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Teng L, Sun Y, Chen J, Wang C, Urbach JM, Kobe B, Ye N, Zeng Q. Exon shuffling and alternative splicing of ROCO genes in brown algae enables a diverse repertoire of candidate immune receptors. FRONTIERS IN PLANT SCIENCE 2024; 15:1445022. [PMID: 39246816 PMCID: PMC11378527 DOI: 10.3389/fpls.2024.1445022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024]
Abstract
The ROCO family is a family of GTPases characterized by a central ROC-COR tandem domain. Interest in the structure and function of ROCO proteins has increased with the identification of their important roles in human disease. Nevertheless, the functions of most ROCO proteins are still unknown. In the present study, we characterized the structure, evolution, and expression of ROCOs in four species of brown algae. Brown algae have a larger number of ROCO proteins than other organisms reported to date. Phylogenetic analyses showed that ROCOs have an ancient origin, likely originated in prokaryotes. ROCOs in brown algae clustered into four groups and showed no strong relationship with red algae or green algae. Brown algal ROCOs retain the ancestral LRR-ROC-COR domain arrangement, which is found in prokaryotes, plants and some basal metazoans. Remarkably, individual LRR motifs in ROCO genes are each encoded by separate exons and exhibit intense exon shuffling and diversifying selection. Furthermore, the tandem LRR exons exhibit alternative splicing to generate multiple transcripts. Both exon shuffling and alternative splicing of LRR repeats may be important mechanisms for generating diverse ligand-binding specificities as immune receptors. Besides their potential immune role, expression analysis shows that many ROCO genes are responsive to other stress conditions, suggesting they could participate in multiple signal pathways, not limited to the immune response. Our results substantially enhance our understanding of the structure and function of this mysterious gene family.
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Affiliation(s)
- Linhong Teng
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Yuhuan Sun
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Jiayi Chen
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Chenghui Wang
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Jonathan M Urbach
- Ragon Institute of Mass General Brigham, MIT, and Harvard, Cambridge, MA, United States
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Naihao Ye
- National Key Laboratory of Mariculture Biobreeding and Sustainable Production, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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Holmes G, Ferguson SR, Lewis PA, Echeverri K. LRRK2 kinase activity is necessary for development and regeneration in Nematostella vectensis. Neural Dev 2024; 19:16. [PMID: 39118162 PMCID: PMC11308222 DOI: 10.1186/s13064-024-00193-3] [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: 10/31/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The starlet sea anemone, Nematostella vectensis, is an emerging model organism with a high regenerative capacity, which was recently found to possess an orthologue to the human Leucine Rich Repeat Kinase 2 (LRRK2) gene. Mutations in this gene are the most common cause of inherited Parkinson's Disease (PD), highlighting the importance of understanding its function. Despite two decades of research, however, the function of LRRK2 is not well established. METHODS To investigate the function of LRRKs in Nematostella vectensis, we applied small molecule inhibitors targeting the kinase activity of LRRK2 to examine its function in development, homeostasis and regeneration in Nematostella vectensis. RESULTS In vivo analyses inhibiting the kinase function of this enzyme demonstrated a role of nvLRRK2 in development and regeneration of N. vectensis. These findings implicate a developmental role of LRRK2 in Nematostella, adding to the expanding knowledge of its physiological function. CONCLUSIONS Our work introduces a new model organism with which to study LRRK biology. We report that LRRK kinase activity is necessary for the development and regeneration of Nematostella. Given the short generation time, genetic trackability and in vivo imaging capabilities, this work introduces Nematostella vectensis as a new model in which to study genes linked to neurodegenerative diseases such as Parkinson's.
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Affiliation(s)
- Grace Holmes
- Royal Veterinary College, University of London, Camden, London, NW1 0TU, UK
| | - Sophie R Ferguson
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA, 02543, USA
| | - Patrick Alfryn Lewis
- Royal Veterinary College, University of London, Camden, London, NW1 0TU, UK.
- UCL Queen Square Institute of Neurology, University of London, London, WC1N 3BG, UK.
| | - Karen Echeverri
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA, 02543, USA.
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3
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Benítez‐Fernández R, Josa‐Prado F, Sánchez E, Lao Y, García‐Rubia A, Cumella J, Martínez A, Palomo V, de Castro F. Efficacy of a benzothiazole-based LRRK2 inhibitor in oligodendrocyte precursor cells and in a murine model of multiple sclerosis. CNS Neurosci Ther 2024; 30:e14552. [PMID: 38287523 PMCID: PMC10808848 DOI: 10.1111/cns.14552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 01/31/2024] Open
Abstract
AIMS Multiple sclerosis (MS) is a chronic neurological disease that currently lacks effective curative treatments. There is a need to find effective therapies, especially to reverse the progressive demyelination and neuronal damage. Oligodendrocytes form the myelin sheath around axons in the central nervous system (CNS) and oligodendrocyte precursor cells (OPCs) undergo mechanisms that enable spontaneously the partial repair of damaged lesions. The aim of this study was to discover small molecules with potential effects in demyelinating diseases, including (re)myelinating properties. METHODS Recently, it has been shown how LRRK2 inhibition promotes oligodendrogliogenesis and therefore an efficient repair or myelin damaged lesions. Here we explored small molecules inhibiting LRRK2 as potential enhancers of primary OPCs proliferation and differentiation, and their potential impact on the clinical score of experimental autoimmune encephalomyelitys (EAE) mice, a validated model of the most frequent clinical form of MS, relapsing-remitting MS. RESULTS One of the LRRK2 inhibitors presented in this study promoted the proliferation and differentiation of OPC primary cultures. When tested in the EAE murine model of MS, it exerted a statistically significant reduction of the clinical burden of the animals, and histological evidence revealed how the treated animals presented a reduced lesion area in the spinal cord. CONCLUSIONS For the first time, a small molecule with LRRK2 inhibition properties presented (re)myelinating properties in primary OPCs cultures and potentially in the in vivo murine model. This study provides an in vivo proof of concept for a LRRK2 inhibitor, confirming its potential for the treatment of MS.
