, USA
| | - Kaylia Duncan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Erica R. Gansemer
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Kaihua Liu
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Reed C. Adajar
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Udayan Apte
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, Kansas, USA
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - D. Thomas Rutkowski
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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18
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Christianson JC, Jarosch E, Sommer T. Mechanisms of substrate processing during ER-associated protein degradation. Nat Rev Mol Cell Biol 2023; 24:777-796. [PMID: 37528230 DOI: 10.1038/s41580-023-00633-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 08/03/2023]
Abstract
Maintaining proteome integrity is essential for long-term viability of all organisms and is overseen by intrinsic quality control mechanisms. The secretory pathway of eukaryotes poses a challenge for such quality assurance as proteins destined for secretion enter the endoplasmic reticulum (ER) and become spatially segregated from the cytosolic machinery responsible for disposal of aberrant (misfolded or otherwise damaged) or superfluous polypeptides. The elegant solution provided by evolution is ER-membrane-bound ubiquitylation machinery that recognizes misfolded or surplus proteins or by-products of protein biosynthesis in the ER and delivers them to 26S proteasomes for degradation. ER-associated protein degradation (ERAD) collectively describes this specialized arm of protein quality control via the ubiquitin-proteasome system. But, instead of providing a single strategy to remove defective or unwanted proteins, ERAD represents a collection of independent processes that exhibit distinct yet overlapping selectivity for a wide range of substrates. Not surprisingly, ER-membrane-embedded ubiquitin ligases (ER-E3s) act as central hubs for each of these separate ERAD disposal routes. In these processes, ER-E3s cooperate with a plethora of specialized factors, coordinating recognition, transport and ubiquitylation of undesirable secretory, membrane and cytoplasmic proteins. In this Review, we focus on substrate processing during ERAD, highlighting common threads as well as differences between the many routes via ERAD.
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Affiliation(s)
- John C Christianson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
| | - Ernst Jarosch
- Max-Delbrück-Centrer for Molecular Medicine in Helmholtz Association, Berlin-Buch, Germany
| | - Thomas Sommer
- Max-Delbrück-Centrer for Molecular Medicine in Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt Universität zu Berlin, Berlin, Germany.
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19
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Zhang X, Luo Z, Li J, Lin Y, Li Y, Li W. Sestrin2 in diabetes and diabetic complications. Front Endocrinol (Lausanne) 2023; 14:1274686. [PMID: 37920252 PMCID: PMC10619741 DOI: 10.3389/fendo.2023.1274686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023] Open
Abstract
Diabetes is a global health problem which is accompanied with multi-systemic complications. It is of great significance to elucidate the pathogenesis and to identify novel therapies of diabetes and diabetic complications. Sestrin2, a stress-inducible protein, is primarily involved in cellular responses to various stresses. It plays critical roles in regulating a series of cellular events, such as oxidative stress, mitochondrial function and endoplasmic reticulum stress. Researches investigating the correlations between Sestrin2, diabetes and diabetic complications are increasing in recent years. This review incorporates recent findings, demonstrates the diverse functions and regulating mechanisms of Sestrin2, and discusses the potential roles of Sestrin2 in the pathogenesis of diabetes and diabetic complications, hoping to highlight a promising therapeutic direction.
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Affiliation(s)
- Xiaodan Zhang
- Department of Endocrinology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zirui Luo
- The Second Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Jiahong Li
- The Second Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Yaxuan Lin
- The Second Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Yu Li
- Department of Endocrinology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wangen Li
- Department of Endocrinology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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20
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Ishiwata-Kimata Y, Kimata Y. Fundamental and Applicative Aspects of the Unfolded Protein Response in Yeasts. J Fungi (Basel) 2023; 9:989. [PMID: 37888245 PMCID: PMC10608004 DOI: 10.3390/jof9100989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
Upon the dysfunction or functional shortage of the endoplasmic reticulum (ER), namely, ER stress, eukaryotic cells commonly provoke a protective gene expression program called the unfolded protein response (UPR). The molecular mechanism of UPR has been uncovered through frontier genetic studies using Saccharomyces cerevisiae as a model organism. Ire1 is an ER-located transmembrane protein that directly senses ER stress and is activated as an RNase. During ER stress, Ire1 promotes the splicing of HAC1 mRNA, which is then translated into a transcription factor that induces the expression of various genes, including those encoding ER-located molecular chaperones and protein modification enzymes. While this mainstream intracellular UPR signaling pathway was elucidated in the 1990s, new intriguing insights have been gained up to now. For instance, various additional factors allow UPR evocation strictly in response to ER stress. The UPR machineries in other yeasts and fungi, including pathogenic species, are another important research topic. Moreover, industrially beneficial yeast strains carrying an enforced and enlarged ER have been produced through the artificial and constitutive induction of the UPR. In this article, we review canonical and up-to-date insights concerning the yeast UPR, mainly from the viewpoint of the functions and regulation of Ire1 and HAC1.
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Affiliation(s)
| | - Yukio Kimata
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
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21
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Nagaraj B, James AW, Mathivanan A, Nachiappan V. Impairment of RPN4, a transcription factor, induces ER stress and lipid abnormality in Saccharomyces cerevisiae. Mol Cell Biochem 2023; 478:2127-2139. [PMID: 36703093 DOI: 10.1007/s11010-022-04623-w] [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: 05/04/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023]
Abstract
Accumulation of misfolded/unfolded proteins in the endoplasmic reticulum (ER) induces ER stress. The transcription factor RPN4 {"Regulatory Particle Non-ATPase"} regulates protein homeostasis by degrading proteins that elude proper folding or assembly via the proteasomal degradation pathway. Here, we studied the lipid alterations exerted by Saccharomyces cerevisiae to mitigate (ER) stress during adaptive responses in rpn4∆ cells. The loss of RPN4-induced ER stress increased phospholipid synthesis, leading to altered membrane structures and accumulation of neutral lipids, causing an increase in lipid droplets (LDs). There was a significant upregulation of genes involved in neutral lipid and membrane lipid synthesis in rpn4∆ cells. Overexpression of RPN4 restored the defects caused by rpn4∆ cells. Thus, our study provides new insight that RPN4 impacts lipid homeostasis.
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Affiliation(s)
- Bhanupriya Nagaraj
- Biomembrane Lab, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Trichy, Tamil Nadu, 620 024, India
| | - Antonisamy William James
- Biomembrane Lab, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Trichy, Tamil Nadu, 620 024, India
- Departments of Medicine and Cancer Biology, College of Medicine & Life Sciences, Toledo, USA
| | - Arul Mathivanan
- Biomembrane Lab, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Trichy, Tamil Nadu, 620 024, India
| | - Vasanthi Nachiappan
- Biomembrane Lab, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Trichy, Tamil Nadu, 620 024, India.
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22
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Lai CC, Chiu WY, Chen YT, Wu CL, Lee FJS. The SNARE-associated protein Sft2 functions in Imh1-mediated SNARE recycling transport upon ER stress. Mol Biol Cell 2023; 34:ar112. [PMID: 37610835 PMCID: PMC10559307 DOI: 10.1091/mbc.e23-01-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Vesicular trafficking involving SNARE proteins play a crucial role in the delivery of cargo to the target membrane. Arf-like protein 1 (Arl1) is an important regulator of the endosomal trans-Golgi network (TGN) and secretory trafficking. In yeast, ER stress-enhances Arl1 activation and Golgin Imh1 recruitment to the late-Golgi. Although Arl1 and Imh1 are critical for GARP-mediated endosomal SNARE-recycling transport in response to ER stress, their downstream effectors are unknown. Here, we report that the SNARE-associated protein Sft2 acts downstream of the Arl1-Imh1 axis to regulate SNARE recycling upon ER stress. We first demonstrated that Sft2 is required for Tlg1/Snc1 SNARE-recycling transport under tunicamycin-induced ER stress. Interestingly, we found that Imh1 regulates Tlg2 retrograde transport to the late-Golgi under ER stress, which in turn is required for Sft2 targeting to the late-Golgi. We further showed that Sft2 with 40 amino acids deleted from the N-terminus exhibits defective mediation of SNARE recycling and decreased association with Tlg1 under ER stress. Finally, we demonstrated that Sft2 is required for GARP-dependent endosome-to-Golgi transport in the absence of Rab protein Ypt6. This study highlights Sft2 as a critical downstream effector of the Arl1-Imh1 axis, mediating the endosome-to-Golgi transport of SNAREs.
