1
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Yokoyama T, Yamagata Y, Honna S, Mizuno S, Katagiri S, Oi R, Nogi T, Hizukuri Y, Akiyama Y. S2P intramembrane protease RseP degrades small membrane proteins and suppresses the cytotoxicity of intrinsic toxin HokB. mBio 2023; 14:e0108623. [PMID: 37409810 PMCID: PMC10470546 DOI: 10.1128/mbio.01086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/25/2023] [Indexed: 07/07/2023] Open
Abstract
The site2-protease (S2P) family of intramembrane proteases (IMPs) is conserved in all kingdoms of life and cleaves transmembrane proteins within the membrane to regulate and maintain various cellular activities. RseP, an Escherichia coli S2P peptidase, is involved in the regulation of gene expression through the regulated cleavage of the two target membrane proteins (RseA and FecR) and in membrane quality control through the proteolytic elimination of remnant signal peptides. RseP is expected to have additional substrates and to be involved in other cellular processes. Recent studies have shown that cells express small membrane proteins (SMPs; single-spanning membrane proteins of approximately 50-100 amino acid residues) with crucial cellular functions. However, little is known about their metabolism, which affects their functions. This study investigated the possible RseP-catalyzed cleavage of E. coli SMPs based on the apparent similarity of the sizes and structures of SMPs to those of remnant signal peptides. We screened SMPs cleaved by RseP in vivo and in vitro and identified 14 SMPs, including HokB, an endogenous toxin that induces persister formation, as potential substrates. We demonstrated that RseP suppresses the cytotoxicity and biological functions of HokB. The identification of several SMPs as novel potential substrates of RseP provides a clue to a comprehensive understanding of the cellular roles of RseP and other S2P peptidases and highlights a novel aspect of the regulation of SMPs. IMPORTANCE Membrane proteins play an important role in cell activity and survival. Thus, understanding their dynamics, including proteolytic degradation, is crucial. E. coli RseP, an S2P family intramembrane protease, cleaves membrane proteins to regulate gene expression in response to environmental changes and to maintain membrane quality. To identify novel substrates of RseP, we screened small membrane proteins (SMPs), a group of proteins that have recently been shown to have diverse cellular functions, and identified 14 potential substrates. We also showed that RseP suppresses the cytotoxicity of the intrinsic toxin, HokB, an SMP that has been reported to induce persister cell formation, by degrading it. These findings provide new insights into the cellular roles of S2P peptidases and the functional regulation of SMPs.
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Affiliation(s)
- Tatsuhiko Yokoyama
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yutaro Yamagata
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Saisei Honna
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Shinya Mizuno
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Shizuka Katagiri
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Rika Oi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Yohei Hizukuri
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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2
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Bohg C, Öster C, Türkaydin B, Lisurek M, Sanchez-Carranza P, Lange S, Utesch T, Sun H, Lange A. The opening dynamics of the lateral gate regulates the activity of rhomboid proteases. SCIENCE ADVANCES 2023; 9:eadh3858. [PMID: 37467320 PMCID: PMC10355837 DOI: 10.1126/sciadv.adh3858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
Rhomboid proteases hydrolyze substrate helices within the lipid bilayer to release soluble domains from the membrane. Here, we investigate the mechanism of activity regulation for this unique but wide-spread protein family. In the model rhomboid GlpG, a lateral gate formed by transmembrane helices TM2 and TM5 was previously proposed to allow access of the hydrophobic substrate to the shielded hydrophilic active site. In our study, we modified the gate region and either immobilized the gate by introducing a maleimide-maleimide (M2M) crosslink or weakened the TM2/TM5 interaction network through mutations. We used solid-state nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations, and molecular docking to investigate the resulting effects on structure and dynamics on the atomic level. We find that variants with increased dynamics at TM5 also exhibit enhanced activity, whereas introduction of a crosslink close to the active site strongly reduces activity. Our study therefore establishes a strong link between the opening dynamics of the lateral gate in rhomboid proteases and their enzymatic activity.
