1
|
Vitali DG, Fonseca D, Carvalho P. The derlin Dfm1 couples retrotranslocation of a folded protein domain to its proteasomal degradation. J Cell Biol 2024; 223:e202308074. [PMID: 38448163 PMCID: PMC11066878 DOI: 10.1083/jcb.202308074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/05/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Endoplasmic reticulum (ER) proteins are degraded by proteasomes in the cytosol through ER-associated degradation (ERAD). This process involves the retrotranslocation of substrates across the ER membrane, their ubiquitination, and membrane extraction by the Cdc48/Npl4/Ufd1 ATPase complex prior to delivery to proteasomes for degradation. How the presence of a folded luminal domain affects substrate retrotranslocation and this event is coordinated with subsequent ERAD steps remains unknown. Here, using a model substrate with a folded luminal domain, we showed that Cdc48 ATPase activity is sufficient to drive substrate retrotranslocation independently of ERAD membrane components. However, the complete degradation of the folded luminal domain required substrate-tight coupling of retrotranslocation and proteasomal degradation, which was ensured by the derlin Dfm1. Mutations in Dfm1 intramembrane rhomboid-like or cytosolic Cdc48-binding regions resulted in partial degradation of the substrate with accumulation of its folded domain. Our study revealed Dfm1 as a critical regulator of Cdc48-driven retrotranslocation and highlights the importance of coordinating substrate retrotranslocation and degradation during ERAD.
Collapse
Affiliation(s)
- Daniela G. Vitali
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Daniel Fonseca
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| |
Collapse
|
2
|
Yang J, Carvalho LAR, Ji S, Chen S, Moreira R, Verhelst SHL. 4-Oxo-β-Lactams as Novel Inhibitors for Rhomboid Proteases. Chembiochem 2023; 24:e202300418. [PMID: 37671979 DOI: 10.1002/cbic.202300418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 09/07/2023]
Abstract
Intramembrane serine proteases (rhomboid proteases) are involved in a variety of biological processes and are implicated in several diseases. Here, we report 4-oxo-β-lactams as a novel scaffold for inhibition of rhomboids. We show that they covalently react with the active site and that the covalent bond is sufficiently stable for detection of the covalent rhomboid-lactam complex. 4-Oxo-β-lactams may therefore find future use as both inhibitors and activity-based probes for rhomboid proteases.
Collapse
Affiliation(s)
- Jian Yang
- Laboratory of, Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Luís A R Carvalho
- Department of Pharmaceutical Sciences and Medicines, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Shanping Ji
- Laboratory of, Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Suyuan Chen
- Leibniz Institut für Analytische Wissenschaften - ISAS - e.V, Otto-Hahn Strasse 6b, 44227, Dortmund, Germany
| | - Rui Moreira
- Department of Pharmaceutical Sciences and Medicines, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Steven H L Verhelst
- Laboratory of, Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
- Leibniz Institut für Analytische Wissenschaften - ISAS - e.V, Otto-Hahn Strasse 6b, 44227, Dortmund, Germany
| |
Collapse
|
3
|
Papadopoulou AA, Stelzer W, Silber M, Schlosser C, Spitz C, Haug-Kröper M, Straub T, Müller SA, Lichtenthaler SF, Muhle-Goll C, Langosch D, Fluhrer R. Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage. Sci Rep 2022; 12:20987. [PMID: 36470941 PMCID: PMC9722940 DOI: 10.1038/s41598-022-24772-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Signal-Peptide Peptidase Like-3 (SPPL3) is an intramembrane cleaving aspartyl protease that causes secretion of extracellular domains from type-II transmembrane proteins. Numerous Golgi-localized glycosidases and glucosyltransferases have been identified as physiological SPPL3 substrates. By SPPL3 dependent processing, glycan-transferring enzymes are deactivated inside the cell, as their active site-containing domain is cleaved and secreted. Thus, SPPL3 impacts on glycan patterns of many cellular and secreted proteins and can regulate protein glycosylation. However, the characteristics that make a substrate a favourable candidate for SPPL3-dependent cleavage remain unknown. To gain insights into substrate requirements, we investigated the function of a GxxxG motif located in the transmembrane domain of N-acetylglucosaminyltransferase V (GnTV), a well-known SPPL3 substrate. SPPL3-dependent secretion of the substrate's ectodomain was affected by mutations disrupting the GxxxG motif. Using deuterium/hydrogen exchange and NMR spectroscopy, we studied the effect of these mutations on the helix flexibility of the GnTV transmembrane domain and observed that increased flexibility facilitates SPPL3-dependent shedding and vice versa. This study provides first insights into the characteristics of SPPL3 substrates, combining molecular biology, biochemistry, and biophysical techniques and its results will provide the basis for better understanding the characteristics of SPPL3 substrates with implications for the substrates of other intramembrane proteases.
Collapse
Affiliation(s)
- Alkmini A. Papadopoulou
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Walter Stelzer
- grid.6936.a0000000123222966Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Mara Silber
- grid.7892.40000 0001 0075 5874Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany ,grid.7892.40000 0001 0075 5874Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Christine Schlosser
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Charlotte Spitz
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Martina Haug-Kröper
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Tobias Straub
- grid.5252.00000 0004 1936 973XCore Facility Bioinformatics, Biomedical Center, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Stephan A. Müller
- grid.424247.30000 0004 0438 0426DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
| | - Stefan F. Lichtenthaler
- grid.424247.30000 0004 0438 0426DZNE – German Center for Neurodegenerative Diseases, Munich, Germany ,grid.15474.330000 0004 0477 2438Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany ,grid.452617.3Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Claudia Muhle-Goll
- grid.7892.40000 0001 0075 5874Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany ,grid.7892.40000 0001 0075 5874Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Dieter Langosch
- grid.6936.a0000000123222966Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Regina Fluhrer
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| |
Collapse
|
4
|
Engberg O, Ulbricht D, Döbel V, Siebert V, Frie C, Penk A, Lemberg MK, Huster D. Rhomboid-catalyzed intramembrane proteolysis requires hydrophobic matching with the surrounding lipid bilayer. Sci Adv 2022; 8:eabq8303. [PMID: 36149963 PMCID: PMC9506719 DOI: 10.1126/sciadv.abq8303] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/09/2022] [Indexed: 06/16/2023]
Abstract
Membrane thinning by rhomboid proteins has been proposed to reduce hydrophobic mismatch, providing a unique environment for important functions ranging from intramembrane proteolysis to retrotranslocation in protein degradation. We show by in vitro reconstitution and solid-state nuclear magnetic resonance that the lipid environment of the Escherichia coli rhomboid protease GlpG influences its activity with an optimal hydrophobic membrane thickness between 24 and 26 Å. While phosphatidylcholine membranes are only negligibly altered by GlpG, in an E. coli-relevant lipid mix of phosphatidylethanolamine and phosphatidylglycerol, a thinning by 1.1 Å per leaflet is observed. Protease activity is strongly correlated with membrane thickness and shows no lipid headgroup specificity. We infer from these results that, by adjusting the thickness of specific membrane domains, membrane proteins shape the bilayer for their specific needs.