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Affiliation(s)
- Chun-Chi Lai
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Wan-Yun Chiu
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Yan-Ting Chen
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Chia-Lu Wu
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Fang-Jen S. Lee
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan
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23
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Bartoszewska S, Sławski J, Collawn JF, Bartoszewski R. Dual RNase activity of IRE1 as a target for anticancer therapies. J Cell Commun Signal 2023:10.1007/s12079-023-00784-5. [PMID: 37721642 DOI: 10.1007/s12079-023-00784-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023] Open
Abstract
The unfolded protein response (UPR) is a cellular mechanism that protects cells during stress conditions in which there is an accumulation of misfolded proteins in the endoplasmic reticulum (ER). UPR activates three signaling pathways that function to alleviate stress conditions and promote cellular homeostasis and cell survival. During unmitigated stress conditions, however, UPR activation signaling changes to promote cell death through apoptosis. Interestingly, cancer cells take advantage of this pathway to facilitate survival and avoid apoptosis even during prolonged cell stress conditions. Here, we discuss different signaling pathways associated with UPR and focus specifically on one of the ER signaling pathways activated during UPR, inositol-requiring enzyme 1α (IRE1). The rationale is that the IRE1 pathway is associated with cell fate decisions and recognized as a promising target for cancer therapeutics. Here we discuss IRE1 inhibitors and how they might prove to be an effective cancer therapeutic.
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Affiliation(s)
- Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Jakub Sławski
- Department of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a Street, 50-383, Wrocław, Poland
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Rafał Bartoszewski
- Department of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a Street, 50-383, Wrocław, Poland.
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24
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Chen X, Shi C, He M, Xiong S, Xia X. Endoplasmic reticulum stress: molecular mechanism and therapeutic targets. Signal Transduct Target Ther 2023; 8:352. [PMID: 37709773 PMCID: PMC10502142 DOI: 10.1038/s41392-023-01570-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/17/2023] [Accepted: 07/14/2023] [Indexed: 09/16/2023] Open
Abstract
The endoplasmic reticulum (ER) functions as a quality-control organelle for protein homeostasis, or "proteostasis". The protein quality control systems involve ER-associated degradation, protein chaperons, and autophagy. ER stress is activated when proteostasis is broken with an accumulation of misfolded and unfolded proteins in the ER. ER stress activates an adaptive unfolded protein response to restore proteostasis by initiating protein kinase R-like ER kinase, activating transcription factor 6, and inositol requiring enzyme 1. ER stress is multifaceted, and acts on aspects at the epigenetic level, including transcription and protein processing. Accumulated data indicates its key role in protein homeostasis and other diverse functions involved in various ocular diseases, such as glaucoma, diabetic retinopathy, age-related macular degeneration, retinitis pigmentosa, achromatopsia, cataracts, ocular tumors, ocular surface diseases, and myopia. This review summarizes the molecular mechanisms underlying the aforementioned ocular diseases from an ER stress perspective. Drugs (chemicals, neurotrophic factors, and nanoparticles), gene therapy, and stem cell therapy are used to treat ocular diseases by alleviating ER stress. We delineate the advancement of therapy targeting ER stress to provide new treatment strategies for ocular diseases.
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Affiliation(s)
- Xingyi Chen
- Eye Center of Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
- Hunan Key Laboratory of Ophthalmology, Central South University, 410008, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chaoran Shi
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Meihui He
- Eye Center of Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
- Hunan Key Laboratory of Ophthalmology, Central South University, 410008, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Siqi Xiong
- Eye Center of Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China.
- Hunan Key Laboratory of Ophthalmology, Central South University, 410008, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China.
- Hunan Key Laboratory of Ophthalmology, Central South University, 410008, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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25
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Usmani SA, Kumar M, Arya K, Ali B, Bhardwaj N, Gaur NA, Prasad R, Singh A. Beyond membrane components: uncovering the intriguing world of fungal sphingolipid synthesis and regulation. Res Microbiol 2023; 174:104087. [PMID: 37328042 DOI: 10.1016/j.resmic.2023.104087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
Sphingolipids (SLs) are essential to fungal survival and represent a major class of structural and signaling lipids. Unique SL structures and their biosynthetic enzymes in filamentous fungi make them an ideal drug target. Several studies have contributed towards the functional characterization of specific SL metabolism genes, which have been complemented by advanced lipidomics methods which allow accurate identification and quantification of lipid structures and pathway mapping. These studies have provided a better understanding of SL biosynthesis, degradation and regulation networks in filamentous fungi, which are discussed and elaborated here.
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Affiliation(s)
- Sana Akhtar Usmani
- Department of Biochemistry, University of Lucknow, Lucknow, Uttar Pradesh, 226024, India
| | - Mohit Kumar
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, India; International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Khushboo Arya
- Department of Biochemistry, University of Lucknow, Lucknow, Uttar Pradesh, 226024, India
| | - Basharat Ali
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, India
| | - Nitin Bhardwaj
- Department of Zoology and Environmental Science, Gurukula Kangri Vishwavidyalaya, Haridwar, Uttarakhand 249404, India
| | - Naseem Akhtar Gaur
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Rajendra Prasad
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, India
| | - Ashutosh Singh
- Department of Biochemistry, University of Lucknow, Lucknow, Uttar Pradesh, 226024, India.
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26
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Fukuoka K, Mineo R, Kita S, Fukuda S, Okita T, Kawada-Horitani E, Iioka M, Fujii K, Kawada K, Fujishima Y, Nishizawa H, Maeda N, Shimomura I. ER stress decreases exosome production through adiponectin/T-cadherin-dependent and -independent pathways. J Biol Chem 2023; 299:105114. [PMID: 37524131 PMCID: PMC10474463 DOI: 10.1016/j.jbc.2023.105114] [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: 01/11/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Exosomes, extracellular vesicles (EVs) produced within cells, mediate both the disposal of intracellular waste and communication with distant cells, and they are involved in a variety of disease processes. Although disease modifications of exosome cargos have been well studied, it has been poorly investigated how disease processes, such as endoplasmic reticulum (ER) stress, affect EV production. We previously reported that adiponectin, an adipocyte-secreted salutary factor, increases systemic exosome levels through T-cadherin-mediated enhancement of exosome biogenesis. In the present study, we demonstrated that adiponectin/T-cadherin-dependent EV production was susceptible to ER stress and that low-dose tunicamycin significantly reduced EV production in the presence, but not in the absence, of adiponectin. Moreover, pharmacological or genetic activation of inositol-requiring enzyme 1α, a central regulator of ER stress, downregulated T-cadherin at the mRNA and protein levels as well as attenuated EV production. In addition, adiponectin/T-cadherin-independent EV production was attenuated under ER stress conditions. Repeated administration of tunicamycin to mice decreased circulating small EVs without decreasing tissue T-cadherin expression. Mechanistically, inositol-requiring enzyme 1α activation by silencing of the X-box binding protein 1 transcription factor upregulated the canonical interferon pathway and decreased EV production. The interferon pathway, when it was activated by polyinosinic-polycytidylic acid, also significantly attenuated EV production. Thus, we concluded that ER stress decreases exosome production through adiponectin/T-cadherin-dependent and -independent pathways.