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Affiliation(s)
- Claudia Bohg
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Carl Öster
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Berke Türkaydin
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Michael Lisurek
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Pascal Sanchez-Carranza
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Sascha Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Tillmann Utesch
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Han Sun
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Adam Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
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3
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Contreras W, Bazan JF, Mentrup T. The transmembrane domain of Frey1 harbors a transplantable inhibitory motif for intramembrane proteases. Cell Mol Life Sci 2023; 80:170. [PMID: 37261541 DOI: 10.1007/s00018-023-04823-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
Although aspartic intramembrane-cleaving proteases (I-CLIPs) are crucial switches of multiple signaling pathways and involved in several devastating diseases, little is known about their physiological regulation. We have recently identified Frey regulator of sperm-oocyte fusion 1 (Frey1) as an inhibitory protein of Signal Peptide Peptidase-like 2c (SPPL2c), a member of this protease family. Employing structure modeling along with cell-based inhibition and interaction studies, we identify a short motif within the Frey1 transmembrane domain essential for inhibition of SPPL2c. Intriguingly, this motif can be transplanted to the SPPL2c substrate PLN, thereby transforming it into an inhibitor of this enzyme. It can be adopted for the generation of Notch1-based γ-Secretase inhibitors demonstrating its versatile use among aspartic I-CLIPs. In summary, we describe a mechanism of aspartic I-CLIP inhibition which allows the targeted generation of specific inhibitors of these enzymes and might enable the identification of endogenous negative regulators of these enzymes.
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Affiliation(s)
- Whendy Contreras
- Institute of Physiological Chemistry, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - J Fernando Bazan
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Torben Mentrup
- Institute of Physiological Chemistry, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany.
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4
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Poláchová E, Bach K, Heuten E, Stanchev S, Tichá A, Lampe P, Majer P, Langer T, Lemberg MK, Stříšovský K. Chemical Blockage of the Mitochondrial Rhomboid Protease PARL by Novel Ketoamide Inhibitors Reveals Its Role in PINK1/Parkin-Dependent Mitophagy. J Med Chem 2022; 66:251-265. [PMID: 36540942 PMCID: PMC9841525 DOI: 10.1021/acs.jmedchem.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitochondrial rhomboid protease PARL regulates mitophagy by balancing intramembrane proteolysis of PINK1 and PGAM5. It has been implicated in the pathogenesis of Parkinson's disease, but its investigation as a possible therapeutic target is challenging in this context because genetic deficiency of PARL may result in compensatory mechanisms. To address this problem, we undertook a hitherto unavailable chemical biology strategy. We developed potent PARL-targeting ketoamide inhibitors and investigated the effects of acute PARL suppression on the processing status of PINK1 intermediates and on Parkin activation. This approach revealed that PARL inhibition leads to a robust activation of the PINK1/Parkin pathway without major secondary effects on mitochondrial properties, which demonstrates that the pharmacological blockage of PARL to boost PINK1/Parkin-dependent mitophagy is a feasible approach to examine novel therapeutic strategies for Parkinson's disease. More generally, this study showcases the power of ketoamide inhibitors for cell biological studies of rhomboid proteases.
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Affiliation(s)
- Edita Poláchová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic,First
Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, Czech Republic
| | - Kathrin Bach
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic,Department
of Molecular Genetics, Faculty of Science, Charles University, Viničná 5, Prague 128 44, Czech Republic
| | - Elena Heuten
- Center
for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer
Feld 282, Heidelberg 69120, Germany,Center
for Biochemistry and Cologne Excellence Cluster on Cellular Stress
Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany
| | - Stancho Stanchev
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic
| | - Anežka Tichá
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic
| | - Philipp Lampe
- Institute
for Genetics and Cologne Excellence Cluster on Cellular Stress Responses
in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany
| | - Pavel Majer
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic
| | - Thomas Langer
- Institute
for Genetics and Cologne Excellence Cluster on Cellular Stress Responses
in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany,Center
for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany,Max-Planck-Institute
for Biology of Ageing, Joseph-Stelzmann-Str. 9b, Cologne 50931, Germany
| | - Marius K. Lemberg
- Center
for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer
Feld 282, Heidelberg 69120, Germany,Center
for Biochemistry and Cologne Excellence Cluster on Cellular Stress
Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany,
| | - Kvido Stříšovský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic,
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5
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Siebert V, Silber M, Heuten E, Muhle-Goll C, Lemberg MK. Cleavage of mitochondrial homeostasis regulator PGAM5 by the intramembrane protease PARL is governed by transmembrane helix dynamics and oligomeric state. J Biol Chem 2022; 298:102321. [PMID: 35921890 PMCID: PMC9436811 DOI: 10.1016/j.jbc.2022.102321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/07/2022] Open
Abstract
The intramembrane protease PARL acts as a crucial mitochondrial safeguard by cleaving the mitophagy regulators PINK1 and PGAM5. Depending on the stress level, PGAM5 can either stimulate cell survival or cell death. In contrast to PINK1, which is constantly cleaved in healthy mitochondria and only active when the inner mitochondrial membrane is depolarized, PGAM5 processing is inversely regulated. However, determinants of PGAM5 that indicate it as a conditional substrate for PARL have not been rigorously investigated, and it is unclear how uncoupling the mitochondrial membrane potential affects its processing compared to that of PINK1. Here, we show that several polar transmembrane residues in PGAM5 distant from the cleavage site serve as determinants for its PARL-catalyzed cleavage. Our NMR analysis indicates that a short N-terminal amphipathic helix, followed by a kink and a C-terminal transmembrane helix harboring the scissile peptide bond are key for a productive interaction with PARL. Furthermore, we also show that PGAM5 is stably inserted into the inner mitochondrial membrane until uncoupling the membrane potential triggers its disassembly into monomers, which are then cleaved by PARL. In conclusion, we propose a model in which PGAM5 is slowly processed by PARL-catalyzed cleavage that is influenced by multiple hierarchical substrate features, including a membrane potential–dependent oligomeric switch.
