1
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Weyer Y, Teis D. The Dsc complex and its role in Golgi quality control. Biochem Soc Trans 2024:BST20230375. [PMID: 39324639 DOI: 10.1042/bst20230375] [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: 07/26/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/27/2024]
Abstract
Membrane proteins play crucial roles in cellular functions. However, processes such as the insertion of membrane proteins into the endoplasmic reticulum (ER), their folding into native structures, the assembly of multi-subunit membrane protein complexes, and their targeting from the ER to specific organelles are prone to errors and have a relatively high failure rate. To prevent the accumulation of defective or orphaned membrane proteins, quality control mechanisms assess folding, quantity, and localization of these proteins. This quality control is vital for preserving organelle integrity and maintaining cellular health. In this mini-review, we will focus on how selective membrane protein quality control at the Golgi apparatus, particularly through the defective for SREBP cleavage (Dsc) ubiquitin ligase complex, detects orphaned proteins and prevents their mis-localization to other organelles.
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Affiliation(s)
- Yannick Weyer
- Institute of Molecular Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - David Teis
- Institute of Molecular Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
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2
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Ruger-Herreros C, Svoboda L, Mogk A, Bukau B. Role of J-domain Proteins in Yeast Physiology and Protein Quality Control. J Mol Biol 2024; 436:168484. [PMID: 38331212 DOI: 10.1016/j.jmb.2024.168484] [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: 10/20/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The number of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.
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Affiliation(s)
- Carmen Ruger-Herreros
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n, E-41013 Sevilla, Spain
| | - Lucia Svoboda
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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3
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Kamada Y, Ohnishi Y, Nakashima C, Fujii A, Terakawa M, Hamano I, Nakayamada U, Katoh S, Hirata N, Tateishi H, Fukuda R, Takahashi H, Lukacs GL, Okiyoneda T. HERC3 facilitates ERAD of select membrane proteins by recognizing membrane-spanning domains. J Cell Biol 2024; 223:e202308003. [PMID: 38722278 PMCID: PMC11082371 DOI: 10.1083/jcb.202308003] [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: 08/01/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
Aberrant proteins located in the endoplasmic reticulum (ER) undergo rapid ubiquitination by multiple ubiquitin (Ub) E3 ligases and are retrotranslocated to the cytosol as part of the ER-associated degradation (ERAD). Despite several ERAD branches involving different Ub E3 ligases, the molecular machinery responsible for these ERAD branches in mammalian cells remains not fully understood. Through a series of multiplex knockdown/knockout experiments with real-time kinetic measurements, we demonstrate that HERC3 operates independently of the ER-embedded ubiquitin ligases RNF5 and RNF185 (RNF5/185) to mediate the retrotranslocation and ERAD of misfolded CFTR. While RNF5/185 participates in the ERAD process of both misfolded ABCB1 and CFTR, HERC3 uniquely promotes CFTR ERAD. In vitro assay revealed that HERC3 directly interacts with the exposed membrane-spanning domains (MSDs) of CFTR but not with the MSDs embedded in liposomes. Therefore, HERC3 could play a role in the quality control of MSDs in the cytoplasm and might be crucial for the ERAD pathway of select membrane proteins.
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Affiliation(s)
- Yuka Kamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Yuko Ohnishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Chikako Nakashima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Aika Fujii
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Mana Terakawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ikuto Hamano
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Uta Nakayamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Saori Katoh
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Noriaki Hirata
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hazuki Tateishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ryosuke Fukuda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hirotaka Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), Ehime University, Matsuyama, Japan
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, Canada
- Department of Biochemistry, McGill University, Montréal, Canada
| | - Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
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4
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Hou W, Watson C, Cecconie T, Bolaki MN, Brady JJ, Lu Q, Gatto GJ, Day TA. Biochemical and functional characterization of the p.A165T missense variant of mitochondrial amidoxime-reducing component 1. J Biol Chem 2024; 300:107353. [PMID: 38723751 PMCID: PMC11190489 DOI: 10.1016/j.jbc.2024.107353] [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: 02/28/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
Recent genome-wide association studies have identified a missense variant p.A165T in mitochondrial amidoxime-reducing component 1 (mARC1) that is strongly associated with protection from all-cause cirrhosis and improved prognosis in nonalcoholic steatohepatitis. The precise mechanism of this protective effect is unknown. Substitution of alanine 165 with threonine is predicted to affect mARC1 protein stability and to have deleterious effects on its function. To investigate the mechanism, we have generated a knock-in mutant mARC1 A165T and a catalytically dead mutant C273A (as a control) in human hepatoma HepG2 cells, enabling characterization of protein subcellular distribution, stability, and biochemical functions of the mARC1 mutant protein expressed from its endogenous locus. Compared to WT mARC1, we found that the A165T mutant exhibits significant mislocalization outside of its traditional location anchored in the mitochondrial outer membrane and reduces protein stability, resulting in lower basal levels. We evaluated the involvement of the ubiquitin proteasome system in mARC1 A165T degradation and observed increased ubiquitination and faster degradation of the A165T variant. In addition, we have shown that HepG2 cells carrying the MTARC1 p.A165T variant exhibit lower N-reductive activity on exogenously added amidoxime substrates in vitro. The data from these biochemical and functional assays suggest a mechanism by which the MTARC1 p.A165T variant abrogates enzyme function which may contribute to its protective effect in liver disease.
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Affiliation(s)
- Wangfang Hou
- Respiratory and Immunology Biology Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Christian Watson
- Respiratory and Immunology Biology Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Ted Cecconie
- MEDDesign-NCE-MD SPMB US, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | | | - Quinn Lu
- Respiratory and Immunology Biology Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Gregory J Gatto
- Respiratory and Immunology Biology Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA.
| | - Tovah A Day
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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5
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Mitchem MM, Shrader C, Abedi E, Truman AW. Novel insights into the post-translational modifications of Ydj1/DNAJA1 co-chaperones. Cell Stress Chaperones 2024; 29:1-9. [PMID: 38309209 PMCID: PMC10939075 DOI: 10.1016/j.cstres.2023.11.001] [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: 09/16/2023] [Revised: 10/18/2023] [Accepted: 11/04/2023] [Indexed: 02/05/2024] Open
Abstract
The activity of the Hsp70 molecular chaperone is regulated by a suite of helper co-chaperones that include J-proteins. Studies on J-proteins have historically focused on their expression, localization, and activation of Hsp70. There is growing evidence that the post-translational modifications (PTMs) of chaperones (the chaperone code) fine-tune chaperone function. This mini-review summarizes the current understanding of the role and regulation of PTMs on the major J-proteins Ydj1 and DNAJA1. Understanding these PTMs may provide novel therapeutic avenues for targeting chaperone activity in cancer and neurodegenerative diseases.
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Affiliation(s)
- Megan M Mitchem
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Courtney Shrader
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Elizabeth Abedi
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Andrew W Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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6
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Hayashi M, Kawarasaki T, Nakatsukasa K. Degradation of citrate synthase lacking the mitochondrial targeting sequence is inhibited in cells defective in Hsp70/Hsp40 chaperones under heat stress conditions. FEMS Yeast Res 2024; 24:foad054. [PMID: 38130235 PMCID: PMC10786195 DOI: 10.1093/femsyr/foad054] [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: 09/29/2023] [Revised: 12/02/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023] Open
Abstract
Most nucleus-encoded mitochondrial precursor proteins are synthesized in the cytosol and imported into mitochondria in a post-translational manner. In recent years, the quality control mechanisms of nonimported mitochondrial proteins have been intensively studied. In a previous study, we established that in budding yeast a mutant form of citrate synthase 1 (N∆Cit1) that lacks the N-terminal mitochondrial targeting sequence, and therefore mislocalizes to the cytosol is targeted for proteasomal degradation by the SCFUcc1 ubiquitin ligase complex. Here, we show that Hsp70 and Hsp40 chaperones (Ssa1 and Ydj1 in yeast, respectively) are required for N∆Cit1 degradation under heat stress conditions. In the absence of Hsp70 function, a portion of N∆Cit1-GFP formed insoluble aggregates and cytosolic foci. However, the extent of ubiquitination of N∆Cit1 was unaffected, implying that Hsp70/Hsp40 chaperones are involved in the postubiquitination step of N∆Cit1 degradation. Intriguingly, degradation of cytosolic/peroxisomal gluconeogenic citrate synthase (Cit2), an endogenous substrate for SCFUcc1-mediated proteasomal degradation, was not highly dependent on Hsp70 even under heat stress conditions. These results suggest that mitochondrial citrate synthase is thermally vulnerable in the cytosol, where Hsp70/Hsp40 chaperones are required to facilitate its degradation.
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Affiliation(s)
- Mayuko Hayashi
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Tomoyuki Kawarasaki
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
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7
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Botsch JJ, Junker R, Sorgenfrei M, Ogger PP, Stier L, von Gronau S, Murray PJ, Seeger MA, Schulman BA, Bräuning B. Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE. Nat Commun 2024; 15:410. [PMID: 38195637 PMCID: PMC10776854 DOI: 10.1038/s41467-023-44670-5] [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: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity.
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Affiliation(s)
- J Josephine Botsch
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Roswitha Junker
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Patricia P Ogger
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Luca Stier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Peter J Murray
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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8
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Flagg MP, Lam B, Lam DK, Le TM, Kao A, Slaiwa YI, Hampton RY. Exploring the "misfolding problem" by systematic discovery and analysis of functional-but-degraded proteins. Mol Biol Cell 2023; 34:ar125. [PMID: 37729018 PMCID: PMC10848938 DOI: 10.1091/mbc.e23-06-0248] [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: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
In both health and disease, the ubiquitin-proteasome system (UPS) degrades point mutants that retain partial function but have decreased stability compared with their wild-type counterparts. This class of UPS substrate includes routine translational errors and numerous human disease alleles, such as the most common cause of cystic fibrosis, ΔF508-CFTR. Yet, there is no systematic way to discover novel examples of these "minimally misfolded" substrates. To address that shortcoming, we designed a genetic screen to isolate functional-but-degraded point mutants, and we used the screen to study soluble, monomeric proteins with known structures. These simple parent proteins yielded diverse substrates, allowing us to investigate the structural features, cytotoxicity, and small-molecule regulation of minimal misfolding. Our screen can support numerous lines of inquiry, and it provides broad access to a class of poorly understood but biomedically critical quality-control substrates.