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Affiliation(s)
- Keita Fukuoka
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryohei Mineo
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shunbun Kita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan; Department of Adipose Management, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Shiro Fukuda
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tomonori Okita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Emi Kawada-Horitani
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masahito Iioka
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kohei Fujii
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Keitaro Kawada
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuya Fujishima
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hitoshi Nishizawa
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Norikazu Maeda
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan; Department of Metabolism and Atherosclerosis, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
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27
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Doss EM, Moore JM, Harman BH, Doud EH, Rubenstein EM, Bernstein DA. Characterization of endoplasmic reticulum-associated degradation in the human fungal pathogen Candida albicans. PeerJ 2023; 11:e15897. [PMID: 37645016 PMCID: PMC10461541 DOI: 10.7717/peerj.15897] [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: 05/22/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Background Candida albicans is the most prevalent human fungal pathogen. In immunocompromised individuals, C. albicans can cause serious systemic disease, and patients infected with drug-resistant isolates have few treatment options. The ubiquitin-proteasome system has not been thoroughly characterized in C. albicans. Research from other organisms has shown ubiquitination is important for protein quality control and regulated protein degradation at the endoplasmic reticulum (ER) via ER-associated protein degradation (ERAD). Methods Here we perform the first characterization, to our knowledge, of ERAD in a human fungal pathogen. We generated functional knockouts of C. albicans genes encoding three proteins predicted to play roles in ERAD, the ubiquitin ligases Hrd1 and Doa10 and the ubiquitin-conjugating enzyme Ubc7. We assessed the fitness of each mutant in the presence of proteotoxic stress, and we used quantitative tandem mass tag mass spectrometry to characterize proteomic alterations in yeast lacking each gene. Results Consistent with a role in protein quality control, yeast lacking proteins thought to contribute to ERAD displayed hypersensitivity to proteotoxic stress. Furthermore, each mutant displayed distinct proteomic profiles, revealing potential physiological ERAD substrates, co-factors, and compensatory stress response factors. Among candidate ERAD substrates are enzymes contributing to ergosterol synthesis, a known therapeutic vulnerability of C. albicans. Together, our results provide the first description of ERAD function in C. albicans, and, to our knowledge, any pathogenic fungus.
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Affiliation(s)
- Ellen M. Doss
- Department of Biology, Ball State University, Muncie, Indiana, United States
- Mode of Action and Resistance Management Center of Expertise, Corteva Agriscience, Indianapolis, Indiana, United States
| | - Joshua M. Moore
- Department of Biology, Ball State University, Muncie, Indiana, United States
| | - Bryce H. Harman
- Department of Biology, Ball State University, Muncie, Indiana, United States
| | - Emma H. Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Eric M. Rubenstein
- Department of Biology, Ball State University, Muncie, Indiana, United States
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28
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Nakazawa T, Morimoto T, Maeoka R, Matsuda R, Nakamura M, Nishimura F, Ouji N, Yamada S, Nakagawa I, Park YS, Ito T, Nakase H, Tsujimura T. CIS deletion by CRISPR/Cas9 enhances human primary natural killer cell functions against allogeneic glioblastoma. J Exp Clin Cancer Res 2023; 42:205. [PMID: 37563692 PMCID: PMC10413513 DOI: 10.1186/s13046-023-02770-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common malignant brain tumor and has "immunologically cold" features. Changing GBM to an "immunologically hot" tumor requires a strong trigger that induces initial immune responses in GBM. Allogeneic natural killer cells (NKCs) have gained considerable attention as promising immunotherapeutic tools against cancer, where gene-edited NKCs would result in effective anti-cancer treatment. The present study focused on the immune checkpoint molecule cytokine-inducible SH2-containing protein (CISH, or CIS) as a critical negative regulator in NKCs. METHODS The GBM tumor environment featured with immunological aspect was analyzed with Cancer immunogram and GlioVis. We generated human primary CIS-deleted NKCs (NK dCIS) using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) with single guide RNA targeting genome sites on CIS coding exons. The genome-edited NKCs underwent microarray with differential expression analysis and gene set enrichment analysis (GSEA). The anti-GBM activity of the genome-edited NKCs was evaluated by apoptosis induction effects against allogeneic GBM cells and spheroids. We further detected in vivo antitumor effects using xenograft brain tumor mice. RESULTS We successfully induced human CIS-deleted NKCs (NK dCIS) by combining our specific human NKC expansion method available for clinical application and genome editing technology. CIS gene-specific guide RNA/Cas9 protein complex suppressed CIS expression in the expanded NKCs with high expansion efficacy. Comprehensive gene expression analysis demonstrated increased expression of 265 genes and decreased expression of 86 genes in the NK dCIS. Gene set enrichment analysis revealed that the enriched genes were involved in NKC effector functions. Functional analysis revealed that the NK dCIS had increased interferon (IFN)ɤ and tumor necrosis factor (TNF) production. CIS deletion enhanced NKC-mediated apoptosis induction against allogeneic GBM cells and spheroids. Intracranial administration of the allogeneic NKCs prolonged the overall survival of xenograft brain tumor mice. Furthermore, the NK dCIS extended the overall survival of the mice. CONCLUSION The findings demonstrated the successful induction of human primary NK dCIS with CRISPR/Cas9 with efficient expansion. CIS deletion enhanced the NKC-mediated anti-tumor effects in allogeneic GBM and could be a promising immunotherapeutic alternative for patients with GBM.
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Affiliation(s)
- Tsutomu Nakazawa
- Grandsoul Research Institute for Immunology, Inc, 8-1 Matsui, Uda, Nara, 634-8522, Japan.
- Clinic Grandsoul Nara, Uda, Nara, Japan.
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan.
| | - Takayuki Morimoto
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Ryosuke Maeoka
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Ryosuke Matsuda
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Mitsutoshi Nakamura
- Clinic Grandsoul Nara, Uda, Nara, Japan
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Fumihiko Nishimura
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Noriko Ouji
- Department of Immunology, Nara Medical University, Kashihara, Nara, 634-8522, Japan
| | - Shuichi Yamada
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Ichiro Nakagawa
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Young Soo Park
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Toshihiro Ito
- Department of Immunology, Nara Medical University, Kashihara, Nara, 634-8522, Japan
| | - Hiroyuki Nakase
- Department of Neurosurgery, Nara Medical University, Kashihara, Nara, Japan
| | - Takahiro Tsujimura
- Grandsoul Research Institute for Immunology, Inc, 8-1 Matsui, Uda, Nara, 634-8522, Japan
- Clinic Grandsoul Nara, Uda, Nara, Japan
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29
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De Groeve M, Laukens B, Schotte P. Optimizing expression of Nanobody® molecules in Pichia pastoris through co-expression of auxiliary proteins under methanol and methanol-free conditions. Microb Cell Fact 2023; 22:135. [PMID: 37481525 PMCID: PMC10362571 DOI: 10.1186/s12934-023-02132-z] [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: 04/04/2023] [Accepted: 06/24/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Ablynx NV, a subsidiary of Sanofi, has a long-standing focus on the development of Nanobody® molecules as biopharmaceuticals (Nanobody® is a registered trademark of Ablynx NV). Nanobody molecules are single variable domains, and they have been met with great success part due to their favorable expression properties in several microbial systems. Nevertheless, the search for the host of the future is an ongoing and challenging process. Komagataella phaffi (Pichia pastoris) is one of the most suitable organisms to produce Nanobody molecules. In addition, genetic engineering of Pichia is easy and an effective approach to improve titers. RESULTS Here we report that P. pastoris engineered to co-express genes encoding four auxiliary proteins (HAC1, KAR2, PDI and RPP0), leads to a marked improvement in the expression of Nanobody molecules using the AOX1 methanol induction system. Titer improvement is mainly attributed to HAC1, and its beneficial effect was also observed in a methanol-free expression system. CONCLUSION Our findings are based on over a thousand fed-batch fermentations and offer a valuable guide to produce Nanobody molecules in P. pastoris. The presented differences in expressability between types of Nanobody molecules will be helpful for researchers to select both the type of Nanobody molecule and Pichia strain and may stimulate further the development of a more ecological methanol-free expression platform.