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6
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Vasconcelos-Cardoso M, Batista-Almeida D, Rios-Barros LV, Castro-Gomes T, Girao H. Cellular and molecular mechanisms underlying plasma membrane functionality and integrity. J Cell Sci 2022; 135:275922. [PMID: 35801807 DOI: 10.1242/jcs.259806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plasma membrane not only protects the cell from the extracellular environment, acting as a selective barrier, but also regulates cellular events that originate at the cell surface, playing a key role in various biological processes that are essential for the preservation of cell homeostasis. Therefore, elucidation of the mechanisms involved in the maintenance of plasma membrane integrity and functionality is of utmost importance. Cells have developed mechanisms to ensure the quality of proteins that inhabit the cell surface, as well as strategies to cope with injuries inflicted to the plasma membrane. Defects in these mechanisms can lead to the development or onset of several diseases. Despite the importance of these processes, a comprehensive and holistic perspective of plasma membrane quality control is still lacking. To tackle this gap, in this Review, we provide a thorough overview of the mechanisms underlying the identification and targeting of membrane proteins that are to be removed from the cell surface, as well as the membrane repair mechanisms triggered in both physiological and pathological conditions. A better understanding of the mechanisms underlying protein quality control at the plasma membrane can reveal promising and unanticipated targets for the development of innovative therapeutic approaches.
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Affiliation(s)
- Maria Vasconcelos-Cardoso
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Daniela Batista-Almeida
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Laura Valeria Rios-Barros
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Thiago Castro-Gomes
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Henrique Girao
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
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7
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A single residue deletion in the barley HKT1;5 P189 variant restores plasma membrane localisation but not Na + conductance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183669. [PMID: 34139196 DOI: 10.1016/j.bbamem.2021.183669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
Leaf Na+ exclusion, mediated by plasma membrane-localised Class 1 High-affinity potassium (K+) Transporters (HKTs), is a key mechanism contributing to salinity tolerance of several major crop plants. We determined previously that the leucine to proline residue substitution at position 189 (L189P) in barley HvHKT1;5 disrupts its characteristic plasma membrane localisation and Na+ conductance. Here, we focus on a surprising observation that a single residue deletion of methionine at position 372 (M372del) within the conserved VMMYL motif in plant HKTs, restores plasma membrane localisation but not Na+ conductance in HvHKT1;5 P189. To clarify why the singular M372 deletion regains plasma membrane localisation, we built 3D models and defined α-helical assembly pathways of the P189 M372del mutant, and compared these findings to the wild-type protein, and the HvHKT1;5 L189 variant and its M372del mutant. We find that α-helical association and assembly pathways in HvHKT1;5 proteins fall in two contrasting categories. Inspections of structural flexibility through molecular dynamics simulations revealed that the conformational states of HvHKT1;5 P189 diverge from those of the L189 variant and M372del mutants. We propose that M372del in HvHKT1;5 P189 instigates structural rearrangements allowing routing to the plasma membrane, while the restoration of conductance would require further interventions. We integrate the microscopy, electrophysiology, and biocomputational data and discuss how a profound structural change in HvHKT1;5 P189 M372del impacts its α-helical protein association pathway and flexibility, and how these features underlie a delicate balance leading to restoring plasma membrane localisation but not Na+ conductance.