Collapse
Affiliation(s)
- Oskar Engberg
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - David Ulbricht
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Viola Döbel
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Verena Siebert
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, D-50931 Cologne, Germany
| | - Christian Frie
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, D-50931 Cologne, Germany
| | - Anja Penk
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Marius K. Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, D-50931 Cologne, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107 Leipzig, Germany
| |
Collapse
|
5
|
Bock J, Kühnle N, Knopf JD, Landscheidt N, Lee JG, Ye Y, Lemberg MK. Rhomboid protease RHBDL4 promotes retrotranslocation of aggregation-prone proteins for degradation. Cell Rep 2022; 40:111175. [PMID: 35947953 DOI: 10.1016/j.celrep.2022.111175] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
Collapse
|
6
|
Marchesini MI, Poetsch A, Guidolín LS, Comerci DJ. Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion. Microorganisms 2022; 10:114. [PMID: 35056563 DOI: 10.3390/microorganisms10010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
Collapse
|
7
|
Bohg C, Öster C, Utesch T, Bischoff S, Lange S, Shi C, Sun H, Lange A. A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor. Chem Sci 2021; 12:12754-12762. [PMID: 34703562 PMCID: PMC8494044 DOI: 10.1039/d1sc02146j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022] Open
Abstract
Intramembrane proteolysis plays a fundamental role in many biological and pathological processes. Intramembrane proteases thus represent promising pharmacological targets, but few selective inhibitors have been identified. This is in contrast to their soluble counterparts, which are inhibited by many common drugs, and is in part explained by the inherent difficulty to characterize the binding of drug-like molecules to membrane proteins at atomic resolution. Here, we investigated the binding of two different inhibitors to the bacterial rhomboid protease GlpG, an intramembrane protease characterized by a Ser–His catalytic dyad, using solid-state NMR spectroscopy. H/D exchange of deuterated GlpG can reveal the binding position while chemical shift perturbations additionally indicate the allosteric effects of ligand binding. Finally, we determined the exact binding mode of a rhomboid protease-inhibitor using a combination of solid-state NMR and molecular dynamics simulations. We believe this approach can be widely adopted to study the structure and binding of other poorly characterized membrane protein–ligand complexes in a native-like environment and under physiological conditions. Proton-detected solid-state NMR in combination with molecular docking and molecular dynamics (MD) simulations allow the study of rhomboid protease inhibition under native-like conditions.![]()
Collapse
Affiliation(s)
- Claudia Bohg
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Tillmann Utesch
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Susanne Bischoff
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China Huangshan Road 443 Hefei 230027 People's Republic of China
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Institut für Biologie, Humboldt-Universität zu Berlin Invalidenstraße 42 10115 Berlin Germany
| |
Collapse
|
8
|
Burzenski LM, Low BE, Kohar V, Shultz LD, Wiles MV, Hosur V. Inactive rhomboid proteins RHBDF1 and RHBDF2 (iRhoms): a decade of research in murine models. Mamm Genome 2021; 32:415-26. [PMID: 34477920 DOI: 10.1007/s00335-021-09910-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022]
Abstract
Rhomboid proteases, first discovered in Drosophila, are intramembrane serine proteases. Members of the rhomboid protein family that are catalytically deficient are known as inactive rhomboids (iRhoms). iRhoms have been implicated in wound healing, cancer, and neurological disorders such as Alzheimer’s and Parkinson’s diseases, inflammation, and skin diseases. The past decade of mouse research has shed new light on two key protein domains of iRhoms—the cytosolic N-terminal domain and the transmembrane dormant peptidase domain—suggesting new ways to target multiple intracellular signaling pathways. This review focuses on recent advances in uncovering the unique functions of iRhom protein domains in normal growth and development, growth factor signaling, and inflammation, with a perspective on future therapeutic opportunities.
Collapse
|
9
|
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: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
10
|
Rao B, Li S, Yao D, Wang Q, Xia Y, Jia Y, Shen Y, Cao Y. The cryo-EM structure of an ERAD protein channel formed by tetrameric human Derlin-1. Sci Adv 2021; 7:eabe8591. [PMID: 33658201 PMCID: PMC7929502 DOI: 10.1126/sciadv.abe8591] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/19/2021] [Indexed: 05/24/2023]
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is a process directing misfolded proteins from the ER lumen and membrane to the degradation machinery in the cytosol. A key step in ERAD is the translocation of ER proteins to the cytosol. Derlins are essential for protein translocation in ERAD, but the mechanism remains unclear. Here, we solved the structure of human Derlin-1 by cryo-electron microscopy. The structure shows that Derlin-1 forms a homotetramer that encircles a large tunnel traversing the ER membrane. The tunnel has a diameter of about 12 to 15 angstroms, large enough to allow an α helix to pass through. The structure also shows a lateral gate within the membrane, providing access of transmembrane proteins to the tunnel, and thus, human Derlin-1 forms a protein channel for translocation of misfolded proteins. Our structure is different from the monomeric yeast Derlin structure previously reported, which forms a semichannel with another protein.
Collapse
Affiliation(s)
- Bing Rao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Shaobai Li
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Deqiang Yao
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Qian Wang
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Ying Xia
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Yi Jia
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Yafeng Shen
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China
| | - Yu Cao
- Shanghai Institute of Precision of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, Shanghai 200125, China.
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| |
Collapse
|
11
|
Lysyk L, Brassard R, Arutyunova E, Siebert V, Jiang Z, Takyi E, Morrison M, Young HS, Lemberg MK, O'Donoghue AJ, Lemieux MJ. Insights into the catalytic properties of the mitochondrial rhomboid protease PARL. J Biol Chem 2021; 296:100383. [PMID: 33556373 PMCID: PMC7966987 DOI: 10.1016/j.jbc.2021.100383] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The rhomboid protease PARL is a critical regulator of mitochondrial homeostasis through its cleavage of substrates such as PINK1, PGAM5, and Smac/Diablo, which have crucial roles in mitochondrial quality control and apoptosis. However, the catalytic properties of PARL, including the effect of lipids on the protease, have never been characterized in vitro. To address this, we isolated human PARL expressed in yeast and used FRET-based kinetic assays to measure proteolytic activity in vitro. We show that PARL activity in detergent is enhanced by cardiolipin, a lipid enriched in the mitochondrial inner membrane. Significantly higher turnover rates were observed for PARL reconstituted in proteoliposomes, with Smac/Diablo being cleaved most rapidly at a rate of 1 min−1. In contrast, PGAM5 is cleaved with the highest efficiency (kcat/KM) compared with PINK1 and Smac/Diablo. In proteoliposomes, a truncated β-cleavage form of PARL, a physiological form known to affect mitochondrial fragmentation, is more active than the full-length enzyme for hydrolysis of PINK1, PGAM5, and Smac/Diablo. Multiplex profiling of 228 peptides reveals that PARL prefers substrates with a bulky side chain such as Phe in P1, which is distinct from the preference for small side chain residues typically found with bacterial rhomboid proteases. This study using recombinant PARL provides fundamental insights into its catalytic activity and substrate preferences that enhance our understanding of its role in mitochondrial function and has implications for specific inhibitor design.
Collapse
Affiliation(s)
- Laine Lysyk
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Raelynn Brassard
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Verena Siebert
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Emmanuella Takyi
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Melissa Morrison
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
12
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
| | | |
Collapse
|
13
|
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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 01/07/2023]
|
14
|
Barniol-Xicota M, Verhelst SHL. Isolation of intramembrane proteases in membrane-like environments. Biochim Biophys Acta Biomembr 2020; 1862:183193. [PMID: 31945321 DOI: 10.1016/j.bbamem.2020.183193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/24/2022]
Abstract
Intramembrane proteases (IMPs) are proteolytic enzymes embedded in the lipid bilayer, where they cleave transmembrane substrates. The importance of IMPs relies on their role in a wide variety of cellular processes and diseases. In order to study the activity and function of IMPs, their purified form is often desired. The production of pure and active IMPs has proven to be a challenging task. This process unavoidably requires the use of solubilizing agents that will, to some extent, alter the native environment of these proteases. In this review we present the current solubilization and reconstitution techniques that have been applied to IMPs. In addition, we describe how these techniques had an influence on the activity and structural studies of IMPs, focusing on rhomboid proteases and γ-secretase.
