1
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Bhaduri S, Braza MKE, Stanchev S, Bach K, Tauber M, Al-Bawab R, Liu LJ, Trujillo DF, Solorio-Kirpichyan K, Srivastava A, Sanlley-Hernandez J, O'Donoghue AJ, Lemberg MK, Amario R, Strisovsky K, Neal SE. An in vitro platform for the enzymatic characterization of the rhomboid protease RHBDL4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.13.618094. [PMID: 39415989 PMCID: PMC11483055 DOI: 10.1101/2024.10.13.618094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Rhomboid proteases are ubiquitous intramembrane serine proteases that can cleave transmembrane substrates within lipid bilayers. They exhibit many and diverse functions, such as but not limited to, growth factor signaling, immune and inflammatory response, protein quality control, and parasitic invasion. Human rhomboid protease RHBDL4 has been demonstrated to play a critical role in removing misfolded proteins from the Endoplasmic Reticulum and is implicated in severe diseases such as various cancers and Alzheimer's disease. Therefore, RHBDL4 is expected to constitute an important therapeutic target for such devastating diseases. Despite its critical role in many biological processes, the enzymatic properties of RHBDL4 remain largely unknown. To enable a comprehensive characterization of RHBDL4's kinetics, catalytic parameters, substrate specificity, and binding modality we expressed and purified recombinant RHBDL4, and employed it in a Förster Resonance Energy Transfer-based cleavage assay. Until now, kinetic studies have been limited mostly to bacterial rhomboid proteases. Our in vitro platform offers a new method for studying RHBDL4's enzymatic function and substrate preferences. Furthermore, we developed and tested potential inhibitors using our assay and successfully identifying peptidyl α-ketoamide inhibitors of RHBDL4 that are highly effective against recombinant RHBDL4. We utilize ensemble docking and molecular dynamics (MD) simulations to explore the binding modality of substrate-derived peptides bound to RHBDL4. Our analysis focused on key interactions and dynamic movements within RHBDL4's active site that contributed to binding stability, offering valuable insights for optimizing the non-prime side of RHBDL4 ketoamide inhibitors. In summary, our study offers fundamental insights into RHBDL4's catalytic activities and substrate preferences, laying the foundation for downstream applications such as drug inhibitor screenings and structure-function studies, which will enable the identification of lead drug compounds for RHBDL4.
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2
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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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3
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Megane Penalva YC, Paschkowsky S, Yang J, Recinto SJ, Cinkorpumin J, Hernandez MR, Xiao B, Nitu A, Yee-Li Wu H, Munter HM, Michalski B, Fahnestock M, Pastor W, Bennett DA, Munter LM. Loss of the APP regulator RHBDL4 preserves memory in an Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.579698. [PMID: 38464180 PMCID: PMC10925189 DOI: 10.1101/2024.02.22.579698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Characteristic cerebral pathological changes of Alzheimer's disease (AD) such as glucose hypometabolism or the accumulation of cleavage products of the amyloid precursor protein (APP), known as Aβ peptides, lead to sustained endoplasmic reticulum (ER) stress and neurodegeneration. To preserve ER homeostasis, cells activate their unfolded protein response (UPR). The rhomboid-like-protease 4 (RHBDL4) is an enzyme that participates in the UPR by targeting proteins for proteasomal degradation. We demonstrated previously that RHBLD4 cleaves APP in HEK293T cells, leading to decreased total APP and Aβ. More recently, we showed that RHBDL4 processes APP in mouse primary mixed cortical cultures as well. Here, we aim to examine the physiological relevance of RHBDL4 in the brain. We first found that brain samples from AD patients and an AD mouse model (APPtg) showed increased RHBDL4 mRNA and protein expression. To determine the effects of RHBDL4's absence on APP physiology in vivo, we crossed APPtg mice to a RHBDL4 knockout (R4-/-) model. RHBDL4 deficiency in APPtg mice led to increased total cerebral APP and amyloidogenic processing when compared to APPtg controls. Contrary to expectations, as assessed by cognitive tests, RHBDL4 absence rescued cognition in 5-month-old female APPtg mice. Informed by unbiased RNAseq data, we demonstrated in vitro and in vivo that RHBDL4 absence leads to greater levels of active β-catenin due to decreased proteasomal clearance. Decreased β-catenin activity is known to underlie cognitive defects in APPtg mice and AD. Our work suggests that RHBDL4's increased expression in AD, in addition to regulating APP levels, leads to aberrant degradation of β-catenin, contributing to cognitive impairment.
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Affiliation(s)
- Ylauna Christine Megane Penalva
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
| | - Sandra Paschkowsky
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Sherilyn Junelle Recinto
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
| | | | - Marina Ruelas Hernandez
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
| | - Bin Xiao
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
| | - Albert Nitu
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
| | - Helen Yee-Li Wu
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
| | - Hans Markus Munter
- Department of Human Genetics, McGill University, Montreal, QC, Canada H3A 0C7
| | - Bernadeta Michalski
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - Margaret Fahnestock
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - William Pastor
- Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 0B1
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
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4
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Bach K, Dohnálek J, Škerlová J, Kuzmík J, Poláchová E, Stanchev S, Majer P, Fanfrlík J, Pecina A, Řezáč J, Lepšík M, Borshchevskiy V, Polovinkin V, Strisovsky K. Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency. Eur J Med Chem 2024; 275:116606. [PMID: 38901105 DOI: 10.1016/j.ejmech.2024.116606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
Rhomboid intramembrane serine proteases have been implicated in several pathologies, and emerge as attractive pharmacological target candidates. The most potent and selective rhomboid inhibitors available to date are peptidyl α-ketoamides, but their selectivity for diverse rhomboid proteases and strategies to modulate it in relevant contexts are poorly understood. This gap, together with the lack of suitable in vitro models, hinders ketoamide development for relevant eukaryotic rhomboid enzymes. Here we explore the structure-activity relationship principles of rhomboid inhibiting ketoamides by medicinal chemistry and enzymatic in vitro and in-cell assays with recombinant rhomboid proteases GlpG, human mitochondrial rhomboid PARL and human RHBDL2. We use X-ray crystallography in lipidic cubic phase to understand the binding mode of one of the best ketoamide inhibitors synthesized here containing a branched terminal substituent bound to GlpG. In addition, to extend the interpretation of the co-crystal structure, we use quantum mechanical calculations and quantify the relative importance of interactions along the inhibitor molecule. These combined experimental analyses implicates that more extensive exploration of chemical space at the prime side is unexpectedly powerful for the selectivity of rhomboid inhibiting ketoamides. Together with variations in the peptide sequence at the non-prime side, or its non-peptidic alternatives, this strategy enables targeted tailoring of potent and selective ketoamides towards diverse rhomboid proteases including disease-relevant ones such as PARL and RHBDL2.
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Affiliation(s)
- Kathrin Bach
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; Department of Molecular Genetics, Faculty of Science, Charles University, Viničná 5, Prague, 128 44, Czech Republic
| | - Jan Dohnálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; University of Chemistry and Technology, Technická 5, Prague, 166 28, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Ján Kuzmík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Edita Poláchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague, 121 08, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry) Forschungszentrum Jülich 52428 Jülich, Germany
| | - Vitaly Polovinkin
- ELI Beamlines Centre, ELI ERIC, Za Radnicí 835, 252 41, Dolní Břežany, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic.
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5
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Davies C, Hu RM, Kamitsuka PJ, Morais GN, de Gonzalez RS, Bustin KA, Matthews ML, Parsons WH. Activity-Based Protein Profiling of RHBDL4 Reveals Proteolysis of the Enzyme and a Distinct Inhibitor Profile. ACS Chem Biol 2024; 19:1674-1682. [PMID: 39041925 PMCID: PMC11334910 DOI: 10.1021/acschembio.4c00273] [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: 04/19/2024] [Revised: 06/19/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Rhomboid proteases have fascinated scientists by virtue of their membrane-embedded active sites and proposed involvement in physiological and disease pathways. The human rhomboid protease RHBDL4 has generated particular interest due to its role in endoplasmic reticulum-associated protein degradation and upregulation in several cancers; however, chemical tools for studying this enzyme are currently lacking. Here, we describe the development of an activity-based protein profiling (ABPP) assay for RHBDL4. We have employed this assay to determine that human RHBDL4 undergoes proteolytic processing in cells to produce multiple active proteoforms with truncated C-termini. We have also used this assay to identify chemical scaffolds capable of inhibiting RHBDL4 activity and have observed distinct inhibitor preferences between RHBDL4 and a second human rhomboid protease PARL. Our work demonstrates the power of ABPP technology to characterize active forms of enzymes that might otherwise elude detection and the potential to achieve selective inhibition among the human rhomboid proteases.