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Affiliation(s)
- Matthew P. Flagg
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Breanna Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Darren K. Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Tiffany M. Le
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Andy Kao
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Yousif I. Slaiwa
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Randolph Y. Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
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9
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Anton V, Buntenbroich I, Simões T, Joaquim M, Müller L, Buettner R, Odenthal M, Hoppe T, Escobar-Henriques M. E4 ubiquitin ligase promotes mitofusin turnover and mitochondrial stress response. Mol Cell 2023; 83:2976-2990.e9. [PMID: 37595558 PMCID: PMC10434984 DOI: 10.1016/j.molcel.2023.07.021] [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: 07/08/2022] [Revised: 05/31/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Ubiquitin-dependent control of mitochondrial dynamics is important for protein quality and neuronal integrity. Mitofusins, mitochondrial fusion factors, can integrate cellular stress through their ubiquitylation, which is carried out by multiple E3 enzymes in response to many different stimuli. However, the molecular mechanisms that enable coordinated responses are largely unknown. Here we show that yeast Ufd2, a conserved ubiquitin chain-elongating E4 enzyme, is required for mitochondrial shape adjustments. Under various stresses, Ufd2 translocates to mitochondria and triggers mitofusin ubiquitylation. This elongates ubiquitin chains on mitofusin and promotes its proteasomal degradation, leading to mitochondrial fragmentation. Ufd2 and its human homologue UBE4B also target mitofusin mutants associated with Charcot-Marie-Tooth disease, a hereditary sensory and motor neuropathy characterized by progressive loss of the peripheral nerves. This underscores the pathophysiological importance of E4-mediated ubiquitylation in neurodegeneration. In summary, we identify E4-dependent mitochondrial stress adaptation by linking various metabolic processes to mitochondrial fusion and fission dynamics.
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Affiliation(s)
- Vincent Anton
- Institute for Genetics, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Ira Buntenbroich
- Institute for Genetics, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Tânia Simões
- Institute for Genetics, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Mariana Joaquim
- Institute for Genetics, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Leonie Müller
- Institute for Genetics, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Reinhard Buettner
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany; Institute of Pathology, Medical Faculty, University Hospital, University of Cologne, Germany
| | - Margarete Odenthal
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany; Institute of Pathology, Medical Faculty, University Hospital, University of Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Mafalda Escobar-Henriques
- Institute for Genetics, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Cologne, Germany.
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10
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Hu X, Zou R, Zhang Z, Ji J, Li J, Huo XY, Liu D, Ge MX, Cui MK, Wu MZ, Li ZP, Wang Q, Zhang X, Zhang ZR. UBE4A catalyzes NRF1 ubiquitination and facilitates DDI2-mediated NRF1 cleavage. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194937. [PMID: 37084817 DOI: 10.1016/j.bbagrm.2023.194937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/24/2023] [Accepted: 04/14/2023] [Indexed: 04/23/2023]
Abstract
The transcription factor nuclear factor erythroid 2 like 1 (NFE2L1 or NRF1) regulates constitutive and inducible expression of proteasome subunits and assembly chaperones. The precursor of NRF1 is integrated into the endoplasmic reticulum (ER) and can be retrotranslocated from the ER to the cytosol where it is processed by ubiquitin-directed endoprotease DDI2. DDI2 cleaves and activates NRF1 only when NRF1 is highly polyubiquitinated. It remains unclear how retrotranslocated NRF1 is primed with very long polyubiquitin chain for subsequent processing. Here, we report that E3 ligase UBE4A catalyzes ubiquitination of retrotranslocated NRF1 and promotes its cleavage. Depletion of UBE4A shortens the average length of polyubiquitin chain of NRF1, decreases NRF1 cleavage efficiency and causes accumulation of non-cleaved, inactivated NRF1. Expression of a UBE4A mutant lacking ligase activity impairs the cleavage, likely due to a dominant negative effect. UBE4A interacts with NRF1 and the recombinant UBE4A can promote ubiquitination of retrotranslocated NRF1 in vitro. In addition, knocking out UBE4A reduces transcription of proteasomal subunits in cells. Our results indicate that UBE4A primes NRF1 for DDI2-mediated activation to facilitate expression of proteasomal genes.
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Affiliation(s)
- Xianyan Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Rong Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Zaihui Zhang
- Department of Endocrinology, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, 2 Hengbu Street, Westlake District, Hangzhou 310000, China
| | - Jia Ji
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jiqiang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xin-Yu Huo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Di Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Man-Xi Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Meng-Ke Cui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Ming-Zhi Wu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Zhao-Peng Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Qingchen Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China
| | - Xiaoli Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China.
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11
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Wang Y, Wang Y, Zou Z, Yuan A, Xiao Z, Geng N, Qiao Z, Li W, Ying X, Lu X, Pu J. Hydrogen sulfide alleviates mitochondrial damage and ferroptosis by regulating OPA3-NFS1 axis in doxorubicin-induced cardiotoxicity. Cell Signal 2023; 107:110655. [PMID: 36924813 DOI: 10.1016/j.cellsig.2023.110655] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
Ferroptosis is a major cause of cardiotoxicity induced by doxorubicin (DOX). Previous studies have shown that hydrogen sulfide (H2S) inhibits ferroptosis in cardiomyocytes and myoblasts, but the underlying mechanism has not been fully elucidated. In this study, we investigated the role of H2S in protecting against DOX-induced cardiotoxicity both in vivo and in vitro, and elucidated the potential mechanisms involved. We found that DOX downregulated the expression of glutathione peroxidase 4 (GPX4) and NFS1, and upregulated the expression of acyl-coenzyme A synthetase long-chain family member 4 (ACSL4) expression level, resulting in increased lipid peroxidation and ferroptosis. Additionally, DOX inhibited MFN2 expression and increased DRP1 and FIS1 expression, leading to abnormal mitochondrial structure and function. In contrast, exogenous H2S inhibited DOX-induced ferroptosis by restoring GPX4 and NFS1 expression, and reducing lipid peroxidation in H9C2 cells. This effect was similar to that of the ferroptosis antagonist ferrostatin-1 (Fer-1) in protecting against DOX-induced cardiotoxicity. We further demonstrated that the protective effect of H2S was mediated by the key mitochondrial membrane protein optic atrophy 3 (OPA3), which was downregulated by DOX and restored by exogenous H2S. Overexpression of OPA3 alleviated DOX-induced mitochondrial dysfunction and ferroptosis both in vivo and in vitro. Mechanistically, NFS1 has an inhibitory effect on ferroptosis, and NFS1 deficiency increases the susceptibility of cardiomyocytes to ferroptosis. OPA3 is involved in the regulation of ferroptosis by interacting with NFS1. Post-translationally, DOX promoted OPA3 ubiquitination, while exogenous H2S antagonized OPA3 ubiquitination by promoting OPA3 s-sulfhydration. In summary, our findings suggested that H2S protects against DOX-induced cardiotoxicity by inhibiting ferroptosis via targeting the OPA3-NFS1 axis. This provides a potential therapeutic strategy for the treatment of DOX-induced cardiotoxicity.
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Affiliation(s)
- Yifan Wang
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - Yuehong Wang
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - Zhiguo Zou
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - Ancai Yuan
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - Zemeng Xiao
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - Na Geng
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - ZhiQing Qiao
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - Wenli Li
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
| | - Xiaoying Ying
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China..
| | - Xiyuan Lu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China..
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, Cancer Institute, Shanghai, China
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12
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Guo Z, Liang J. Role of ubiquitin regulatory X domain‑containing protein 3B in the development of hepatocellular carcinoma (Review). Oncol Rep 2023; 49:57. [PMID: 36799187 PMCID: PMC9942258 DOI: 10.3892/or.2023.8494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
The majority of new cases and fatalities from hepatocellular carcinoma (HCC) occur in China; however, the overall morbidity and mortality rates are decreasing. A major risk factor due to the evolving epidemiology is improper lipid metabolism. Although investigations on aberrant lipid metabolism are numerous, there are only a limited number of studies available on proteasomal degradation processes. The degradation process is mainly involved in endoplasmic reticulum stabilization, the balance of lipid metabolism, and physiological functions of Golgi apparatus, endoplasmic reticulum, lysosomes and other organelles, however, this process has been little studied in the development of tumorigenesis. In order to provide some theoretical support for future research on ubiquitin regulatory X domain‑containing protein 3B (UBXN3B), the present review focuses on the role of UBXN3B, which is involved in the stabilization of the endoplasmic reticulum and the maintenance of lipid homeostasis, as well as in the promotion and development of non‑alcoholic fatty liver disease and HCC.
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Affiliation(s)
- Ziwei Guo
- Department of Medical Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Jun Liang
- Department of Medical Oncology, Peking University International Hospital, Beijing 102206, P.R. China,Correspondence to: Professor Jun Liang, Department of Medical Oncology, Peking University International Hospital, Life Park Road, Life Science Park of Zhong Guancun Chang Ping, Beijing 102206, P.R. China, E-mail:
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13
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Kawarasaki T, Nakatsukasa K. Metabolomics analysis of an AAA-ATPase Cdc48-deficient yeast strain. Heliyon 2023; 9:e13219. [PMID: 36761826 PMCID: PMC9905943 DOI: 10.1016/j.heliyon.2023.e13219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
The ubiquitin-specific chaperone AAA-ATPase Cdc48 and its orthologs p97/valosin-containing protein (VCP) in mammals play crucial roles in regulating numerous intracellular pathways via segregase activity, which separates polyubiquitinated targets from membranes or binding partners. Interestingly, high-throughput experiments show that a vast number of metabolic enzymes are modified with ubiquitin. Therefore, Cdc48 may regulate metabolic pathways, for example by acting on the polyubiquitin chains of metabolic enzymes; however, the role of Cdc48 in metabolic regulation remains largely unknown. To begin to analyze the role of Cdc48 in metabolic regulation in yeast, we performed a metabolomics analysis of temperature-sensitive cdc48-3 mutant cells. We found that the amount of metabolites in the glycolytic pathway was altered. Moreover, the pool of nucleotides, as well as the levels of metabolites involved in the tricarboxylic acid cycle and oxidative phosphorylation, increased, whereas the pool of amino acids decreased. These results suggest the involvement of Cdc48 in metabolic regulation in yeast. In addition, because of the roles of p97/VCP in regulating multiple cellular pathways, its inhibition is being considered as a promising anticancer drug target. We propose that the metabolomics study of Cdc48-deficient yeast will be useful as a complement to p97/VCP-related pathological and therapeutic studies.