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Affiliation(s)
- Manu De Groeve
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Bram Laukens
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Peter Schotte
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium.
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30
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Zhao S, Feng H, Jiang D, Yang K, Wang ST, Zhang YX, Wang Y, Liu H, Guo C, Tang TS. ER Ca 2+ overload activates the IRE1α signaling and promotes cell survival. Cell Biosci 2023; 13:123. [PMID: 37400935 DOI: 10.1186/s13578-023-01062-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Maintaining homeostasis of Ca2+ stores in the endoplasmic reticulum (ER) is crucial for proper Ca2+ signaling and key cellular functions. Although Ca2+ depletion has been known to cause ER stress which in turn activates the unfolded protein response (UPR), how UPR sensors/transducers respond to excess Ca2+ when ER stores are overloaded remain largely unclear. RESULTS Here, we report for the first time that overloading of ER Ca2+ can directly sensitize the IRE1α-XBP1 axis. The overloaded ER Ca2+ in TMCO1-deficient cells can cause BiP dissociation from IRE1α, promote the dimerization and stability of the IRE1α protein, and boost IRE1α activation. Intriguingly, attenuation of the over-activated IRE1α-XBP1s signaling by a IRE1α inhibitor can cause a significant cell death in TMCO1-deficient cells. CONCLUSIONS Our data establish a causal link between excess Ca2+ in ER stores and the selective activation of IRE1α-XBP1 axis, underscoring an unexpected role of overload of ER Ca2+ in IRE1α activation and in preventing cell death.
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Affiliation(s)
- Song Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiping Feng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongfang Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keyan Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Si-Tong Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Xin Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Caixia Guo
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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31
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Hrach VL, King WR, Nelson LD, Conklin S, Pollock JA, Patton-Vogt J. The acyltransferase Gpc1 is both a target and an effector of the unfolded protein response in Saccharomyces cerevisiae. J Biol Chem 2023; 299:104884. [PMID: 37269946 PMCID: PMC10331479 DOI: 10.1016/j.jbc.2023.104884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023] Open
Abstract
The unfolded protein response (UPR) is sensitive to proteotoxic and membrane bilayer stress, both of which are sensed by the ER protein Ire1. When activated, Ire1 splices HAC1 mRNA, producing a transcription factor that targets genes involved in proteostasis and lipid metabolism, among others. The major membrane lipid phosphatidylcholine (PC) is subject to phospholipase-mediated deacylation, producing glycerophosphocholine (GPC), followed by reacylation of GPC through the PC deacylation/reacylation pathway (PC-DRP). The reacylation events occur via a two-step process catalyzed first by the GPC acyltransferase Gpc1, followed by acylation of the lyso-PC molecule by Ale1. However, whether Gpc1 is critical for ER bilayer homeostasis is unclear. Using an improved method for C14-choline-GPC radiolabeling, we first show that loss of Gpc1 results in abrogation of PC synthesis through PC-DRP and that Gpc1 colocalizes with the ER. We then probe the role of Gpc1 as both a target and an effector of the UPR. Exposure to the UPR-inducing compounds tunicamycin, DTT, and canavanine results in a Hac1-dependent increase in GPC1 message. Further, cells lacking Gpc1 exhibit increased sensitivity to those proteotoxic stressors. Inositol limitation, known to induce the UPR via bilayer stress, also induces GPC1 expression. Finally, we show that loss of GPC1 induces the UPR. A gpc1Δ mutant displays upregulation of the UPR in strains expressing a mutant form of Ire1 that is unresponsive to unfolded proteins, indicating that bilayer stress is responsible for the observed upregulation. Collectively, our data indicate an important role for Gpc1 in yeast ER bilayer homeostasis.
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Affiliation(s)
- Victoria Lee Hrach
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - William R King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Laura D Nelson
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Shane Conklin
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - John A Pollock
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.
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32
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Popova LG, Khramov DE, Nedelyaeva OI, Volkov VS. Yeast Heterologous Expression Systems for the Study of Plant Membrane Proteins. Int J Mol Sci 2023; 24:10768. [PMID: 37445944 DOI: 10.3390/ijms241310768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Researchers are often interested in proteins that are present in cells in small ratios compared to the total amount of proteins. These proteins include transcription factors, hormones and specific membrane proteins. However, sufficient amounts of well-purified protein preparations are required for functional and structural studies of these proteins, including the creation of artificial proteoliposomes and the growth of protein 2D and 3D crystals. This aim can be achieved by the expression of the target protein in a heterologous system. This review describes the applications of yeast heterologous expression systems in studies of plant membrane proteins. An initial brief description introduces the widely used heterologous expression systems of the baker's yeast Saccharomyces cerevisiae and the methylotrophic yeast Pichia pastoris. S. cerevisiae is further considered a convenient model system for functional studies of heterologously expressed proteins, while P. pastoris has the advantage of using these yeast cells as factories for producing large quantities of proteins of interest. The application of both expression systems is described for functional and structural studies of membrane proteins from plants, namely, K+- and Na+-transporters, various ATPases and anion transporters, and other transport proteins.
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Affiliation(s)
- Larissa G Popova
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Dmitrii E Khramov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Olga I Nedelyaeva
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Vadim S Volkov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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33
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Bhuiyan SH, Bordet G, Bamgbose G, Tulin AV. The Drosophila gene encoding JIG protein (CG14850) is critical for CrebA nuclear trafficking during development. Nucleic Acids Res 2023; 51:5647-5660. [PMID: 37144466 PMCID: PMC10287909 DOI: 10.1093/nar/gkad343] [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] [Received: 01/17/2022] [Revised: 04/16/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Coordination of mitochondrial and nuclear processes is key to the cellular health; however, very little is known about the molecular mechanisms regulating nuclear-mitochondrial crosstalk. Here, we report a novel molecular mechanism controlling the shuttling of CREB (cAMP response element-binding protein) protein complex between mitochondria and nucleoplasm. We show that a previously unknown protein, herein termed as Jig, functions as a tissue-specific and developmental timing-specific coregulator in the CREB pathway. Our results demonstrate that Jig shuttles between mitochondria and nucleoplasm, interacts with CrebA protein and controls its delivery to the nucleus, thus triggering CREB-dependent transcription in nuclear chromatin and mitochondria. Ablating the expression of Jig prevents CrebA from localizing to the nucleoplasm, affecting mitochondrial functioning and morphology and leads to Drosophila developmental arrest at the early third instar larval stage. Together, these results implicate Jig as an essential mediator of nuclear and mitochondrial processes. We also found that Jig belongs to a family of nine similar proteins, each of which has its own tissue- and time-specific expression profile. Thus, our results are the first to describe the molecular mechanism regulating nuclear and mitochondrial processes in a tissue- and time-specific manner.