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Affiliation(s)
- Cassondra
C. Davies
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Ren-Ming Hu
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul J. Kamitsuka
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Gabriel N. Morais
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | | | - Katelyn A. Bustin
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Megan L. Matthews
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - William H. Parsons
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
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6
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Penalva YCM, Paschkowsky S, Recinto SJ, Duchesne A, Hammond T, Spiegler P, Jansen G, Levet C, Charron F, Freeman M, McKinney RA, Trempe JF, Munter LM. Eta-secretase-like processing of the amyloid precursor protein (APP) by the rhomboid protease RHBDL4. J Biol Chem 2024; 300:107541. [PMID: 38992438 PMCID: PMC11345391 DOI: 10.1016/j.jbc.2024.107541] [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: 12/08/2023] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
The amyloid precursor protein (APP) is a key protein in Alzheimer's disease synthesized in the endoplasmic reticulum (ER) and translocated to the plasma membrane where it undergoes proteolytic cleavages by several proteases. Conversely, to other known proteases, we previously elucidated rhomboid protease RHBDL4 as a novel APP processing enzyme where several cleavages likely occur already in the ER. Interestingly, the pattern of RHBDL4-derived large APP C-terminal fragments resembles those generated by the η-secretase or MT5-MMP, which was described to generate so-called Aη fragments. The similarity in large APP C-terminal fragments between both proteases raised the question of whether RHBDL4 may contribute to η-secretase activity and Aη-like fragments. Here, we identified two cleavage sites of RHBDL4 in APP by mass spectrometry, which, intriguingly, lie in close proximity to the MT5-MMP cleavage sites. Indeed, we observed that RHBDL4 generates Aη-like fragments in vitro without contributions of α-, β-, or γ-secretases. Such Aη-like fragments are likely generated in the ER since RHBDL4-derived APP-C-terminal fragments do not reach the cell surface. Inherited, familial APP mutations appear to not affect this processing pathway. In RHBDL4 knockout mice, we observed increased cerebral full-length APP in comparison to wild type (WT) in support of RHBDL4 being a physiologically relevant protease for APP. Furthermore, we found secreted Aη fragments in dissociated mixed cortical cultures from WT mice, however significantly fewer Aη fragments in RHBDL4 knockout cultures. Our data underscores that RHBDL4 contributes to the η-secretease-like processing of APP and that RHBDL4 is a physiologically relevant protease for APP.
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Affiliation(s)
- Ylauna Christine Mégane Penalva
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Sandra Paschkowsky
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Sherilyn Junelle Recinto
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Anthony Duchesne
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Thomas Hammond
- School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Pascal Spiegler
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Gregor Jansen
- School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Clemence Levet
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - François Charron
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal, Québec, Canada
| | - Lisa Marie Munter
- Department of Pharmacology and Therapeutics, McGill University, Bellini Life Sciences, Complex, Montreal, Quebec, Canada; School of Biomedical Sciences (SBMS), McGill University, Bellini Life Sciences Complex, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal, Québec, Canada.
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7
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Lange SM, McFarland MR, Lamoliatte F, Carroll T, Krshnan L, Pérez-Ràfols A, Kwasna D, Shen L, Wallace I, Cole I, Armstrong LA, Knebel A, Johnson C, De Cesare V, Kulathu Y. VCP/p97-associated proteins are binders and debranching enzymes of K48-K63-branched ubiquitin chains. Nat Struct Mol Biol 2024:10.1038/s41594-024-01354-y. [PMID: 38977901 DOI: 10.1038/s41594-024-01354-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/13/2024] [Indexed: 07/10/2024]
Abstract
Branched ubiquitin (Ub) chains constitute a sizable fraction of Ub polymers in human cells. Despite their abundance, our understanding of branched Ub function in cell signaling has been stunted by the absence of accessible methods and tools. Here we identify cellular branched-chain-specific binding proteins and devise approaches to probe K48-K63-branched Ub function. We establish a method to monitor cleavage of linkages within complex Ub chains and unveil ATXN3 and MINDY as debranching enzymes. We engineer a K48-K63 branch-specific nanobody and reveal the molecular basis of its specificity in crystal structures of nanobody-branched Ub chain complexes. Using this nanobody, we detect increased K48-K63-Ub branching following valosin-containing protein (VCP)/p97 inhibition and after DNA damage. Together with our discovery that multiple VCP/p97-associated proteins bind to or debranch K48-K63-linked Ub, these results suggest a function for K48-K63-branched chains in VCP/p97-related processes.
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Affiliation(s)
- Sven M Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Matthew R McFarland
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Thomas Carroll
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Logesvaran Krshnan
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Anna Pérez-Ràfols
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Dominika Kwasna
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Linnan Shen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Iona Wallace
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Isobel Cole
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Lee A Armstrong
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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8
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Zhang Y, Huang X, Zhang L, Gao W, Ma J, Chen T, Yang D. Genome-wide identification, gene expression and haplotype analysis of the rhomboid-like gene family in wheat (Triticum aestivum L.). THE PLANT GENOME 2024; 17:e20435. [PMID: 38348504 DOI: 10.1002/tpg2.20435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/08/2024] [Accepted: 01/23/2024] [Indexed: 07/02/2024]
Abstract
The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through various approaches, including gene structure analysis, evolutionary relationship analysis, promoter cis-acting element analysis, expression pattern analysis, and haplotype analysis. The 41 TaRBL genes were identified and divided into five subfamilies in the wheat genome. RBL family genes were expanded through segmented duplication and purification selection. The cis-element analysis revealed their involvement in various stress responses and plant development. The results of RNA-seq and quantitative real-time-PCR showed that TaRBL genes displayed higher expression levels in developing spike/grain and were differentially regulated under polyethylene glycol, NaCl, and abscisic acid treatments, indicating their roles in grain development and abiotic stress response. A kompetitive allele-specific PCR molecular marker was developed to confirm the single nucleotide polymorphism of TaRBL14a gene in 263 wheat accessions. We found that the elite haplotype TaRBL14a-Hap2 showed a significantly higher 1000-grain weight than TaRBL14a-Hap11 in at least three environments, and the TaRBL14a-Hap2 was positively selected in wheat breeding. The findings will provide a good insight into the evolutionary and functional characteristics of the TaRBL genes family in wheat and lay the foundation for future exploration of the regulatory mechanisms of TaRBL genes in plant growth and development, as well as their response to abiotic stresses.
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Affiliation(s)
- Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoya Huang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Long Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weidong Gao
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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9
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Kandel R, Jung J, Neal S. Proteotoxic stress and the ubiquitin proteasome system. Semin Cell Dev Biol 2024; 156:107-120. [PMID: 37734998 PMCID: PMC10807858 DOI: 10.1016/j.semcdb.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
The ubiquitin proteasome system maintains protein homeostasis by regulating the breakdown of misfolded proteins, thereby preventing misfolded protein aggregates. The efficient elimination is vital for preventing damage to the cell by misfolded proteins, known as proteotoxic stress. Proteotoxic stress can lead to the collapse of protein homeostasis and can alter the function of the ubiquitin proteasome system. Conversely, impairment of the ubiquitin proteasome system can also cause proteotoxic stress and disrupt protein homeostasis. This review examines two impacts of proteotoxic stress, 1) disruptions to ubiquitin homeostasis (ubiquitin stress) and 2) disruptions to proteasome homeostasis (proteasome stress). Here, we provide a mechanistic description of the relationship between proteotoxic stress and the ubiquitin proteasome system. This relationship is illustrated by findings from several protein misfolding diseases, mainly neurodegenerative diseases, as well as from basic biology discoveries from yeast to mammals. In addition, we explore the importance of the ubiquitin proteasome system in endoplasmic reticulum quality control, and how proteotoxic stress at this organelle is alleviated. Finally, we highlight how cells utilize the ubiquitin proteasome system to adapt to proteotoxic stress and how the ubiquitin proteasome system can be genetically and pharmacologically manipulated to maintain protein homeostasis.
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Affiliation(s)
- Rachel Kandel
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Jasmine Jung
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Sonya Neal
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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10
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Knopf JD, Steigleder SS, Korn F, Kühnle N, Badenes M, Tauber M, Theobald SJ, Rybniker J, Adrain C, Lemberg MK. RHBDL4-triggered downregulation of COPII adaptor protein TMED7 suppresses TLR4-mediated inflammatory signaling. Nat Commun 2024; 15:1528. [PMID: 38453906 PMCID: PMC10920636 DOI: 10.1038/s41467-024-45615-2] [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: 02/09/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024] Open
Abstract
The toll-like receptor 4 (TLR4) is a central regulator of innate immunity that primarily recognizes bacterial lipopolysaccharide cell wall constituents to trigger cytokine secretion. We identify the intramembrane protease RHBDL4 as a negative regulator of TLR4 signaling. We show that RHBDL4 triggers degradation of TLR4's trafficking factor TMED7. This counteracts TLR4 transport to the cell surface. Notably, TLR4 activation mediates transcriptional upregulation of RHBDL4 thereby inducing a negative feedback loop to reduce TLR4 trafficking to the plasma membrane. This secretory cargo tuning mechanism prevents the over-activation of TLR4-dependent signaling in an in vitro Mycobacterium tuberculosis macrophage infection model and consequently alleviates septic shock in a mouse model. A hypomorphic RHBDL4 mutation linked to Kawasaki syndrome, an ill-defined inflammatory disorder in children, further supports the pathophysiological relevance of our findings. In this work, we identify an RHBDL4-mediated axis that acts as a rheostat to prevent over-activation of the TLR4 pathway.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Susanne S Steigleder
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Friederike Korn
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Nathalie Kühnle
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Marina Badenes
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- Faculty of Veterinary Medicine, Lusofona University and Faculty of Veterinary Nursing, Polytechnic Institute of Lusofonia, Lisbon, Portugal
| | - Marina Tauber
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931, Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931, Cologne, Germany
| | - Colin Adrain
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany.