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14
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Guo Z, Liang J. Characterization of a lipid droplet and endoplasmic reticulum stress related gene risk signature to evaluate the clinical and biological value in hepatocellular carcinoma. Lipids Health Dis 2022; 21:146. [PMID: 36581927 PMCID: PMC9798721 DOI: 10.1186/s12944-022-01759-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 12/14/2022] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Lipid metabolism and endoplasmic reticulum (ER) stress play an important role in the progression and metastasis of hepatocellular carcinoma (HCC). We aimed to establish lipid droplet (LD)-associated and ER stress-related gene risk signature as prognostic indicators. MATERIALS AND METHODS Literature searches for LD-associated proteins was screened and validated in The Cancer Genome Atlas (TCGA) and International Cancer Genome Collaboratory (ICGC) databases. A total of 371 samples were enrolled from the TCGA RNA-seq dataset (training cohort) and 240 samples from IGGC RNA-seq dataset (validation cohort). A 10-gene risk signature was established by the last absolute shrinkage and selection operator (LASSO) regression analysis. The prognostic value of the risk signature was evaluated by Cox regression, Kaplan-Meier and ROC Curve analyses. Biological features associated with LD and ER stress-related factors were explored by functional analysis and in vitro experiment. RESULTS Based on the medical literatures, 124 lipid droplet-associated proteins were retrieved, and three genes failed to establish a valid prognostic model. ER stress was considered as an important component by functional analysis. A 10-gene risk signature compared the clinicopathology characteristics, immunosuppressive events and a nomogram in HCC patients. CONCLUSION LD-associated and ER stress-related gene risk signatures highlighted poor prognosis for clinicopathological features, positively correlate with macrophages and T cell immunoglobulin and mucin-3 (TIM-3) expression in the tumor microenvironment, and might act as independent prognostic factors.
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Affiliation(s)
- Ziwei Guo
- grid.449412.ePeking University International Hospital, Beijing, China ,grid.412474.00000 0001 0027 0586Peking University Cancer Hospital and Institute, Beijing, China
| | - Jun Liang
- grid.449412.ePeking University International Hospital, Beijing, China ,grid.412474.00000 0001 0027 0586Peking University Cancer Hospital and Institute, Beijing, China
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15
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Sagarika P, Yadav K, Sahi C. Volleying plasma membrane proteins from birth to death: Role of J-domain proteins. Front Mol Biosci 2022; 9:1072242. [PMID: 36589230 PMCID: PMC9798423 DOI: 10.3389/fmolb.2022.1072242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
The function, stability, and turnover of plasma membrane (PM) proteins are crucial for cellular homeostasis. Compared to soluble proteins, quality control of plasma membrane proteins is extremely challenging. Failure to meet the high quality control standards is detrimental to cellular and organismal health. J-domain proteins (JDPs) are among the most diverse group of chaperones that collaborate with other chaperones and protein degradation machinery to oversee cellular protein quality control (PQC). Although fragmented, the available literature from different models, including yeast, mammals, and plants, suggests that JDPs assist PM proteins with their synthesis, folding, and trafficking to their destination as well as their degradation, either through endocytic or proteasomal degradation pathways. Moreover, some JDPs interact directly with the membrane to regulate the stability and/or functionality of proteins at the PM. The deconvoluted picture emerging is that PM proteins are relayed from one JDP to another throughout their life cycle, further underscoring the versatility of the Hsp70:JDP machinery in the cell.
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16
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Mehrtash AB, Hochstrasser M. Elements of the ERAD ubiquitin ligase Doa10 regulating sequential poly-ubiquitylation of its targets. iScience 2022; 25:105351. [PMID: 36325070 PMCID: PMC9619350 DOI: 10.1016/j.isci.2022.105351] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/16/2022] [Accepted: 10/11/2022] [Indexed: 11/29/2022] Open
Abstract
In ER-associated degradation (ERAD), misfolded ER proteins are degraded by the proteasome after undergoing ubiquitylation. Yeast Doa10 (human MARCHF6/TEB4) is a membrane-embedded E3 ubiquitin ligase that functions with E2s Ubc6 and Ubc7. Ubc6 attaches a single ubiquitin to substrates, which is extended by Ubc7 to form a polyubiquitin chain. We show the conserved C-terminal element (CTE) of Doa10 promotes E3-mediated Ubc6 activity. Doa10 substrates undergoing an alternative ubiquitylation mechanism are still degraded in CTE-mutant cells. Structure prediction by AlphaFold2 suggests the CTE binds near the catalytic RING-CH domain, implying a direct role in substrate ubiquitylation, and we confirm this interaction using intragenic suppression. Truncation analysis defines a minimal E2-binding region of Doa10; structural predictions suggest that Doa10 forms a retrotranslocation channel and that E2s bind within the cofactor-binding region defined here. These results provide mechanistic insight into how Doa10, and potentially other ligases, interact with their cofactors and mediate ERAD. The conserved Doa10 C-terminus promotes E3-mediated activity of Ubc6 The minimal E2-binding region of Doa10 includes TMs 1–9 The N- and C-terminus of Doa10 interact, likely forming an ERAD protein channel
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Affiliation(s)
- Adrian B. Mehrtash
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520 CT, USA
| | - Mark Hochstrasser
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520 CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
- Corresponding author
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17
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Pranke IM, Chevalier B, Premchandar A, Baatallah N, Tomaszewski KF, Bitam S, Tondelier D, Golec A, Stolk J, Lukacs GL, Hiemstra PS, Dadlez M, Lomas DA, Irving JA, Delaunay-Moisan A, van Anken E, Hinzpeter A, Sermet-Gaudelus I, Edelman A. Keratin 8 is a scaffolding and regulatory protein of ERAD complexes. Cell Mol Life Sci 2022; 79:503. [PMID: 36045259 DOI: 10.1007/s00018-022-04528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/03/2022]
Abstract
Early recognition and enhanced degradation of misfolded proteins by the endoplasmic reticulum (ER) quality control and ER-associated degradation (ERAD) cause defective protein secretion and membrane targeting, as exemplified for Z-alpha-1-antitrypsin (Z-A1AT), responsible for alpha-1-antitrypsin deficiency (A1ATD) and F508del-CFTR (cystic fibrosis transmembrane conductance regulator) responsible for cystic fibrosis (CF). Prompted by our previous observation that decreasing Keratin 8 (K8) expression increased trafficking of F508del-CFTR to the plasma membrane, we investigated whether K8 impacts trafficking of soluble misfolded Z-A1AT protein. The subsequent goal of this study was to elucidate the mechanism underlying the K8-dependent regulation of protein trafficking, focusing on the ERAD pathway. The results show that diminishing K8 concentration in HeLa cells enhances secretion of both Z-A1AT and wild-type (WT) A1AT with a 13-fold and fourfold increase, respectively. K8 down-regulation triggers ER failure and cellular apoptosis when ER stress is jointly elicited by conditional expression of the µs heavy chains, as previously shown for Hrd1 knock-out. Simultaneous K8 silencing and Hrd1 knock-out did not show any synergistic effect, consistent with K8 acting in the Hrd1-governed ERAD step. Fractionation and co-immunoprecipitation experiments reveal that K8 is recruited to ERAD complexes containing Derlin2, Sel1 and Hrd1 proteins upon expression of Z/WT-A1AT and F508del-CFTR. Treatment of the cells with c407, a small molecule inhibiting K8 interaction, decreases K8 and Derlin2 recruitment to high-order ERAD complexes. This was associated with increased Z-A1AT secretion in both HeLa and Z-homozygous A1ATD patients' respiratory cells. Overall, we provide evidence that K8 acts as an ERAD modulator. It may play a scaffolding protein role for early-stage ERAD complexes, regulating Hrd1-governed retrotranslocation initiation/ubiquitination processes. Targeting K8-containing ERAD complexes is an attractive strategy for the pharmacotherapy of A1ATD.
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Affiliation(s)
- Iwona Maria Pranke
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France.
| | - Benoit Chevalier
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France
| | - Aiswarya Premchandar
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106, Warsaw, Poland
| | - Nesrine Baatallah
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France
| | - Kamil F Tomaszewski
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France
| | - Sara Bitam
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France
| | - Danielle Tondelier
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France
| | - Anita Golec
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France
| | - Jan Stolk
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montréal, QC, Canada.,Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michal Dadlez
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106, Warsaw, Poland
| | - David A Lomas
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, WC1E 6JF, UK
| | - James A Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, WC1E 6JF, UK
| | - Agnes Delaunay-Moisan
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Eelco van Anken
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Alexandre Hinzpeter
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France
| | - Isabelle Sermet-Gaudelus
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France.,Cystic Fibrosis Center, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Aleksander Edelman
- Inserm, U1151, CNRS UMR 8253, Université de Paris, 160 rue de Vaugirard, 75015, Paris, France.