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34
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Fauzee YNBM, Yoshida Y, Kimata Y. Endoplasmic stress sensor Ire1 is involved in cytosolic/nuclear protein quality control in Pichia pastoris cells independent of HAC1. Front Microbiol 2023; 14:1157146. [PMID: 37415818 PMCID: PMC10321714 DOI: 10.3389/fmicb.2023.1157146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023] Open
Abstract
In eukaryotic species, dysfunction of the endoplasmic reticulum (ER), namely, ER stress, provokes a cytoprotective transcription program called the unfolded protein response (UPR). The UPR is triggered by transmembrane ER-stress sensors, including Ire1, which acts as an endoribonuclease to splice and mature the mRNA encoding the transcription factor Hac1 in many fungal species. Through analyses of the methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii), we revealed a previously unknown function of Ire1. In P. pastoris cells, the IRE1 knockout mutation (ire1Δ) and HAC1 knockout mutation (hac1Δ) caused only partially overlapping gene expression changes. Protein aggregation and the heat shock response (HSR) were induced in ire1Δ cells but not in hac1Δ cells even under non-stress conditions. Moreover, Ire1 was further activated upon high-temperature culturing and conferred heat stress resistance to P. pastoris cells. Our findings cumulatively demonstrate an intriguing case in which the UPR machinery controls cytosolic protein folding status and the HSR, which is known to be activated upon the accumulation of unfolded proteins in the cytosol and/or nuclei.
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35
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Kostina A, Lewis-Israeli YR, Abdelhamid M, Gabalski MA, Volmert BD, Lankerd H, Huang AR, Wasserman AH, Lydic T, Chan C, Olomu I, Aguirre A. ER stress and lipid imbalance drive embryonic cardiomyopathy in a human heart organoid model of pregestational diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544081. [PMID: 37333095 PMCID: PMC10274758 DOI: 10.1101/2023.06.07.544081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Congenital heart defects constitute the most common birth defect in humans, affecting approximately 1% of all live births. The incidence of congenital heart defects is exacerbated by maternal conditions, such as diabetes during the first trimester. Our ability to mechanistically understand these disorders is severely limited by the lack of human models and the inaccessibility to human tissue at relevant stages. Here, we used an advanced human heart organoid model that recapitulates complex aspects of heart development during the first trimester to model the effects of pregestational diabetes in the human embryonic heart. We observed that heart organoids in diabetic conditions develop pathophysiological hallmarks like those previously reported in mouse and human studies, including ROS-mediated stress and cardiomyocyte hypertrophy, among others. Single cell RNA-seq revealed cardiac cell type specific-dysfunction affecting epicardial and cardiomyocyte populations, and suggested alterations in endoplasmic reticulum function and very long chain fatty acid lipid metabolism. Confocal imaging and LC-MS lipidomics confirmed our observations and showed that dyslipidemia was mediated by fatty acid desaturase 2 (FADS2) mRNA decay dependent on IRE1-RIDD signaling. We also found that the effects of pregestational diabetes could be reversed to a significant extent using drug interventions targeting either IRE1 or restoring healthy lipid levels within organoids, opening the door to new preventative and therapeutic strategies in humans.
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Affiliation(s)
- Aleksandra Kostina
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
| | - Yonatan R. Lewis-Israeli
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
| | - Mishref Abdelhamid
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Division of Neonatology, Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Mitchell A. Gabalski
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
| | - Brett D. Volmert
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
| | - Haley Lankerd
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
| | - Amanda R. Huang
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
| | - Aaron H. Wasserman
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
| | - Todd Lydic
- Department of Physiology, Michigan State University, MI, USA
| | - Christina Chan
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
| | - Isoken Olomu
- Division of Neonatology, Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Aitor Aguirre
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, USA
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36
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Korpys-Woźniak P, Celińska E. Molecular background of HAC1-driven improvement in the secretion of recombinant protein in Yarrowia lipolytica based on comparative transcriptomics. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 38:e00801. [PMID: 37234569 PMCID: PMC10206436 DOI: 10.1016/j.btre.2023.e00801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023]
Abstract
While the unfolded protein response (UPR) and its major regulator - transcription factor Hac1 are well-conserved across Eukarya, species-specific variations are repeatedly reported. Here we investigated molecular mechanisms by which co-over-expression of HAC1 improves secretion of a recombinant protein (r-Prot) in Yarrowia lipolytica, using comparative transcriptomics. Co-over-expression of HAC1 caused an >2-fold increase in secreted r-Prot, but its intracellular levels were decreased. The unconventional splicing rate of the HAC1 mRNA was counted through transcript sequencing. Multiple biological processes were affected in the HAC1-and-r-Prot co-over-expressing strain, including ribosome biogenesis, nuclear and mitochondrial events, cell cycle arrest, attenuation of gene expression by RNA polymerase III and II, as well as modulation of proteolysis and RNA metabolism; but whether the HAC1 co-over-expression/induction was the actual causative agent for these changes, was not always clear. We settled that the expression of the "conventional" HAC1 targets (KAR2 and PDI1) is not affected by its over-expression.
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37
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Sosa-Carrillo S, Galez H, Napolitano S, Bertaux F, Batt G. Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches. Nat Commun 2023; 14:3028. [PMID: 37231013 DOI: 10.1038/s41467-023-38807-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
Optimizing the production of recombinant proteins is a problem of major industrial and pharmaceutical importance. Secretion of the protein by the host cell considerably simplifies downstream purification processes. However, for many proteins, this is also the limiting production step. Current solutions involve extensive engineering of the chassis cell to facilitate protein trafficking and limit protein degradation triggered by excessive secretion-associated stress. Here, we propose instead a regulation-based strategy in which induction is dynamically adjusted to an optimal strength based on the current stress level of the cells. Using a small collection of hard-to-secrete proteins, a bioreactor-based platform with automated cytometry measurements, and a systematic assay to quantify secreted protein levels, we demonstrate that the secretion sweet spot is indicated by the appearance of a subpopulation of cells that accumulate high amounts of proteins, decrease growth, and face significant stress, that is, experience a secretion burnout. In these cells, adaptations capabilities are overwhelmed by a too strong production. Using these notions, we show for a single-chain antibody variable fragment that secretion levels can be improved by 70% by dynamically keeping the cell population at optimal stress levels using real-time closed-loop control.
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Affiliation(s)
| | - Henri Galez
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - Sara Napolitano
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - François Bertaux
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
- Lesaffre International, 101 rue de Menin, Marcq-en-Baroeul, France
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France.
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38
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Liu Z, Nan P, Gong Y, Tian L, Zheng Y, Wu Z. Endoplasmic reticulum stress-triggered ferroptosis via the XBP1-Hrd1-Nrf2 pathway induces EMT progression in diabetic nephropathy. Biomed Pharmacother 2023; 164:114897. [PMID: 37224754 DOI: 10.1016/j.biopha.2023.114897] [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: 03/29/2023] [Revised: 05/06/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023] Open
Abstract
Diabetic nephropathy (DN) is characterized by tubulointerstitial fibrosis caused by epithelial-mesenchymal transition (EMT) of renal tubular epithelial cells. Although ferroptosis promotes DN development, the specific pathological process that is affected by ferroptosis in DN remains unclear. Herein, EMT-related changes, including increased α-smooth muscle actin (α-SMA) and Vimentin expression and decreased E-cadherin expression, were observed in the renal tissues of streptozotocin-induced DN mice and high glucose-cultured human renal proximal tubular (HK-2) cells. Treatment with ferrostatin-1 (Fer-1) ameliorated these changes and rescued renal pathological injury in diabetic mice. Interestingly, endoplasmic reticulum stress (ERS) was activated during EMT progression in DN. Inhibiting ERS improved the expression of EMT-associated indicators and further rescued the characteristic changes in ferroptosis caused by high glucose, including reactive oxygen species (ROS) accumulation, iron overload, increased lipid peroxidation product generation, and reduced mitochondrial cristae. Moreover, overexpression of XBP1 increased Hrd1 expression and inhibited NFE2-related factor 2 (Nrf2) expression, which could enhance cell susceptibility to ferroptosis. Co-immunoprecipitation (Co-IP) and ubiquitylation assays indicated that Hrd1 interacted with and ubiquitinated Nrf2 under high-glucose conditions. Collectively, our results demonstrated that ERS triggers ferroptosis-related EMT progression through the XBP1-Hrd1-Nrf2 pathway, which provides new insights into potential mechanisms for delaying EMT progression in DN.