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Affiliation(s)
- Rocío Benítez‐Fernández
- Centro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
- Instituto Cajal‐CSICMadridSpain
| | | | | | | | | | - José Cumella
- Instituto de Química Médica, IQM‐CSICMadridSpain
| | - Ana Martínez
- Centro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
- Centro de Investigaciones Biomédicas en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos IIIMadridSpain
| | - Valle Palomo
- Centro de Investigaciones Biomédicas en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos IIIMadridSpain
- Instituto Madrileño de Estudios AvanzadosIMDEA NanocienciaMadridSpain
- Unidad de Nanobiotecnología Asociada al Centro Nacional de Biotecnología (CNB‐CSIC)MadridSpain
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4
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Holmes G, Ferguson SR, Lewis PA, Echeverri K. LRRK2 kinase activity is necessary for development and regeneration in Nematostella vectensis. RESEARCH SQUARE 2023:rs.3.rs-3525606. [PMID: 37986927 PMCID: PMC10659525 DOI: 10.21203/rs.3.rs-3525606/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background The starlet sea anemone, Nematostella vectensis, is an emerging model organism with a high regenerative capacity, which was recently found to possess an orthologue to the human LRRK2 gene (nvLRRK2). The leucine rich repeat kinase 2 (LRRK2) gene, when mutated, is the most common cause of inherited Parkinson's Disease (PD). Its protein product (LRRK2) has implications in a variety of cellular processes, however, the full function of LRRK2 is not well established. Current research is focusing on understanding the function of LRRK2, including both its physiological role as well as its pathobiological underpinnings. Methods We used bioinformatics to determine the cross-species conservation of LRRK2, then applied drugs targeting the kinase activity of LRRK2 to examine its function in development, homeostasis and regeneration in Nematostella vectensis. Results An in-silico characterization and phylogenetic analysis of nvLRRK2 comparing it to human LRRK2 highlighted key conserved motifs and residues. In vivo analyses inhibiting the kinase function of this enzyme demonstrated a role of nvLRRK2 in development and regeneration of N. vectensis. These findings implicate a developmental role of LRRK2 in Nematostella, adding to the expanding knowledge of its physiological function. Conclusions Our work introduces a new model organism with which to study LRRK biology. We show a necessity for LRRK2 in development and regeneration. Given the short generation time, genetic trackability and in vivo imaging capabilities, this work introduces Nematostella vectensis as a new model in which to study genes linked to neurodegenerative diseases such as Parkinson's.
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5
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Reimer JM, Dickey AM, Lin YX, Abrisch RG, Mathea S, Chatterjee D, Fay EJ, Knapp S, Daugherty MD, Reck-Peterson SL, Leschziner AE. Structure of LRRK1 and mechanisms of autoinhibition and activation. Nat Struct Mol Biol 2023; 30:1735-1745. [PMID: 37857821 PMCID: PMC10643122 DOI: 10.1038/s41594-023-01109-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/24/2023] [Indexed: 10/21/2023]
Abstract
Leucine Rich Repeat Kinase 1 and 2 (LRRK1 and LRRK2) are homologs in the ROCO family of proteins in humans. Despite their shared domain architecture and involvement in intracellular trafficking, their disease associations are strikingly different: LRRK2 is involved in familial Parkinson's disease while LRRK1 is linked to bone diseases. Furthermore, Parkinson's disease-linked mutations in LRRK2 are typically autosomal dominant gain-of-function while those in LRRK1 are autosomal recessive loss-of-function. Here, to understand these differences, we solved cryo-EM structures of LRRK1 in its monomeric and dimeric forms. Both differ from the corresponding LRRK2 structures. Unlike LRRK2, which is sterically autoinhibited as a monomer, LRRK1 is sterically autoinhibited in a dimer-dependent manner. LRRK1 has an additional level of autoinhibition that prevents activation of the kinase and is absent in LRRK2. Finally, we place the structural signatures of LRRK1 and LRRK2 in the context of the evolution of the LRRK family of proteins.
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Affiliation(s)
- Janice M Reimer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Andrea M Dickey
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yu Xuan Lin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Robert G Abrisch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Sebastian Mathea
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Deep Chatterjee
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Elizabeth J Fay
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Stefan Knapp
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Matthew D Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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6
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Urwyler-Rösselet C, Tanghe G, Devos M, Hulpiau P, Saeys Y, Declercq W. Functions of the RIP kinase family members in the skin. Cell Mol Life Sci 2023; 80:285. [PMID: 37688617 PMCID: PMC10492769 DOI: 10.1007/s00018-023-04917-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2023] [Accepted: 08/08/2023] [Indexed: 09/11/2023]
Abstract
The receptor interacting protein kinases (RIPK) are a family of serine/threonine kinases that are involved in the integration of various stress signals. In response to several extracellular and/or intracellular stimuli, RIP kinases engage signaling cascades leading to the activation of NF-κB and mitogen-activated protein kinases, cell death, inflammation, differentiation and Wnt signaling and can have kinase-dependent and kinase-independent functions. Although it was previously suggested that seven RIPKs are part of the RIPK family, phylogenetic analysis indicates that there are only five genuine RIPKs. RIPK1 and RIPK3 are mainly involved in controlling and executing necroptosis in keratinocytes, while RIPK4 controls proliferation and differentiation of keratinocytes and thereby can act as a tumor suppressor in skin. Therefore, in this review we summarize and discuss the functions of RIPKs in skin homeostasis as well as the signaling pathways involved.
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Affiliation(s)
- Corinne Urwyler-Rösselet
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Giel Tanghe
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Michael Devos
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Paco Hulpiau
- VIB Center for Inflammation Research, Ghent, Belgium
- Howest University of Applied Sciences, Brugge, Belgium
| | - Yvan Saeys
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium
| | - Wim Declercq
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- VIB Center for Inflammation Research, Ghent, Belgium.
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7
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Ito G, Utsunomiya-Tate N. Overview of the Impact of Pathogenic LRRK2 Mutations in Parkinson's Disease. Biomolecules 2023; 13:biom13050845. [PMID: 37238714 DOI: 10.3390/biom13050845] [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: 03/08/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large protein kinase that physiologically phosphorylates and regulates the function of several Rab proteins. LRRK2 is genetically implicated in the pathogenesis of both familial and sporadic Parkinson's disease (PD), although the underlying mechanism is not well understood. Several pathogenic mutations in the LRRK2 gene have been identified, and in most cases the clinical symptoms that PD patients with LRRK2 mutations develop are indistinguishable from those of typical PD. However, it has been shown that the pathological manifestations in the brains of PD patients with LRRK2 mutations are remarkably variable when compared to sporadic PD, ranging from typical PD pathology with Lewy bodies to nigral degeneration with deposition of other amyloidogenic proteins. The pathogenic mutations in LRRK2 are also known to affect the functions and structure of LRRK2, the differences in which may be partly attributable to the variations observed in patient pathology. In this review, in order to help researchers unfamiliar with the field to understand the mechanism of pathogenesis of LRRK2-associated PD, we summarize the clinical and pathological manifestations caused by pathogenic mutations in LRRK2, their impact on the molecular function and structure of LRRK2, and their historical background.
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Affiliation(s)
- Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
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8
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Hadisurya M, Li L, Kuwaranancharoen K, Wu X, Lee ZC, Alcalay RN, Padmanabhan S, Tao WA, Iliuk A. Quantitative proteomics and phosphoproteomics of urinary extracellular vesicles define putative diagnostic biosignatures for Parkinson's disease. COMMUNICATIONS MEDICINE 2023; 3:64. [PMID: 37165152 PMCID: PMC10172329 DOI: 10.1038/s43856-023-00294-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/27/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been recognized as genetic risk factors for Parkinson's disease (PD). However, compared to cancer, fewer genetic mutations contribute to the cause of PD, propelling the search for protein biomarkers for early detection of the disease. METHODS Utilizing 138 urine samples from four groups, healthy individuals (control), healthy individuals with G2019S mutation in the LRRK2 gene (non-manifesting carrier/NMC), PD individuals without G2019S mutation (idiopathic PD/iPD), and PD individuals with G2019S mutation (LRRK2 PD), we applied a proteomics strategy to determine potential diagnostic biomarkers for PD from urinary extracellular vesicles (EVs). RESULTS After efficient isolation of urinary EVs through chemical affinity followed by mass spectrometric analyses of EV peptides and enriched phosphopeptides, we identify and quantify 4476 unique proteins and 2680 unique phosphoproteins. We detect multiple proteins and phosphoproteins elevated in PD EVs that are known to be involved in important PD pathways, in particular the autophagy pathway, as well as neuronal cell death, neuroinflammation, and formation of amyloid fibrils. We establish a panel of proteins and phosphoproteins as novel candidates for disease biomarkers and substantiate the biomarkers using machine learning, ROC, clinical correlation, and in-depth network analysis. Several putative disease biomarkers are further partially validated in patients with PD using parallel reaction monitoring (PRM) and immunoassay for targeted quantitation. CONCLUSIONS These findings demonstrate a general strategy of utilizing biofluid EV proteome/phosphoproteome as an outstanding and non-invasive source for a wide range of disease exploration.