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11
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Yamamoto S, Kiyatake N, Kaneko A, Shimamura M, Yoshida T, Shimizu S. Mouse transient receptor potential melastatin 2 (TRPM2) isoform 7 attenuates full-length mouse TRPM2 activity through reductions in its expression by targeting it to ER-associated degradation. Genes Cells 2024; 29:254-269. [PMID: 38247314 DOI: 10.1111/gtc.13097] [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: 04/05/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Transient receptor potential melastatin 2 (TRPM2) assembles into tetramers to function as an oxidative stress-sensitive Ca2+ channel at the surface membrane. Limited information is currently available on the 10 protein isoforms of mouse TRPM2 (mTRPM2) identified. This study investigated whether these isoforms function as Ca2+ channels and examined their effects on full-length mTRPM2 activity using the HEK 293 cell exogenous expression system. Only full-length mTRPM2, isoform 1 localized to the surface membrane and was activated by oxidative stress. Isoform 7 was clearly recognized by protein quality control systems and degraded by endoplasmic reticulum-associated degradation after transmembrane proteolysis. In the co-expression system, the activation and expression of full-length mTRPM2 were attenuated by its co-expression with isoform 7, but not with the other isoforms. This decrease in the expression of full-length mTRPM2 was recovered by the proteasomal inhibitor. The present results suggest that isoforms other than isoform 1 did not function as oxidative stress-sensitive channels and also that only isoform 7 attenuated the activation of full-length mTRPM2 by targeting it to endoplasmic reticulum-associated degradation. The present study will provide important information on the functional nature of mTRPM2 isoforms for the elucidation of their roles in physiological and patho-physiological responses in vivo using mouse models.
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Affiliation(s)
| | - Naoto Kiyatake
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
| | - Akihiro Kaneko
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
| | - Masanao Shimamura
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
| | - Takashi Yoshida
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
| | - Shunichi Shimizu
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
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12
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Dulloo I, Tellier M, Levet C, Chikh A, Zhang B, Blaydon DC, Webb CM, Kelsell DP, Freeman M. Cleavage of the pseudoprotease iRhom2 by the signal peptidase complex reveals an ER-to-nucleus signaling pathway. Mol Cell 2024; 84:277-292.e9. [PMID: 38183983 DOI: 10.1016/j.molcel.2023.12.012] [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: 11/29/2022] [Revised: 09/18/2023] [Accepted: 12/08/2023] [Indexed: 01/08/2024]
Abstract
iRhoms are pseudoprotease members of the rhomboid-like superfamily and are cardinal regulators of inflammatory and growth factor signaling; they function primarily by recognizing transmembrane domains of their clients. Here, we report a mechanistically distinct nuclear function of iRhoms, showing that both human and mouse iRhom2 are non-canonical substrates of signal peptidase complex (SPC), the protease that removes signal peptides from secreted proteins. Cleavage of iRhom2 generates an N-terminal fragment that enters the nucleus and modifies the transcriptome, in part by binding C-terminal binding proteins (CtBPs). The biological significance of nuclear iRhom2 is indicated by elevated levels in skin biopsies of patients with psoriasis, tylosis with oesophageal cancer (TOC), and non-epidermolytic palmoplantar keratoderma (NEPPK); increased iRhom2 cleavage in a keratinocyte model of psoriasis; and nuclear iRhom2 promoting proliferation of keratinocytes. Overall, this work identifies an unexpected SPC-dependent ER-to-nucleus signaling pathway and demonstrates that iRhoms can mediate nuclear signaling.
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Affiliation(s)
- Iqbal Dulloo
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Michael Tellier
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Clémence Levet
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Anissa Chikh
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Boyan Zhang
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Diana C Blaydon
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Catherine M Webb
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - David P Kelsell
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Matthew Freeman
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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13
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Daskivich GJ, Brodsky JL. The generation of detergent-insoluble clipped fragments from an ERAD substrate in mammalian cells. Sci Rep 2023; 13:21508. [PMID: 38057493 PMCID: PMC10700608 DOI: 10.1038/s41598-023-48769-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Proteostasis ensures the proper synthesis, folding, and trafficking of proteins and is required for cellular and organellar homeostasis. This network also oversees protein quality control within the cell and prevents accumulation of aberrant proteins, which can lead to cellular dysfunction and disease. For example, protein aggregates irreversibly disrupt proteostasis and can exert gain-of-function toxic effects. Although this process has been examined in detail for cytosolic proteins, how endoplasmic reticulum (ER)-tethered, aggregation-prone proteins are handled is ill-defined. To determine how a membrane protein with a cytoplasmic aggregation-prone domain is routed for ER-associated degradation (ERAD), we analyzed a new model substrate, TM-Ubc9ts. In yeast, we previously showed that TM-Ubc9ts ERAD requires Hsp104, which is absent in higher cells. In transient and stable HEK293 cells, we now report that TM-Ubc9ts degradation is largely proteasome-dependent, especially at elevated temperatures. In contrast to yeast, clipped TM-Ubc9ts polypeptides, which are stabilized upon proteasome inhibition, accumulate and are insoluble at elevated temperatures. TM-Ubc9ts cleavage is independent of the intramembrane protease RHBDL4, which clips other classes of ERAD substrates. These studies highlight an unappreciated mechanism underlying the degradation of aggregation-prone substrates in the ER and invite further work on other proteases that contribute to ERAD.
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Affiliation(s)
- Grant J Daskivich
- A320 Langley Hall, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jeffrey L Brodsky
- A320 Langley Hall, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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14
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Meng Z, Rodriguez Ehrenfried A, Tan CL, Steffens LK, Kehm H, Zens S, Lauenstein C, Paul A, Schwab M, Förster JD, Salek M, Riemer AB, Wu H, Eckert C, Leonhardt CS, Strobel O, Volkmar M, Poschke I, Offringa R. Transcriptome-based identification of tumor-reactive and bystander CD8 + T cell receptor clonotypes in human pancreatic cancer. Sci Transl Med 2023; 15:eadh9562. [PMID: 37967201 DOI: 10.1126/scitranslmed.adh9562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is generally refractory to immune checkpoint blockade, although patients with genetically unstable tumors can show modest therapeutic benefit. We previously demonstrated the presence of tumor-reactive CD8+ T cells in PDAC samples. Here, we charted the tumor-infiltrating T cell repertoire in PDAC by combining single-cell transcriptomics with functional testing of T cell receptors (TCRs) for reactivity against autologous tumor cells. On the basis of a comprehensive dataset including 93 tumor-reactive and 65 bystander TCR clonotypes, we delineated a gene signature that effectively distinguishes between these T cell subsets in PDAC, as well as in other tumor indications. This revealed a high frequency of tumor-reactive TCR clonotypes in three genetically unstable samples. In contrast, the T cell repertoire in six genetically stable PDAC tumors was largely dominated by bystander T cells. Nevertheless, multiple tumor-reactive TCRs were successfully identified in each of these samples, thereby providing a perspective for personalized immunotherapy in this treatment-resistant indication.
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Affiliation(s)
- Zibo Meng
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
| | - Aaron Rodriguez Ehrenfried
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Helmholtz-Institute for Translational Oncology by DKFZ (HI-TRON), 55131 Mainz, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Chin Leng Tan
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Laura K Steffens
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Hannes Kehm
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Zens
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Claudia Lauenstein
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Alina Paul
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Marius Schwab
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Jonas D Förster
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
- Division of Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, 69120 Heidelberg, Germany
| | - Mogjiborahman Salek
- Division of Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, 69120 Heidelberg, Germany
| | - Angelika B Riemer
- Division of Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, 69120 Heidelberg, Germany
| | - Heshui Wu
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
| | - Christoph Eckert
- Pathology Institute, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Carl-Stephan Leonhardt
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael Volkmar
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Helmholtz-Institute for Translational Oncology by DKFZ (HI-TRON), 55131 Mainz, Germany
| | - Isabel Poschke
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, 69120 Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Rienk Offringa
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, 69120 Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
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15
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Han SI, Nakakuki M, Nakagawa Y, Wang Y, Araki M, Yamamoto Y, Tokiwa H, Takeda H, Mizunoe Y, Motomura K, Ohno H, Kainoh K, Murayama Y, Aita Y, Takeuchi Y, Osaki Y, Miyamoto T, Sekiya M, Matsuzaka T, Yahagi N, Sone H, Daitoku H, Sato R, Kawano H, Shimano H. Rhomboid protease RHBDL4/RHBDD1 cleaves SREBP-1c at endoplasmic reticulum monitoring and regulating fatty acids. PNAS NEXUS 2023; 2:pgad351. [PMID: 37954160 PMCID: PMC10637267 DOI: 10.1093/pnasnexus/pgad351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023]
Abstract
The endoplasmic reticulum (ER)-embedded transcription factors, sterol regulatory element-binding proteins (SREBPs), master regulators of lipid biosynthesis, are transported to the Golgi for proteolytic activation to tune cellular cholesterol levels and regulate lipogenesis. However, mechanisms by which the cell responds to the levels of saturated or unsaturated fatty acids remain underexplored. Here, we show that RHBDL4/RHBDD1, a rhomboid family protease, directly cleaves SREBP-1c at the ER. The p97/VCP, AAA-ATPase complex then acts as an auxiliary segregase to extract the remaining ER-embedded fragment of SREBP-1c. Importantly, the enzymatic activity of RHBDL4 is enhanced by saturated fatty acids (SFAs) but inhibited by polyunsaturated fatty acids (PUFAs). Genetic deletion of RHBDL4 in mice fed on a Western diet enriched in SFAs and cholesterol prevented SREBP-1c from inducing genes for lipogenesis, particularly for synthesis and incorporation of PUFAs, and secretion of lipoproteins. The RHBDL4-SREBP-1c pathway reveals a regulatory system for monitoring fatty acid composition and maintaining cellular lipid homeostasis.