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Affiliation(s)
- Zijun Liu
- NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China; Tianjin Key Laboratory of Metabolic Diseases, Tianjin Medical University, Tianjin 300134, China.
| | - Ping Nan
- Department of Obster & Gynecol, Shengli Oilfield Center Hospital, Dongying, Shandong 257000, China.
| | - Yihui Gong
- NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China; Tianjin Key Laboratory of Metabolic Diseases, Tianjin Medical University, Tianjin 300134, China.
| | - Ling Tian
- NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China; Tianjin Key Laboratory of Metabolic Diseases, Tianjin Medical University, Tianjin 300134, China.
| | - Yin Zheng
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China; Shandong Institute of Endocrine and Metabolic Diseases, Jinan, Shandong 250021, China.
| | - Zhongming Wu
- NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China; Tianjin Key Laboratory of Metabolic Diseases, Tianjin Medical University, Tianjin 300134, China; Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China; Shandong Institute of Endocrine and Metabolic Diseases, Jinan, Shandong 250021, China.
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Xiao C, Xue S, Pan Y, Liu X, Huang M. Overexpression of genes by stress-responsive promoters increases protein secretion in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2023; 39:203. [PMID: 37209206 DOI: 10.1007/s11274-023-03646-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/22/2023]
Abstract
Recombinant proteins produced by cell factories are now widely used in various fields. Many efforts have been made to improve the secretion capacity of cell factories to meet the increasing demand for recombinant proteins. Recombinant protein production usually causes cell stress in the endoplasmic reticulum (ER). The overexpression of key genes possibly removes limitations in protein secretion. However, inappropriate gene expression may have negative effects. There is a need for dynamic control of genes adapted to cellular status. In this study, we constructed and characterized synthetic promoters that were inducible under ER stress conditions in Saccharomyces cerevisiae. The unfolded protein response element UPRE2, responding to stress with a wide dynamic range, was assembled with various promoter core regions, resulting in UPR-responsive promoters. Synthetic responsive promoters regulated gene expression by responding to stress level, which reflected the cellular status. The engineered strain using synthetic responsive promoters P4UPRE2 - TDH3 and P4UPRE2 - TEF1 for co-expression of ERO1 and SLY1 had 95% higher α-amylase production compared with the strain using the native promoters PTDH3 and PTEF1. This work showed that UPR-responsive promoters were useful in the metabolic engineering of yeast strains for tuning genes to support efficient protein production.
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Affiliation(s)
- Chufan Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Songlyu Xue
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Xiufang Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China.
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40
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Phuong HT, Ishiwata-Kimata Y, Kimata Y. An ER-accumulated mutant of yeast Pma1 causes membrane-related stress to induce the unfolded protein response. Biochem Biophys Res Commun 2023; 667:58-63. [PMID: 37209563 DOI: 10.1016/j.bbrc.2023.05.044] [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: 04/24/2023] [Accepted: 05/13/2023] [Indexed: 05/22/2023]
Abstract
Upon dysfunction of the endoplasmic reticulum (ER), namely ER stress, eukaryotic cells provoke the unfolded protein response (UPR), which is triggered by ER stress sensors including Ire1. While the ER luminal domain of Ire1 is known to directly recognize misfolded soluble proteins accumulated in the ER, the transmembrane domain of Ire1 is involved in its self-association and activation upon membrane lipid-related abnormalities, which are so-called lipid bilayer stress (LBS). Here we inquired how the ER accumulation of misfolded transmembrane proteins induces the UPR. In yeast Saccharomyces cerevisiae cells, a multi-transmembrane protein, Pma1, is not transported to the cell surface but aggregates on the ER membrane when carrying a point mutation (Pma1-2308). Here, we show that GFP-tagged Ire1 co-localized with the Pma1-2308-mCherry puncta. This co-localization and the UPR induced by Pma1-2308-mCherry were compromised by a point mutation in Ire1 that specifically impairs its activation upon LBS. We presume that Pma1-2308-mCherry locally affects the properties (probably the thickness) of the ER membrane at its aggregation sites, where Ire1 is then recruited, self-associated, and then activated.
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Affiliation(s)
- Huong Thi Phuong
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan; Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet road, Cau Giay, Ha Noi, Viet Nam
| | - Yuki Ishiwata-Kimata
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Yukio Kimata
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
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41
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Wu S, Lin W. Endoplasmic reticulum associated degradation is essential for maintaining the viability or function of mature myelinating cells in adults. Glia 2023; 71:1360-1376. [PMID: 36708285 PMCID: PMC10023378 DOI: 10.1002/glia.24346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/29/2023]
Abstract
Endoplasmic reticulum associated degradation (ERAD) is responsible for recognition and degradation of unfolded or misfolded proteins in the ER. Sel1L is essential for the ERAD activity of Sel1L-Hrd1 complex, the best-known ERAD machinery. Using a continuous Sel1L knockout mouse model (CNP/Cre; Sel1LloxP/loxP mice), our previous studies showed that Sel1L knockout in myelinating cells, oligodendrocytes in the central nervous system (CNS) and Schwann cells in the peripheral nervous system (PNS), leads to adult-onset myelin abnormalities in the CNS and PNS. Because Sel1L is deleted in myelinating cells of CNP/Cre; Sel1LloxP/loxP mice starting at very early stage of differentiation, it is impossible to rule out the possibility that the adult-onset myelin abnormalities in these mice results from developmental myelination defects caused by Sel1L knockout in myelinating cells during development. Thus, using an inducible Sel1L knockout mouse model (PLP/CreERT ; Sel1LloxP/loxP mice) that has normal, intact myelin and myelinating cells in the adult CNS and PNS prior to tamoxifen treatment, we sought to determine if Sel1L knockout in mature myelinating cells of adult mice leads to myelin abnormalities in the CNS and PNS. We showed that Sel1L knockout in mature myelinating cells caused ERAD impairment, ER stress and UPR activation. Interesting, Sel1L knockout in mature oligodendrocytes impaired their myelinating function by suppressing myelin protein translation, and resulted in progressive myelin thinning in the adult CNS. Conversely, Sel1L knockout in mature Schwann cells led to Schwann cell apoptosis and demyelination in the adult PNS. These findings demonstrate the essential roles of ERAD in mature myelinating cells in the adult CNS and PNS under physiological conditions.
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Affiliation(s)
- Shuangchan Wu
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, United States, 55455
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, United States, 55455
| | - Wensheng Lin
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, United States, 55455
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, United States, 55455
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Pal D, De K, Yates TB, Kolape J, Muchero W. Mutating novel interaction sites in NRP1 reduces SARS-CoV-2 spike protein internalization. iScience 2023; 26:106274. [PMID: 36910328 PMCID: PMC9957656 DOI: 10.1016/j.isci.2023.106274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
The global pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has become a severe global health problem because of its rapid spread. Both Ace2 and NRP1 provide initial viral binding sites for SARS-CoV-2. Here, we show that cysteine residues located in the vestigial plasminogen-apple-nematode (PAN) domain of NRP1 are necessary for SARS-CoV-2 spike protein internalization. Mutating novel cysteine residues in the PAN altered NRP1 stability and downstream activation of extracellular signal-regulated kinase (ERK) signaling pathway and impaired its interaction with the spike protein. This resulted in a significant reduction in spike protein abundance in Vero-E6 cells for the original, alpha, and delta SARS-CoV-2 variants even in the presence of the Ace2. Moreover, mutating these cysteine residues in NRP1 significantly lowered its association with Plexin-A1. As the spike protein is a critical component for targeted therapy, our biochemical study may represent a distinct mechanism to develop a path for future therapeutic discovery.