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18
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Trenner J, Monaghan J, Saeed B, Quint M, Shabek N, Trujillo M. Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:93-121. [PMID: 35226816 DOI: 10.1146/annurev-arplant-102720-012310] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Posttranslational modifications add complexity and diversity to cellular proteomes. One of the most prevalent modifications across eukaryotes is ubiquitination, which is orchestrated by E3 ubiquitin ligases. U-box-containing E3 ligases have massively expanded in the plant kingdom and have diversified into plant U-box proteins (PUBs). PUBs likely originated from two or three ancestral forms, fusing with diverse functional subdomains that resulted in neofunctionalization. Their emergence and diversification may reflect adaptations to stress during plant evolution, reflecting changes in the needs of plant proteomes to maintain cellular homeostasis. Through their close association with protein kinases, they are physically linked to cell signaling hubs and activate feedback loops by dynamically pairing with E2-ubiquitin-conjugating enzymes to generate distinct ubiquitin polymers that themselves act as signals. Here, we complement current knowledgewith comparative genomics to gain a deeper understanding of PUB function, focusing on their evolution and structural adaptations of key U-box residues, as well as their various roles in plant cells.
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Affiliation(s)
- Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | | | - Bushra Saeed
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA;
| | - Marco Trujillo
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
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19
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SLC26A9 is selected for endoplasmic reticulum associated degradation (ERAD) via Hsp70-dependent targeting of the soluble STAS domain. Biochem J 2021; 478:4203-4220. [PMID: 34821356 PMCID: PMC8826537 DOI: 10.1042/bcj20210644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
SLC26A9, a member of the solute carrier protein family, transports chloride ions across various epithelia. SLC26A9 also associates with other ion channels and transporters linked to human health, and in some cases these heterotypic interactions are essential to support the biogenesis of both proteins. Therefore, understanding how this complex membrane protein is initially folded might provide new therapeutic strategies to overcome deficits in the function of SLC26A9 partners, one of which is associated with Cystic Fibrosis. To this end, we developed a novel yeast expression system for SLC26A9. This facile system has been used extensively with other ion channels and transporters to screen for factors that oversee protein folding checkpoints. As commonly observed for other channels and transporters, we first noted that a substantial fraction of SLC26A9 is targeted for endoplasmic reticulum associated degradation (ERAD), which destroys folding-compromised proteins in the early secretory pathway. We next discovered that ERAD selection requires the Hsp70 chaperone, which can play a vital role in ERAD substrate selection. We then created SLC26A9 mutants and found that the transmembrane-rich domain of SLC26A9 was quite stable, whereas the soluble cytosolic STAS domain was responsible for Hsp70-dependent ERAD. To support data obtained in the yeast model, we were able to recapitulate Hsp70-facilitated ERAD of the STAS domain in human tissue culture cells. These results indicate that a critical barrier to nascent membrane protein folding can reside within a specific soluble domain, one that is monitored by components associated with the ERAD machinery.
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20
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Marei WFA, Leroy JLMR. Cellular Stress Responses in Oocytes: Molecular Changes and Clinical Implications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1387:171-189. [PMID: 34921349 DOI: 10.1007/5584_2021_690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The oocyte may be exposed to several sources of stress during its growth and maturation, which may lead to reduced fertility. Unfolded protein responses (UPRs) play a central role to maintain cell survival and repair. Transcription of heat shock proteins (HSPs) is a key element to facilitate reestablishment of cellular homeostasis. Unlike somatic cells, cellular mechanisms by which oocytes can sense and respond to stress are not well described. In here, we provide an overview about the impact of cellular stress, particularly due to lipotoxicity, oxidative stress, and heat stress on oocyte developmental competence. Next, we focus on the expression of HSPs in oocytes and their potential role in UPRs in oocytes and embryos. This is based on a comprehensive shotgun proteomic analysis of mature bovine oocytes performed in our laboratory, as well as a literature review. The topic is discussed in light of our understanding of similar mechanisms in other cell types and the limited transcriptional activity in oocytes. More fundamental research is needed both at the transcriptomic and proteomic levels to further understand cell stress response mechanisms in oocytes and early developing embryos, their critical interactions, and their long-term effects. Strategies to provide targeted external support to prevent or reduce cell stress levels during oocyte maturation or early embryo development under maternal metabolic stress conditions should be developed to maximize the odds of producing good quality embryos and guarantee optimal viability.
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Affiliation(s)
- Waleed F A Marei
- Gamete Research Centre, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium. .,Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
| | - Jo L M R Leroy
- Gamete Research Centre, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
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21
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Kumari D, Fisher EA, Brodsky JL. Hsp40s play distinct roles during the initial stages of apolipoprotein B biogenesis. Mol Biol Cell 2021; 33:ar15. [PMID: 34910568 PMCID: PMC9236142 DOI: 10.1091/mbc.e21-09-0436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Apolipoprotein B (ApoB) is the primary component of atherogenic lipoproteins, which transport serum fats and cholesterol. Therefore, elevated levels of circulating ApoB are a primary risk factor for cardiovascular disease. During ApoB biosynthesis in the liver and small intestine under nutrient-rich conditions, ApoB cotranslationally translocates into the endoplasmic reticulum (ER) and is lipidated and ultimately secreted. Under lipid-poor conditions, ApoB is targeted for ER Associated Degradation (ERAD). Although prior work identified select chaperones that regulate ApoB biogenesis, the contributions of cytoplasmic Hsp40s are undefined. To this end, we screened ApoB-expressing yeast and determined that a class A ER-associated Hsp40, Ydj1, associates with and facilitates the ERAD of ApoB. Consistent with these results, a homologous Hsp40, DNAJA1, functioned similarly in rat hepatoma cells. DNAJA1 deficient cells also secreted hyperlipidated lipoproteins, in accordance with attenuated ERAD. In contrast to the role of DNAJA1 during ERAD, DNAJB1-a class B Hsp40-helped stabilize ApoB. Depletion of DNAJA1 and DNAJB1 also led to opposing effects on ApoB ubiquitination. These data represent the first example in which different Hsp40s exhibit disparate effects during regulated protein biogenesis in the ER, and highlight distinct roles that chaperones can play on a single ERAD substrate.
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Affiliation(s)
- Deepa Kumari
- Department of Biological Sciences, A320 Langley Hall, Fifth & Ruskin Ave, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Edward A Fisher
- Department of Medicine, Leon H. Charney Division of Cardiology, Cardiovascular Research Center, New York University Grossman School of Medicine, New York, United States
| | - Jeffrey L Brodsky
- Department of Biological Sciences, A320 Langley Hall, Fifth & Ruskin Ave, University of Pittsburgh, Pittsburgh, PA 15260 USA
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22
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Sun Z, Guerriero CJ, Brodsky JL. Substrate ubiquitination retains misfolded membrane proteins in the endoplasmic reticulum for degradation. Cell Rep 2021; 36:109717. [PMID: 34551305 PMCID: PMC8503845 DOI: 10.1016/j.celrep.2021.109717] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/11/2021] [Accepted: 08/25/2021] [Indexed: 11/28/2022] Open
Abstract
To maintain secretory pathway fidelity, misfolded proteins are commonly retained in the endoplasmic reticulum (ER) and selected for ER-associated degradation (ERAD). Soluble misfolded proteins use ER chaperones for retention, but the machinery that restricts aberrant membrane proteins to the ER is unclear. In fact, some misfolded membrane proteins escape the ER and traffic to the lysosome/vacuole. To this end, we describe a model substrate, SZ*, that contains an ER export signal but is also targeted for ERAD. We observe decreased ER retention when chaperone-dependent SZ* ubiquitination is compromised. In addition, appending a linear tetra-ubiquitin motif onto SZ* overrides ER export. By screening known ubiquitin-binding proteins, we then positively correlate SZ* retention with Ubx2 binding. Deletion of Ubx2 also inhibits the retention of another misfolded membrane protein. Our results indicate that polyubiquitination is sufficient to retain misfolded membrane proteins in the ER prior to ERAD. Sun et al. characterize how misfolded membrane proteins are delivered for either ERAD or post-ER degradation in the secretory pathway. By using a model substrate that can access both pathways, they show that substrate retention requires chaperone-dependent substrate ubiquitination and interaction with a conserved ER membrane protein, Ubx2.
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Affiliation(s)
- Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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23
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Chen Q, Liu R, Wu Y, Wei S, Wang Q, Zheng Y, Xia R, Shang X, Yu F, Yang X, Liu L, Huang X, Wang Y, Xie Q. ERAD-related E2 and E3 enzymes modulate the drought response by regulating the stability of PIP2 aquaporins. THE PLANT CELL 2021; 33:2883-2898. [PMID: 34015125 PMCID: PMC8408458 DOI: 10.1093/plcell/koab141] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/12/2021] [Indexed: 05/20/2023]
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is known to regulate plant responses to diverse stresses, yet its underlying molecular mechanisms and links to various stress signaling pathways are poorly understood. Here, we show that the ERAD component ubiquitin-conjugating enzyme UBC32 positively regulates drought tolerance in Arabidopsis thaliana by targeting the aquaporins PIP2;1 and PIP2;2 for degradation. Furthermore, we demonstrate that the RING-type ligase Rma1 acts together with UBC32 and that the E2 activity of UBC32 is essential for the ubiquitination of Rma1. This complex ubiquitinates a phosphorylated form of PIP2;1 at Lys276 to promote its degradation, thereby enhancing plant drought tolerance. Extending these molecular insights into crops, we show that overexpression of Arabidopsis UBC32 also improves drought tolerance in rice (Oryza sativa). Thus, beyond uncovering the molecular basis of an ERAD-regulated stress response, our study suggests multiple potential strategies for engineering crops with improved drought tolerance.