Collapse
Affiliation(s)
- Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium.
| | - Steven H L Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium; Leibniz Institute for Analytical Sciences, ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
| |
Collapse
|
15
|
Began J, Cordier B, Březinová J, Delisle J, Hexnerová R, Srb P, Rampírová P, Kožíšek M, Baudet M, Couté Y, Galinier A, Veverka V, Doan T, Strisovsky K. Rhomboid intramembrane protease YqgP licenses bacterial membrane protein quality control as adaptor of FtsH AAA protease. EMBO J 2020; 39:e102935. [PMID: 31930742 PMCID: PMC7231995 DOI: 10.15252/embj.2019102935] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
Magnesium homeostasis is essential for life and depends on magnesium transporters, whose activity and ion selectivity need to be tightly controlled. Rhomboid intramembrane proteases pervade the prokaryotic kingdom, but their functions are largely elusive. Using proteomics, we find that Bacillus subtilis rhomboid protease YqgP interacts with the membrane‐bound ATP‐dependent processive metalloprotease FtsH and cleaves MgtE, the major high‐affinity magnesium transporter in B. subtilis. MgtE cleavage by YqgP is potentiated in conditions of low magnesium and high manganese or zinc, thereby protecting B. subtilis from Mn2+/Zn2+ toxicity. The N‐terminal cytosolic domain of YqgP binds Mn2+ and Zn2+ ions and facilitates MgtE cleavage. Independently of its intrinsic protease activity, YqgP acts as a substrate adaptor for FtsH, a function that is necessary for degradation of MgtE. YqgP thus unites protease and pseudoprotease function, hinting at the evolutionary origin of rhomboid pseudoproteases such as Derlins that are intimately involved in eukaryotic ER‐associated degradation (ERAD). Conceptually, the YqgP‐FtsH system we describe here is analogous to a primordial form of “ERAD” in bacteria and exemplifies an ancestral function of rhomboid‐superfamily proteins.
Collapse
Affiliation(s)
- Jakub Began
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Baptiste Cordier
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Jana Březinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jordan Delisle
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Petra Rampírová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Mathieu Baudet
- CEA, Inserm, IRIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Yohann Couté
- CEA, Inserm, IRIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Thierry Doan
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France.,Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7255, Aix Marseille Univ, Marseille Cedex 20, France
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| |
Collapse
|
16
|
Affiliation(s)
- Sandra Paschkowsky
- Department of Pharmacology & Therapeutics, McGill University, Bellini Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Jacqueline Melissa Hsiao
- Department of Biochemistry, McGill University, McIntyre Building, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Jason C. Young
- Department of Biochemistry, McGill University, McIntyre Building, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Bellini Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| |
Collapse
|
17
|
Abstract
Rhomboid intramembrane proteases are bound to lipid membranes, where they dock and cleave other transmembrane substrates. How the lipid membrane surrounding the protease impacts the conformational dynamics of the protease is essential to understand because it informs on the reaction coordinate of substrate binding. Atomistic molecular dynamics simulations allow us to probe protein motions and characterize the coupling between protein and lipids. Simulations performed here on GlpG, the rhomboid protease from Escherichia coli, indicate that the thickness of the lipid membrane close to GlpG depends on both the composition of the lipid membrane and the conformation of GlpG. Transient binding of a lipid headgroup at the active site of the protease, as observed in some of the simulations reported here, suggests that a lipid headgroup might compete with the substrate for access to the GlpG active site. Interactions identified between lipid headgroups and the protein influence the dynamics of lipid interactions close to the substrate-binding site. These observations suggest that the lipid membrane environment shapes the energy profile of the substrate-docking region of the enzyme reaction coordinate.
Collapse
Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
| |
Collapse
|
18
|
Gaffney KA, Hong H. The rhomboid protease GlpG has weak interaction energies in its active site hydrogen bond network. J Gen Physiol 2018; 151:282-291. [PMID: 30420443 PMCID: PMC6400518 DOI: 10.1085/jgp.201812047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023] Open
Abstract
Rhomboid proteases are membrane-integrated enzymes that hydrolyze peptide bonds in the transmembrane domains of protein substrates. Gaffney and Hong experimentally determine interaction energies between active site residues to reveal weak coupling, which may explain the slow proteolysis mediated by GlpG. Intramembrane rhomboid proteases are of particular interest because of their function to hydrolyze a peptide bond of a substrate buried in the membrane. Crystal structures of the bacterial rhomboid protease GlpG have revealed a catalytic dyad (Ser201-His254) and oxyanion hole (His150/Asn154/the backbone amide of Ser201) surrounded by the protein matrix and contacting a narrow water channel. Although multiple crystal structures have been solved, the catalytic mechanism of GlpG is not completely understood. Because it is a serine protease, hydrogen bonding interactions between the active site residues are thought to play a critical role in the catalytic cycle. Here, we dissect the interaction energies among the active site residues His254, Ser201, and Asn154 of Escherichia coli GlpG, which form a hydrogen bonding network. We combine double mutant cycle analysis with stability measurements using steric trapping. In mild detergent, the active site residues are weakly coupled with interaction energies (ΔΔGInter) of ‒1.4 kcal/mol between His254 and Ser201 and ‒0.2 kcal/mol between Ser201 and Asn154. Further, by analyzing the propagation of single mutations of the active site residues, we find that these residues are important not only for function but also for the folding cooperativity of GlpG. The weak interaction between Ser and His in the catalytic dyad may partly explain the unusually slow proteolysis by GlpG compared with other canonical serine proteases. Our result suggests that the weak hydrogen bonds in the active site are sufficient to carry out the proteolytic function of rhomboid proteases.
Collapse
Affiliation(s)
- Kristen A Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Heedeok Hong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI .,Department of Chemistry, Michigan State University, East Lansing, MI
| |
Collapse
|
19
|
Tichá A, Collis B, Strisovsky K. The Rhomboid Superfamily: Structural Mechanisms and Chemical Biology Opportunities. Trends Biochem Sci 2018; 43:726-39. [DOI: 10.1016/j.tibs.2018.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/08/2018] [Accepted: 06/30/2018] [Indexed: 12/27/2022]
|
20
|
Lee MY, Kang JS, Go RE, Byun YS, Wi YJ, Hwang KA, Choi JH, Kim HC, Choi KC, Nam KH. Collagen-Induced Arthritis Analysis in Rhbdf2 Knockout Mouse. Biomol Ther (Seoul) 2018; 26:298-305. [PMID: 29223140 PMCID: PMC5933897 DOI: 10.4062/biomolther.2017.103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/02/2022] Open
Abstract
Rhomboid family member 2 gene (Rhbdf2) is an inactive homologue lacking essential catalytic residues of rhomboid intramembrane serine proteases. The protein is necessary for maturation of tumor necrosis factor-alpha (TNF-α) converting enzyme, which is the molecule responsible for the release of TNF-α. In this study, Rhbdf2 knockout (KO) mice were produced by CRISPR/CAS9. To see the effects of the failure of TNF-α release induced by Rhbdf2 gene KO, collagen-induced arthritis (CIA), which is the representative TNF-α related disease, was induced in the Rhbdf2 mutant mouse using chicken collagen type II. The severity of the CIA was measured by traditional clinical scores and histopathological analysis of hind limb joints. A rota-rod test and grip strength test were employed to evaluate the severity of CIA based on losses of physical functions. The results indicated that Rhbdf2 mutant mice showed clear alleviation of the clinical severity of CIA as demonstrated by the significantly lower severity indexes. Moreover, a grip strength test was shown to be useful for the evaluation of physical functional losses by CIA. Overall, the results showed that the Rhbdf2 gene has a significant effect on the induction of CIA, which is related to TNF-α.