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Affiliation(s)
- Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Li Li
- Tymora Analytical Operations, West Lafayette, IN, 47906, USA
| | | | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Zheng-Chi Lee
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- West Lafayette Junior/Senior High School, West Lafayette, IN, 47906, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Shalini Padmanabhan
- The Michael J. Fox Foundation for Parkinson's Research, New York City, NY, 10163, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.
- Tymora Analytical Operations, West Lafayette, IN, 47906, USA.
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
| | - Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.
- Tymora Analytical Operations, West Lafayette, IN, 47906, USA.
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9
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Is Glial Dysfunction the Key Pathogenesis of LRRK2-Linked Parkinson's Disease? Biomolecules 2023; 13:biom13010178. [PMID: 36671564 PMCID: PMC9856048 DOI: 10.3390/biom13010178] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Leucine rich-repeat kinase 2 (LRRK2) is the most well-known etiologic gene for familial Parkinson's disease (PD). Its gene product is a large kinase with multiple functional domains that phosphorylates a subset of Rab small GTPases. However, studies of autopsy cases with LRRK2 mutations indicate a varied pathology, and the molecular functions of LRRK2 and its relationship to PD pathogenesis are largely unknown. Recently, non-autonomous neurodegeneration associated with glial cell dysfunction has attracted attention as a possible mechanism of dopaminergic neurodegeneration. Molecular studies of LRRK2 in astrocytes and microglia have also suggested that LRRK2 is involved in the regulation of lysosomal and other organelle dynamics and inflammation. In this review, we describe the proposed functions of LRRK2 in glial cells and discuss its involvement in the pathomechanisms of PD.
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10
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Helton LG, Rideout HJ, Herberg FW, Kennedy EJ. Leucine rich repeat kinase 2 (
LRRK2
) peptide modulators: Recent advances and future directions. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leah G. Helton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
| | - Hardy J. Rideout
- Center for Clinical, Experimental Surgery, and Translational Research Biomedical Research Foundation of the Academy of Athens Athens Greece
| | - Friedrich W. Herberg
- Department of Biochemistry Institute for Biology, University of Kassel Kassel Germany
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
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11
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Rosenbusch KE, Oun A, Sanislav O, Lay ST, Keizer-Gunnink I, Annesley SJ, Fisher PR, Dolga AM, Kortholt A. A Conserved Role for LRRK2 and Roco Proteins in the Regulation of Mitochondrial Activity. Front Cell Dev Biol 2021; 9:734554. [PMID: 34568343 PMCID: PMC8455996 DOI: 10.3389/fcell.2021.734554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/16/2021] [Indexed: 01/02/2023] Open
Abstract
Parkinson's Disease (PD) is the second most common neurodegenerative disease world-wide. Mutations in the multidomain protein Leucine Rich Repeat Kinase 2 (LRRK2) are the most frequent cause of hereditary PD. Furthermore, recent data suggest that independent of mutations, increased kinase activity of LRRK2 plays an essential role in PD pathogenesis. Isolated mitochondria of tissue samples from PD patients carrying LRRK2 mutations display a significant impairment of mitochondrial function. However, due to the complexity of the mitochondrial signaling network, the role of LRRK2 in mitochondrial metabolism is still not well understood. Previously we have shown that D. discoideum Roco4 is a suitable model to study the activation mechanism of LRRK2 in vivo. To get more insight in the LRRK2 pathways regulating mitochondrial activity we used this Roco4 model system in combination with murine RAW macrophages. Here we show that both Dictyostelium roco4 knockout and cells expressing PD-mutants show behavioral and developmental phenotypes that are characteristic for mitochondrial impairment. Mitochondrial activity measured by Seahorse technology revealed that the basal respiration of D. discoideum roco4- cells is significantly increased compared to the WT strain, while the basal and maximal respiration values of cells overexpressing Roco4 are reduced compared to the WT strain. Consistently, LRRK2 KO RAW 264.7 cells exhibit higher maximal mitochondrial respiration activity compared to the LRRK2 parental RAW264.7 cells. Measurement on isolated mitochondria from LRRK2 KO and parental RAW 264.7 cells revealed no difference in activity compared to the parental cells. Furthermore, neither D. discoideum roco4- nor LRRK2 KO RAW 264.7 showed a difference in either the number or the morphology of mitochondria compared to their respective parental strains. This suggests that the observed effects on the mitochondrial respiratory in cells are indirect and that LRRK2/Roco proteins most likely require other cytosolic cofactors to elicit mitochondrial effects.
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Affiliation(s)
| | - Asmaa Oun
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands.,Groningen Research Institute of Pharmacy (GRIP), Molecular Pharmacology XB10, Groningen, Netherlands.,Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Oana Sanislav
- Department of Physiology Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Sui T Lay
- Department of Physiology Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Ineke Keizer-Gunnink
- Department of Physiology Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Sarah J Annesley
- Department of Physiology Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Paul R Fisher
- Department of Physiology Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Amalia M Dolga
- Groningen Research Institute of Pharmacy (GRIP), Molecular Pharmacology XB10, Groningen, Netherlands
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands.,Department of Pharmacology, Faculty of Medicine, Suleyman Demirel University, Isparta, Turkey
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12
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Li X, Qi Z, Ni D, Lu S, Chen L, Chen X. Markov State Models and Molecular Dynamics Simulations Provide Understanding of the Nucleotide-Dependent Dimerization-Based Activation of LRRK2 ROC Domain. Molecules 2021; 26:5647. [PMID: 34577121 PMCID: PMC8467336 DOI: 10.3390/molecules26185647] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 01/26/2023] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are recognized as the most frequent cause of Parkinson's disease (PD). As a multidomain ROCO protein, LRRK2 is characterized by the presence of both a Ras-of-complex (ROC) GTPase domain and a kinase domain connected through the C-terminal of an ROC domain (COR). The bienzymatic ROC-COR-kinase catalytic triad indicated the potential role of GTPase domain in regulating kinase activity. However, as a functional GTPase, the detailed intrinsic regulation of the ROC activation cycle remains poorly understood. Here, combining extensive molecular dynamics simulations and Markov state models, we disclosed the dynamic structural rearrangement of ROC's homodimer during nucleotide turnover. Our study revealed the coupling between dimerization extent and nucleotide-binding state, indicating a nucleotide-dependent dimerization-based activation scheme adopted by ROC GTPase. Furthermore, inspired by the well-known R1441C/G/H PD-relevant mutations within the ROC domain, we illuminated the potential allosteric molecular mechanism for its pathogenetic effects through enabling faster interconversion between inactive and active states, thus trapping ROC in a prolonged activated state, while the implicated allostery could provide further guidance for identification of regulatory allosteric pockets on the ROC complex. Our investigations illuminated the thermodynamics and kinetics of ROC homodimer during nucleotide-dependent activation for the first time and provided guidance for further exploiting ROC as therapeutic targets for controlling LRRK2 functionality in PD treatment.