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Affiliation(s)
- Qian Chen
- State Key Laboratory of Agrobiotechnology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruijun Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shaowei Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunna Zheng
- State Key Laboratory of Agrobiotechnology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ran Xia
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoling Shang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Feifei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoyuan Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijing Liu
- School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiahe Huang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingchun Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Author for correspondence:
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24
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Burns GD, Hilal OE, Sun Z, Reutter KR, Preston GM, Augustine AA, Brodsky JL, Guerriero CJ. Distinct classes of misfolded proteins differentially affect the growth of yeast compromised for proteasome function. FEBS Lett 2021; 595:2383-2394. [PMID: 34358326 DOI: 10.1002/1873-3468.14172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/24/2021] [Accepted: 07/29/2021] [Indexed: 11/09/2022]
Abstract
Maintenance of the proteome (proteostasis) is essential for cellular homeostasis and prevents cytotoxic stress responses that arise from protein misfolding. However, little is known about how different types of misfolded proteins impact homeostasis, especially when protein degradation pathways are compromised. We examined the effects of misfolded protein expression on yeast growth by characterizing a suite of substrates possessing the same aggregation-prone domain but engaging different quality control pathways. We discovered that treatment with a proteasome inhibitor was more toxic in yeast expressing misfolded membrane proteins, and this growth defect was mirrored in yeast lacking a proteasome-specific transcription factor, Rpn4p. These results highlight weaknesses in the proteostasis network's ability to handle the stress arising from an accumulation of misfolded membrane proteins.
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Affiliation(s)
- Grace D Burns
- Department of Biological Sciences, University of Pittsburgh, PA, USA
| | - Olivia E Hilal
- Department of Biological Sciences, University of Pittsburgh, PA, USA
| | - Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, PA, USA
| | | | - G Michael Preston
- Department of Biological Sciences, University of Pittsburgh, PA, USA
| | | | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, PA, USA
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25
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Goeckeler-Fried JL, Aldrin Denny R, Joshi D, Hill C, Larsen MB, Chiang AN, Frizzell RA, Wipf P, Sorscher EJ, Brodsky JL. Improved correction of F508del-CFTR biogenesis with a folding facilitator and an inhibitor of protein ubiquitination. Bioorg Med Chem Lett 2021; 48:128243. [PMID: 34246753 DOI: 10.1016/j.bmcl.2021.128243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/25/2022]
Abstract
A growing number of diseases are linked to the misfolding of integral membrane proteins, and many of these proteins are targeted for ubiquitin-proteasome-dependent degradation. One such substrate is a mutant form of the Cystic Fibrosis Transmembrane Conductance Regulator (F508del-CFTR). Protein folding "correctors" that repair the F508del-CFTR folding defect have entered the clinic, but they are unlikely to protect the entire protein from degradation. To increase the pool of F508del-CFTR protein that is available for correction by existing treatments, we determined a structure-activity relationship to improve the efficacy and reduce the toxicity of an inhibitor of the E1 ubiquitin activating enzyme that facilitates F508del-CFTR maturation. A resulting lead compound lacked measurable toxicity and improved the ability of an FDA-approved corrector to augment F508del-CFTR folding, transport the protein to the plasma membrane, and maintain its activity. These data support a proof-of-concept that modest inhibition of substrate ubiquitination improves the activity of small molecule correctors to treat CF and potentially other protein conformational disorders.
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Affiliation(s)
| | - Rajiah Aldrin Denny
- Department of Inflammation & Immunology, Pfizer Inc., Cambridge, MA 02139, USA
| | - Disha Joshi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Clare Hill
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mads B Larsen
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Annette N Chiang
- Department of Biological Science, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Raymond A Frizzell
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Jeffrey L Brodsky
- Department of Biological Science, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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26
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Feder ZA, Ali A, Singh A, Krakowiak J, Zheng X, Bindokas VP, Wolfgeher D, Kron SJ, Pincus D. Subcellular localization of the J-protein Sis1 regulates the heat shock response. J Cell Biol 2021; 220:211600. [PMID: 33326013 PMCID: PMC7748816 DOI: 10.1083/jcb.202005165] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/13/2020] [Accepted: 11/06/2020] [Indexed: 12/24/2022] Open
Abstract
Cells exposed to heat shock induce a conserved gene expression program, the heat shock response (HSR), encoding protein homeostasis (proteostasis) factors. Heat shock also triggers proteostasis factors to form subcellular quality control bodies, but the relationship between these spatial structures and the HSR is unclear. Here we show that localization of the J-protein Sis1, a cofactor for the chaperone Hsp70, controls HSR activation in yeast. Under nonstress conditions, Sis1 is concentrated in the nucleoplasm, where it promotes Hsp70 binding to the transcription factor Hsf1, repressing the HSR. Upon heat shock, Sis1 forms an interconnected network with other proteostasis factors that spans the nucleolus and the surface of the endoplasmic reticulum. We propose that localization of Sis1 to this network directs Hsp70 activity away from Hsf1 in the nucleoplasm, leaving Hsf1 free to induce the HSR. In this manner, Sis1 couples HSR activation to the spatial organization of the proteostasis network.
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Affiliation(s)
- Zoë A Feder
- Whitehead Institute for Biomedical Research, Cambridge, MA
| | - Asif Ali
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE.,Department of Biomedical Engineering, University of Delaware, Newark, DE.,Department of Mathematical Sciences, University of Delaware, Newark, DE.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE
| | | | - Xu Zheng
- Whitehead Institute for Biomedical Research, Cambridge, MA.,State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Vytas P Bindokas
- Integrated Light Microscopy Core Facility, University of Chicago, Chicago, IL
| | - Donald Wolfgeher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA.,Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL.,Center for Physics of Evolving Systems, University of Chicago, Chicago, IL
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27
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Flagg MP, Wangeline MA, Holland SR, Duttke SH, Benner C, Neal S, Hampton RY. Inner-nuclear-membrane-associated degradation employs Dfm1-independent retrotranslocation and alleviates misfolded transmembrane-protein toxicity. Mol Biol Cell 2021; 32:521-537. [PMID: 33566711 PMCID: PMC8101470 DOI: 10.1091/mbc.e20-11-0720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 11/11/2022] Open
Abstract
Before their delivery to and degradation by the 26S proteasome, misfolded transmembrane proteins of the endoplasmic reticulum (ER) and inner-nuclear membrane (INM) must be extracted from lipid bilayers. This extraction process, known as retrotranslocation, requires both quality-control E3 ubiquitin ligases and dislocation factors that diminish the energetic cost of dislodging the transmembrane segments of a protein. Recently, we showed that retrotranslocation of all ER transmembrane proteins requires the Dfm1 rhomboid pseudoprotease. However, we did not investigate whether Dfm1 also mediated retrotranslocation of transmembrane substrates in the INM, which is contiguous with the ER but functionally separated from it by nucleoporins. Here, we show that canonical retrotranslocation occurs during INM-associated degradation (INMAD) but proceeds independently of Dfm1. Despite this independence, ER-associated degradation (ERAD)-M and INMAD cooperate to mitigate proteotoxicity. We show a novel misfolded-transmembrane-protein toxicity that elicits genetic suppression, demonstrating the cell's ability to tolerate a toxic burden of misfolded transmembrane proteins without functional INMAD or ERAD-M. This strikingly contrasted the suppression of the dfm1Δ null, which leads to the resumption of ERAD-M through HRD-complex remodeling. Thus, we conclude that INM retrotranslocation proceeds through a novel, private channel that can be studied by virtue of its role in alleviating membrane-associated proteotoxicity.
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Affiliation(s)
- Matthew P. Flagg
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Margaret A. Wangeline
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Sarah R. Holland
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Sascha H. Duttke
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Sonya Neal
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Randolph Y. Hampton
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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28
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The Degron Architecture of Squalene Monooxygenase and How Specific Lipids Calibrate Levels of This Key Cholesterol Synthesis Enzyme. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 32979157 DOI: 10.1007/5584_2020_583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Cholesterol synthesis is a fundamental process that contributes to cellular cholesterol homeostasis. Cells execute transcriptional and post-translational mechanisms to control the abundance of enzymes of the cholesterol synthesis pathway, consequently affecting cholesterol production. One such highly tuned enzyme is squalene monooxygenase (SM), which catalyzes a rate-limiting step in the pathway. A well-characterized mechanism is the cholesterol-mediated degradation of SM. Notably, lipids (cholesterol, plasmalogens, squalene, and unsaturated fatty acids) can act as cellular signals that either promote or reduce SM degradation. The N-terminal region of SM consists of the shortest known cholesterol-responsive degron, characterized by atypical membrane anchoring structures, namely a re-entrant loop and an amphipathic helix. SM also undergoes non-canonical ubiquitination on serine, a relatively uncommon attachment site for ubiquitination. The structure of the catalytic domain of SM has been solved, providing insights into the catalytic mechanisms and modes of inhibition by well-known SM inhibitors, some of which have been effective in lowering cholesterol levels in animal models. Certain human cancers have been linked to dysregulation of SM levels and activity, further emphasizing the relevance of SM in health and disease.
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29
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Rao B, Li S, Yao D, Wang Q, Xia Y, Jia Y, Shen Y, Cao Y. The cryo-EM structure of an ERAD protein channel formed by tetrameric human Derlin-1. SCIENCE ADVANCES 2021; 7:eabe8591. [PMID: 33658201 PMCID: PMC7929502 DOI: 10.1126/sciadv.abe8591] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/19/2021] [Indexed: 05/24/2023]
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is a process directing misfolded proteins from the ER lumen and membrane to the degradation machinery in the cytosol. A key step in ERAD is the translocation of ER proteins to the cytosol. Derlins are essential for protein translocation in ERAD, but the mechanism remains unclear. Here, we solved the structure of human Derlin-1 by cryo-electron microscopy. The structure shows that Derlin-1 forms a homotetramer that encircles a large tunnel traversing the ER membrane. The tunnel has a diameter of about 12 to 15 angstroms, large enough to allow an α helix to pass through. The structure also shows a lateral gate within the membrane, providing access of transmembrane proteins to the tunnel, and thus, human Derlin-1 forms a protein channel for translocation of misfolded proteins. Our structure is different from the monomeric yeast Derlin structure previously reported, which forms a semichannel with another protein.
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Affiliation(s)
- Bing Rao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Shaobai Li
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Deqiang Yao
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Qian Wang
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Ying Xia
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Yi Jia
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Yafeng Shen
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Yu Cao
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China.