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8
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Yokoyama T, Niinae T, Tsumagari K, Imami K, Ishihama Y, Hizukuri Y, Akiyama Y. The Escherichia coli S2P intramembrane protease RseP regulates ferric citrate uptake by cleaving the sigma factor regulator FecR. J Biol Chem 2021; 296:100673. [PMID: 33865858 PMCID: PMC8144685 DOI: 10.1016/j.jbc.2021.100673] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli RseP, a member of the site-2 protease family of intramembrane proteases, is involved in the activation of the σE extracytoplasmic stress response and elimination of signal peptides from the cytoplasmic membrane. However, whether RseP has additional cellular functions is unclear. In this study, we used mass spectrometry-based quantitative proteomic analysis to search for new substrates that might reveal unknown physiological roles for RseP. Our data showed that the levels of several Fec system proteins encoded by the fecABCDE operon (fec operon) were significantly decreased in an RseP-deficient strain. The Fec system is responsible for the uptake of ferric citrate, and the transcription of the fec operon is controlled by FecI, an alternative sigma factor, and its regulator FecR, a single-pass transmembrane protein. Assays with a fec operon expression reporter demonstrated that the proteolytic activity of RseP is essential for the ferric citrate-dependent upregulation of the fec operon. Analysis using the FecR protein and FecR-derived model proteins showed that FecR undergoes sequential processing at the membrane and that RseP participates in the last step of this sequential processing to generate the N-terminal cytoplasmic fragment of FecR that participates in the transcription of the fec operon with FecI. A shortened FecR construct was not dependent on RseP for activation, confirming this cleavage step is the essential and sufficient role of RseP. Our study unveiled that E. coli RseP performs the intramembrane proteolysis of FecR, a novel physiological role that is essential for regulating iron uptake by the ferric citrate transport system.
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Affiliation(s)
- Tatsuhiko Yokoyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomoya Niinae
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuya Tsumagari
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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9
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Miyake T, Hizukuri Y, Akiyama Y. Involvement of a Membrane-Bound Amphiphilic Helix in Substrate Discrimination and Binding by an Escherichia coli S2P Peptidase RseP. Front Microbiol 2020; 11:607381. [PMID: 33329500 PMCID: PMC7728848 DOI: 10.3389/fmicb.2020.607381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/05/2020] [Indexed: 11/21/2022] Open
Abstract
Intramembrane proteases (IMPs) are a unique class of proteases that catalyze the proteolysis within the membrane and regulate diverse cellular processes in various organisms. RseP, an Escherichia coli site-2 protease (S2P) family IMP, is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-σE) protein RseA. Extracytoplasmic stresses trigger a sequential cleavage of RseA, in which first DegS cleaves off its periplasmic domain, and RseP catalyzes the second cleavage of RseA. The two tandem-arranged periplasmic PDZ (PDZ tandem) domains of RseP serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP IMP domain. However, RseP’s substrate recognition mechanism is not fully understood. Here, we found that a periplasmic region of RseP, located downstream of the PDZ tandem, contains a segment (named H1) predicted to form an amphiphilic helix. Bacterial S2P homologs with various numbers of PDZ domains have a similar amphiphilic helix in the corresponding region. We demonstrated that the H1 segment forms a partially membrane-embedded amphiphilic helix on the periplasmic surface of the membrane. Systematic and random mutagenesis analyses revealed that the H1 helix is important for the stability and proteolytic function of RseP and that mutations in the H1 segment can affect the PDZ-mediated substrate discrimination. Cross-linking experiments suggested that H1 directly interacts with the DegS-cleaved form of RseA. We propose that H1 acts as an adaptor required for proper arrangement of the PDZ tandem domain to perform its filter function and for substrate positioning for its efficient cleavage.
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Affiliation(s)
- Takuya Miyake
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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10
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Hitzenberger M, Götz A, Menig S, Brunschweiger B, Zacharias M, Scharnagl C. The dynamics of γ-secretase and its substrates. Semin Cell Dev Biol 2020; 105:86-101. [DOI: 10.1016/j.semcdb.2020.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022]
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11
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Zaucha J, Heinzinger M, Kulandaisamy A, Kataka E, Salvádor ÓL, Popov P, Rost B, Gromiha MM, Zhorov BS, Frishman D. Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins. Brief Bioinform 2020; 22:5872174. [PMID: 32672331 DOI: 10.1093/bib/bbaa132] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
Membrane proteins are unique in that they interact with lipid bilayers, making them indispensable for transporting molecules and relaying signals between and across cells. Due to the significance of the protein's functions, mutations often have profound effects on the fitness of the host. This is apparent both from experimental studies, which implicated numerous missense variants in diseases, as well as from evolutionary signals that allow elucidating the physicochemical constraints that intermembrane and aqueous environments bring. In this review, we report on the current state of knowledge acquired on missense variants (referred to as to single amino acid variants) affecting membrane proteins as well as the insights that can be extrapolated from data already available. This includes an overview of the annotations for membrane protein variants that have been collated within databases dedicated to the topic, bioinformatics approaches that leverage evolutionary information in order to shed light on previously uncharacterized membrane protein structures or interaction interfaces, tools for predicting the effects of mutations tailored specifically towards the characteristics of membrane proteins as well as two clinically relevant case studies explaining the implications of mutated membrane proteins in cancer and cardiomyopathy.