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Affiliation(s)
- Song-Iee Han
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Masanori Nakakuki
- Pharmaceutical Research Center, Mochida Pharmaceutical Co., Ltd., Gotemba, Shizuoka 412-8524, Japan
| | - Yoshimi Nakagawa
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Division of Complex Biosystem Research, Department of Research and Development, Institute of Natural Medicine, University of Toyama, Toyama, Toyama 930-0194, Japan
| | - Yunong Wang
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Masaya Araki
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Hiroaki Tokiwa
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, Daigaku-Nishi, Gifu 501-1196, Japan
| | - Hiroyuki Takeda
- Division of Proteo Drug Discovery Sciences, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Yuhei Mizunoe
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kaori Motomura
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroshi Ohno
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenta Kainoh
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuki Murayama
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuichi Aita
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshinori Takeuchi
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshinori Osaki
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Takafumi Miyamoto
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Motohiro Sekiya
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Naoya Yahagi
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hirohito Sone
- Department of Internal Medicine, Faculty of Medicine, Niigata University, Niigata, Niigata 951-8510, Japan
| | - Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryuichiro Sato
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, Nutri-Life Science Laboratory, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hiroyuki Kawano
- Pharmaceutical Research Center, Mochida Pharmaceutical Co., Ltd., Gotemba, Shizuoka 412-8524, Japan
| | - Hitoshi Shimano
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-0004, Japan
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16
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Christianson JC, Jarosch E, Sommer T. Mechanisms of substrate processing during ER-associated protein degradation. Nat Rev Mol Cell Biol 2023; 24:777-796. [PMID: 37528230 DOI: 10.1038/s41580-023-00633-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 08/03/2023]
Abstract
Maintaining proteome integrity is essential for long-term viability of all organisms and is overseen by intrinsic quality control mechanisms. The secretory pathway of eukaryotes poses a challenge for such quality assurance as proteins destined for secretion enter the endoplasmic reticulum (ER) and become spatially segregated from the cytosolic machinery responsible for disposal of aberrant (misfolded or otherwise damaged) or superfluous polypeptides. The elegant solution provided by evolution is ER-membrane-bound ubiquitylation machinery that recognizes misfolded or surplus proteins or by-products of protein biosynthesis in the ER and delivers them to 26S proteasomes for degradation. ER-associated protein degradation (ERAD) collectively describes this specialized arm of protein quality control via the ubiquitin-proteasome system. But, instead of providing a single strategy to remove defective or unwanted proteins, ERAD represents a collection of independent processes that exhibit distinct yet overlapping selectivity for a wide range of substrates. Not surprisingly, ER-membrane-embedded ubiquitin ligases (ER-E3s) act as central hubs for each of these separate ERAD disposal routes. In these processes, ER-E3s cooperate with a plethora of specialized factors, coordinating recognition, transport and ubiquitylation of undesirable secretory, membrane and cytoplasmic proteins. In this Review, we focus on substrate processing during ERAD, highlighting common threads as well as differences between the many routes via ERAD.
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Affiliation(s)
- John C Christianson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
| | - Ernst Jarosch
- Max-Delbrück-Centrer for Molecular Medicine in Helmholtz Association, Berlin-Buch, Germany
| | - Thomas Sommer
- Max-Delbrück-Centrer for Molecular Medicine in Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt Universität zu Berlin, Berlin, Germany.
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17
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Hsiao JM, Penalva YCM, Wu HYL, Xiao B, Jansen G, Dejgaard K, Young JC, Munter LM. Putative Protein Interactome of the Rhomboid Protease RHBDL4. Biochemistry 2023; 62:1209-1218. [PMID: 36857408 DOI: 10.1021/acs.biochem.2c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The physiological functions of the rhomboid-related protein 4 (RHBDL4) are emerging, but their molecular details remain unclear. Because increased expression of RHBDL4 has been clinically linked to poorer outcomes in cancer patients, this association urgently demands a better understanding of RHBDL4. To elucidate the molecular interactions and pathways that RHBDL4 may be involved in, we conducted proximity-dependent biotin identification (BioID) assays. Our analyses corroborated several of the expected protein interactors such as the transitional endoplasmic reticulum (ER) ATPase VCP/p97 (TERA), but they also described novel putative interactors including IRS4, PGAM5, and GORS2. Using proximity-ligation assays, we validated VCP/p97, COPB, and VRK2 as proteins that are in proximity to RHBDL4. Overall, our results support the emerging functions of RHBDL4 in ER quality control and also point toward putative RHBDL4 functions in protein membrane insertion and membrane organization and trafficking.
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Affiliation(s)
| | - Ylauna Christine Mégane Penalva
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 2B4, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Helen Yee-Li Wu
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Bin Xiao
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Gregor Jansen
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Kurt Dejgaard
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Jason C Young
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
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18
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Bhaduri S, Scott NA, Neal SE. The Role of the Rhomboid Superfamily in ER Protein Quality Control: From Mechanisms and Functions to Diseases. Cold Spring Harb Perspect Biol 2023; 15:a041248. [PMID: 35940905 PMCID: PMC9899648 DOI: 10.1101/cshperspect.a041248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The endoplasmic reticulum (ER) is an essential organelle in eukaryotic cells and is a major site for protein folding, modification, and lipid synthesis. Perturbations within the ER, such as protein misfolding and high demand for protein folding, lead to dysregulation of the ER protein quality control network and ER stress. Recently, the rhomboid superfamily has emerged as a critical player in ER protein quality control because it has diverse cellular functions, including ER-associated degradation (ERAD), endosome Golgi-associated degradation (EGAD), and ER preemptive quality control (ERpQC). This breadth of function both illustrates the importance of the rhomboid superfamily in health and diseases and emphasizes the necessity of understanding their mechanisms of action. Because dysregulation of rhomboid proteins has been implicated in various diseases, such as neurological disorders and cancers, they represent promising potential therapeutic drug targets. This review provides a comprehensive account of the various roles of rhomboid proteins in the context of ER protein quality control and discusses their significance in health and disease.
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Affiliation(s)
- Satarupa Bhaduri
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Nicola A Scott
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Sonya E Neal
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
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19
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Kandel R, Jung J, Syau D, Kuo T, Songster L, Horn C, Chapman C, Aguayo A, Duttke S, Benner C, Neal SE. Yeast derlin Dfm1 employs a chaperone-like function to resolve misfolded membrane protein stress. PLoS Biol 2023; 21:e3001950. [PMID: 36689475 PMCID: PMC9894555 DOI: 10.1371/journal.pbio.3001950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/02/2023] [Accepted: 12/07/2022] [Indexed: 01/24/2023] Open
Abstract
Protein aggregates are a common feature of diseased and aged cells. Membrane proteins comprise a quarter of the proteome, and yet, it is not well understood how aggregation of membrane proteins is regulated and what effects these aggregates can have on cellular health. We have determined in yeast that the derlin Dfm1 has a chaperone-like activity that influences misfolded membrane protein aggregation. We establish that this function of Dfm1 does not require recruitment of the ATPase Cdc48 and it is distinct from Dfm1's previously identified function in dislocating misfolded membrane proteins from the endoplasmic reticulum (ER) to the cytosol for degradation. Additionally, we assess the cellular impacts of misfolded membrane proteins in the absence of Dfm1 and determine that misfolded membrane proteins are toxic to cells in the absence of Dfm1 and cause disruptions to proteasomal and ubiquitin homeostasis.
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Affiliation(s)
- Rachel Kandel
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Jasmine Jung
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Della Syau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Tiffany Kuo
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Livia Songster
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Casey Horn
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Claire Chapman
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Analine Aguayo
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Sascha Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Christopher Benner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Sonya E. Neal
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
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20
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Bloemeke N, Meighen‐Berger K, Hitzenberger M, Bach NC, Parr M, Coelho JPL, Frishman D, Zacharias M, Sieber SA, Feige MJ. Intramembrane client recognition potentiates the chaperone functions of calnexin. EMBO J 2022; 41:e110959. [PMID: 36314723 PMCID: PMC9753464 DOI: 10.15252/embj.2022110959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
One-third of the human proteome is comprised of membrane proteins, which are particularly vulnerable to misfolding and often require folding assistance by molecular chaperones. Calnexin (CNX), which engages client proteins via its sugar-binding lectin domain, is one of the most abundant ER chaperones, and plays an important role in membrane protein biogenesis. Based on mass spectrometric analyses, we here show that calnexin interacts with a large number of nonglycosylated membrane proteins, indicative of additional nonlectin binding modes. We find that calnexin preferentially bind misfolded membrane proteins and that it uses its single transmembrane domain (TMD) for client recognition. Combining experimental and computational approaches, we systematically dissect signatures for intramembrane client recognition by calnexin, and identify sequence motifs within the calnexin TMD region that mediate client binding. Building on this, we show that intramembrane client binding potentiates the chaperone functions of calnexin. Together, these data reveal a widespread role of calnexin client recognition in the lipid bilayer, which synergizes with its established lectin-based substrate binding. Molecular chaperones thus can combine different interaction modes to support the biogenesis of the diverse eukaryotic membrane proteome.
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Affiliation(s)
- Nicolas Bloemeke
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Kevin Meighen‐Berger
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Manuel Hitzenberger
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Nina C Bach
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Marina Parr
- Department of Bioinformatics, TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Joao PL Coelho
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Dmitrij Frishman
- Department of Bioinformatics, TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Martin Zacharias
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Stephan A Sieber
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Matthias J Feige
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
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21
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Rhomboid protease RHBDL4 promotes retrotranslocation of aggregation-prone proteins for degradation. Cell Rep 2022; 40:111175. [PMID: 35947953 PMCID: PMC9437926 DOI: 10.1016/j.celrep.2022.111175] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/02/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
Protein degradation is fundamentally important to ensure cell homeostasis. In the endoplasmic reticulum (ER), the ER-associated degradation (ERAD) pathway targets incorrectly folded and unassembled proteins for turnover by the cytoplasmic proteasome. Previously, we showed that the rhomboid protease RHBDL4, together with p97, mediates membrane protein degradation. However, whether RHBDL4 acts in concert with additional ERAD components is unclear, and its full substrate spectrum remains to be defined. Here, we show that, in addition to membrane proteins, RHBDL4 cleaves aggregation-prone luminal ERAD substrates. Since mutations of the RHBDL4 rhomboid domain led to stabilization of substrates at the cytoplasmic side, we hypothesize that, analogous to the homolog ERAD factor derlin, RHBDL4 is directly involved in substrate retrotranslocation. RHBDL4's interaction with the erlin ERAD complex and reciprocal interaction of rhomboid substrates with erlins suggest that RHBDL4 and erlins form a complex that clips substrates and thereby rescues aggregation-prone peptides in the ER from aggregation.