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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30
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Ryder BD, Matlahov I, Bali S, Vaquer-Alicea J, van der Wel PCA, Joachimiak LA. Regulatory inter-domain interactions influence Hsp70 recruitment to the DnaJB8 chaperone. Nat Commun 2021; 12:946. [PMID: 33574241 PMCID: PMC7878476 DOI: 10.1038/s41467-021-21147-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 01/15/2021] [Indexed: 01/18/2023] Open
Abstract
The Hsp40/Hsp70 chaperone families combine versatile folding capacity with high substrate specificity, which is mainly facilitated by Hsp40s. The structure and function of many Hsp40s remain poorly understood, particularly oligomeric Hsp40s that suppress protein aggregation. Here, we used a combination of biochemical and structural approaches to shed light on the domain interactions of the Hsp40 DnaJB8, and how they may influence recruitment of partner Hsp70s. We identify an interaction between the J-Domain (JD) and C-terminal domain (CTD) of DnaJB8 that sequesters the JD surface, preventing Hsp70 interaction. We propose a model for DnaJB8-Hsp70 recruitment, whereby the JD-CTD interaction of DnaJB8 acts as a reversible switch that can control the binding of Hsp70. These findings suggest that the evolutionarily conserved CTD of DnaJB8 is a regulatory element of chaperone activity in the proteostasis network.
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Affiliation(s)
- Bryan D Ryder
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Neuroscience Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands.
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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31
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Potential Physiological Relevance of ERAD to the Biosynthesis of GPI-Anchored Proteins in Yeast. Int J Mol Sci 2021; 22:ijms22031061. [PMID: 33494405 PMCID: PMC7865462 DOI: 10.3390/ijms22031061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/19/2022] Open
Abstract
Misfolded and/or unassembled secretory and membrane proteins in the endoplasmic reticulum (ER) may be retro-translocated into the cytoplasm, where they undergo ER-associated degradation, or ERAD. The mechanisms by which misfolded proteins are recognized and degraded through this pathway have been studied extensively; however, our understanding of the physiological role of ERAD remains limited. This review describes the biosynthesis and quality control of glycosylphosphatidylinositol (GPI)-anchored proteins and briefly summarizes the relevance of ERAD to these processes. While recent studies suggest that ERAD functions as a fail-safe mechanism for the degradation of misfolded GPI-anchored proteins, several pieces of evidence suggest an intimate interaction between ERAD and the biosynthesis of GPI-anchored proteins.
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32
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Ninagawa S, George G, Mori K. Mechanisms of productive folding and endoplasmic reticulum-associated degradation of glycoproteins and non-glycoproteins. Biochim Biophys Acta Gen Subj 2020; 1865:129812. [PMID: 33316349 DOI: 10.1016/j.bbagen.2020.129812] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The quality of proteins destined for the secretory pathway is ensured by two distinct mechanisms in the endoplasmic reticulum (ER): productive folding of newly synthesized proteins, which is assisted by ER-localized molecular chaperones and in most cases also by disulfide bond formation and transfer of an oligosaccharide unit; and ER-associated degradation (ERAD), in which proteins unfolded or misfolded in the ER are recognized and processed for delivery to the ER membrane complex, retrotranslocated through the complex with simultaneous ubiquitination, extracted by AAA-ATPase to the cytosol, and finally degraded by the proteasome. SCOPE OF REVIEW We describe the mechanisms of productive folding and ERAD, with particular attention to glycoproteins versus non-glycoproteins, and to yeast versus mammalian systems. MAJOR CONCLUSION Molecular mechanisms of the productive folding of glycoproteins and non-glycoproteins mediated by molecular chaperones and protein disulfide isomerases are well conserved from yeast to mammals. Additionally, mammals have gained an oligosaccharide structure-dependent folding cycle for glycoproteins. The molecular mechanisms of ERAD are also well conserved from yeast to mammals, but redundant expression of yeast orthologues in mammals has been encountered, particularly for components involved in recognition and processing of glycoproteins and components of the ER membrane complex involved in retrotranslocation and simultaneous ubiquitination of glycoproteins and non-glycoproteins. This may reflect an evolutionary consequence of increasing quantity or quality needs toward mammals. GENERAL SIGNIFICANCE The introduction of innovative genome editing technology into analysis of the mechanisms of mammalian ERAD, as exemplified here, will provide new insights into the pathogenesis of various diseases.
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Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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33
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Zhang L, Qin Y, Wu G, Wang J, Cao J, Wang Y, Wu D, Yang K, Zhao Z, He L, Lyu J, Li H, Gu H. PRRG4 promotes breast cancer metastasis through the recruitment of NEDD4 and downregulation of Robo1. Oncogene 2020; 39:7196-7208. [PMID: 33037408 DOI: 10.1038/s41388-020-01494-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/19/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022]
Abstract
Metastasis is responsible for the death of most breast cancer patients. Robo1 has been implicated as a tumor suppressor for various cancers including breast cancer. However, it is not well understood how Robo1 expression is regulated during tumorigenesis. In this study, we uncovered that the transmembrane proline rich γ-carboxyglutamic acid protein 4 (PRRG4) promotes breast cancer metastasis by downregulating Robo1. Analysis of mRNA expression data in The Cancer Genome Atlas and immunohistochemistry assay on breast tumor samples showed that PRRG4 expression was higher in breast tumors than in normal breast tissues. Experiments with PRRG4 knockdown and overexpression revealed that PRRG4 promoted migration and invasion of breast cancer cells, and enhanced metastasis in an experimental metastasis model. Mechanistically, we found that PRRG4 via its LPSY and PPPY motifs recruited the E3 ubiquitin ligase NEDD4, which induced ubiquitination and degradation of Robo1, thus contributing to migration and invasion of breast cancer cells. In addition, PRRG4 interacted with and enhanced protein tyrosine kinase Src and FAK activation. Overall, our data support a model that PRRG4 via NEDD4 downregulates the Robo1, resulting in the activation of Src and FAK and promoting breast cancer metastasis. PRRG4 may be a novel target for treating metastatic breast cancer.
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Affiliation(s)
- Lingling Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yaqian Qin
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Guang Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jieyi Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jiawei Cao
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yaqi Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Du Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kaiyan Yang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhiguang Zhao
- Department of Pathology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Licai He
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Hongzhi Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Haihua Gu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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Peck Justice SA, Barron MP, Qi GD, Wijeratne HRS, Victorino JF, Simpson ER, Vilseck JZ, Wijeratne AB, Mosley AL. Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome. J Biol Chem 2020; 295:16219-16238. [PMID: 32878984 PMCID: PMC7705321 DOI: 10.1074/jbc.ra120.014576] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Temperature-sensitive (TS) missense mutants have been foundational for characterization of essential gene function. However, an unbiased approach for analysis of biochemical and biophysical changes in TS missense mutants within the context of their functional proteomes is lacking. We applied MS-based thermal proteome profiling (TPP) to investigate the proteome-wide effects of missense mutations in an application that we refer to as mutant thermal proteome profiling (mTPP). This study characterized global impacts of temperature sensitivity-inducing missense mutations in two different subunits of the 26S proteasome. The majority of alterations identified by RNA-Seq and global proteomics were similar between the mutants, which could suggest that a similar functional disruption is occurring in both missense variants. Results from mTPP, however, provide unique insights into the mechanisms that contribute to the TS phenotype in each mutant, revealing distinct changes that were not obtained using only steady-state transcriptome and proteome analyses. Computationally, multisite λ-dynamics simulations add clear support for mTPP experimental findings. This work shows that mTPP is a precise approach to measure changes in missense mutant-containing proteomes without the requirement for large amounts of starting material, specific antibodies against proteins of interest, and/or genetic manipulation of the biological system. Although experiments were performed under permissive conditions, mTPP provided insights into the underlying protein stability changes that cause dramatic cellular phenotypes observed at nonpermissive temperatures. Overall, mTPP provides unique mechanistic insights into missense mutation dysfunction and connection of genotype to phenotype in a rapid, nonbiased fashion.
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Affiliation(s)
- Sarah A Peck Justice
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Monica P Barron
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Guihong D Qi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - H R Sagara Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - José F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ed R Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA; Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University, Indianapolis, Indiana, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jonah Z Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Aruna B Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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Singh A, Vashistha N, Heck J, Tang X, Wipf P, Brodsky JL, Hampton RY. Direct involvement of Hsp70 ATP hydrolysis in Ubr1-dependent quality control. Mol Biol Cell 2020; 31:2669-2686. [PMID: 32966159 PMCID: PMC7927186 DOI: 10.1091/mbc.e20-08-0541] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Chaperones can mediate both protein folding and degradation. This process is referred to as protein triage, which demands study to reveal mechanisms of quality control for both basic scientific and translational purposes. In yeast, many misfolded proteins undergo chaperone-dependent ubiquitination by the action of the E3 ligases Ubr1 and San1, allowing detailed study of protein triage. In cells, both HSP70 and HSP90 mediated substrate ubiquitination, and the canonical ATP cycle was required for HSP70’s role: we have found that ATP hydrolysis by HSP70, the nucleotide exchange activity of Sse1, and the action of J-proteins are all needed for Ubr1-mediated quality control. To discern whether chaperones were directly involved in Ubr1-mediated ubiquitination, we developed a bead-based assay with covalently immobilized but releasable misfolded protein to obviate possible chaperone effects on substrate physical state or transport. In this in vitro assay, only HSP70 was required, along with its ATPase cycle and relevant cochaperones, for Ubr1-mediated ubiquitination. The requirement for the HSP70 ATP cycle in ubiquitination suggests a possible model of triage in which efficiently folded proteins are spared, while slow-folding or nonfolding proteins are iteratively tagged with ubiquitin for subsequent degradation.