Collapse
Affiliation(s)
- Min-Young Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 28116, Republic of Korea.,Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ju-Seong Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 28116, Republic of Korea
| | - Ryeo-Eun Go
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Yong-Sub Byun
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 28116, Republic of Korea
| | - Young Jin Wi
- Department of Life Science, College of Natureal Sciences, Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Kyung-A Hwang
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jae-Hoon Choi
- Department of Life Science, College of Natureal Sciences, Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyoung-Chin Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 28116, Republic of Korea
| | - Kyung-Chul Choi
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 28116, Republic of Korea
| |
Collapse
|
21
|
Yang J, Barniol-Xicota M, Nguyen MT, Ticha A, Strisovsky K, Verhelst SH. Benzoxazin-4-ones as novel, easily accessible inhibitors for rhomboid proteases. Bioorg Med Chem Lett 2018; 28:1423-1427. [DOI: 10.1016/j.bmcl.2017.12.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 12/13/2022]
|
22
|
Goel P, Jumpertz T, Mikles DC, Tichá A, Nguyen MTN, Verhelst S, Hubalek M, Johnson DC, Bachovchin DA, Ogorek I, Pietrzik CU, Strisovsky K, Schmidt B, Weggen S. Discovery and Biological Evaluation of Potent and Selective N-Methylene Saccharin-Derived Inhibitors for Rhomboid Intramembrane Proteases. Biochemistry 2017; 56:6713-6725. [PMID: 29185711 DOI: 10.1021/acs.biochem.7b01066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhomboids are intramembrane serine proteases and belong to the group of structurally and biochemically most comprehensively characterized membrane proteins. They are highly conserved and ubiquitously distributed in all kingdoms of life and function in a wide range of biological processes, including epidermal growth factor signaling, mitochondrial dynamics, and apoptosis. Importantly, rhomboids have been associated with multiple diseases, including Parkinson's disease, type 2 diabetes, and malaria. However, despite a thorough understanding of many structural and functional aspects of rhomboids, potent and selective inhibitors of these intramembrane proteases are still not available. In this study, we describe the computer-based rational design, chemical synthesis, and biological evaluation of novel N-methylene saccharin-based rhomboid protease inhibitors. Saccharin inhibitors displayed inhibitory potency in the submicromolar range, effectiveness against rhomboids both in vitro and in live Escherichia coli cells, and substantially improved selectivity against human serine hydrolases compared to those of previously known rhomboid inhibitors. Consequently, N-methylene saccharins are promising new templates for the development of rhomboid inhibitors, providing novel tools for probing rhomboid functions in physiology and disease.
Collapse
Affiliation(s)
- Parul Goel
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany.,Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Thorsten Jumpertz
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - David C Mikles
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Anežka Tichá
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Minh T N Nguyen
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Steven Verhelst
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, University of Leuven , Herestraat 49, Box 802, 3000 Leuven, Belgium
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Darren C Johnson
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Isabella Ogorek
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Claus U Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz , Duesbergweg 6, 55128 Mainz, Germany
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Boris Schmidt
- Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Sascha Weggen
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| |
Collapse
|
23
|
Tichá A, Stanchev S, Vinothkumar KR, Mikles DC, Pachl P, Began J, Škerle J, Švehlová K, Nguyen MTN, Verhelst SHL, Johnson DC, Bachovchin DA, Lepšík M, Majer P, Strisovsky K. General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases. Cell Chem Biol 2017; 24:1523-1536.e4. [PMID: 29107700 PMCID: PMC5746060 DOI: 10.1016/j.chembiol.2017.09.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/19/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022]
Abstract
Rhomboid-family intramembrane proteases regulate important biological processes and have been associated with malaria, cancer, and Parkinson's disease. However, due to the lack of potent, selective, and pharmacologically compliant inhibitors, the wide therapeutic potential of rhomboids is currently untapped. Here, we bridge this gap by discovering that peptidyl α-ketoamides substituted at the ketoamide nitrogen by hydrophobic groups are potent rhomboid inhibitors active in the nanomolar range, surpassing the currently used rhomboid inhibitors by up to three orders of magnitude. Such peptidyl ketoamides show selectivity for rhomboids, leaving most human serine hydrolases unaffected. Crystal structures show that these compounds bind the active site of rhomboid covalently and in a substrate-like manner, and kinetic analysis reveals their reversible, slow-binding, non-competitive mechanism. Since ketoamides are clinically used pharmacophores, our findings uncover a straightforward modular way for the design of specific inhibitors of rhomboid proteases, which can be widely applicable in cell biology and drug discovery. N-substituted peptidyl α-ketoamides are nanomolar inhibitors of rhomboid proteases Peptidyl ketoamides inhibit rhomboids covalently, reversibly, and non-competitively The peptide and ketoamide substituent independently modulate potency and selectivity Peptidyl ketoamides are selective for rhomboids, sparing most human serine proteases
Collapse
Affiliation(s)
- Anežka Tichá
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Kutti R Vinothkumar
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David C Mikles
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Jakub Began
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, Prague 128 44, Czech Republic
| | - Jan Škerle
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43, Czech Republic
| | - Kateřina Švehlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Minh T N Nguyen
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Steven H L Verhelst
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany; KU Leuven - University of Leuven, Herestraat 49, Box 802, 3000 Leuven, Belgium
| | - Darren C Johnson
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 428, New York, NY 10065, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 428, New York, NY 10065, USA
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic.
| |
Collapse
|
24
|
Düsterhöft S, Künzel U, Freeman M. Rhomboid proteases in human disease: Mechanisms and future prospects. Biochim Biophys Acta Mol Cell Res 2017; 1864:2200-2209. [PMID: 28460881 DOI: 10.1016/j.bbamcr.2017.04.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/19/2023]
Abstract
Rhomboids are intramembrane serine proteases that cleave the transmembrane helices of substrate proteins, typically releasing luminal/extracellular domains from the membrane. They are conserved in all branches of life and there is a growing recognition of their association with a wide range of human diseases. Human rhomboids, for example, have been implicated in cancer, metabolic disease and neurodegeneration, while rhomboids in apicomplexan parasites appear to contribute to their invasion of host cells. Recent advances in our knowledge of the structure and the enzyme function of rhomboids, and increasing efforts to identify specific inhibitors, are beginning to provide important insight into the prospect of rhomboids becoming future therapeutic targets. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
Collapse
Affiliation(s)
- Stefan Düsterhöft
- Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom
| | - Ulrike Künzel
- Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom
| | - Matthew Freeman
- Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom.
| |
Collapse
|
25
|
Miao F, Zhang M, Zhao Y, Li X, Yao R, Wu F, Huang R, Li K, Miao S, Ma C, Ju H, Song W, Wang L. RHBDD1 upregulates EGFR via the AP-1 pathway in colorectal cancer. Oncotarget 2017; 8:25251-25260. [PMID: 28445956 PMCID: PMC5421926 DOI: 10.18632/oncotarget.15694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/24/2017] [Indexed: 01/08/2023] Open
Abstract
Our previous study showed that RHBDD1 can activate the EGFR signaling pathway to promote colorectal cancer growth. In the present study, EGFR was decreased when RHBDD1 was knocked down or inactivated. Further analysis found that c-Jun and EGFR protein expression was decreased in RHBDD1 knockdown and inactivated cells. c-Jun overexpression in RHBDD1-inactivated cells rescued EGFR expression in a dose-dependent manner. RHBDD1 overexpression in RHBDD1-inactivated cells restored EGFR expression, but this effect was counteracted by c-Jun knockdown. Furthermore, EGFR and c-Jun were attenuated in the RHBDD1 knockdown and inactivated groups in animal tumor models. Tissue microarray assays demonstrated a correlation between RHBDD1 and EGFR in colorectal cancer patients. Therefore, our findings indicate that RHBDD1 stimulates EGFR expression by promoting the AP-1 pathway.