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22
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Vasconcelos-Cardoso M, Batista-Almeida D, Rios-Barros LV, Castro-Gomes T, Girao H. Cellular and molecular mechanisms underlying plasma membrane functionality and integrity. J Cell Sci 2022; 135:275922. [PMID: 35801807 DOI: 10.1242/jcs.259806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plasma membrane not only protects the cell from the extracellular environment, acting as a selective barrier, but also regulates cellular events that originate at the cell surface, playing a key role in various biological processes that are essential for the preservation of cell homeostasis. Therefore, elucidation of the mechanisms involved in the maintenance of plasma membrane integrity and functionality is of utmost importance. Cells have developed mechanisms to ensure the quality of proteins that inhabit the cell surface, as well as strategies to cope with injuries inflicted to the plasma membrane. Defects in these mechanisms can lead to the development or onset of several diseases. Despite the importance of these processes, a comprehensive and holistic perspective of plasma membrane quality control is still lacking. To tackle this gap, in this Review, we provide a thorough overview of the mechanisms underlying the identification and targeting of membrane proteins that are to be removed from the cell surface, as well as the membrane repair mechanisms triggered in both physiological and pathological conditions. A better understanding of the mechanisms underlying protein quality control at the plasma membrane can reveal promising and unanticipated targets for the development of innovative therapeutic approaches.
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Affiliation(s)
- Maria Vasconcelos-Cardoso
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Daniela Batista-Almeida
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Laura Valeria Rios-Barros
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Thiago Castro-Gomes
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Henrique Girao
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
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23
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De Backer J, Van Breusegem F, De Clercq I. Proteolytic Activation of Plant Membrane-Bound Transcription Factors. FRONTIERS IN PLANT SCIENCE 2022; 13:927746. [PMID: 35774815 PMCID: PMC9237531 DOI: 10.3389/fpls.2022.927746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/23/2022] [Indexed: 06/03/2023]
Abstract
Due to the presence of a transmembrane domain, the subcellular mobility plan of membrane-bound or membrane-tethered transcription factors (MB-TFs) differs from that of their cytosolic counterparts. The MB-TFs are mostly locked in (sub)cellular membranes, until they are released by a proteolytic cleavage event or when the transmembrane domain (TMD) is omitted from the transcript due to alternative splicing. Here, we review the current knowledge on the proteolytic activation mechanisms of MB-TFs in plants, with a particular focus on regulated intramembrane proteolysis (RIP), and discuss the analogy with the proteolytic cleavage of MB-TFs in animal systems. We present a comprehensive inventory of all known and predicted MB-TFs in the model plant Arabidopsis thaliana and examine their experimentally determined or anticipated subcellular localizations and membrane topologies. We predict proteolytically activated MB-TFs by the mapping of protease recognition sequences and structural features that facilitate RIP in and around the TMD, based on data from metazoan intramembrane proteases. Finally, the MB-TF functions in plant responses to environmental stresses and in plant development are considered and novel functions for still uncharacterized MB-TFs are forecasted by means of a regulatory network-based approach.
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Affiliation(s)
- Jonas De Backer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Inge De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
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24
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Lastun VL, Levet C, Freeman M. The mammalian rhomboid protein RHBDL4 protects against endoplasmic reticulum stress by regulating the morphology and distribution of ER sheets. J Biol Chem 2022; 298:101935. [PMID: 35436469 PMCID: PMC9136127 DOI: 10.1016/j.jbc.2022.101935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
In metazoans, the architecture of the endoplasmic reticulum (ER) differs between cell types and undergoes major changes throughout the cell cycle and according to physiological needs. Although much is known about how the different ER morphologies are generated and maintained, especially ER tubules, how context-dependent changes in ER shape and distribution are regulated and the factors involved are less well characterized, as are the factors that contribute to the positioning of the ER within the cell. By overexpression and KO experiments, we show that the levels of RHBDL4, an ER-resident rhomboid protease, modulate the shape and distribution of the ER, especially during conditions that require rapid changes in the ER sheet distribution, such as ER stress. We demonstrate that RHBDL4 interacts with cytoskeleton-linking membrane protein 63 (CLIMP-63), a protein involved in ER sheet stabilization, as well as with the cytoskeleton. Furthermore, we found that mice lacking RHBDL4 are sensitive to ER stress and develop liver steatosis, a phenotype associated with unresolved ER stress. Taken together, these data suggest a new physiological role for RHBDL4 and also imply that this function does not require its enzymatic activity.
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25
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Shibuya K, Ebihara K, Ebihara C, Sawayama N, Isoda M, Yamamuro D, Takahashi M, Nagashima S, Ishibashi S. AAA-ATPase valosin-containing protein binds the transcription factor SREBP1 and promotes its proteolytic activation by rhomboid protease RHBDL4. J Biol Chem 2022; 298:101936. [PMID: 35430252 PMCID: PMC9127370 DOI: 10.1016/j.jbc.2022.101936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/24/2022] Open
Abstract
Valosin-containing protein (VCP) is a member of AAA-ATPase superfamily involved in various cellular functions. To investigate the pathophysiological role of VCP in metabolic disorders, we generated knock-in mice bearing an A232E mutation in VCP, a known human VCP pathogenic variant. When heterozygous mutant mice (A232E/+) were fed a high-fat diet, we observed that fatty liver was ameliorated and the proteolytic processing of the transcription factor sterol regulatory element-binding protein 1 (SREBP1) was impaired. Further co-immunoprecipitation analysis in wildtype mice revealed interactions of VCP with SREBP1 and a rhomboid protease, RHBDL4, in the liver, and these interactions were attenuated in A232E/+ mice. Consistent with these results, we show that knockdown or chemical inhibition of VCP or RHBDL4 in human hepatocytes impaired the proteolytic processing of SREBP1. Finally, we found that knockdown of E3 ligases such as glycoprotein 78 and HMG-CoA reductase degradation protein 1 disrupted the interaction of VCP with SREBP1 and impaired the proteolytic processing of SREBP1. These results suggest that VCP recognizes ubiquitinylated SREBP1 and recruits it to RHBDL4 to promote its proteolytic processing. The present study reveals a novel proteolytic processing pathway of SREBP1 and may lead to development of new therapeutic strategies to treat fatty liver diseases.
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Affiliation(s)
- Koji Shibuya
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Ken Ebihara
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan.
| | - Chihiro Ebihara
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Nagisa Sawayama
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Masayo Isoda
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Daisuke Yamamuro
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Manabu Takahashi
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Shuichi Nagashima
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Shun Ishibashi
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
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26
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Rai M, Curley M, Coleman Z, Demontis F. Contribution of proteases to the hallmarks of aging and to age-related neurodegeneration. Aging Cell 2022; 21:e13603. [PMID: 35349763 PMCID: PMC9124314 DOI: 10.1111/acel.13603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/10/2022] [Accepted: 03/13/2022] [Indexed: 12/20/2022] Open
Abstract
Protein quality control ensures the degradation of damaged and misfolded proteins. Derangement of proteostasis is a primary cause of aging and age-associated diseases. The ubiquitin-proteasome and autophagy-lysosome play key roles in proteostasis but, in addition to these systems, the human genome encodes for ~600 proteases, also known as peptidases. Here, we examine the role of proteases in aging and age-related neurodegeneration. Proteases are present across cell compartments, including the extracellular space, and their substrates encompass cellular constituents, proteins with signaling functions, and misfolded proteins. Proteolytic processing by proteases can lead to changes in the activity and localization of substrates or to their degradation. Proteases cooperate with the autophagy-lysosome and ubiquitin-proteasome systems but also have independent proteolytic roles that impact all hallmarks of cellular aging. Specifically, proteases regulate mitochondrial function, DNA damage repair, cellular senescence, nutrient sensing, stem cell properties and regeneration, protein quality control and stress responses, and intercellular signaling. The capacity of proteases to regulate cellular functions translates into important roles in preserving tissue homeostasis during aging. Consequently, proteases influence the onset and progression of age-related pathologies and are important determinants of health span. Specifically, we examine how certain proteases promote the progression of Alzheimer's, Huntington's, and/or Parkinson's disease whereas other proteases protect from neurodegeneration. Mechanistically, cleavage by proteases can lead to the degradation of a pathogenic protein and hence impede disease pathogenesis. Alternatively, proteases can generate substrate byproducts with increased toxicity, which promote disease progression. Altogether, these studies indicate the importance of proteases in aging and age-related neurodegeneration.
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Affiliation(s)
- Mamta Rai
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Michelle Curley
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Zane Coleman
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Fabio Demontis
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
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27
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Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Mechanism-based traps enable protease and hydrolase substrate discovery. Nature 2022; 602:701-707. [PMID: 35173328 PMCID: PMC8866121 DOI: 10.1038/s41586-022-04414-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/07/2022] [Indexed: 12/28/2022]
Abstract
Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.