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Affiliation(s)
- Debjani Pal
- Radioisotope Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kuntal De
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Timothy B. Yates
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN 37996, USA
| | - Jaydeep Kolape
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Wellington Muchero
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN 37996, USA
- Corresponding author
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Massoudi D, Gorman S, Kuo YM, Iwawaki T, Oakes SA, Papa FR, Gould DB. Deletion of the Unfolded Protein Response Transducer IRE1α Is Detrimental to Aging Photoreceptors and to ER Stress-Mediated Retinal Degeneration. Invest Ophthalmol Vis Sci 2023; 64:30. [PMID: 37097227 PMCID: PMC10148664 DOI: 10.1167/iovs.64.4.30] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Purpose The unfolded protein response (UPR) is triggered when the protein folding capacity of the endoplasmic reticulum (ER) is overwhelmed and misfolded proteins accumulate in the ER, a condition referred to as ER stress. IRE1α is an ER-resident protein that plays major roles in orchestrating the UPR. Several lines of evidence implicate the UPR and its transducers in neurodegenerative diseases, including retinitis pigmentosa (RP), a group of inherited diseases that cause progressive dysfunction and loss of rod and cone photoreceptors. This study evaluated the contribution of IRE1α to photoreceptor development, homeostasis, and degeneration. Methods We used a conditional gene targeting strategy to selectively inactivate Ire1α in mouse rod photoreceptors. We used a combination of optical coherence tomography (OCT) imaging, histology, and electroretinography (ERG) to assess longitudinally the effect of IRE1α deficiency in retinal development and function. Furthermore, we evaluated the IRE1α-deficient retina responses to tunicamycin-induced ER stress and in the context of RP caused by the rhodopsin mutation RhoP23H. Results OCT imaging, histology, and ERG analyses did not reveal abnormalities in IRE1α-deficient retinas up to 3 months old. However, by 6 months of age, the Ire1α mutant animals showed reduced outer nuclear layer thickness and deficits in retinal function. Furthermore, conditional inactivation of Ire1α in rod photoreceptors accelerated retinal degeneration caused by the RhoP23H mutation. Conclusions These data suggest that IRE1α is dispensable for photoreceptor development but important for photoreceptor homeostasis in aging retinas and for protecting against ER stress-mediated photoreceptor degeneration.
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Affiliation(s)
- Dawiyat Massoudi
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Seán Gorman
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Yien-Ming Kuo
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Takao Iwawaki
- Division of Cell Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
| | - Scott A Oakes
- Department of Pathology, Pritzker School of Medicine, University of Chicago, Chicago, Illinois, United States
| | - Feroz R Papa
- Department of Medicine, Diabetes Center, Quantitative Biosciences Institute and Lung Biology Center University of California, San Francisco, San Francisco, California, United States
| | - Douglas B Gould
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Department of Anatomy, Institute for Human Genetics, Cardiovascular Research Institute, Bakar Aging Research Institute, University of California, San Francisco, California, United States
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Aria H, Rezaei M. Immunogenic cell death inducer peptides: A new approach for cancer therapy, current status and future perspectives. Biomed Pharmacother 2023; 161:114503. [PMID: 36921539 DOI: 10.1016/j.biopha.2023.114503] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/23/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Immunogenic Cell Death (ICD) is a type of cell death that kills tumor cells by stimulating the adaptive immune response against other tumor cells. ICD depends on the endoplasmic reticulum (ER) stress and the secretion of Damage-Associated Molecular Patterns (DAMP) by the dying tumor cell. DAMPs recruit innate immune cells such as Dendritic Cells (DC), triggering a cancer-specific immune response such as cytotoxic T lymphocytes (CTLs) to eliminate remaining cancer cells. ICD is accompanied by several hallmarks in dying cells, such as surface translocation of ER chaperones, calreticulin (CALR), and extracellular secretion of DAMPs such as high mobility group protein B1 (HMGB1) and adenosine triphosphate (ATP). Therapeutic peptides can kill bacteria and tumor cells thus affecting the immune system. They have high specificity and affinity for their targets, small size, appropriate cell membrane penetration, short half-life, and simple production processes. Peptides are interesting agents for immunomodulation since they may overcome the limitations of other therapeutics. Thus, the development of peptides affecting the TME and active antitumoral immunity has been actively pursued. On the other hand, several peptides have been recently identified to trigger ICD and anti-cancer responses. In the present review, we review previous studies on peptide-induced ICD, their mechanism, their targets, and markers. They include anti-microbial peptides (AMPs), cationic or mitochondrial targeting, checkpoint inhibitors, antiapoptotic inhibitors, and "don't eat me" inhibitor peptides. Also, peptides will be investigated potentially inducing ICD that is divided into ER stressors, ATPase inhibitors, and anti-microbial peptides.
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Affiliation(s)
- Hamid Aria
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Marzieh Rezaei
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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45
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Nguyen NH, Brodsky JL. The cellular pathways that maintain the quality control and transport of diverse potassium channels. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194908. [PMID: 36638864 PMCID: PMC9908860 DOI: 10.1016/j.bbagrm.2023.194908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Potassium channels are multi-subunit transmembrane proteins that permit the selective passage of potassium and play fundamental roles in physiological processes, such as action potentials in the nervous system and organismal salt and water homeostasis, which is mediated by the kidney. Like all ion channels, newly translated potassium channels enter the endoplasmic reticulum (ER) and undergo the error-prone process of acquiring post-translational modifications, folding into their native conformations, assembling with other subunits, and trafficking through the secretory pathway to reach their final destinations, most commonly the plasma membrane. Disruptions in these processes can result in detrimental consequences, including various human diseases. Thus, multiple quality control checkpoints evolved to guide potassium channels through the secretory pathway and clear potentially toxic, aggregation-prone misfolded species. We will summarize current knowledge on the mechanisms underlying potassium channel quality control in the secretory pathway, highlight diseases associated with channel misfolding, and suggest potential therapeutic routes.
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Affiliation(s)
- Nga H Nguyen
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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Howell-Bray T, Byrne L. The effect of prions on cellular metabolism: The metabolic impact of the [RNQ +] prion and potential role of native Rnq1p. RESEARCH SQUARE 2023:rs.3.rs-2511186. [PMID: 36909567 PMCID: PMC10002837 DOI: 10.21203/rs.3.rs-2511186/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Within the field of amyloid and prion disease there is a need for a more comprehensive understanding of the fundamentals of disease biology. In order to facilitate the progression treatment and underpin comprehension of toxicity, fundamental understanding of the disruption to normal cellular biochemistry and trafficking is needed. Here, by removing the complex biochemistry of the brain, we have utilised known prion forming strains of Saccharomyces cerevisiae carrying different conformational variants of the Rnq1p to obtain Liquid Chromatography-Mass Spectrometry (LC-MS) metabolic profiles and identify key perturbations of prion presence. These studies reveal that prion containing [RNQ+] cells display a significant reduction in amino acid biosynthesis and distinct perturbations in sphingolipid metabolism, with significant downregulation in metabolites within these pathways. Moreover, that native Rnq1p appears to downregulate ubiquinone biosynthesis pathways within cells, suggesting that Rnq1p may play a lipid/mevalonate-based cytoprotective role as a regulator of ubiquinone production. These findings contribute to the understanding of how prion proteins interact in vivo in both their prion and non-prion confirmations and indicate potential targets for the mitigation of these effects. We demonstrate specific sphingolipid centred metabolic disruptions due to prion presence and give insight into a potential cytoprotective role of the native Rnq1 protein. This provides evidence of metabolic similarities between yeast and mammalian cells as a consequence of prion presence and establishes the application of metabolomics as a tool to investigate prion/amyloid-based phenomena.