Collapse
Affiliation(s)
- Fei Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Mengmeng Zhang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Yuechao Zhao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Xiaolu Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Rongyan Yao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Fan Wu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Rong Huang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Kai Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Shiying Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Changwu Ma
- Department of Medical Oncology, Chifeng Municipal Hospital, Chifeng 024000, China
| | - Hongge Ju
- Department of Pathology, Baotou Medical College, Baotou 014040, China.,Department of Pathology, The First Affiliated Hospital of Baotou Medical College, Baotou 014010, China
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Linfang Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| |
Collapse
|
26
|
Arutyunova E, Panigrahi R, Strisovsky K, Lemieux MJ. Production of Recombinant Rhomboid Proteases. Methods Enzymol 2017; 584:255-78. [PMID: 28065266 DOI: 10.1016/bs.mie.2016.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Rhomboid proteases are intramembrane enzymes that hydrolyze peptide bonds of transmembrane proteins in the lipid bilayer. They play a variety of roles in key biological events and are linked to several disease states. Over the last decade a great deal of structural and functional knowledge has been generated on this fascinating class of proteases. Both structural and kinetic analyses require milligram amounts of protein, which may be challenging for membrane proteins such as rhomboids. Here, we present a detailed protocol for optimization of expression and purification of three rhomboid proteases from Escherichia coli (ecGlpG), Haemophilus influenzae (hiGlpG), and Providencia stuartii (AarA). We discuss the optimization of expression conditions, such as concentration of inducing agent, induction time, and temperature, as well as purification protocol with precise details for each step. The provided protocol yields 1-2.5mg of rhomboid enzyme per liter of bacterial culture and can assist in structural and functional studies of intramembrane proteases.
Collapse
|
27
|
Tichá A, Stanchev S, Škerle J, Began J, Ingr M, Švehlová K, Polovinkin L, Růžička M, Bednárová L, Hadravová R, Poláchová E, Rampírová P, Březinová J, Kašička V, Majer P, Strisovsky K. Sensitive Versatile Fluorogenic Transmembrane Peptide Substrates for Rhomboid Intramembrane Proteases. J Biol Chem 2017; 292:2703-2713. [PMID: 28069810 DOI: 10.1074/jbc.m116.762849] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/05/2017] [Indexed: 11/06/2022] Open
Abstract
Rhomboid proteases are increasingly being explored as potential drug targets, but their potent and specific inhibitors are not available, and strategies for inhibitor development are hampered by the lack of widely usable and easily modifiable in vitro activity assays. Here we address this bottleneck and report on the development of new fluorogenic transmembrane peptide substrates, which are cleaved by several unrelated rhomboid proteases, can be used both in detergent micelles and in liposomes, and contain red-shifted fluorophores that are suitable for high-throughput screening of compound libraries. We show that nearly the entire transmembrane domain of the substrate is important for efficient cleavage, implying that it extensively interacts with the enzyme. Importantly, we demonstrate that in the detergent micelle system, commonly used for the enzymatic analyses of intramembrane proteolysis, the cleavage rate strongly depends on detergent concentration, because the reaction proceeds only in the micelles. Furthermore, we show that the catalytic efficiency and selectivity toward a rhomboid substrate can be dramatically improved by targeted modification of the sequence of its P5 to P1 region. The fluorogenic substrates that we describe and their sequence variants should find wide use in the detection of activity and development of inhibitors of rhomboid proteases.
Collapse
Affiliation(s)
- Anežka Tichá
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the First Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, and
| | - Stancho Stanchev
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Jan Škerle
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43
| | - Jakub Began
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, Prague 128 44
| | - Marek Ingr
- the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43.,the Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Faculty of Technology, nám. T.G. Masaryka 5555, 76001, Zlín, Czech Republic
| | - Kateřina Švehlová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Lucie Polovinkin
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43
| | - Martin Růžička
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43
| | - Lucie Bednárová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Romana Hadravová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Edita Poláchová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Petra Rampírová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Jana Březinová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Václav Kašička
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Pavel Majer
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Kvido Strisovsky
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10,
| |
Collapse
|
28
|
Cordier B, Lemberg M. Probing the Activity of Eukaryotic Rhomboid Proteases In Vitro. Methods Enzymol 2017; 584:99-126. [DOI: 10.1016/bs.mie.2016.09.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
29
|
Cooley JW, Abdine A, Brown M, Chavez J, Lada B, JiJi RD, Ubarretxena-Belandia I. A New Method to Determine the Transmembrane Conformation of Substrates in Intramembrane Proteolysis by Deep-UV Resonance Raman Spectroscopy. Methods Enzymol 2017; 584:207-28. [PMID: 28065264 DOI: 10.1016/bs.mie.2016.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present a new method based on deep-UV resonance Raman spectroscopy to determine the backbone conformation of intramembrane protease substrates. The classical amide vibrational modes reporting on the conformation of just the transmembrane region of the substrate can be resolved from solvent exchangeable regions outside the detergent micelle by partial deuteration of the solvent. In the presence of isotopically triple-labeled intramembrane protease, these amide modes can be accurately measured to monitor the transmembrane conformation of the substrate during intramembrane proteolysis.
Collapse
|
30
|
Abstract
Rhomboids are ubiquitous intramembrane serine proteases that are involved in various signaling pathways. This fascinating class of proteases harbors an active site buried within the lipid milieu. High-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed the catalytic mechanism for rhomboid-mediated proteolysis; however, a quantitative characterization was lacking. Assessing an enzyme's catalytic parameters is important for understanding the details of its proteolytic reaction and regulatory mechanisms. To assay rhomboid protease activity, many challenges exist such as the lipid environment and lack of known substrates. Here, we summarize various enzymatic assays developed over the last decade to study rhomboid protease activity. We present detailed protocols for gel-shift and FRET-based assays, and calculation of KM and Vmax to measure catalytic parameters, using detergent solubilized rhomboids with TatA, the only known substrate for bacterial rhomboids, and the model substrate fluorescently labeled casein.