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Affiliation(s)
- Jan Zaucha
- Department of Bioinformatics of the TUM School of Life Sciences Weihenstephan in Freising, Germany
| | - Michael Heinzinger
- Department of Informatics, Bioinformatics and Computational Biology of the TUM Faculty of Informatics in Garching, Germany
| | - A Kulandaisamy
- Department of Biotechnology of the IIT Bhupat and Jyoti Mehta School of BioSciences in Madras, India
| | - Evans Kataka
- Department of Bioinformatics of the TUM School of Life Sciences Weihenstephan in Freising, Germany
| | - Óscar Llorian Salvádor
- Department of Informatics, Bioinformatics and Computational Biology of the TUM Faculty of Informatics in Garching, Germany
| | - Petr Popov
- Center for Computational and Data-Intensive Science and Engineering of the Skolkovo Institute of Science and Technology in Moscow, Russia
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology at the TUM Faculty of Informatics in Garching, Germany
| | | | - Boris S Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University in Hamilton, Canada
| | - Dmitrij Frishman
- Department of Bioinformatics at the TUM School of Life Sciences Weihenstephan in Freising, Germany
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12
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The Metastable XBP1u Transmembrane Domain Defines Determinants for Intramembrane Proteolysis by Signal Peptide Peptidase. Cell Rep 2020; 26:3087-3099.e11. [PMID: 30865896 DOI: 10.1016/j.celrep.2019.02.057] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/07/2018] [Accepted: 02/14/2019] [Indexed: 11/23/2022] Open
Abstract
Unspliced XBP1 mRNA encodes XBP1u, the transcriptionally inert variant of the unfolded protein response (UPR) transcription factor XBP1s. XBP1u targets its mRNA-ribosome-nascent-chain-complex to the endoplasmic reticulum (ER) to facilitate UPR activation and prevents overactivation. Yet, its membrane association is controversial. Here, we use cell-free translocation and cellular assays to define a moderately hydrophobic stretch in XBP1u that is sufficient to mediate insertion into the ER membrane. Mutagenesis of this transmembrane (TM) region reveals residues that facilitate XBP1u turnover by an ER-associated degradation route that is dependent on signal peptide peptidase (SPP). Furthermore, the impact of these mutations on TM helix dynamics was assessed by residue-specific amide exchange kinetics, evaluated by a semi-automated algorithm. Based on our results, we suggest that SPP-catalyzed intramembrane proteolysis of TM helices is not only determined by their conformational flexibility, but also by side-chain interactions near the scissile peptide bond with the enzyme's active site.
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13
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Knopf JD, Landscheidt N, Pegg CL, Schulz BL, Kühnle N, Chao CW, Huck S, Lemberg MK. Intramembrane protease RHBDL4 cleaves oligosaccharyltransferase subunits to target them for ER-associated degradation. J Cell Sci 2020; 133:jcs243790. [PMID: 32005703 DOI: 10.1242/jcs.243790] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 08/31/2023] Open
Abstract
The endoplasmic reticulum (ER)-resident intramembrane rhomboid protease RHBDL4 generates metastable protein fragments and together with the ER-associated degradation (ERAD) machinery provides a clearance mechanism for aberrant and surplus proteins. However, the endogenous substrate spectrum and with that the role of RHBDL4 in physiological ERAD is mainly unknown. Here, we use a substrate trapping approach in combination with quantitative proteomics to identify physiological RHBDL4 substrates. This revealed oligosaccharyltransferase (OST) complex subunits such as the catalytic active subunit STT3A as substrates for the RHBDL4-dependent ERAD pathway. RHBDL4-catalysed cleavage inactivates OST subunits by triggering dislocation into the cytoplasm and subsequent proteasomal degradation. RHBDL4 thereby controls the abundance and activity of OST, suggesting a novel link between the ERAD machinery and glycosylation tuning.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nina Landscheidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nathalie Kühnle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Chao-Wei Chao
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Simon Huck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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14
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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] [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.
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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
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15
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Götz A, Högel P, Silber M, Chaitoglou I, Luy B, Muhle-Goll C, Scharnagl C, Langosch D. Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer's Disease Mutant of APP. Sci Rep 2019; 9:5321. [PMID: 30926830 PMCID: PMC6440955 DOI: 10.1038/s41598-019-41766-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Cleavage of the amyloid precursor protein's (APP) transmembrane domain (TMD) by γ-secretase is a crucial step in the aetiology of Alzheimer's Disease (AD). Mutations in the APP TMD alter cleavage and lead to familial forms of AD (FAD). The majority of FAD mutations shift the preference of initial cleavage from ε49 to ε48, thus raising the AD-related Aβ42/Aβ40 ratio. The I45T mutation is among the few FAD mutations that do not alter ε-site preference, while it dramatically reduces the efficiency of ε-cleavage. Here, we investigate the impact of the I45T mutation on the backbone dynamics of the substrate TMD. Amide exchange experiments and molecular dynamics simulations in solvent and a lipid bilayer reveal an increased stability of amide hydrogen bonds at the ζ- and γ-cleavage sites. Stiffening of the H-bond network is caused by an additional H-bond between the T45 side chain and the TMD backbone, which alters dynamics within the cleavage domain. In particular, the increased H-bond stability inhibits an upward movement of the ε-sites in the I45T mutant. Thus, an altered presentation of ε-sites to the active site of γ-secretase as a consequence of restricted local flexibility provides a rationale for reduced ε-cleavage efficiency of the I45T mutant.