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Das E, Sahu KK, Roy I. The functional role of Ire1 in regulating autophagy and proteasomal degradation under prolonged proteotoxic stress. FEBS J 2023. [PMID: 36757110 DOI: 10.1111/febs.16747] [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: 05/11/2022] [Revised: 12/23/2022] [Accepted: 02/08/2023] [Indexed: 02/10/2023]
Abstract
Inhibition of endoribonuclease/kinase Ire1 has shown beneficial effects in many proteotoxicity-induced pathology models. The mechanism by which this occurs has not been elucidated completely. Using a proteotoxic yeast model of Huntington's disease, we show that the deletion of Ire1 led to lower protein aggregation at longer time points. The rate of protein degradation was higher in ΔIre1 cells. We monitored the two major protein degradation mechanisms in the cell. The increase in expression of Rpn4, coding for the transcription factor controlling proteasome biogenesis, was higher in ΔIre1 cells. The chymotrypsin-like proteasomal activity was also significantly enhanced in these cells at later time points of aggregation. The gene and protein expression levels of the autophagy gene Atg8 were higher in ΔIre1 than in wild-type cells. Significant increase in autophagy flux was also seen in ΔIre1 cells at later time points of aggregation. The results suggest that the deletion of Ire1 activates UPR-independent arms of the proteostasis network, especially under conditions of aggravated stress. Thus, the inhibition of Ire1 may regulate UPR-independent cellular stress-response pathways under prolonged stress.
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Affiliation(s)
- Eshita Das
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, India
| | - Kiran Kumari Sahu
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, India
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Shah A, Huck I, Duncan K, Gansemer ER, Apte U, Stamnes MA, Rutkowski DT. Interference with the HNF4-dependent gene regulatory network diminishes ER stress in hepatocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527889. [PMID: 36798396 PMCID: PMC9934629 DOI: 10.1101/2023.02.09.527889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
In all eukaryotic cell types, the unfolded protein response (UPR) upregulates factors that promote protein folding and misfolded protein clearance to help alleviate endoplasmic reticulum (ER) stress. Yet ER stress in the liver is uniquely accompanied by the suppression of metabolic genes, the coordination and purpose of which is largely unknown. Here, we used unsupervised machine learning to identify a cluster of correlated genes that were profoundly suppressed by persistent ER stress in the liver. These genes, which encode diverse functions including metabolism, coagulation, drug detoxification, and bile synthesis, are likely targets of the master regulator of hepatocyte differentiation HNF4α. The response of these genes to ER stress was phenocopied by liver-specific deletion of HNF4 α. Strikingly, while deletion of HNF4α exacerbated liver injury in response to an ER stress challenge, it also diminished UPR activation and partially preserved ER ultrastructure, suggesting attenuated ER stress. Conversely, pharmacological maintenance of hepatocyte identity in vitro enhanced sensitivity to stress. Several pathways potentially link HNF4α to ER stress sensitivity, including control of expression of the tunicamycin transporter MFSD2A; modulation of IRE1/XBP1 signaling; and regulation of Pyruvate Dehydrogenase. Together, these findings suggest that HNF4α activity is linked to hepatic ER homeostasis through multiple mechanisms.
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Affiliation(s)
- Anit Shah
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Ian Huck
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, KS
| | - Kaylia Duncan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Erica R. Gansemer
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Udayan Apte
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, KS
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA
| | - D. Thomas Rutkowski
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA
- Department of Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, IA
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Bhaduri S, Scott NA, Neal SE. The Role of the Rhomboid Superfamily in ER Protein Quality Control: From Mechanisms and Functions to Diseases. Cold Spring Harb Perspect Biol 2023; 15:a041248. [PMID: 35940905 PMCID: PMC9899648 DOI: 10.1101/cshperspect.a041248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The endoplasmic reticulum (ER) is an essential organelle in eukaryotic cells and is a major site for protein folding, modification, and lipid synthesis. Perturbations within the ER, such as protein misfolding and high demand for protein folding, lead to dysregulation of the ER protein quality control network and ER stress. Recently, the rhomboid superfamily has emerged as a critical player in ER protein quality control because it has diverse cellular functions, including ER-associated degradation (ERAD), endosome Golgi-associated degradation (EGAD), and ER preemptive quality control (ERpQC). This breadth of function both illustrates the importance of the rhomboid superfamily in health and diseases and emphasizes the necessity of understanding their mechanisms of action. Because dysregulation of rhomboid proteins has been implicated in various diseases, such as neurological disorders and cancers, they represent promising potential therapeutic drug targets. This review provides a comprehensive account of the various roles of rhomboid proteins in the context of ER protein quality control and discusses their significance in health and disease.
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Affiliation(s)
- Satarupa Bhaduri
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Nicola A Scott
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Sonya E Neal
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
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50
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Wang W, Lu J, Yang WC, Spear ED, Michaelis S, Matunis MJ. Analysis of a degron-containing reporter protein GFP-CL1 reveals a role for SUMO1 in cytosolic protein quality control. J Biol Chem 2023; 299:102851. [PMID: 36587767 PMCID: PMC9898758 DOI: 10.1016/j.jbc.2022.102851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Misfolded proteins are recognized and degraded through protein quality control (PQC) pathways, which are essential for maintaining proteostasis and normal cellular functions. Defects in PQC can result in disease, including cancer, cardiovascular disease, and neurodegeneration. The small ubiquitin-related modifiers (SUMOs) were previously implicated in the degradation of nuclear misfolded proteins, but their functions in cytoplasmic PQC are unclear. Here, in a systematic screen of SUMO protein mutations in the budding yeast Saccharomyces cerevisiae, we identified a mutant allele (Smt3-K38A/K40A) that sensitizes cells to proteotoxic stress induced by amino acid analogs. Smt3-K38A/K40A mutant strains also exhibited a defect in the turnover of a soluble PQC model substrate containing the CL1 degron (NES-GFP-Ura3-CL1) localized in the cytoplasm, but not the nucleus. Using human U2OS SUMO1- and SUMO2-KO cell lines, we observed a similar SUMO-dependent pathway for degradation of the mammalian degron-containing PQC reporter protein, GFP-CL1, also only in the cytoplasm but not the nucleus. Moreover, we found that turnover of GFP-CL1 in the cytoplasm was uniquely dependent on SUMO1 but not the SUMO2 paralogue. Additionally, we showed that turnover of GFP-CL1 in the cytoplasm is dependent on the AAA-ATPase, Cdc48/p97. Cellular fractionation studies and analysis of a SUMO1-GFP-CL1 fusion protein revealed that SUMO1 promotes cytoplasmic misfolded protein degradation by maintaining substrate solubility. Collectively, our findings reveal a conserved and previously unrecognized role for SUMO1 in regulating cytoplasmic PQC and provide valuable insights into the roles of sumoylation in PQC-associated diseases.
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Affiliation(s)
- Wei Wang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jian Lu
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Wei-Chih Yang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Eric D Spear
- Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Susan Michaelis
- Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA.
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