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Affiliation(s)
- Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Adam T Beattie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Lucie Kafkova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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28
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Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion. Microorganisms 2022; 10:microorganisms10010114. [PMID: 35056563 PMCID: PMC8778405 DOI: 10.3390/microorganisms10010114] [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: 11/17/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023] Open
Abstract
Rhomboids are intramembrane serine proteases highly conserved in the three domains of life. Their key roles in eukaryotes are well understood but their contribution to bacterial physiology is still poorly characterized. Here we demonstrate that Brucella abortus, the etiological agent of the zoonosis called brucellosis, encodes an active rhomboid protease capable of cleaving model heterologous substrates like Drosophila melanogaster Gurken and Providencia stuartii TatA. To address the impact of rhomboid deletion on B. abortus physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. About 50% of the B. abortus predicted proteome was identified by quantitative proteomics under two experimental conditions and 108 differentially represented proteins were detected. Membrane associated proteins that showed variations in concentration in the mutant were considered as potential rhomboid targets. This class included nitric oxide reductase subunit C NorC (Q2YJT6) and periplasmic protein LptC involved in LPS transport to the outer membrane (Q2YP16). Differences in secretory proteins were also addressed. Differentially represented proteins included a putative lytic murein transglycosylase (Q2YIT4), nitrous-oxide reductase NosZ (Q2YJW2) and high oxygen affinity Cbb3-type cytochrome c oxidase subunit (Q2YM85). Deletion of rhomboid had no obvious effect in B. abortus virulence. However, rhomboid overexpression had a negative impact on growth under static conditions, suggesting an effect on denitrification enzymes and/or high oxygen affinity cytochrome c oxidase required for growth in low oxygen tension conditions.
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Conformational surveillance of Orai1 by a rhomboid intramembrane protease prevents inappropriate CRAC channel activation. Mol Cell 2021; 81:4784-4798.e7. [PMID: 34800360 PMCID: PMC8657799 DOI: 10.1016/j.molcel.2021.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/14/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Calcium influx through plasma membrane calcium release-activated calcium (CRAC) channels, which are formed of hexamers of Orai1, is a potent trigger for many important biological processes, most notably in T cell-mediated immunity. Through a bioinformatics-led cell biological screen, we have identified Orai1 as a substrate for the rhomboid intramembrane protease RHBDL2. We show that RHBDL2 prevents stochastic calcium signaling in unstimulated cells through conformational surveillance and cleavage of inappropriately activated Orai1. A conserved disease-linked proline residue is responsible for RHBDL2’s recognizing the active conformation of Orai1, which is required to sharpen switch-like signaling triggered by store-operated calcium entry. Loss of RHBDL2 control of CRAC channel activity causes severe dysregulation of downstream CRAC channel effectors, including transcription factor activation, inflammatory cytokine expression, and T cell activation. We propose that this surveillance function may represent an ancient activity of rhomboid proteases in degrading unwanted signaling proteins. A screen for transmembrane substrates of the rhomboid intramembrane protease RHBDL2 RHBDL2 cleaves the CRAC channel protein Orai1 when it is inappropriately activated Conformational change in these calcium channels is recognized by RHBDL2 An Orai1 mutant that cannot be cleaved by RHBDL2 causes a human disease syndrome
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Wang L, Liu XX, Yang YM, Wang Y, Song YY, Gao S, Li LY, Zhang ZS. RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression. Cancer Cell Int 2021; 21:590. [PMID: 34736454 PMCID: PMC8567583 DOI: 10.1186/s12935-021-02277-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023] Open
Abstract
Background The rhomboids are a family of multi-transmembrane proteins, many of which have been implicated in facilitating tumor progression. Little is yet known, however, about rhomboid-associated biomarkers in cancers. An analysis of such biomarkers could yield important insights into the role of the rhomboids in cancer pathology. Methods In this study, we carried out the univariate Cox regression analysis and compared gene expression patterns of several rhomboid genes in 30 types of cancers by using The Cancer Genome Atlas (TCGA) database and the methods delineated in Gene Expression Profiling Interactive Analysis (GEPIA). We then used datasets GSE47032, GSE126964, GSE68417 and 75 paired pathological specimens to verify the influences of the rhomboid genes in cancer progression. Moreover, we carried out Weighted Gene Correlation Network Analysis (WGCNA) to investigate gene-related functions and we exploited potential correlations between rhomboid genes expression and immune cell infiltration in cancer tissues. Furthermore, we constructed gene-knockdown cancer cell lines to investigate rhomboid gene functions. Results We find that kidney renal clear cell carcinoma (KIRC) disease progression is affected by fluctuations in the expression of a number of the rhomboid family of genes and, more specifically, high levels of RHBDF2 gene expression are a good indicator of poor prognosis of the disease, as patients with high RHBDF2 expression levels exhibit less favorable survival rates compared to those with low RHBDF2 levels. Silencing of the RHBDF2 gene in KIRC cell lines leads to significantly diminished cell proliferation and migration; this is in good agreement with the identification of an enhanced presence of a number of cell growth and migration promoting signaling molecules in KIRC tumors. We found that, although high level of RHBDF2 correlated with increased infiltration of lymphocytes in cancer tissues, artificially overexpressed RHBDF2 led to an inhibition of the activity of the infiltrated immune cells through sustaining PD-L1 protein level. Furthermore, we show that RHBDF2 related cell migration and PD-L1 regulation were potentially mediated by EGFR signaling pathway. Conclusions RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression and may serve as a critical prognostic biomarker for the disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02277-0.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Xiu-Xiu Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Yu-Meng Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Yan Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Yuan-Yuan Song
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Shan Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Lu-Yuan Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
| | - Zhi-Song Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
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Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Rep 2021; 37:109840. [PMID: 34686332 PMCID: PMC8641752 DOI: 10.1016/j.celrep.2021.109840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/19/2021] [Accepted: 09/27/2021] [Indexed: 01/13/2023] Open
Abstract
Nearly one-third of proteins are initially targeted to the endoplasmic reticulum (ER) membrane, where they are correctly folded and then delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) moves these clients from the ER membrane to the cytosol, a process known as retrotranslocation. Our recent work in Saccharomyces cerevisiae reveals a derlin rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated ERAD membrane substrates. In this study, we identify conserved residues of Dfm1 that are critical for retrotranslocation. We find several retrotranslocation-deficient Loop 1 mutants that display impaired binding to membrane substrates. Furthermore, Dfm1 possesses lipid thinning function to facilitate in the removal of ER membrane substrates, and this feature is conserved in its human homolog, Derlin-1, further implicating that derlin-mediated retrotranslocation is a well-conserved process.
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Affiliation(s)
- Anahita Nejatfard
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Wauer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Satarupa Bhaduri
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam Conn
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Saroj Gourkanti
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Narinderbir Singh
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Tiffany Kuo
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Kandel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
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Koch L, Kespohl B, Agthe M, Schumertl T, Düsterhöft S, Lemberg MK, Lokau J, Garbers C. Interleukin-11 (IL-11) receptor cleavage by the rhomboid protease RHBDL2 induces IL-11 trans-signaling. FASEB J 2021; 35:e21380. [PMID: 33566379 DOI: 10.1096/fj.202002087r] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Interleukin-11 (IL-11) is a pleiotropic cytokine with both pro- and anti-inflammatory properties. It activates its target cells via binding to the membrane-bound IL-11 receptor (IL-11R), which then recruits a homodimer of the ubiquitously expressed, signal-transducing receptor gp130. Besides this classic signaling pathway, IL-11 can also bind to soluble forms of the IL-11R (sIL-11R), and IL-11/sIL-11R complexes activate cells via the induction of gp130 homodimerization (trans-signaling). We have previously reported that the metalloprotease ADAM10 cleaves the membrane-bound IL-11R and thereby generates sIL-11R. In this study, we identify the rhomboid intramembrane protease RHBDL2 as a so far unrecognized alternative sheddase that can efficiently trigger IL-11R secretion. We determine the cleavage site used by RHBDL2, which is located in the extracellular part of the receptor in close proximity to the plasma membrane, between Ala-370 and Ser-371. Furthermore, we identify critical amino acid residues within the transmembrane helix that are required for IL-11R proteolysis. We also show that ectopically expressed RHBDL2 is able to cleave the IL-11R within the early secretory pathway and not only at the plasma membrane, indicating that its subcellular localization plays a central role in controlling its activity. Moreover, RHBDL2-derived sIL-11R is biologically active and able to perform IL-11 trans-signaling. Finally, we show that the human mutation IL-11R-A370V does not impede IL-11 classic signaling, but prevents RHBDL2-mediated IL-11R cleavage.