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Affiliation(s)
- Xinyi Li
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, China;
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China;
| | - Zengxin Qi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China;
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Huashan Hospital, Fudan University, Shanghai 200040, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai 200433, China
| | - Duan Ni
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China;
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China;
| | - Liang Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China;
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Huashan Hospital, Fudan University, Shanghai 200040, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai 200433, China
| | - Xiangyu Chen
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, China;
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13
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Leschziner AE, Reck-Peterson SL. Structural Biology of LRRK2 and its Interaction with Microtubules. Mov Disord 2021; 36:2494-2504. [PMID: 34423856 PMCID: PMC9290818 DOI: 10.1002/mds.28755] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/02/2022] Open
Abstract
Mutations in leucine rich repeat kinase 2 (LRRK2) are a major cause of familial Parkinson's disease (PD) and a risk factor for its sporadic form. LRRK2 hyperactivity has also been reported in sporadic PD, making LRRK2 an appealing target for PD small‐molecule therapeutics. At a cellular level, increasing evidence suggests that LRRK2 regulates membrane trafficking. Under some conditions LRRK2 also associates with microtubules, the cellular tracks used by dynein and kinesin motors to move membranes. At a structural level, however, relatively little was known about LRRK2. An important step toward bridging this gap took place last year with the publication of structures of LRRK2's cytosolic and microtubule‐bound forms. Here, we review the main findings from these studies and discuss what we see as the major challenges going forward with a focus on areas that will require structural information. We also introduce the structural techniques—cryo‐electron microscopy and cryo‐electron tomography—that were instrumental to solving the structures of LRRK2. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
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Affiliation(s)
- Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, California, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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14
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Herman EK, Greninger A, van der Giezen M, Ginger ML, Ramirez-Macias I, Miller HC, Morgan MJ, Tsaousis AD, Velle K, Vargová R, Záhonová K, Najle SR, MacIntyre G, Muller N, Wittwer M, Zysset-Burri DC, Eliáš M, Slamovits CH, Weirauch MT, Fritz-Laylin L, Marciano-Cabral F, Puzon GJ, Walsh T, Chiu C, Dacks JB. Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. BMC Biol 2021; 19:142. [PMID: 34294116 PMCID: PMC8296547 DOI: 10.1186/s12915-021-01078-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. RESULTS Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. CONCLUSIONS In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.
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Affiliation(s)
- Emily K Herman
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Alex Greninger
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
- Department of Laboratory Medicine, University of Washington Medical Center, Montlake, USA
| | - Mark van der Giezen
- Centre for Organelle Research, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Michael L Ginger
- School of Applied Sciences, Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK
| | - Inmaculada Ramirez-Macias
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Department of Cardiology, Hospital Clinico Universitario Virgen de la Arrixaca. Instituto Murciano de Investigación Biosanitaria. Centro de Investigación Biomedica en Red-Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Haylea C Miller
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
- CSIRO, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
| | - Matthew J Morgan
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | | | - Katrina Velle
- Department of Biology, University of Massachusetts, Amherst, UK
| | - Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kristína Záhonová
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Sebastian Rodrigo Najle
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Catalonia, Spain
| | - Georgina MacIntyre
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Norbert Muller
- Institute of Parasitology, Vetsuisse Faculty Bern, University of Bern, Bern, Switzerland
| | - Mattias Wittwer
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, Spiez, Switzerland
| | - Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | | | - Francine Marciano-Cabral
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Geoffrey J Puzon
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | - Charles Chiu
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Department of Life Sciences, The Natural History Museum, London, UK.
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15
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Chittoor-Vinod VG, Nichols RJ, Schüle B. Genetic and Environmental Factors Influence the Pleomorphy of LRRK2 Parkinsonism. Int J Mol Sci 2021; 22:1045. [PMID: 33494262 PMCID: PMC7864502 DOI: 10.3390/ijms22031045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 12/25/2022] Open
Abstract
Missense mutations in the LRRK2 gene were first identified as a pathogenic cause of Parkinson's disease (PD) in 2004. Soon thereafter, a founder mutation in LRRK2, p.G2019S (rs34637584), was described, and it is now estimated that there are approximately 100,000 people worldwide carrying this risk variant. While the clinical presentation of LRRK2 parkinsonism has been largely indistinguishable from sporadic PD, disease penetrance and age at onset can be quite variable. In addition, its neuropathological features span a wide range from nigrostriatal loss with Lewy body pathology, lack thereof, or atypical neuropathology, including a large proportion of cases with concomitant Alzheimer's pathology, hailing LRRK2 parkinsonism as the "Rosetta stone" of parkinsonian disorders, which provides clues to an understanding of the different neuropathological trajectories. These differences may result from interactions between the LRRK2 mutant protein and other proteins or environmental factors that modify LRRK2 function and, thereby, influence pathobiology. This review explores how potential genetic and biochemical modifiers of LRRK2 function may contribute to the onset and clinical presentation of LRRK2 parkinsonism. We review which genetic modifiers of LRRK2 influence clinical symptoms, age at onset, and penetrance, what LRRK2 mutations are associated with pleomorphic LRRK2 neuropathology, and which environmental modifiers can augment LRRK2 mutant pathophysiology. Understanding how LRRK2 function is influenced and modulated by other interactors and environmental factors-either increasing toxicity or providing resilience-will inform targeted therapeutic development in the years to come. This will allow the development of disease-modifying therapies for PD- and LRRK2-related neurodegeneration.
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Affiliation(s)
| | - R. Jeremy Nichols
- Department Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Birgitt Schüle
- Department Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
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16
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The 14-3-3 Proteins as Important Allosteric Regulators of Protein Kinases. Int J Mol Sci 2020; 21:ijms21228824. [PMID: 33233473 PMCID: PMC7700312 DOI: 10.3390/ijms21228824] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Phosphorylation by kinases governs many key cellular and extracellular processes, such as transcription, cell cycle progression, differentiation, secretion and apoptosis. Unsurprisingly, tight and precise kinase regulation is a prerequisite for normal cell functioning, whereas kinase dysregulation often leads to disease. Moreover, the functions of many kinases are regulated through protein–protein interactions, which in turn are mediated by phosphorylated motifs and often involve associations with the scaffolding and chaperon protein 14-3-3. Therefore, the aim of this review article is to provide an overview of the state of the art on 14-3-3-mediated kinase regulation, focusing on the most recent mechanistic insights into these important protein–protein interactions and discussing in detail both their structural aspects and functional consequences.