Collapse
|
31
|
Arutyunova E, Smithers CC, Corradi V, Espiritu AC, Young HS, Tieleman DP, Lemieux MJ. Probing catalytic rate enhancement during intramembrane proteolysis. Biol Chem 2016; 397:907-19. [DOI: 10.1515/hsz-2016-0124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Rhomboids are ubiquitous intramembrane serine proteases involved in various signaling pathways. While the high-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed an active site comprised of a serine-histidine dyad and an extensive oxyanion hole, the molecular details of rhomboid catalysis were unclear because substrates are unknown for most of the family members. Here we used the only known physiological pair of AarA rhomboid with its psTatA substrate to decipher the contribution of catalytically important residues to the reaction rate enhancement. An MD-refined homology model of AarA was used to identify residues important for catalysis. We demonstrated that the AarA active site geometry is strict and intolerant to alterations. We probed the roles of H83 and N87 oxyanion hole residues and determined that substitution of H83 either abolished AarA activity or reduced the transition state stabilization energy (ΔΔG‡) by 3.1 kcal/mol; substitution of N87 decreased ΔΔG‡ by 1.6–3.9 kcal/mol. Substitution M154, a residue conserved in most rhomboids that stabilizes the catalytic general base, to tyrosine, provided insight into the mechanism of nucleophile generation for the catalytic dyad. This study provides a quantitative evaluation of the role of several residues important for hydrolytic efficiency and oxyanion stabilization during intramembrane proteolysis.
Collapse
|
32
|
Abstract
Rhomboid-family intramembrane serine proteases are evolutionarily widespread. Their functions in different organisms are gradually being uncovered and already suggest medical relevance for infectious diseases and cancer. In contrast to these advances, selective inhibitors that could serve as efficient tools for investigation of physiological functions of rhomboids, validation of their disease relevance or as templates for drug development are lacking. In this review I extract what is known about rhomboid protease mechanism and specificity, examine the currently used inhibitors, their mechanism of action and limitations, and conclude by proposing routes for future development of rhomboid protease inhibitors.
Collapse
Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic.
| |
Collapse
|
33
|
Lastun VL, Grieve AG, Freeman M. Substrates and physiological functions of secretase rhomboid proteases. Semin Cell Dev Biol 2016; 60:10-8. [PMID: 27497690 DOI: 10.1016/j.semcdb.2016.07.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/26/2016] [Accepted: 07/31/2016] [Indexed: 02/01/2023]
Abstract
Rhomboids are conserved intramembrane serine proteases with widespread functions. They were the earliest discovered members of the wider rhomboid-like superfamily of proteases and pseudoproteases. The secretase class of rhomboid proteases, distributed through the secretory pathway, are the most numerous in eukaryotes, but our knowledge of them is limited. Here we aim to summarise all that has been published on secretase rhomboids in a concise encyclopaedia of the enzymes, their substrates, and their biological roles. We also discuss emerging themes of how these important enzymes are regulated.
Collapse
|
34
|
Lemberg MK, Adrain C. Inactive rhomboid proteins: New mechanisms with implications in health and disease. Semin Cell Dev Biol 2016; 60:29-37. [PMID: 27378062 DOI: 10.1016/j.semcdb.2016.06.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/25/2016] [Accepted: 06/30/2016] [Indexed: 12/23/2022]
Abstract
Rhomboids, proteases containing an unusual membrane-integral serine protease active site, were first identified in Drosophila, where they fulfill an essential role in epidermal growth factor receptor signaling, by cleaving membrane-tethered growth factor precursors. It has recently become apparent that eukaryotic genomes harbor conserved catalytically inactive rhomboid protease homologs, including derlins and iRhoms. Here we highlight how loss of proteolytic activity was followed in evolution by impressive functional diversification, enabling these pseudoproteases to fulfill crucial roles within the secretory pathway, including protein degradation, trafficking regulation, and inflammatory signaling. We distil the current understanding of the roles of rhomboid pseudoproteases in development and disease. Finally, we address mechanistically how versatile features of proteolytically active rhomboids have been elaborated to serve the sophisticated functions of their pseudoprotease cousins. By comparing functional and structural clues, we highlight common principles shared by the rhomboid superfamily, and make mechanistic predictions.
Collapse
Affiliation(s)
- Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Colin Adrain
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
| |
Collapse
|
35
|
Noy PJ, Swain RK, Khan K, Lodhia P, Bicknell R. Sprouting angiogenesis is regulated by shedding of the C-type lectin family 14, member A (CLEC14A) ectodomain, catalyzed by rhomboid-like 2 protein (RHBDL2). FASEB J 2016; 30:2311-23. [PMID: 26939791 DOI: 10.1096/fj.201500122r] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/18/2016] [Indexed: 11/11/2022]
Abstract
C-type lectin family 14, member A (CLEC14A), is a single-pass transmembrane glycoprotein that is overexpressed in tumor endothelial cells, and it promotes sprouting angiogenesis and modulates endothelial function via interactions with extracellular matrix proteins. Here, we show that CLEC14A is cleaved by rhomboid-like protein 2 (RHBDL2), one of 3 catalytic mammalian rhomboid-like (RHBDL) proteases, but that it is not cleaved by RHBDL1 or -3. Site-directed mutagenesis identified the precise site at which RHBDL2 cleaves CLEC14A, and targeted, small interfering RNAs that knockdown endogenous CLEC14A and RHBDL2 in human endothelial cells validated the specificity of CLEC14A shedding by RHBDL2. Loss of endogenous cleaved CLEC14A increased endothelial migration 2-fold, whereas that addition of recombinant cleaved CLEC14A inhibited the sprouting of human and murine endothelial cells 3-fold in several in vitro models. We assessed the in vivo role of cleaved CLEC14A in angiogenesis by using the rodent subcutaneous sponge implant model, and we found that CLEC14A protein inhibited vascular density by >50%. Finally, we show that cleaved CLEC14A binds to sprouting endothelial tip cells. Our data show that the ectodomain of CLEC14A regulates sprouting angiogenesis and suggests a role for RHBDL2 in endothelial function.-Noy, P. J., Swain, R. K., Khan, K., Lodhia, P., Bicknell, R. Sprouting angiogenesis is regulated by shedding of the C-type lectin family 14, member A (CLEC14A) ectodomain, catalyzed by rhomboid-like 2 protein (RHBDL2).
Collapse
Affiliation(s)
- Peter J Noy
- Angiogenesis Laboratory, Institutes for Cardiovascular Sciences and Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Rajeeb K Swain
- Angiogenesis Laboratory, Institutes for Cardiovascular Sciences and Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kabir Khan
- Angiogenesis Laboratory, Institutes for Cardiovascular Sciences and Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Puja Lodhia
- Angiogenesis Laboratory, Institutes for Cardiovascular Sciences and Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Roy Bicknell
- Angiogenesis Laboratory, Institutes for Cardiovascular Sciences and Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
36
|
|
37
|
Abstract
In Drosophila, rhomboid proteases are active cardinal regulators of epidermal growth factor receptor (EGFR) signaling pathway. iRhom1 and iRhom2, which are inactive homologs of rhomboid intramembrane serine proteases, are lacking essential catalytic residues. These are necessary for maturation and traffickingof tumor necrosis factor-alpha (TNF-α) converting enzyme (TACE) from endoplasmic reticulum (ER) to plasma membrane through Golgi, and associated with the fates of various ligands for EGFR. Recent studies have clarifiedthat the activation or downregulation of EGFR signaling pathways by alteration of iRhoms are connected to several human diseases including tylosis with esophageal cancer (TOC) which is the autosomal dominant syndrom, breast cancer, and Alzheimer's disease. Thus, this review focuses on our understanding of iRhoms and the involved mechanisms in the cellular processes.