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Affiliation(s)
- Lydia Koch
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Birte Kespohl
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Maria Agthe
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Tim Schumertl
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Stefan Düsterhöft
- Institute of Molecular Pharmacology, RWTH Aachen University, Aachen, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Juliane Lokau
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Christoph Garbers
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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33
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Wolf LM, Lambert AM, Haenlin J, Boutros M. EVI/WLS function is regulated by ubiquitination and linked to ER-associated degradation by ERLIN2. J Cell Sci 2021; 134:271857. [PMID: 34406391 PMCID: PMC8435288 DOI: 10.1242/jcs.257790] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
WNT signalling is important for development in all metazoans and is associated with various human diseases. The ubiquitin–proteasome system (UPS) and regulatory endoplasmic reticulum-associated degradation (ERAD) have been implicated in the production of WNT proteins. Here, we investigated how the WNT secretory factor EVI (also known as WLS) is ubiquitylated, recognised by ERAD components and subsequently removed from the secretory pathway. We performed a focused immunoblot-based RNAi screen for factors that influence EVI/WLS protein stability. We identified the VCP-binding proteins FAF2 and UBXN4 as novel interaction partners of EVI/WLS and showed that ERLIN2 links EVI/WLS to the ubiquitylation machinery. Interestingly, we also found that EVI/WLS is ubiquitylated and degraded in cells irrespective of their level of WNT production. This K11, K48 and K63-linked ubiquitylation is mediated by the E2 ubiquitin-conjugating enzymes UBE2J2, UBE2K and UBE2N, but is independent of the E3 ubiquitin ligases HRD1 (also known as SYVN1) and GP78 (also known as AMFR). Taken together, our study identifies factors that link the UPS to the WNT secretory pathway and provides mechanistic details of the fate of an endogenous substrate of regulatory ERAD in mammalian cells. This article has an associated First Person interview with the first author of the paper. Summary: The WNT secretory factor EVI/WLS is ubiquitylated and linked to ER-associated degradation by multiple proteins, providing insight into the link between WNT signalling and the ubiquitin–proteasome system.
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Affiliation(s)
- Lucie M Wolf
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
| | - Annika M Lambert
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
| | - Julie Haenlin
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
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34
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Lemberg MK, Strisovsky K. Maintenance of organellar protein homeostasis by ER-associated degradation and related mechanisms. Mol Cell 2021; 81:2507-2519. [PMID: 34107306 DOI: 10.1016/j.molcel.2021.05.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/19/2022]
Abstract
Protein homeostasis mechanisms are fundamentally important to match cellular needs and to counteract stress conditions. A fundamental challenge is to understand how defective proteins are recognized and extracted from cellular organelles to be degraded in the cytoplasm. The endoplasmic reticulum (ER)-associated degradation (ERAD) pathway is the best-understood organellar protein quality control system. Here, we review new insights into the mechanism of recognition and retrotranslocation of client proteins in ERAD. In addition to the membrane-integral ERAD E3 ubiquitin ligases, we highlight one protein family that is remarkably often involved in various aspects of membrane protein quality control and protein dislocation: the rhomboid superfamily, which includes derlins and intramembrane serine proteases. Rhomboid-like proteins have been found to control protein homeostasis in the ER, but also in other eukaryotic organelles and in bacteria, pointing toward conserved principles of membrane protein quality control across organelles and evolution.
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Affiliation(s)
- Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany.
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czechia.
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35
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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Kong KYE, Coelho JPL, Feige MJ, Khmelinskii A. Quality control of mislocalized and orphan proteins. Exp Cell Res 2021; 403:112617. [PMID: 33930402 DOI: 10.1016/j.yexcr.2021.112617] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022]
Abstract
A healthy and functional proteome is essential to cell physiology. However, this is constantly being challenged as most steps of protein metabolism are error-prone and changes in the physico-chemical environment can affect protein structure and function, thereby disrupting proteome homeostasis. Among a variety of potential mistakes, proteins can be targeted to incorrect compartments or subunits of protein complexes may fail to assemble properly with their partners, resulting in the formation of mislocalized and orphan proteins, respectively. Quality control systems are in place to handle these aberrant proteins, and to minimize their detrimental impact on cellular functions. Here, we discuss recent findings on quality control mechanisms handling mislocalized and orphan proteins. We highlight common principles involved in their recognition and summarize how accumulation of these aberrant molecules is associated with aging and disease.
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Affiliation(s)
| | - João P L Coelho
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Matthias J Feige
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
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37
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Van Kersavond T, Konopatzki R, van der Plassche MAT, Yang J, Verhelst SHL. Rapid synthesis of internal peptidyl α-ketoamides by on resin oxidation for the construction of rhomboid protease inhibitors. RSC Adv 2021; 11:4196-4199. [PMID: 35424368 PMCID: PMC8694341 DOI: 10.1039/d0ra10614c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/01/2021] [Accepted: 01/08/2021] [Indexed: 11/21/2022] Open
Abstract
Rhomboid proteases are intramembrane serine proteases, which are involved in a wide variety of biological processes and have been implied in various human diseases. Recently, peptidyl α-ketoamides have been reported as rhomboid inhibitors with high potency and selectivity – owing to their interaction with both the primed and non-primed site of the target protease. However, their synthesis has been performed by solution phase chemistry. Here, we report a solid phase strategy towards ketoamides as rhomboid protease inhibitors, allowing rapid synthesis and optimization. We found that the primed site binding part of inhibitors is crucial for potency. Rhomboid intramembrane serine proteases are involved in various biological processes. A solid phase synthesis of internal α-ketoamides reported here shows that primed site elements are crucial for rhomboid protease inhibition.![]()
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Affiliation(s)
| | | | | | - Jian Yang
- KU Leuven
- Department of Cellular and Molecular Medicine
- Laboratory of Chemical Biology
- 3000 Leuven
- Belgium
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS
- 44227 Dortmund
- Germany
- KU Leuven
- Department of Cellular and Molecular Medicine
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38
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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: 42] [Impact Index Per Article: 10.5] [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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39
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Adrain C, Cavadas M. The complex life of rhomboid pseudoproteases. FEBS J 2020; 287:4261-4283. [DOI: 10.1111/febs.15548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Colin Adrain
- Instituto Gulbenkian de Ciência (IGC) Oeiras Portugal
- Centre for Cancer Research and Cell Biology Queen's University Belfast UK
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40
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Kandel RR, Neal SE. The role of rhomboid superfamily members in protein homeostasis: Mechanistic insight and physiological implications. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118793. [PMID: 32645330 PMCID: PMC7434706 DOI: 10.1016/j.bbamcr.2020.118793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/30/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
Cells are equipped with protein quality control pathways in order to maintain a healthy proteome; a process known as protein homeostasis. Dysfunction in protein homeostasis leads to the development of many diseases that are associated with proteinopathies. Recently, the rhomboid superfamily has attracted much attention concerning their involvement in protein homeostasis. While their functional role has become much clearer in the last few years, their systemic significance in mammals remains elusive. Here we delineate the current knowledge of rhomboids in protein quality control and how these functions are integrated at the organismal level.
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Affiliation(s)
- Rachel R Kandel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States of America.
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Oommen D, Kizhakkedath P, Jawabri AA, Varghese DS, Ali BR. Proteostasis Regulation in the Endoplasmic Reticulum: An Emerging Theme in the Molecular Pathology and Therapeutic Management of Familial Hypercholesterolemia. Front Genet 2020; 11:570355. [PMID: 33173538 PMCID: PMC7538668 DOI: 10.3389/fgene.2020.570355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/31/2020] [Indexed: 02/05/2023] Open
Abstract
Familial hypercholesterolemia (FH) is an autosomal genetic disease characterized by high serum low-density lipoprotein (LDL) content leading to premature coronary artery disease. The main genetic and molecular causes of FH are mutations in low-density lipoprotein receptor gene (LDLR) resulting in the non-clearance of LDL from the blood by hepatocytes and consequently the formation of plaques. LDLR is synthesized and glycosylated in the endoplasmic reticulum (ER) and then transported to the plasma membrane via Golgi. It is estimated that more than 50% of reported FH-causing mutations in LDLR result in misfolded proteins that are transport-defective and hence retained in ER. ER accumulation of misfolded proteins causes ER-stress and activates unfolded protein response (UPR). UPR aids protein folding, blocks further protein synthesis, and eliminates misfolded proteins via ER-associated degradation (ERAD) to alleviate ER stress. Various studies demonstrated that ER-retained LDLR mutants are subjected to ERAD. Interestingly, chemical chaperones and genetic or pharmacological inhibition of ERAD have been reported to rescue the transport defective mutant LDLR alleles from ERAD and restore their ER-Golgi transport resulting in the expression of functional plasma membrane LDLR. This suggests the possibility of pharmacological modulation of proteostasis in the ER as a therapeutic strategy for FH. In this review, we picture a detailed analysis of UPR and the ERAD processes activated by ER-retained LDLR mutants associated with FH. In addition, we discuss and critically evaluate the potential role of chemical chaperones and ERAD modulators in the therapeutic management of FH.
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Affiliation(s)
- Deepu Oommen
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Praseetha Kizhakkedath
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Aseel A Jawabri
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center for Health Sciences, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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42
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Lysyk L, Brassard R, Touret N, Lemieux MJ. PARL Protease: A Glimpse at Intramembrane Proteolysis in the Inner Mitochondrial Membrane. J Mol Biol 2020; 432:5052-5062. [DOI: 10.1016/j.jmb.2020.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 01/07/2023]
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43
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Tang D, Sandoval W, Lam C, Haley B, Liu P, Xue D, Roy D, Patapoff T, Louie S, Snedecor B, Misaghi S. UBR E3 ligases and the PDIA3 protease control degradation of unfolded antibody heavy chain by ERAD. J Cell Biol 2020; 219:151862. [PMID: 32558906 PMCID: PMC7337499 DOI: 10.1083/jcb.201908087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 12/01/2022] Open
Abstract
Accumulation of unfolded antibody chains in the ER triggers ER stress that may lead to reduced productivity in therapeutic antibody manufacturing processes. We identified UBR4 and UBR5 as ubiquitin E3 ligases involved in HC ER-associated degradation. Knockdown of UBR4 and UBR5 resulted in intracellular accumulation, enhanced secretion, and reduced ubiquitination of HC. In concert with these E3 ligases, PDIA3 was shown to cleave ubiquitinated HC molecules to accelerate HC dislocation. Interestingly, UBR5, and to a lesser degree UBR4, were down-regulated as cellular demand for antibody expression increased in CHO cells during the production phase, or in plasma B cells. Reducing UBR4/UBR5 expression before the production phase increased antibody productivity in CHO cells, possibly by redirecting antibody molecules from degradation to secretion. Altogether we have characterized a novel proteolysis/proteasome-dependent pathway involved in degradation of unfolded antibody HC. Proteins characterized in this pathway may be novel targets for CHO cell engineering.