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Affiliation(s)
- Amanjot Singh
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
| | - Nidhi Vashistha
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
| | - Jarrod Heck
- Adaptive Biotechnologies Corp., Seattle, WA 98102
| | - Xin Tang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Randolph Y Hampton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
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Buck TM, Zeng X, Cantrell PS, Cattley RT, Hasanbasri Z, Yates ME, Nguyen D, Yates NA, Brodsky JL. The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation. Mol Cell Proteomics 2020; 19:1896-1909. [PMID: 32868373 DOI: 10.1074/mcp.ra120.002050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/06/2020] [Indexed: 01/13/2023] Open
Abstract
Studies in the yeast Saccharomyces cerevisiae have helped define mechanisms underlying the activity of the ubiquitin-proteasome system (UPS), uncover the proteasome assembly pathway, and link the UPS to the maintenance of cellular homeostasis. However, the spectrum of UPS substrates is incompletely defined, even though multiple techniques-including MS-have been used. Therefore, we developed a substrate trapping proteomics workflow to identify previously unknown UPS substrates. We first generated a yeast strain with an epitope tagged proteasome subunit to which a proteasome inhibitor could be applied. Parallel experiments utilized inhibitor insensitive strains or strains lacking the tagged subunit. After affinity isolation, enriched proteins were resolved, in-gel digested, and analyzed by high resolution liquid chromatography-tandem MS. A total of 149 proteasome partners were identified, including all 33 proteasome subunits. When we next compared data between inhibitor sensitive and resistant cells, 27 proteasome partners were significantly enriched. Among these proteins were known UPS substrates and proteins that escort ubiquitinated substrates to the proteasome. We also detected Erg25 as a high-confidence partner. Erg25 is a methyl oxidase that converts dimethylzymosterol to zymosterol, a precursor of the plasma membrane sterol, ergosterol. Because Erg25 is a resident of the endoplasmic reticulum (ER) and had not previously been directly characterized as a UPS substrate, we asked whether Erg25 is a target of the ER associated degradation (ERAD) pathway, which most commonly mediates proteasome-dependent destruction of aberrant proteins. As anticipated, Erg25 was ubiquitinated and associated with stalled proteasomes. Further, Erg25 degradation depended on ERAD-associated ubiquitin ligases and was regulated by sterol synthesis. These data expand the cohort of lipid biosynthetic enzymes targeted for ERAD, highlight the role of the UPS in maintaining ER function, and provide a novel tool to uncover other UPS substrates via manipulations of our engineered strain.
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Affiliation(s)
- Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA
| | - Pamela S Cantrell
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA
| | - Richard T Cattley
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA
| | - Zikri Hasanbasri
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Megan E Yates
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Diep Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nathan A Yates
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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Neal S, Syau D, Nejatfard A, Nadeau S, Hampton RY. HRD Complex Self-Remodeling Enables a Novel Route of Membrane Protein Retrotranslocation. iScience 2020; 23:101493. [PMID: 32891886 PMCID: PMC7481253 DOI: 10.1016/j.isci.2020.101493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/09/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022] Open
Abstract
ER-associated degradation (ERAD) targets misfolded ER proteins for degradation. Retrotranslocation, a key feature of ERAD, entails removal of ubiquitinated substrates into the cytosol for proteasomal destruction. Recently, it has been shown that the Hrd1 E3 ligase forms a retrotranslocation channel for luminal (ERAD-L) substrates. Conversely, our studies found that integral membrane (ERAD-M) substrates exit the ER through a distinct pathway mediated by the Dfm1 rhomboid protein. Those studies also revealed a second, Hrd1-dependent pathway of ERAD-M retrotranslocation can arise in dfm1Δ null. Here we show that, in the dfm1Δ null, the HRD complex undergoes remodeling to a form that mediates ERAD-M retrotranslocation. Specifically, Hrd1's normally present stochiometric partner Hrd3 is efficiently removed during suppressive remodeling, allowing Hrd1 to function in this novel capacity. Neither Hrd1 autoubiquitination nor its cytosolic domain is required for suppressive ERAD-M retrotranslocation. Thus, the HRD complex displays remarkable functional flexibility in response to ER stress.
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Affiliation(s)
- Sonya Neal
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Della Syau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Anahita Nejatfard
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Samantha Nadeau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Randolph Y Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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Lopata A, Kniss A, Löhr F, Rogov VV, Dötsch V. Ubiquitination in the ERAD Process. Int J Mol Sci 2020; 21:ijms21155369. [PMID: 32731622 PMCID: PMC7432864 DOI: 10.3390/ijms21155369] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 01/08/2023] Open
Abstract
In this review, we focus on the ubiquitination process within the endoplasmic reticulum associated protein degradation (ERAD) pathway. Approximately one third of all synthesized proteins in a cell are channeled into the endoplasmic reticulum (ER) lumen or are incorporated into the ER membrane. Since all newly synthesized proteins enter the ER in an unfolded manner, folding must occur within the ER lumen or co-translationally, rendering misfolding events a serious threat. To prevent the accumulation of misfolded protein in the ER, proteins that fail the quality control undergo retrotranslocation into the cytosol where they proceed with ubiquitination and degradation. The wide variety of misfolded targets requires on the one hand a promiscuity of the ubiquitination process and on the other hand a fast and highly processive mechanism. We present the various ERAD components involved in the ubiquitination process including the different E2 conjugating enzymes, E3 ligases, and E4 factors. The resulting K48-linked and K11-linked ubiquitin chains do not only represent a signal for degradation by the proteasome but are also recognized by the AAA+ ATPase Cdc48 and get in the process of retrotranslocation modified by enzymes bound to Cdc48. Lastly we discuss the conformations adopted in particular by K48-linked ubiquitin chains and their importance for degradation.
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Hu X, Wang L, Wang Y, Ji J, Li J, Wang Z, Li C, Zhang Y, Zhang ZR. RNF126-Mediated Reubiquitination Is Required for Proteasomal Degradation of p97-Extracted Membrane Proteins. Mol Cell 2020; 79:320-331.e9. [DOI: 10.1016/j.molcel.2020.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 12/13/2022]
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40
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Chua NK, Coates HW, Brown AJ. Squalene monooxygenase: a journey to the heart of cholesterol synthesis. Prog Lipid Res 2020; 79:101033. [DOI: 10.1016/j.plipres.2020.101033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
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Schmidt CC, Vasic V, Stein A. Doa10 is a membrane protein retrotranslocase in ER-associated protein degradation. eLife 2020; 9:56945. [PMID: 32588820 PMCID: PMC7319771 DOI: 10.7554/elife.56945] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
In endoplasmic reticulum-associated protein degradation (ERAD), membrane proteins are ubiquitinated, extracted from the membrane, and degraded by the proteasome. The cytosolic ATPase Cdc48 drives extraction by pulling on polyubiquitinated substrates. How hydrophobic transmembrane (TM) segments are moved from the phospholipid bilayer into cytosol, often together with hydrophilic and folded ER luminal protein parts, is not known. Using a reconstituted system with purified proteins from Saccharomyces cerevisiae, we show that the ubiquitin ligase Doa10 (Teb-4/MARCH6 in animals) is a retrotranslocase that facilitates membrane protein extraction. A substrate’s TM segment interacts with the membrane-embedded domain of Doa10 and then passively moves into the aqueous phase. Luminal substrate segments cross the membrane in an unfolded state. Their unfolding occurs on the luminal side of the membrane by cytoplasmic Cdc48 action. Our results reveal how a membrane-bound retrotranslocase cooperates with the Cdc48 ATPase in membrane protein extraction. The inside of a cell contains many different compartments called organelles, which are separated by membranes. Each organelle is composed of a unique set of proteins and performs specific roles in the cell. The endoplasmic reticulum, or ER for short, is an organelle where many proteins are produced. Most of these proteins are then released from the cell or sorted to other organelles. The ER has a strict quality control system that ensures any faulty proteins are quickly marked for the cell to destroy. However, the destruction process itself does not happen in the ER, so faulty proteins first need to leave this organelle. This is achieved by a group of proteins known as endoplasmic reticulum-associated protein degradation machinery (or ERAD for short). To extract a faulty protein from the ER, proteins of the ER and outside the ER cooperate. First, an ERAD protein called Doa10 attaches a small protein tag called ubiquitin to the faulty proteins to mark them for destruction. Then, outside of the ER, a protein called Cdc48 ‘grabs’ the ubiquitin tag and pulls. But that is only part of the story. Many of the proteins made by the ER have tethers that anchor them firmly to the membrane, making them much harder to remove. To get a better idea of how the extraction works, Schmidt et al. rebuilt the ERAD machinery in a test tube. This involved purifying proteins from yeast and inserting them into artificial membranes, allowing closer study of each part of the process. This revealed that attaching ubiquitin tags to faulty proteins is only one part of Doa10's role; it also participates in the extraction itself. Part of Doa10 resides within the membrane, and this ‘membrane-spanning domain’ can interact with faulty proteins, loosening their membrane anchors. At the same time, Cdc48 pulls from the outside. This pulling force causes the faulty proteins to unfold, allowing them to pass through the membrane. Given these findings, the next step is to find out exactly how Doa10 works by looking at its three-dimensional structure. This could have implications not only for the study of ERAD, but of similar quality control processes in other organelles too. A build-up of faulty proteins can cause diseases like neurodegeneration, so understanding how cells remove faulty proteins could help future medical research.
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Affiliation(s)
- Claudia C Schmidt
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vedran Vasic
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander Stein
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Fukuda R, Okiyoneda T. Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Ubiquitylation as a Novel Pharmaceutical Target for Cystic Fibrosis. Pharmaceuticals (Basel) 2020; 13:ph13040075. [PMID: 32331485 PMCID: PMC7243099 DOI: 10.3390/ph13040075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/22/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene decrease the structural stability and function of the CFTR protein, resulting in cystic fibrosis. Recently, the effect of CFTR-targeting combination therapy has dramatically increased, and it is expected that add-on drugs that modulate the CFTR surrounding environment will further enhance their effectiveness. Various interacting proteins have been implicated in the structural stability of CFTR and, among them, molecules involved in CFTR ubiquitylation are promising therapeutic targets as regulators of CFTR degradation. This review focuses on the ubiquitylation mechanism that contributes to the stability of mutant CFTR at the endoplasmic reticulum (ER) and post-ER compartments and discusses the possibility as a pharmacological target for cystic fibrosis (CF).