Collapse
Affiliation(s)
- Min-Young Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Kyung-Chul Choi
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| |
Collapse
|
38
|
Strisovsky K. Why cells need intramembrane proteases - a mechanistic perspective. FEBS J 2016; 283:1837-45. [DOI: 10.1111/febs.13638] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/19/2015] [Accepted: 12/24/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Prague Czech Republic
| |
Collapse
|
39
|
Wolf EV, Zeissler A, Verhelst SHL. Inhibitor Fingerprinting of Rhomboid Proteases by Activity-Based Protein Profiling Reveals Inhibitor Selectivity and Rhomboid Autoprocessing. ACS Chem Biol 2015. [PMID: 26218717 DOI: 10.1021/acschembio.5b00514] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rhomboid proteases were discovered almost 15 years ago and are structurally the best characterized intramembrane proteases. Apart from the general serine protease inhibitor 3,4-dichloro-isocoumarin (DCI) and a few crystal structures of the Escherichia coli rhomboid GlpG with other inhibitors, there is surprisingly little information about inhibitors of rhomboids from other species, probably because of a lack of general methods to measure inhibition against different rhomboid species. We here present activity-based protein profiling (ABPP) as a general method to screen rhomboids for their activity and inhibition. Using ABPP, we compare the inhibitory capacity of 50 small molecules against 13 different rhomboids. We find one new pan rhomboid inhibitor and several inhibitors that display selectivity. We also demonstrate that inhibition profile and sequence similarity of rhomboids are not related, which suggests that related rhomboids may be selectively inhibited. Finally, by making use of the here discovered inhibitors, we were able to show that two bacterial rhomboids autoprocess themselves in their N-terminal part.
Collapse
Affiliation(s)
- Eliane V. Wolf
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Annett Zeissler
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Steven H. L. Verhelst
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| |
Collapse
|
40
|
Abstract
Proteases regulate a myriad of cell functions, both in normal and disease states. In addition to protein turnover, they regulate a range of signaling processes, including those mediated by Eph receptors and their ephrin ligands. A variety of proteases is reported to directly cleave Ephs and/or ephrins under different conditions, to promote receptor and/or ligand shedding, and regulate receptor/ligand internalisation and signaling. They also cleave other adhesion proteins in response to Eph-ephrin interactions, to indirectly facilitate Eph-mediated functions. Proteases thus contribute to Eph/ephrin mediated changes in cell-cell and cell-matrix interactions, in cell morphology and in cell migration and invasion, in a manner which appears to be tightly regulated by, and co-ordinated with, Eph signaling. This review summarizes the current literature describing the function and regulation of protease activities during Eph/ephrin-mediated cell signaling.
Collapse
Affiliation(s)
- Lakmali Atapattu
- a Department of Biochemistry and Molecular Biology ; Monash University , Victoria ; Australia
| | | | | |
Collapse
|
41
|
Wolf EV, Seybold M, Hadravová R, Strisovsky K, Verhelst SHL. Activity-Based Protein Profiling of Rhomboid Proteases in Liposomes. Chembiochem 2015; 16:1616-21. [PMID: 26032951 DOI: 10.1002/cbic.201500213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 11/07/2022]
Abstract
Although activity-based protein profiling (ABPP) has been used to study a variety of enzyme classes, its application to intramembrane proteases is still in its infancy. Intramembrane proteolysis is an important biochemical mechanism for activating proteins residing within the membrane in a dormant state. Rhomboid proteases (intramembrane serine proteases) are embedded in the lipid bilayers of membranes and occur in all phylogenetic domains. The study of purified rhomboid proteases has mainly been performed in detergent micelle environments. Here we report on the reconstitution of rhomboids in liposomes. Using ABPP, we have been able to detect active rhomboids in large and giant unilamellar vesicles. We have found that the inhibitor profiles of rhomboids in micelles and liposomes are similar, thus validating previous inhibitor screenings. Moreover, fluorescence microscopy experiments on the liposomes constitute the first steps towards activity-based imaging of rhomboid proteases in membrane environments.
Collapse
Affiliation(s)
- Eliane V Wolf
- Center for Integrated Protein Science Munich, Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising (Germany)
| | - Martin Seybold
- Center for Integrated Protein Science Munich, Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising (Germany)
| | - Romana Hadravová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague, 166 10 (Czech Republic)
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague, 166 10 (Czech Republic)
| | - Steven H L Verhelst
- Center for Integrated Protein Science Munich, Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising (Germany). .,Leibniz Institut für Analytische Wissenschaften, ISAS, e.V. Otto-Hahn-Strasse 6b, 44227 Dortmund (Germany). .,Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, Box 802, 3000 Leuven (Belgium).
| |
Collapse
|
42
|
Rastew E, Morf L, Singh U. Entamoeba histolytica rhomboid protease 1 has a role in migration and motility as validated by two independent genetic approaches. Exp Parasitol 2015; 154:33-42. [PMID: 25889553 DOI: 10.1016/j.exppara.2015.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/24/2015] [Accepted: 04/08/2015] [Indexed: 11/25/2022]
Abstract
Rhomboid proteins represent a recently discovered family of intramembrane proteases present in a broad range of organisms and with increasing links to human diseases. The enteric parasite Entamoeba histolytica has evolved multiple mechanisms to adapt to the human host environment and establish infection. Our recent studies identified EhROM1 as a functional E. histolytica rhomboid protease with roles in adhesion to and phagocytosis of host cells. Since those studies were performed in a non-virulent strain, roles in parasite virulence could not be assessed. We focused this study on the comparison and validation of two genetic manipulation techniques: overexpression of a dominant-negative catalytic mutant of EhROM1 and knock down of EhROM1 using a RNAi-based silencing approach followed by functional studies of phenotypic analyses in virulent parasites. Both the EhROM1 catalytic mutant and parasites with EhROM1 downregulation were reduced in cytotoxicity, hemolytic activity, and directional and non-directional transwell migration. Importantly, the role for EhROM1 in cell migration mimics similar roles for rhomboid proteases from mammalian and apicomplexan systems. However, the EhROM1 catalytic mutant and EhROM1 downregulation parasites had different phenotypes for erythrophagocytosis, while complement resistance was not affected in either strain. In summary, in this study we genetically manipulated E. histolytica rhomboid protease EhROM1 by two different approaches and identified similarly attenuated phenotypes by both approaches, suggesting a novel role for EhROM1 in amebic motility.
Collapse
Affiliation(s)
- Elena Rastew
- Department of Internal Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Morf
- Department of Internal Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Upinder Singh
- Department of Internal Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
43
|
Affiliation(s)
- Matthew Freeman
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom;
| |
Collapse
|
44
|
Abstract
Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases.