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Grants
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Helmholtz-Gemeinschaft (Helmholtz Association)
- Leibniz Supercomputing Centre: Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften, Boltzmannstraße 1, 85748 Garching bei München, Germany, WEB: https://www.lrz.de Gauss Centre for Supercomputing: GCS-Geschäftsstelle Bonn, Ahrstrasse 45, 53175 Bonn, Germany, WEB: http://www.gauss-centre.eu
- Center for Integrated Protein Science: Munich Center For Integrated Protein Science (CIPSM), Butenandtstr. 5 - 13, 81377 Munich, Germany, WEB: http://www.cipsm.de/ Leibniz Supercomputing Centre: Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften, Boltzmannstraße 1, 85748 Garching bei München, Germany, WEB: https://www.lrz.de
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Affiliation(s)
- Alexander Götz
- Lehrstuhl für Physik synthetischer Biosysteme (E14), Technische Universität München, Maximus-von-Imhof Forum 4, 85354, Freising, Germany
| | - Philipp Högel
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Mara Silber
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Iro Chaitoglou
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Christina Scharnagl
- Lehrstuhl für Physik synthetischer Biosysteme (E14), Technische Universität München, Maximus-von-Imhof Forum 4, 85354, Freising, Germany.
| | - Dieter Langosch
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
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16
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Recinto SJ, Paschkowsky S, Munter LM. An alternative processing pathway of APP reveals two distinct cleavage modes for rhomboid protease RHBDL4. Biol Chem 2018; 399:1399-1408. [DOI: 10.1515/hsz-2018-0259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/28/2018] [Indexed: 02/02/2023]
Abstract
AbstractSince the first genetic description of a rhomboid inDrosophila melanogaster, tremendous efforts have been geared towards elucidating the proteolytic mechanism of this particular class of intramembrane proteases. In particular, mammalian rhomboid proteases sparked our interest and we aimed to investigate the human homologue RHBDL4. In light of our recent finding of the amyloid precursor protein (APP) family as efficient substrates of RHBDL4, we were enticed to further study the specific proteolytic mechanism of this enzyme by comparing cleavage patterns of wild type APP and APP TMS chimeras. Here, we demonstrate that the introduction of positively charged amino acid residues in the TMS redirects the RHBDL4-mediated cleavage of APP from its ectodomain closer towards the TMS, possibly inducing an ER-associated degradation (ERAD) of the substrate. In addition, we concluded that the cytoplasmic tail and proposed palmitoylation sites in the ectodomain of APP are not essential for the RHBDL4-mediated APP processing. In summary, our previously identified APP ectodomain cleavages by RHBDL4 are a subsidiary mechanism to the proposed RHBDL4-mediated ERAD of substrates likely through a single cleavage near or within the TMS.