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Jones RD, Enam C, Ibarra R, Borror HR, Mostoller KE, Fredrickson EK, Lin J, Chuang E, March Z, Shorter J, Ravid T, Kleiger G, Gardner RG. The extent of Ssa1/Ssa2 Hsp70 chaperone involvement in nuclear protein quality control degradation varies with the substrate. Mol Biol Cell 2019; 31:221-233. [PMID: 31825716 PMCID: PMC7001477 DOI: 10.1091/mbc.e18-02-0121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protein misfolding is a recurring phenomenon that cells must manage; otherwise misfolded proteins can aggregate and become toxic should they persist. To counter this burden, cells have evolved protein quality control (PQC) mechanisms that manage misfolded proteins. Two classes of systems that function in PQC are chaperones that aid in protein folding and ubiquitin-protein ligases that ubiquitinate misfolded proteins for proteasomal degradation. How folding and degradative PQC systems interact and coordinate their respective functions is not yet fully understood. Previous studies of PQC degradation pathways in the endoplasmic reticulum and cytosol have led to the prevailing idea that these pathways require the activity of Hsp70 chaperones. Here, we find that involvement of the budding yeast Hsp70 chaperones Ssa1 and Ssa2 in nuclear PQC degradation varies with the substrate. In particular, nuclear PQC degradation mediated by the yeast ubiquitin-protein ligase San1 often involves Ssa1/Ssa2, but San1 substrate recognition and ubiquitination can proceed without these Hsp70 chaperone functions in vivo and in vitro. Our studies provide new insights into the variability of Hsp70 chaperone involvement with a nuclear PQC degradation pathway.
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Affiliation(s)
- Ramon D Jones
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Charisma Enam
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Rebeca Ibarra
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154
| | - Heather R Borror
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | | | | | - JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Edward Chuang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Zachary March
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, -Jerusalem 91904, Israel
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, WA 98195
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Nakatsukasa K, Kawarasaki T, Moriyama A. Heterologous expression and functional analysis of the F-box protein Ucc1 from other yeast species in Saccharomyces cerevisiae. J Biosci Bioeng 2019; 128:704-709. [DOI: 10.1016/j.jbiosc.2019.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
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45
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Lautenschäger J, Kaminski Schierle GS. Mitochondrial degradation of amyloidogenic proteins - A new perspective for neurodegenerative diseases. Prog Neurobiol 2019; 181:101660. [PMID: 31301323 DOI: 10.1016/j.pneurobio.2019.101660] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/02/2019] [Accepted: 07/04/2019] [Indexed: 01/09/2023]
Abstract
This perspective article outlines mechanisms of mitochondrial import and protein degradation and how these have been linked to alpha-synuclein and Amyloid beta (Aβ) homeostasis. Our aim is to underpin and stimulate the debate on the recent conception of mitochondria as protein degrading organelles, which suggests that mitochondria are more directly involved in neurodegenerative diseases than previously assumed.
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Affiliation(s)
- Janin Lautenschäger
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| | - Gabriele S Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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46
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Sun Z, Brodsky JL. Protein quality control in the secretory pathway. J Cell Biol 2019; 218:3171-3187. [PMID: 31537714 PMCID: PMC6781448 DOI: 10.1083/jcb.201906047] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 12/23/2022] Open
Abstract
Protein folding is inherently error prone, especially in the endoplasmic reticulum (ER). Even with an elaborate network of molecular chaperones and protein folding facilitators, misfolding can occur quite frequently. To maintain protein homeostasis, eukaryotes have evolved a series of protein quality-control checkpoints. When secretory pathway quality-control pathways fail, stress response pathways, such as the unfolded protein response (UPR), are induced. In addition, the ER, which is the initial hub of protein biogenesis in the secretory pathway, triages misfolded proteins by delivering substrates to the proteasome or to the lysosome/vacuole through ER-associated degradation (ERAD) or ER-phagy. Some misfolded proteins escape the ER and are instead selected for Golgi quality control. These substrates are targeted for degradation after retrieval to the ER or delivery to the lysosome/vacuole. Here, we discuss how these guardian pathways function, how their activities intersect upon induction of the UPR, and how decisions are made to dispose of misfolded proteins in the secretory pathway.
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Affiliation(s)
- Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
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47
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Anelli T, Panina-Bordignon P. How to Avoid a No-Deal ER Exit. Cells 2019; 8:cells8091051. [PMID: 31500301 PMCID: PMC6769657 DOI: 10.3390/cells8091051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 01/01/2023] Open
Abstract
Efficiency and fidelity of protein secretion are achieved thanks to the presence of different steps, located sequentially in time and space along the secretory compartment, controlling protein folding and maturation. After entering into the endoplasmic reticulum (ER), secretory proteins attain their native structure thanks to specific chaperones and enzymes. Only correctly folded molecules are allowed by quality control (QC) mechanisms to leave the ER and proceed to downstream compartments. Proteins that cannot fold properly are instead retained in the ER to be finally destined to proteasomal degradation. Exiting from the ER requires, in most cases, the use of coated vesicles, departing at the ER exit sites, which will fuse with the Golgi compartment, thus releasing their cargoes. Protein accumulation in the ER can be caused by a too stringent QC or by ineffective transport: these situations could be deleterious for the organism, due to the loss of the secreted protein, and to the cell itself, because of abnormal increase of protein concentration in the ER. In both cases, diseases can arise. In this review, we will describe the pathophysiology of protein folding and transport between the ER and the Golgi compartment.
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Affiliation(s)
- Tiziana Anelli
- Vita-Salute San Raffaele University, 20132 Milan, Italy.
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy.
| | - Paola Panina-Bordignon
- Vita-Salute San Raffaele University, 20132 Milan, Italy.
- Division of Neuroscience, IRCCS Ospedale San Raffaele, 20132 Milan, Italy.
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Werner HM, Estabrooks SK, Preston GM, Brodsky JL, Horne WS. Exploring the Functional Consequences of Protein Backbone Alteration in Ubiquitin through Native Chemical Ligation. Chembiochem 2019; 20:2346-2350. [PMID: 31059184 DOI: 10.1002/cbic.201900225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Indexed: 01/21/2023]
Abstract
Ubiquitin (Ub) plays critical roles in myriad protein degradation and signaling networks in the cell. We report herein Ub mimetics based on backbones that blend natural and artificial amino acid units. The variants were prepared by a modular route based on native chemical ligation. Biological assays show that some are enzymatically polymerized onto protein substrates, and that the resulting Ub tags are recognized for downstream pathways. These results advance the size and complexity of folded proteins mimicked by artificial backbones and expand the functional scope of such agents.
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Affiliation(s)
- Halina M Werner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Samuel K Estabrooks
- Department of Biological Sciences, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - G Michael Preston
- Department of Biological Sciences, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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Scheffer J, Hasenjäger S, Taxis C. Degradation of integral membrane proteins modified with the photosensitive degron module requires the cytosolic endoplasmic reticulum-associated degradation pathway. Mol Biol Cell 2019; 30:2558-2570. [PMID: 31411939 PMCID: PMC6740197 DOI: 10.1091/mbc.e18-12-0754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Protein quality mechanisms are fundamental for proteostasis of eukaryotic cells. Endoplasmic reticulum–associated degradation (ERAD) is a well-studied pathway that ensures quality control of secretory and endoplasmic reticulum (ER)–resident proteins. Different branches of ERAD are involved in degradation of malfolded secretory proteins, depending on the localization of the misfolded part, the ER lumen (ERAD-L), the ER membrane (ERAD-M), and the cytosol (ERAD-C). Here we report that modification of several ER transmembrane proteins with the photosensitive degron (psd) module resulted in light-dependent degradation of the membrane proteins via the ERAD-C pathway. We found dependency on the ubiquitylation machinery including the ubiquitin-activating enzyme Uba1, the ubiquitin-conjugating enzymes Ubc6 and Ubc7, and the ubiquitin–protein ligase Doa10. Moreover, we found involvement of the Cdc48 AAA-ATPase complex members Ufd1 and Npl4, as well as the proteasome, in degradation of Sec62-myc-psd. Thus, our work shows that ERAD-C substrates can be systematically generated via synthetic degron constructs, which facilitates future investigations of the ERAD-C pathway.
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Affiliation(s)
- Johannes Scheffer
- Department of Chemistry/Biochemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Sophia Hasenjäger
- Department of Biology/Genetics, Philipps-University Marburg, 35043 Marburg, Germany
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-University Marburg, 35043 Marburg, Germany
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50
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Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP. Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science 2019; 363:363/6429/eaav4467. [PMID: 30792274 DOI: 10.1126/science.aav4467] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
Abstract
Chloroplasts contain thousands of nucleus-encoded proteins that are imported from the cytosol by translocases in the chloroplast envelope membranes. Proteolytic regulation of the translocases is critically important, but little is known about the underlying mechanisms. We applied forward genetics and proteomics in Arabidopsis to identify factors required for chloroplast outer envelope membrane (OEM) protein degradation. We identified SP2, an Omp85-type β-barrel channel of the OEM, and CDC48, a cytosolic AAA+ (ATPase associated with diverse cellular activities) chaperone. Both proteins acted in the same pathway as the ubiquitin E3 ligase SP1, which regulates OEM translocase components. SP2 and CDC48 cooperated to bring about retrotranslocation of ubiquitinated substrates from the OEM (fulfilling conductance and motor functions, respectively), enabling degradation of the substrates by the 26S proteasome in the cytosol. Such chloroplast-associated protein degradation (CHLORAD) is vital for organellar functions and plant development.
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Affiliation(s)
- Qihua Ling
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - William Broad
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Raphael Trösch
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Mats Töpel
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Amy Baldwin
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK. .,Department of Biology, University of Leicester, Leicester LE1 7RH, UK
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