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17
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Taylor SS, Kaila-Sharma P, Weng JH, Aoto P, Schmidt SH, Knapp S, Mathea S, Herberg FW. Kinase Domain Is a Dynamic Hub for Driving LRRK2 Allostery. Front Mol Neurosci 2020; 13:538219. [PMID: 33122997 PMCID: PMC7573214 DOI: 10.3389/fnmol.2020.538219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
Protein kinases and GTPases are the two major molecular switches that regulate much of biology, and both of these domains are embedded within the large multi-domain Leucine-Rich Repeat Kinase 2 (LRRK2). Mutations in LRRK2 are the most common cause of familial Parkinson's disease (PD) and are also implicated in Crohn's disease. The recent Cryo-Electron Microscopy (Cryo-EM) structure of the four C-terminal domains [ROC COR KIN WD40 (RCKW)] of LRRK2 includes both of the catalytic domains. Although the important allosteric N-terminal domains are missing in the Cryo-EM structure this structure allows us to not only explore the conserved features of the kinase domain, which is trapped in an inactive and open conformation but also to observe the direct allosteric cross-talk between the two domains. To define the unique features of the kinase domain and to better understand the dynamic switch mechanism that allows LRRK2 to toggle between its inactive and active conformations, we have compared the LRRK2 kinase domain to Src, BRaf, and PKA. We also compare and contrast the two canonical glycine-rich loop motifs in LRRK2 that anchor the nucleotide: the G-Loop in protein kinases that anchors ATP and the P-Loop in GTPases that anchors GTP. The RCKW structure also provides a template for the cross-talk between the kinase and GTPase domains and brings new mechanistic insights into the physiological function of LRRK2 and how the kinase domain, along with key phosphorylation sites, can serve as an allosteric hub for mediating conformational changes.
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Pallavi Kaila-Sharma
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Phillip Aoto
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Sven H Schmidt
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Sebastian Mathea
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
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18
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Allosteric modulation of the GTPase activity of a bacterial LRRK2 homolog by conformation-specific Nanobodies. Biochem J 2020; 477:1203-1218. [PMID: 32167135 PMCID: PMC7135905 DOI: 10.1042/bcj20190843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 01/02/2023]
Abstract
Mutations in the Parkinson's disease (PD)-associated protein leucine-rich repeat kinase 2 (LRRK2) commonly lead to a reduction of GTPase activity and increase in kinase activity. Therefore, strategies for drug development have mainly been focusing on the design of LRRK2 kinase inhibitors. We recently showed that the central RocCOR domains (Roc: Ras of complex proteins; COR: C-terminal of Roc) of a bacterial LRRK2 homolog cycle between a dimeric and monomeric form concomitant with GTP binding and hydrolysis. PD-associated mutations can slow down GTP hydrolysis by stabilizing the protein in its dimeric form. Here, we report the identification of two Nanobodies (NbRoco1 and NbRoco2) that bind the bacterial Roco protein (CtRoco) in a conformation-specific way, with a preference for the GTP-bound state. NbRoco1 considerably increases the GTP turnover rate of CtRoco and reverts the decrease in GTPase activity caused by a PD-analogous mutation. We show that NbRoco1 exerts its effect by allosterically interfering with the CtRoco dimer–monomer cycle through the destabilization of the dimeric form. Hence, we provide the first proof of principle that allosteric modulation of the RocCOR dimer–monomer cycle can alter its GTPase activity, which might present a potential novel strategy to overcome the effect of LRRK2 PD mutations.
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19
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Levy DR, Udgata A, Tourlomousis P, Symmons MF, Hopkins LJ, Bryant CE, Gay NJ. The Parkinson's disease-associated kinase LRRK2 regulates genes required for cell adhesion, polarization, and chemotaxis in activated murine macrophages. J Biol Chem 2020; 295:10857-10867. [PMID: 32111741 PMCID: PMC7397110 DOI: 10.1074/jbc.ra119.011842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/21/2020] [Indexed: 11/06/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) encodes a complex protein that includes kinase and GTPase domains. Genome-wide association studies have identified dominant LRRK2 alleles that predispose their carriers to late-onset idiotypic Parkinson's disease (PD) and also to autoimmune disorders such as Crohn's disease. Considerable evidence indicates that PD initiation and progression involve activation of innate immune functions in microglia, which are brain-resident macrophages. Here we asked whether LRRK2 modifies inflammatory signaling and how this modification might contribute to PD and Crohn's disease. We used RNA-Seq-based high-resolution transcriptomics to compare gene expression in activated primary macrophages derived from WT and Lrrk2 knockout mice. Remarkably, expression of a single gene, Rap guanine nucleotide exchange factor 3 (Rapgef3), was strongly up-regulated in the absence of LRRK2 and down-regulated in its presence. We observed similar regulation of Rapgef3 expression in cells treated with a highly specific inhibitor of LRRK2 protein kinase activity. Rapgef3 encodes an exchange protein, activated by cAMP 1 (EPAC-1), a guanine nucleotide exchange factor that activates the small GTPase Rap-1. Rap-1 mediates cell adhesion, polarization, and directional motility, and our results indicate that LRRK2 modulates chemotaxis of microglia and macrophages. Dominant PD-associated LRRK2 alleles may suppress EPAC-1 activity, further restricting motility and preventing efficient migration of microglia to sites of neuronal damage. Functional analysis in vivo in a subclinical infection model also indicated that Lrrk2 subtly modifies the inflammatory response. These results indicate that LRRK2 modulates the expression of genes involved in murine immune cell chemotaxis.
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Affiliation(s)
- Daniel R Levy
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Atul Udgata
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Panagiotis Tourlomousis
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
| | - Martyn F Symmons
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Lee J Hopkins
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
| | - Clare E Bryant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
| | - Nicholas J Gay
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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20
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Mills RD, Liang LY, Lio DSS, Mok YF, Mulhern TD, Cao G, Griffin M, Kenche VB, Culvenor JG, Cheng HC. The Roc-COR tandem domain of leucine-rich repeat kinase 2 forms dimers and exhibits conventional Ras-like GTPase properties. J Neurochem 2019; 147:409-428. [PMID: 30091236 DOI: 10.1111/jnc.14566] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 12/18/2022]
Abstract
The Parkinson's disease (PD)-causative leucine-rich repeat kinase 2 (LRRK2) belongs to the Roco family of G-proteins comprising a Ras-of-complex (Roc) domain followed by a C-terminal of Roc (COR) domain in tandem (called Roc-COR domain). Two prokaryotic Roc-COR domains have been characterized as 'G proteins activated by guanine nucleotide-dependent dimerization' (GADs), which require dimerization for activation of their GTPase activity and bind guanine nucleotides with relatively low affinities. Additionally, LRRK2 Roc domain in isolation binds guanine nucleotides with relatively low affinities. As such, LRRK2 GTPase domain was predicted to be a GAD. Herein, we describe the design and high-level expression of human LRRK2 Roc-COR domain (LRRK2 Roc-COR). Biochemical analyses of LRRK2 Roc-COR reveal that it forms homodimers, with the C-terminal portion of COR mediating its dimerization. Furthermore, it co-purifies and binds Mg2+ GTP/GDP at 1 : 1 stoichiometry, and it hydrolyzes GTP with Km and kcat of 22 nM and 4.70 × 10-4 min-1 , respectively. Thus, even though LRRK2 Roc-COR forms GAD-like homodimers, it exhibits conventional Ras-like GTPase properties, with high-affinity binding of Mg2+ -GTP/GDP and low intrinsic catalytic activity. The PD-causative Y1699C mutation mapped to the COR domain was previously reported to reduce the GTPase activity of full-length LRRK2. In contrast, this mutation induces no change in the GTPase activity, and only slight perturbations in the secondary structure contents of LRRK2 Roc-COR. As this mutation does not directly affect the GTPase activity of the isolated Roc-COR tandem, it is possible that the effects of this mutation on full-length LRRK2 occur via other functional domains. Open Practices Open Science: This manuscript was awarded with the Open Materials Badge. For more information see: https://cos.io/our-services/open-science-badges/.