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Affiliation(s)
- Danming Tang
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Cynthia Lam
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA
| | - Peter Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Di Xue
- Department of Research Biology, Genentech Inc., South San Francisco, CA
| | - Deepankar Roy
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Tom Patapoff
- Department of Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA
| | - Salina Louie
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Brad Snedecor
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
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Fenech EJ, Lari F, Charles PD, Fischer R, Laétitia-Thézénas M, Bagola K, Paton AW, Paton JC, Gyrd-Hansen M, Kessler BM, Christianson JC. Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling. eLife 2020; 9:e57306. [PMID: 32614325 PMCID: PMC7332293 DOI: 10.7554/elife.57306] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/11/2020] [Indexed: 12/25/2022] Open
Abstract
Ubiquitin ligases (E3s) embedded in the endoplasmic reticulum (ER) membrane regulate essential cellular activities including protein quality control, calcium flux, and sterol homeostasis. At least 25 different, transmembrane domain (TMD)-containing E3s are predicted to be ER-localised, but for most their organisation and cellular roles remain poorly defined. Using a comparative proteomic workflow, we mapped over 450 protein-protein interactions for 21 stably expressed, full-length E3s. Bioinformatic analysis linked ER-E3s and their interactors to multiple homeostatic, regulatory, and metabolic pathways. Among these were four membrane-embedded interactors of RNF26, a polytopic E3 whose abundance is auto-regulated by ubiquitin-proteasome dependent degradation. RNF26 co-assembles with TMEM43, ENDOD1, TMEM33 and TMED1 to form a complex capable of modulating innate immune signalling through the cGAS-STING pathway. This RNF26 complex represents a new modulatory axis of STING and innate immune signalling at the ER membrane. Collectively, these data reveal the broad scope of regulation and differential functionalities mediated by ER-E3s for both membrane-tethered and cytoplasmic processes.
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Affiliation(s)
- Emma J Fenech
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Federica Lari
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Philip D Charles
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Marie Laétitia-Thézénas
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Katrin Bagola
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of AdelaideAdelaideAustralia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of AdelaideAdelaideAustralia
| | - Mads Gyrd-Hansen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - John C Christianson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research CentreOxfordUnited Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Botnar Research CentreOxfordUnited Kingdom
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45
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Abstract
Rhomboid intramembrane serine proteases are present in all kingdoms of life, but as we do not know their substrates in many species, it remains puzzling why rhomboids are among the most-conserved integral membrane proteins. Two new studies in The EMBO Journal by Began et al and Liu et al now link bacterial rhomboid proteases to membrane protein degradation, showing striking similarities to what is known about eukaryotic rhomboid family proteins, thus pointing toward a conserved membrane surveillance mechanism.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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46
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Liu G, Beaton SE, Grieve AG, Evans R, Rogers M, Strisovsky K, Armstrong FA, Freeman M, Exley RM, Tang CM. Bacterial rhomboid proteases mediate quality control of orphan membrane proteins. EMBO J 2020; 39:e102922. [PMID: 32337752 PMCID: PMC7232013 DOI: 10.15252/embj.2019102922] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023] Open
Abstract
Although multiprotein membrane complexes play crucial roles in bacterial physiology and virulence, the mechanisms governing their quality control remain incompletely understood. In particular, it is not known how unincorporated, orphan components of protein complexes are recognised and eliminated from membranes. Rhomboids, the most widespread and largest superfamily of intramembrane proteases, are known to play key roles in eukaryotes. In contrast, the function of prokaryotic rhomboids has remained enigmatic. Here, we show that the Shigella sonnei rhomboid proteases GlpG and the newly identified Rhom7 are involved in membrane protein quality control by specifically targeting components of respiratory complexes, with the metastable transmembrane domains (TMDs) of rhomboid substrates protected when they are incorporated into a functional complex. Initial cleavage by GlpG or Rhom7 allows subsequent degradation of the orphan substrate. Given the occurrence of this strategy in an evolutionary ancient organism and the presence of rhomboids in all domains of life, it is likely that this form of quality control also mediates critical events in eukaryotes and protects cells from the damaging effects of orphan proteins.
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Affiliation(s)
- Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Stephen E Beaton
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Adam G Grieve
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rhiannon Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Miranda Rogers
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Praha 6, Czech Republic
| | | | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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47
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The Metastable XBP1u Transmembrane Domain Defines Determinants for Intramembrane Proteolysis by Signal Peptide Peptidase. Cell Rep 2020; 26:3087-3099.e11. [PMID: 30865896 DOI: 10.1016/j.celrep.2019.02.057] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/07/2018] [Accepted: 02/14/2019] [Indexed: 11/23/2022] Open
Abstract
Unspliced XBP1 mRNA encodes XBP1u, the transcriptionally inert variant of the unfolded protein response (UPR) transcription factor XBP1s. XBP1u targets its mRNA-ribosome-nascent-chain-complex to the endoplasmic reticulum (ER) to facilitate UPR activation and prevents overactivation. Yet, its membrane association is controversial. Here, we use cell-free translocation and cellular assays to define a moderately hydrophobic stretch in XBP1u that is sufficient to mediate insertion into the ER membrane. Mutagenesis of this transmembrane (TM) region reveals residues that facilitate XBP1u turnover by an ER-associated degradation route that is dependent on signal peptide peptidase (SPP). Furthermore, the impact of these mutations on TM helix dynamics was assessed by residue-specific amide exchange kinetics, evaluated by a semi-automated algorithm. Based on our results, we suggest that SPP-catalyzed intramembrane proteolysis of TM helices is not only determined by their conformational flexibility, but also by side-chain interactions near the scissile peptide bond with the enzyme's active site.
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48
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Knopf JD, Landscheidt N, Pegg CL, Schulz BL, Kühnle N, Chao CW, Huck S, Lemberg MK. Intramembrane protease RHBDL4 cleaves oligosaccharyltransferase subunits to target them for ER-associated degradation. J Cell Sci 2020; 133:jcs243790. [PMID: 32005703 DOI: 10.1242/jcs.243790] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 08/31/2023] Open
Abstract
The endoplasmic reticulum (ER)-resident intramembrane rhomboid protease RHBDL4 generates metastable protein fragments and together with the ER-associated degradation (ERAD) machinery provides a clearance mechanism for aberrant and surplus proteins. However, the endogenous substrate spectrum and with that the role of RHBDL4 in physiological ERAD is mainly unknown. Here, we use a substrate trapping approach in combination with quantitative proteomics to identify physiological RHBDL4 substrates. This revealed oligosaccharyltransferase (OST) complex subunits such as the catalytic active subunit STT3A as substrates for the RHBDL4-dependent ERAD pathway. RHBDL4-catalysed cleavage inactivates OST subunits by triggering dislocation into the cytoplasm and subsequent proteasomal degradation. RHBDL4 thereby controls the abundance and activity of OST, suggesting a novel link between the ERAD machinery and glycosylation tuning.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nina Landscheidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nathalie Kühnle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Chao-Wei Chao
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Simon Huck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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Rhomboid-Like-2 Intramembrane Protease Mediates Metalloprotease-Independent Regulation of Cadherins. Int J Mol Sci 2019; 20:ijms20235958. [PMID: 31783481 PMCID: PMC6928865 DOI: 10.3390/ijms20235958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/25/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022] Open
Abstract
Cadherins are a major family of cell-cell adhesive receptors, which are implicated in development, tissue homeostasis, and cancer. Here, we show a novel mechanism of post-translational regulation of E-cadherin in cancer cells by an intramembrane protease of the Rhomboid family, RHBDL2, which leads to the shedding of E-cadherin extracellular domain. In addition, our data indicate that RHBDL2 mediates a similar activity on VE-cadherin, which is selectively expressed by endothelial cells. We show that RHBDL2 promotes cell migration, which is consistent with its ability to interfere with the functional role of cadherins as negative regulators of motility; moreover, the two players appear to lie in the same functional pathway. Importantly, we show that RHBDL2 expression is induced by the inflammatory chemokine TNFα. The E-cadherin extracellular domain is known to be released by metalloproteases (MMPs); however, here, we provide evidence of a novel MMP-independent, TNFα inducible, E-cadherin processing mechanism that is mediated by RHBDL2. Thus, the intramembrane protease RHBDL2 is a novel regulator of cadherins promoting cell motility.
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50
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Beard HA, Barniol-Xicota M, Yang J, Verhelst SHL. Discovery of Cellular Roles of Intramembrane Proteases. ACS Chem Biol 2019; 14:2372-2388. [PMID: 31287658 DOI: 10.1021/acschembio.9b00404] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intramembrane proteases (IMPs) are localized within lipid bilayers of membranes-either the cell membrane or membranes of various organelles. Cleavage of substrates often results in release from the membrane, leading to a downstream biological effect. This mechanism allows different signaling events to happen through intramembrane proteolysis. Over the years, various mechanistically distinct families of IMPs have been discovered, but the research progress has generally been slower than for soluble proteases due to the challenges associated with membrane proteins. In this review we summarize how each mechanistic family of IMPs was discovered, which chemical tools are available for the study of IMPs, and which techniques have been developed for the discovery of IMP substrates. Finally, we discuss the various roles in cellular physiology of some of these IMPs.
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Affiliation(s)
- Hester A. Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Jian Yang
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Steven H. L. Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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