Collapse
Affiliation(s)
- Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Pauline M Skiba
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Nicola Gale
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Michelle W Mak
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
45
|
Parente J, Casabuono A, Ferrari MC, Paggi RA, De Castro RE, Couto AS, Giménez MI. A rhomboid protease gene deletion affects a novel oligosaccharide N-linked to the S-layer glycoprotein of Haloferax volcanii. J Biol Chem 2014; 289:11304-11317. [PMID: 24596091 DOI: 10.1074/jbc.m113.546531] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhomboid proteases occur in all domains of life; however, their physiological role is not completely understood, and nothing is known of the biology of these enzymes in Archaea. One of the two rhomboid homologs of Haloferax volcanii (RhoII) is fused to a zinc finger domain. Chromosomal deletion of rhoII was successful, indicating that this gene is not essential for this organism; however, the mutant strain (MIG1) showed reduced motility and increased sensitivity to novobiocin. Membrane preparations of MIG1 were enriched in two glycoproteins, identified as the S-layer glycoprotein and an ABC transporter component. The H. volcanii S-layer glycoprotein has been extensively used as a model to study haloarchaeal protein N-glycosylation. HPLC analysis of oligosaccharides released from the S-layer glycoprotein after PNGase treatment revealed that MIG1 was enriched in species with lower retention times than those derived from the parent strain. Mass spectrometry analysis showed that the wild type glycoprotein released a novel oligosaccharide species corresponding to GlcNAc-GlcNAc(Hex)2-(SQ-Hex)6 in contrast to the mutant protein, which contained the shorter form GlcNAc2(Hex)2-SQ-Hex-SQ. A glycoproteomics approach of the wild type glycopeptide fraction revealed Asn-732 peptide fragments linked to the sulfoquinovose-containing oligosaccharide. This work describes a novel N-linked oligosaccharide containing a repeating SQ-Hex unit bound to Asn-732 of the H. volcanii S-layer glycoprotein, a position that had not been reported as glycosylated. Furthermore, this study provides the first insight on the biological role of rhomboid proteases in Archaea, suggesting a link between protein glycosylation and this protease family.
Collapse
Affiliation(s)
- Juliana Parente
- From the Centro de Investigación en Hidratos de Carbono, Departamento de Química Orgánica, Facultad de Ciencias, Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, Buenos Aires, Argentina and
| | - Adriana Casabuono
- From the Centro de Investigación en Hidratos de Carbono, Departamento de Química Orgánica, Facultad de Ciencias, Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, Buenos Aires, Argentina and
| | - María Celeste Ferrari
- the Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-Consejo Nacional de Investigaciones Científicas y Técnicas, Funes 3250 4to nivel, 7600 Mar del Plata, Provincia de Buenos Aires, Argentina
| | - Roberto Alejandro Paggi
- the Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-Consejo Nacional de Investigaciones Científicas y Técnicas, Funes 3250 4to nivel, 7600 Mar del Plata, Provincia de Buenos Aires, Argentina
| | - Rosana Esther De Castro
- the Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-Consejo Nacional de Investigaciones Científicas y Técnicas, Funes 3250 4to nivel, 7600 Mar del Plata, Provincia de Buenos Aires, Argentina
| | - Alicia Susana Couto
- From the Centro de Investigación en Hidratos de Carbono, Departamento de Química Orgánica, Facultad de Ciencias, Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, Buenos Aires, Argentina and
| | - María Inés Giménez
- the Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-Consejo Nacional de Investigaciones Científicas y Técnicas, Funes 3250 4to nivel, 7600 Mar del Plata, Provincia de Buenos Aires, Argentina.
| |
Collapse
|
46
|
Abstract
A primary mode of regulating receptor tyrosine kinase (RTK) signaling is to control access of ligand to its receptor. Many RTK ligands are synthesized as transmembrane proteins. Frequently, the active ligand must be released from the membrane by proteolysis before signaling can occur. Here, we discuss RTK ligand shedding and describe the proteases that catalyze it in flies and mammals. We focus principally on the control of EGF receptor ligand shedding, but also refer to ligands of other RTKs. Two prominent themes emerge. First, control by regulated trafficking and cellular compartmentalization of the proteases and their ligand substrates plays a key role in shedding. Second, many external signals converge on the shedding proteases and their control machinery. Proteases therefore act as regulatory hubs that integrate information that the cell receives and translate it into precise outgoing signals. The activation of signaling by proteases is therefore an essential element of the cellular communication machinery.
Collapse
Affiliation(s)
- Colin Adrain
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | | |
Collapse
|
47
|
Sibley LD. The roles of intramembrane proteases in protozoan parasites. Biochim Biophys Acta 2013; 1828:2908-15. [PMID: 24099008 DOI: 10.1016/j.bbamem.2013.04.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/02/2013] [Accepted: 04/11/2013] [Indexed: 11/30/2022]
Abstract
Intramembrane proteolysis is widely conserved throughout different forms of life, with three major types of proteases being known for their ability to cleave peptide bonds directly within the transmembrane domains of their substrates. Although intramembrane proteases have been extensively studied in humans and model organisms, they have only more recently been investigated in protozoan parasites, where they turn out to play important and sometimes unexpected roles. Signal peptide peptidases are involved in endoplasmic reticulum (ER) quality control and signal peptide degradation from exported proteins. Recent studies suggest that repurposing inhibitors developed for blocking presenilins may be useful for inhibiting the growth of Plasmodium, and possibly other protozoan parasites, by blocking signal peptide peptidases. Rhomboid proteases, originally described in the fly, are also widespread in parasites, and are especially expanded in apicomplexans. Their study in parasites has revealed novel roles that expand our understanding of how these proteases function. Within this diverse group of parasites, rhomboid proteases contribute to processing of adhesins involved in attachment, invasion, intracellular replication, phagocytosis, and immune evasion, placing them at the vertex of host-parasite interactions. This article is part of a Special Issue entitled: Intramembrane Proteases.
Collapse
Affiliation(s)
- L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
48
|
Vinothkumar KR, Freeman M. Intramembrane proteolysis by rhomboids: catalytic mechanisms and regulatory principles. Curr Opin Struct Biol 2013; 23:851-8. [DOI: 10.1016/j.sbi.2013.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/06/2013] [Accepted: 07/19/2013] [Indexed: 12/20/2022]
|
49
|
Wolf EV, Zeißler A, Vosyka O, Zeiler E, Sieber S, Verhelst SH. A new class of rhomboid protease inhibitors discovered by activity-based fluorescence polarization. PLoS One 2013; 8:e72307. [PMID: 23991088 DOI: 10.1371/journal.pone.0072307] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/10/2013] [Indexed: 01/01/2023] Open
Abstract
Rhomboids are intramembrane serine proteases that play diverse biological roles, including some that are of potential therapeutical relevance. Up to date, rhomboid inhibitor assays are based on protein substrate cleavage. Although rhomboids have an overlapping substrate specificity, substrates cannot be used universally. To overcome the need for substrates, we developed a screening assay using fluorescence polarization activity-based protein profiling (FluoPol ABPP) that is compatible with membrane proteases. With FluoPol ABPP, we identified new inhibitors for the E. coli rhomboid GlpG. Among these was a structural class that has not yet been reported as rhomboid inhibitors: β-lactones. They form covalent and irreversible complexes with the active site serine of GlpG. The presence of alkyne handles on the β-lactones also allowed activity-based labeling. Overall, these molecules represent a new scaffold for future inhibitor and activity-based probe development, whereas the assay will allow inhibitor screening of ill-characterized membrane proteases.
Collapse
|
50
|
Abstract
Rhomboid protease was first discovered in Drosophila. Mutation of the fly gene interfered with growth factor signaling and produced a characteristic phenotype of a pointed head skeleton. The name rhomboid has since been widely used to describe a large family of related membrane proteins that have diverse biological functions but share a common catalytic core domain composed of six membrane-spanning segments. Most rhomboid proteases cleave membrane protein substrates near the N terminus of their transmembrane domains. How these proteases function within the confines of the membrane is not completely understood. Recent progress in crystallographic analysis of the Escherichia coli rhomboid protease GlpG in complex with inhibitors has provided new insights into the catalytic mechanism of the protease and its conformational change. Improved biochemical assays have also identified a substrate sequence motif that is specifically recognized by many rhomboid proteases.
Collapse
Affiliation(s)
- Ya Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA.
| | | | | |
Collapse
|