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17
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Zhou H, Yu H, Zhao X, Yang L, Huang X. Molecular dynamics simulations investigate the pathway of substrate entry active site of rhomboid protease. J Biomol Struct Dyn 2018; 37:3445-3455. [PMID: 30175657 DOI: 10.1080/07391102.2018.1517609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Rhomboid proteases can catalyze peptide bond cleavage and participate in abundant biological processes encompassing all branches of life; however, the pathway for substrate entry into its active site remains ambiguous. Here, the two possible pathways are preliminarily determined through molecular dynamics: One pathway is between Tm2 and Tm5, and the other is between Loop3 and Loop5. Then, the umbrella sampling simulations are performed to investigate the more feasible pathway for substrate entry. The results show that free energy barriers along the two pathways are similar; in the pathway 1, Trp236 and Trp157 as pivotal residues are responsible for the rotation of substrate in the binding process; in the pathway 2, among some important residues, the residue His150 plays an important role in substrate entry. Further, combining with previous experiment results, it is concluded that the substrate is inclined to enter into the active site along pathway 2. Our results are important for further understanding the function and catalysis mechanism of rhomboid proteases. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hua Zhou
- a Institute of Theoretical Chemistry , Jilin University , Changchun , China
| | - Hui Yu
- b College of Chemistry and Biology , Beihua University , Jilin , China
| | - Xi Zhao
- a Institute of Theoretical Chemistry , Jilin University , Changchun , China
| | - Lianjuan Yang
- c The Fungal Reference Laboratory of Shanghai Dermatology Hospital , Shanghai , China
| | - Xuri Huang
- a Institute of Theoretical Chemistry , Jilin University , Changchun , China
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18
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Lichtenthaler SF, Lemberg MK, Fluhrer R. Proteolytic ectodomain shedding of membrane proteins in mammals-hardware, concepts, and recent developments. EMBO J 2018; 37:e99456. [PMID: 29976761 PMCID: PMC6068445 DOI: 10.15252/embj.201899456] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/05/2018] [Accepted: 06/18/2018] [Indexed: 12/14/2022] Open
Abstract
Proteolytic removal of membrane protein ectodomains (ectodomain shedding) is a post-translational modification that controls levels and function of hundreds of membrane proteins. The contributing proteases, referred to as sheddases, act as important molecular switches in processes ranging from signaling to cell adhesion. When deregulated, ectodomain shedding is linked to pathologies such as inflammation and Alzheimer's disease. While proteases of the "a disintegrin and metalloprotease" (ADAM) and "beta-site APP cleaving enzyme" (BACE) families are widely considered as sheddases, in recent years a much broader range of proteases, including intramembrane and soluble proteases, were shown to catalyze similar cleavage reactions. This review demonstrates that shedding is a fundamental process in cell biology and discusses the current understanding of sheddases and their substrates, molecular mechanisms and cellular localizations, as well as physiological functions of protein ectodomain shedding. Moreover, we provide an operational definition of shedding and highlight recent conceptual advances in the field. While new developments in proteomics facilitate substrate discovery, we expect that shedding is not a rare exception, but rather the rule for many membrane proteins, and that many more interesting shedding functions await discovery.
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Affiliation(s)
- Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, Klinikum rechts der Isar, School of Medicine, and Institute for Advanced Study, Technical University Munich, Munich, Germany
- Munich Center for Systems Neurology (SyNergy), Munich, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Regina Fluhrer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedizinisches Centrum (BMC), Ludwig-Maximilians University of Munich, Munich, Germany
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19
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Voytyuk I, De Strooper B, Chávez-Gutiérrez L. Modulation of γ- and β-Secretases as Early Prevention Against Alzheimer's Disease. Biol Psychiatry 2018; 83:320-327. [PMID: 28918941 DOI: 10.1016/j.biopsych.2017.08.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 01/18/2023]
Abstract
The genetic evidence implicating amyloid-β in the initial stage of Alzheimer's disease is unequivocal. However, the long biochemical and cellular prodromal phases of the disease suggest that dementia is the result of a series of molecular and cellular cascades whose nature and connections remain unknown. Therefore, it is unlikely that treatments directed at amyloid-β will have major clinical effects in the later stages of the disease. We discuss the two major candidate therapeutic targets to lower amyloid-β in a preventive mode, i.e., γ- and β-secretase; the rationale behind these two targets; and the current state of the field.
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Affiliation(s)
- Iryna Voytyuk
- KU Leuven Department for Neurosciences, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Bart De Strooper
- KU Leuven Department for Neurosciences, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; UK Dementia Research Institute, University College, London, United Kingdom.
| | - Lucía Chávez-Gutiérrez
- KU Leuven Department for Neurosciences, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
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20
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Martin SJ. The FEBS Journal in 2018 - putting a bit of color in your life, and your figures. FEBS J 2018; 285:4-7. [PMID: 29314600 DOI: 10.1111/febs.14365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Seamus Martin holds the Smurfit Chair of Medical Genetics at the Smurfit Institute of Genetics, Trinity College Dublin, Ireland. He works on all aspects of cell death control and is especially interested in the links between cell death, cell stress and inflammation. He received the GlaxoSmithKline Award of The Biochemical Society (2006) and The RDS-Irish Times Boyle Medal (2015) for his work on the role of caspases in apoptosis and was elected to the Royal Irish Academy in 2006 and EMBO in 2009. He is the Editor-in-Chief of The FEBS Journal since 2014.
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Affiliation(s)
- Seamus J Martin
- The FEBS Journal Editorial Office, Cambridge, UK.,Department of Genetics, Trinity College, Dublin, Ireland
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21
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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] [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
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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.