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Affiliation(s)
- Ryan D Mills
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Lung-Yu Liang
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia.,Cell Signaling Research Laboratories, University of Melbourne, Parkville, Victoria, Australia
| | - Daisy Sio-Seng Lio
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia.,Cell Signaling Research Laboratories, University of Melbourne, Parkville, Victoria, Australia
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Terrence D Mulhern
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - George Cao
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Vijaya B Kenche
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia.,Florey Neuroscience Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Janetta G Culvenor
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia.,Cell Signaling Research Laboratories, University of Melbourne, Parkville, Victoria, Australia
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21
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Seol W, Nam D, Son I. Rab GTPases as Physiological Substrates of LRRK2 Kinase. Exp Neurobiol 2019; 28:134-145. [PMID: 31138985 PMCID: PMC6526114 DOI: 10.5607/en.2019.28.2.134] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
LRRK2 (Leucine-Rich Repeat Kinase 2) is a gene whose specific mutations cause Parkinson's disease (PD), the most common neurodegenerative movement disorder. LRRK2 harbors GTPase and kinase activities, two enzyme activities that play critical roles in the regulation of cellular signal transduction. Among the several LRRK2 pathogenic mutations, the most prevalent G2019S mutation increases its kinase activity when compared with the wild-type (WT), suggesting that LRRK2 kinase substrates are potential culprits of PD pathogenesis. Although there were several studies to identify LRRK2 kinase substrates, most of them mainly employed in vitro kinase assays. Therefore, it remains uncertain whether the identified substrates were real physiological substrates. However, efforts to determine physiological LRRK2 kinase substrates have recently identified several members of the Rab GTPase family as physiological LRRK2 kinase substrates. A conserved threonine or serine in the switch II domain of certain Rab GTPase family members (Rab3A/B/C/D, Rab5A/B, Rab8A/B, Rab10, Rab12, Rab29, Rab35 and Rab43) has been pinpointed to be phosphorylated by LRRK2 in cells using sophisticated phosphoproteomics technology in combination with LRRK2-specific kinase inhibitors. The Rab GTPases regulate vesicle trafficking, suggesting that LRRK2 may be a regulator of such vesicle trafficking, confirming previously suggested LRRK2 functions. However, how the consequence of the LRRK2-mediated Rab phosphorylation is related to PD pathogenesis is not clear. This review briefly summarizes the recent results about LRRK2-mediated Rab phosphorylation studies.
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Affiliation(s)
- Wongi Seol
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| | - Daleum Nam
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| | - Ilhong Son
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
- Department of Neurology, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
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Agrahari AK, Doss GPC, Siva R, Magesh R, Zayed H. Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach. J Theor Biol 2019; 469:163-171. [PMID: 30844370 DOI: 10.1016/j.jtbi.2019.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
The G2019S substitution in the Leucine-rich repeat kinase 2 (LRRK2) is significantly associated with Parkinson's disease (PD). This substitution was identified in both familial and sporadic forms of PD with a higher frequency. Few computational studies have reported the impact of G2019S substitution on inhibitors of the kinase domain of LRRK2. However, no computational study deeply investigated the possible impact of the G2019S substitution on the kinase domain in its Apo conformation. Therefore, in this study, we used 200 ns molecular dynamic simulation using the GROMACS 5.1.4 package software to investigate the impact of the G2019S substitution on the structure of the kinase domain of LRRK2. Our results indicate that the G2019S substitution affects the dynamics and stability of LRRK2 by decreasing the flexibility and increasing the compactness of the kinase domain and showing its tendency to be in an active conformation for long time interval because of the high energy barrier between active and inactive conformation. This study predicts the molecular pathogenicity mechanism of the G2019S on patients with PD and provides a potential platform for developing therapeutics for patients with PD that harbor this amino acid substitution.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University (DU), Porur, Chennai, 600116, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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Waschbüsch D, Hübel N, Ossendorf E, Lobbestael E, Baekelandt V, Lindsay AJ, McCaffrey MW, Khan AR, Barnekow A. Rab32 interacts with SNX6 and affects retromer-dependent Golgi trafficking. PLoS One 2019; 14:e0208889. [PMID: 30640902 PMCID: PMC6331118 DOI: 10.1371/journal.pone.0208889] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 11/26/2018] [Indexed: 12/18/2022] Open
Abstract
The Rab family of small GTPases regulate various aspects of cellular dynamics in eukaryotic cells. Membrane trafficking has emerged as central to the functions of leucine-rich repeat kinase 2 (LRRK2), which is associated with inherited and sporadic forms of Parkinson's disease (PD). Rabs act as both regulators of the catalytic activity and targets for serine/threonine phosphorylation by LRRK2. Rab32, Rab38 and Rab29 have been shown to regulate LRRK2 sub-cellular localization through direct interactions. Recently, Rab29 was shown to escort LRRK2 to the Golgi apparatus and activate the phosphorylation of Rab8 and Rab10. Rab32 is linked to multiple cellular functions including endosomal trafficking, mitochondrial dynamics, and melanosome biogenesis. A missense mutation in Rab32 has also recently been linked to PD. Here, we demonstrate that Rab32 directly interacts with sorting nexin 6 (SNX6). SNX6 is a transient subunit of the retromer, an endosome-Golgi retrieval complex whose Vps35 subunit is strongly associated with PD. We could further show that localization of cation-independent mannose-6-phosphate receptors, which are recycled to the trans-Golgi network (TGN) by the retromer, was affected by both Rab32 and SNX6. These data imply that Rab32 is linked to SNX6/retromer trafficking at the Golgi, and also suggests a possible connection between the retromer and Rab32 in the trafficking and biological functions of LRRK2.
