1
|
Schillinger J, Koci M, Bravo-Rodriguez K, Heilmann G, Kaschani F, Kaiser M, Beuck C, Luecke H, Huber R, Hellerschmied D, Burston SG, Ehrmann M. High resolution analysis of proteolytic substrate processing. J Biol Chem 2024; 300:107812. [PMID: 39313096 PMCID: PMC11513451 DOI: 10.1016/j.jbc.2024.107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 08/27/2024] [Accepted: 09/17/2024] [Indexed: 09/25/2024] Open
Abstract
Members of the widely conserved high temperature requirement A (HtrA) family of serine proteases are involved in multiple aspects of protein quality control. In this context, they have been shown to efficiently degrade misfolded proteins or protein fragments. However, recent reports suggest that folded proteins can also be native substrates. To gain a deeper understanding of how folded proteins are initially processed and subsequently degraded into short peptides by human HTRA1, we established an integrated and quantitative approach using time-resolved mass spectrometry, CD spectroscopy, and bioinformatics. The resulting data provide high-resolution information on up to 178 individual proteolytic sites within folded ANXA1 (consisting of 346 amino acids), the relative frequency of cuts at each proteolytic site, the preferences of the protease for the amino acid sequence surrounding the scissile bond, as well as the degrees of sequential structural relaxation and unfolding of the substrate that occur during progressive degradation. Our workflow provides precise molecular insights into protease-substrate interactions, which could be readily adapted to address other posttranslational modifications such as phosphorylation in dynamic protein complexes.
Collapse
Affiliation(s)
- Jasmin Schillinger
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Michelle Koci
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | | | - Geronimo Heilmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Farnusch Kaschani
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Hartmut Luecke
- Nova School of Science and Technology, Lisbon, Portugal; Department of Biophysics, University of California, Irvine, California, USA
| | - Robert Huber
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany; Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Doris Hellerschmied
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Steven G Burston
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol, United Kingdom
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.
| |
Collapse
|
2
|
Beaufort N, Ingendahl L, Merdanovic M, Schmidt A, Podlesainski D, Richter T, Neumann T, Kuszner M, Vetter IR, Stege P, Burston SG, Filipovic A, Ruiz-Blanco YB, Bravo-Rodriguez K, Mieres-Perez J, Beuck C, Uebel S, Zobawa M, Schillinger J, Malik R, Todorov-Völgyi K, Rey J, Roberti A, Hagemeier B, Wefers B, Müller SA, Wurst W, Sanchez-Garcia E, Zimmermann A, Hu XY, Clausen T, Huber R, Lichtenthaler SF, Schmuck C, Giese M, Kaiser M, Ehrmann M, Dichgans M. Rational correction of pathogenic conformational defects in HTRA1. Nat Commun 2024; 15:5944. [PMID: 39013852 PMCID: PMC11252331 DOI: 10.1038/s41467-024-49982-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Abstract
Loss-of-function mutations in the homotrimeric serine protease HTRA1 cause cerebral vasculopathy. Here, we establish independent approaches to achieve the functional correction of trimer assembly defects. Focusing on the prototypical R274Q mutation, we identify an HTRA1 variant that promotes trimer formation thus restoring enzymatic activity in vitro. Genetic experiments in Htra1R274Q mice further demonstrate that expression of this protein-based corrector in trans is sufficient to stabilize HtrA1-R274Q and restore the proteomic signature of the brain vasculature. An alternative approach employs supramolecular chemical ligands that shift the monomer-trimer equilibrium towards proteolytically active trimers. Moreover, we identify a peptidic ligand that activates HTRA1 monomers. Our findings open perspectives for tailored protein repair strategies.