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22
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Shokhen M, Albeck A. How does the exosite of rhomboid protease affect substrate processing and inhibition? Protein Sci 2017; 26:2355-2366. [PMID: 28884847 DOI: 10.1002/pro.3294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 09/03/2017] [Indexed: 12/24/2022]
Abstract
Rhomboid proteases constitute a family of intramembrane serine proteases ubiquitous in all forms of life. They differ in many aspects from their soluble counterparts. We applied molecular dynamics (MD) computational approach to address several challenging issues regarding their catalytic mechanism: How does the exosite of GlpG rhomboid protease control the kinetics efficiency of substrate hydrolysis? What is the mechanism of inhibition by the non-competitive peptidyl aldehyde inhibitors bound to the GlpG rhomboid active site (AS)? What is the underlying mechanism that explains the hypothesis that GlpG rhomboid protease is not adopted for the hydrolysis of short peptides that do not contain a transmembrane domain (TMD)? Two fundamental features of rhomboid catalysis, the enzyme recognition and discrimination of substrates by TMD interactions in the exosite, and the concerted mechanism of non-covalent pre-catalytic complex to covalent tetrahedral complex (TC) conversion, provide answers to these mechanistic questions.
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Affiliation(s)
- Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
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23
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Langosch D, Steiner H. Substrate processing in intramembrane proteolysis by γ-secretase - the role of protein dynamics. Biol Chem 2017; 398:441-453. [PMID: 27845877 DOI: 10.1515/hsz-2016-0269] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/08/2016] [Indexed: 01/31/2023]
Abstract
Intramembrane proteases comprise a number of different membrane proteins with different types of catalytic sites. Their common denominator is cleavage within the plane of the membrane, which usually results in peptide bond scission within the transmembrane helices of their substrates. Despite recent progress in the determination of high-resolution structures, as illustrated here for the γ-secretase complex and its substrate C99, it is still unknown how these enzymes function and how they distinguish between substrates and non-substrates. In principle, substrate/non-substrate discrimination could occur at the level of substrate binding and/or cleavage. Focusing on the γ-secretase/C99 pair, we will discuss recent observations suggesting that global motions within a substrate transmembrane helix may be much more important for defining a substrate than local unraveling at cleavage sites.
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Düsterhöft S, Künzel U, Freeman M. Rhomboid proteases in human disease: Mechanisms and future prospects. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 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] [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.
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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.
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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] [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.
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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,
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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.
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28
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Abstract
Intramembrane serine proteases of the rhomboid family are widespread, and their gradually uncovered functions in different organisms already suggest medical relevance for infectious diseases and cancer. However, selective inhibitors that could serve as research tools for rhomboids, for validation of their disease relevance, or as templates for drug development are lacking. Here I summarize the current knowledge about rhomboid protease mechanism and specificity, overview the currently used inhibitors, and conclude by proposing avenues for future development of rhomboid protease inhibitors.
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Affiliation(s)
- K Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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29
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Strisovsky K. Rhomboid protease inhibitors: Emerging tools and future therapeutics. Semin Cell Dev Biol 2016; 60:52-62. [PMID: 27567709 DOI: 10.1016/j.semcdb.2016.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/16/2016] [Accepted: 08/24/2016] [Indexed: 02/01/2023]
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.
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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.
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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] [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.
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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.
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Parsons WH, Kolar MJ, Kamat SS, Cognetta AB, Hulce JJ, Saez E, Kahn BB, Saghatelian A, Cravatt BF. AIG1 and ADTRP are atypical integral membrane hydrolases that degrade bioactive FAHFAs. Nat Chem Biol 2016; 12:367-372. [PMID: 27018888 PMCID: PMC4837090 DOI: 10.1038/nchembio.2051] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/05/2016] [Indexed: 12/04/2022]
Abstract
Enzyme classes may contain outlier members that share mechanistic, but not sequence or structural relatedness with more common representatives. The functional annotation of such exceptional proteins can be challenging. Here, we use activity-based profiling to discover that the poorly characterized multipass transmembrane proteins AIG1 and ADTRP are atypical hydrolytic enzymes that depend on conserved threonine and histidine residues for catalysis. Both AIG1 and ADTRP hydrolyze bioactive fatty-acid esters of hydroxy-fatty acids (FAHFAs), but not other major classes of lipids. We discover multiple cell-active, covalent inhibitors of AIG1 and show that these agents block FAHFA hydrolysis in mammalian cells. These results indicate that AIG1 and ADTRP are founding members of an evolutionarily conserved class of transmembrane threonine hydrolases involved in bioactive lipid metabolism. More generally, our findings demonstrate how chemical proteomics can excavate potential cases of convergent/parallel protein evolution that defy conventional sequence- and structure-based predictions.
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Affiliation(s)
- William H Parsons
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Matthew J Kolar
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California 92037, United States
| | - Siddhesh S Kamat
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Armand B Cognetta
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Jonathan J Hulce
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Enrique Saez
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Alan Saghatelian
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California 92037, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
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