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Affiliation(s)
- Dieter Waschbüsch
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Nicole Hübel
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
| | - Edith Ossendorf
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
| | - Evy Lobbestael
- Laboratory for Neurobiology and Gene Therapy, KU Leuven, Leuven, Belgium
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, KU Leuven, Leuven, Belgium
| | - Andrew J. Lindsay
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Mary W. McCaffrey
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- * E-mail: (AK); (AB)
| | - Angelika Barnekow
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
- * E-mail: (AK); (AB)
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Structure and nucleotide-induced conformational dynamics of the Chlorobium tepidum Roco protein. Biochem J 2019; 476:51-66. [PMID: 30538153 DOI: 10.1042/bcj20180803] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
The LRR (leucine-rich repeat)-Roc (Ras of complex proteins)-COR (C-terminal of Roc) domains are central to the action of nearly all Roco proteins, including the Parkinson's disease-associated protein LRRK2 (leucine-rich repeat kinase 2). We previously demonstrated that the Roco protein from Chlorobium tepidum (CtRoco) undergoes a dimer-monomer cycle during the GTPase reaction, with the protein being mainly dimeric in the nucleotide-free and GDP (guanosine-5'-diphosphate)-bound states and monomeric in the GTP (guanosine-5'-triphosphate)-bound state. Here, we report a crystal structure of CtRoco in the nucleotide-free state showing for the first time the arrangement of the LRR-Roc-COR. This structure reveals a compact dimeric arrangement and shows an unanticipated intimate interaction between the Roc GTPase domains in the dimer interface, involving residues from the P-loop, the switch II loop, the G4 region and a loop which we named the 'Roc dimerization loop'. Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) is subsequently used to highlight structural alterations induced by individual steps along the GTPase cycle. The structure and HDX-MS data propose a pathway linking nucleotide binding to monomerization and relaying the conformational changes via the Roc switch II to the LRR and COR domains. Together, this work provides important new insights in the regulation of the Roco proteins.
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Wauters L, Versées W, Kortholt A. Roco Proteins: GTPases with a Baroque Structure and Mechanism. Int J Mol Sci 2019; 20:ijms20010147. [PMID: 30609797 PMCID: PMC6337361 DOI: 10.3390/ijms20010147] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/21/2018] [Accepted: 12/25/2018] [Indexed: 01/05/2023] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of genetically inherited Parkinson’s Disease (PD). LRRK2 is a large, multi-domain protein belonging to the Roco protein family, a family of GTPases characterized by a central RocCOR (Ras of complex proteins/C-terminal of Roc) domain tandem. Despite the progress in characterizing the GTPase function of Roco proteins, there is still an ongoing debate concerning the working mechanism of Roco proteins in general, and LRRK2 in particular. This review consists of two parts. First, an overview is given of the wide evolutionary range of Roco proteins, leading to a variety of physiological functions. The second part focusses on the GTPase function of the RocCOR domain tandem central to the action of all Roco proteins, and progress in the understanding of its structure and biochemistry is discussed and reviewed. Finally, based on the recent work of our and other labs, a new working hypothesis for the mechanism of Roco proteins is proposed.
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Affiliation(s)
- Lina Wauters
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.
- Department of Cell Biochemistry, University of Groningen, NL-9747 AG Groningen, The Netherlands.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, NL-9747 AG Groningen, The Netherlands.
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Roco Proteins and the Parkinson's Disease-Associated LRRK2. Int J Mol Sci 2018; 19:ijms19124074. [PMID: 30562929 PMCID: PMC6320773 DOI: 10.3390/ijms19124074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 02/08/2023] Open
Abstract
Small G-proteins are structurally-conserved modules that function as molecular on-off switches. They function in many different cellular processes with differential specificity determined by the unique effector-binding surfaces, which undergo conformational changes during the switching action. These switches are typically standalone monomeric modules that form transient heterodimers with specific effector proteins in the 'on' state, and cycle to back to the monomeric conformation in the 'off' state. A new class of small G-proteins called "Roco" was discovered about a decade ago; this class is distinct from the typical G-proteins in several intriguing ways. Their switch module resides within a polypeptide chain of a large multi-domain protein, always adjacent to a unique domain called COR, and its effector kinase often resides within the same polypeptide. As such, the mechanisms of action of the Roco G-proteins are likely to differ from those of the typical G-proteins. Understanding these mechanisms is important because aberrant activity in the human Roco protein LRRK2 is associated with the pathogenesis of Parkinson's disease. This review provides an update on the current state of our understanding of the Roco G-proteins and the prospects of targeting them for therapeutic purposes.
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Taymans JM, Chartier-Harlin MC. In silico and Wet Bench Interactomics Sheds Light on the Similitudes and Differences between Human ROCO Proteins. Proteomics 2018; 18:e1800103. [PMID: 29791783 DOI: 10.1002/pmic.201800103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/09/2018] [Indexed: 11/10/2022]
Abstract
Defining a common and specific function for homologs of a novel protein family is not a trivial task. In their recent study, Tomkins and colleagues have addressed this challenge for the ROCO protein family by exploring interactomes of its four human members: MASL1, DAPK1, LRRK1, and LRRK2. ROCO proteins are characterized by a Ras-GTPase domain embedded in complex multidomain proteins and a functional descriptor for this protein family has been elusive despite accumulating research, particularly for LRRK2, a protein implicated in Parkinson's disease. Tomkins et al. have combined an in silico weighted literature mining approach with novel interactomics data obtained on protein chips for all four proteins under strictly comparable conditions. The combination of these approaches has allowed the prudent formulation of common functions for ROCO proteins, including their involvement in stress response and cell projection organization. In addition, the study also confirms functional specificity for the individual ROCOs with such functions as cell death and apoptosis assigned to DAPK1, cellular, and neuronal development associated with LRRK1 and intracellular transport and organization assigned to LRRK2.
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Affiliation(s)
- Jean-Marc Taymans
- UMR-S1172 Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer CHU Lille, Inserm and Université de Lille, Team "Early Stages of Parkinson's disease", Lille, 59000, France
| | - Marie-Christine Chartier-Harlin
- UMR-S1172 Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer CHU Lille, Inserm and Université de Lille, Team "Early Stages of Parkinson's disease", Lille, 59000, France
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Gilsbach BK, Eckert M, Gloeckner CJ. Regulation of LRRK2: insights from structural and biochemical analysis. Biol Chem 2018; 399:637-642. [DOI: 10.1515/hsz-2018-0132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/14/2018] [Indexed: 12/11/2022]
Abstract
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multi-domain protein and its mutations can lead to Parkinson’s disease. Recent studies on LRRK2 and homologue proteins have advanced our mechanistic understanding of LRRK2 regulation. Here, we summarize the available data on the biochemistry and structure of LRRK2 and postulate three possible layers of regulation, translocation, monomer-dimer equilibrium and intramolecular activation of domains.
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Affiliation(s)
- Bernd K. Gilsbach
- DZNE-German Center for Neurodegenerative Diseases , Otfried-Müller Str. 23 , D-72076 Tübingen , Germany
| | - Marita Eckert
- DZNE-German Center for Neurodegenerative Diseases , Otfried-Müller Str. 23 , D-72076 Tübingen , Germany
| | - Christian Johannes Gloeckner
- DZNE-German Center for Neurodegenerative Diseases , Otfried-Müller Str. 23 , D-72076 Tübingen , Germany
- University of Tübingen, Institute for Ophthalmic Research, Center for Ophthalmology , Elfriede-Aulhorn-Str. 7 , D-72076 Tübingen , Germany
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Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W. A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover. Nat Commun 2017; 8:1008. [PMID: 29044096 PMCID: PMC5714945 DOI: 10.1038/s41467-017-01103-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 08/18/2017] [Indexed: 11/24/2022] Open
Abstract
Mutations in LRRK2 are a common cause of genetic Parkinson's disease (PD). LRRK2 is a multi-domain Roco protein, harbouring kinase and GTPase activity. In analogy with a bacterial homologue, LRRK2 was proposed to act as a GTPase activated by dimerization (GAD), while recent reports suggest LRRK2 to exist under a monomeric and dimeric form in vivo. It is however unknown how LRRK2 oligomerization is regulated. Here, we show that oligomerization of a homologous bacterial Roco protein depends on the nucleotide load. The protein is mainly dimeric in the nucleotide-free and GDP-bound states, while it forms monomers upon GTP binding, leading to a monomer-dimer cycle during GTP hydrolysis. An analogue of a PD-associated mutation stabilizes the dimer and decreases the GTPase activity. This work thus provides insights into the conformational cycle of Roco proteins and suggests a link between oligomerization and disease-associated mutations in LRRK2.