Collapse
Affiliation(s)
- Nathalie Beaufort
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Linda Ingendahl
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Melisa Merdanovic
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Andree Schmidt
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), LMU Munich, Munich, Germany
| | - David Podlesainski
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Tim Richter
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Thorben Neumann
- Organic Chemistry, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Michael Kuszner
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Ingrid R Vetter
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Patricia Stege
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Steven G Burston
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol, UK
| | - Anto Filipovic
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Kenny Bravo-Rodriguez
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Joel Mieres-Perez
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Department of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, Germany
| | - Christine Beuck
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Stephan Uebel
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Monika Zobawa
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Jasmin Schillinger
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Katalin Todorov-Völgyi
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Juliana Rey
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Annabell Roberti
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Birte Hagemeier
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Developmental Genetics (IDG), Helmholtz Zentrum München, Neuherberg, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Developmental Genetics (IDG), Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Technische Universität München-Weihenstephan, Freising, Germany
| | - Elsa Sanchez-Garcia
- Department of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, Germany
| | - Alexander Zimmermann
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Xiao-Yu Hu
- College of Material Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Robert Huber
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carsten Schmuck
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Michael Giese
- Organic Chemistry, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| |
Collapse
|
3
|
Chen S, Puri A, Bell B, Fritsche J, Palacios HH, Balch M, Sprunger ML, Howard MK, Ryan JJ, Haines JN, Patti GJ, Davis AA, Jackrel ME. HTRA1 disaggregates α-synuclein amyloid fibrils and converts them into non-toxic and seeding incompetent species. Nat Commun 2024; 15:2436. [PMID: 38499535 PMCID: PMC10948756 DOI: 10.1038/s41467-024-46538-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/01/2024] [Indexed: 03/20/2024] Open
Abstract
Parkinson's disease (PD) is closely linked to α-synuclein (α-syn) misfolding and accumulation in Lewy bodies. The PDZ serine protease HTRA1 degrades fibrillar tau, which is associated with Alzheimer's disease, and inactivating mutations to mitochondrial HTRA2 are implicated in PD. Here, we report that HTRA1 inhibits aggregation of α-syn as well as FUS and TDP-43, which are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. The protease domain of HTRA1 is necessary and sufficient for inhibiting aggregation, yet this activity is proteolytically-independent. Further, HTRA1 disaggregates preformed α-syn fibrils, rendering them incapable of seeding aggregation of endogenous α-syn, while reducing HTRA1 expression promotes α-syn seeding. HTRA1 remodels α-syn fibrils by targeting the NAC domain, the key domain catalyzing α-syn amyloidogenesis. Finally, HTRA1 detoxifies α-syn fibrils and prevents formation of hyperphosphorylated α-syn accumulations in primary neurons. Our findings suggest that HTRA1 may be a therapeutic target for a range of neurodegenerative disorders.
Collapse
Affiliation(s)
- Sheng Chen
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Anuradhika Puri
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Braxton Bell
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Joseph Fritsche
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Hector H Palacios
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Maurie Balch
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Macy L Sprunger
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Matthew K Howard
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Jeremy J Ryan
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Jessica N Haines
- Department of Neurology, Washington University, St. Louis, MO, 63130, USA
| | - Gary J Patti
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University, St. Louis, MO, 63130, USA
| | - Albert A Davis
- Department of Neurology, Washington University, St. Louis, MO, 63130, USA
| | - Meredith E Jackrel
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA.
| |
Collapse
|
4
|
Merle DA, Sen M, Armento A, Stanton CM, Thee EF, Meester-Smoor MA, Kaiser M, Clark SJ, Klaver CCW, Keane PA, Wright AF, Ehrmann M, Ueffing M. 10q26 - The enigma in age-related macular degeneration. Prog Retin Eye Res 2023; 96:101154. [PMID: 36513584 DOI: 10.1016/j.preteyeres.2022.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
Despite comprehensive research efforts over the last decades, the pathomechanisms of age-related macular degeneration (AMD) remain far from being understood. Large-scale genome wide association studies (GWAS) were able to provide a defined set of genetic aberrations which contribute to disease risk, with the strongest contributors mapping to distinct regions on chromosome 1 and 10. While the chromosome 1 locus comprises factors of the complement system with well-known functions, the role of the 10q26-locus in AMD-pathophysiology remains enigmatic. 10q26 harbors a cluster of three functional genes, namely PLEKHA1, ARMS2 and HTRA1, with most of the AMD-associated genetic variants mapping to the latter two genes. High linkage disequilibrium between ARMS2 and HTRA1 has kept association studies from reliably defining the risk-causing gene for long and only very recently the genetic risk region has been narrowed to ARMS2, suggesting that this is the true AMD gene at this locus. However, genetic associations alone do not suffice to prove causality and one or more of the 14 SNPs on this haplotype may be involved in long-range control of gene expression, leaving HTRA1 and PLEKHA1 still suspects in the pathogenic pathway. Both, ARMS2 and HTRA1 have been linked to extracellular matrix homeostasis, yet their exact molecular function as well as their role in AMD pathogenesis remains to be uncovered. The transcriptional regulation of the 10q26 locus adds an additional level of complexity, given, that gene-regulatory as well as epigenetic alterations may influence expression levels from 10q26 in diseased individuals. Here, we provide a comprehensive overview on the 10q26 locus and its three gene products on various levels of biological complexity and discuss current and future research strategies to shed light on one of the remaining enigmatic spots in the AMD landscape.
Collapse
Affiliation(s)
- David A Merle
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department of Ophthalmology, Medical University of Graz, 8036, Graz, Austria.
| | - Merve Sen
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Angela Armento
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Chloe M Stanton
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eric F Thee
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Simon J Clark
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands; Department of Ophthalmology, Radboudumc, 6525EX, Nijmegen, Netherlands; Institute of Molecular and Clinical Ophthalmology Basel, CH-4031, Basel, Switzerland
| | - Pearse A Keane
- Institute for Health Research, Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, EC1V 2PD, UK
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany.
| |
Collapse
|