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Affiliation(s)
- Egon Deyaert
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Lina Wauters
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Giambattista Guaitoli
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
- Eberhard Karls University, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Albert Konijnenberg
- Department of Chemistry, Biomolecular & Analytical Mass Spectrometry group, University of Antwerp, 2020, Antwerp, Belgium
| | - Margaux Leemans
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Susanne Terheyden
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
- Structural Biology Group, Max-Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Rodrigo Gallardo
- VIB Center for Brain & Disease Research, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PB 802, 3000, Leuven, Belgium
| | | | | | - Henderikus Pots
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Peter J M Van Haastert
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Frank Sobott
- Department of Chemistry, Biomolecular & Analytical Mass Spectrometry group, University of Antwerp, 2020, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
- Eberhard Karls University, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Rouslan Efremov
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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Neuronal death signaling pathways triggered by mutant LRRK2. Biochem Soc Trans 2017; 45:123-129. [PMID: 28202665 DOI: 10.1042/bst20160256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/11/2016] [Accepted: 10/14/2016] [Indexed: 11/17/2022]
Abstract
Autosomal dominantly inherited mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease. While considerable progress has been made in understanding its function and the many different cellular activities in which it participates, a clear understanding of the mechanism(s) of the induction of neuronal death by mutant forms of LRRK2 remains elusive. Although several in vivo models have documented the progressive loss of dopaminergic neurons of the substantia nigra, more complete interrogations of the modality of neuronal death have been gained from cellular models. Overexpression of mutant LRRK2 in neuronal-like cell lines or in primary neurons induces an apoptotic type of cell death involving components of the extrinsic as well as intrinsic death pathways. While informative, these studies are limited by their reliance upon isolated neuronal cells; and the pathways triggered by mutant LRRK2 in neurons may be further refined or modulated by extracellular signals. Nevertheless, the identification of specific cell death-associated signaling events set in motion by the dominant action of mutant LRRK2, the loss of an inhibitory function of wild-type LRRK2, or a combination of the two, expands the landscape of potential therapeutic targets for future intervention in the clinic.
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A proteomic analysis of LRRK2 binding partners reveals interactions with multiple signaling components of the WNT/PCP pathway. Mol Neurodegener 2017; 12:54. [PMID: 28697798 PMCID: PMC5505151 DOI: 10.1186/s13024-017-0193-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/20/2017] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Autosomal-dominant mutations in the Park8 gene encoding Leucine-rich repeat kinase 2 (LRRK2) have been identified to cause up to 40% of the genetic forms of Parkinson's disease. However, the function and molecular pathways regulated by LRRK2 are largely unknown. It has been shown that LRRK2 serves as a scaffold during activation of WNT/β-catenin signaling via its interaction with the β-catenin destruction complex, DVL1-3 and LRP6. In this study, we examine whether LRRK2 also interacts with signaling components of the WNT/Planar Cell Polarity (WNT/PCP) pathway, which controls the maturation of substantia nigra dopaminergic neurons, the main cell type lost in Parkinson's disease patients. METHODS Co-immunoprecipitation and tandem mass spectrometry was performed in a mouse substantia nigra cell line (SN4741) and human HEK293T cell line in order to identify novel LRRK2 binding partners. Inhibition of the WNT/β-catenin reporter, TOPFlash, was used as a read-out of WNT/PCP pathway activation. The capacity of LRRK2 to regulate WNT/PCP signaling in vivo was tested in Xenopus laevis' early development. RESULTS Our proteomic analysis identified that LRRK2 interacts with proteins involved in WNT/PCP signaling such as the PDZ domain-containing protein GIPC1 and Integrin-linked kinase (ILK) in dopaminergic cells in vitro and in the mouse ventral midbrain in vivo. Moreover, co-immunoprecipitation analysis revealed that LRRK2 binds to two core components of the WNT/PCP signaling pathway, PRICKLE1 and CELSR1, as well as to FLOTILLIN-2 and CULLIN-3, which regulate WNT secretion and inhibit WNT/β-catenin signaling, respectively. We also found that PRICKLE1 and LRRK2 localize in signalosomes and act as dual regulators of WNT/PCP and β-catenin signaling. Accordingly, analysis of the function of LRRK2 in vivo, in X. laevis revelaed that LRKK2 not only inhibits WNT/β-catenin pathway, but induces a classical WNT/PCP phenotype in vivo. CONCLUSIONS Our study shows for the first time that LRRK2 activates the WNT/PCP signaling pathway through its interaction to multiple WNT/PCP components. We suggest that LRRK2 regulates the balance between WNT/β-catenin and WNT/PCP signaling, depending on the binding partners. Since this balance is crucial for homeostasis of midbrain dopaminergic neurons, we hypothesize that its alteration may contribute to the pathophysiology of Parkinson's disease.
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Nguyen APT, Moore DJ. Understanding the GTPase Activity of LRRK2: Regulation, Function, and Neurotoxicity. ADVANCES IN NEUROBIOLOGY 2017; 14:71-88. [PMID: 28353279 DOI: 10.1007/978-3-319-49969-7_4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most frequent cause of Parkinson's disease (PD) with late-onset and autosomal-dominant inheritance. LRRK2 belongs to the ROCO superfamily of proteins, characterized by a Ras-of-complex (Roc) GTPase domain in tandem with a C-terminal-of-Roc (COR) domain. LRRK2 also contains a protein kinase domain adjacent to the Roc-COR tandem domain in addition to multiple repeat domains. Disease-causing familial mutations cluster within the Roc-COR tandem and kinase domains of LRRK2, where they act to either impair GTPase activity or enhance kinase activity. Familial LRRK2 mutations share in common the capacity to induce neuronal toxicity in cultured cells. While the contribution of the frequent G2019S mutation, located within the kinase domain, to kinase activity and neurotoxicity has been extensively investigated, the contribution of GTPase activity has received less attention. The GTPase domain has been shown to play an important role in regulating kinase activity, in dimerization, and in mediating the neurotoxic effects of LRRK2. Accordingly, the GTPase domain has emerged as a potential therapeutic target for inhibiting the pathogenic effects of LRRK2 mutations. Many important mechanisms remain to be elucidated, including how the GTPase cycle of LRRK2 is regulated, whether GTPase effectors exist for LRRK2, and how GTPase activity contributes to the overall functional output of LRRK2. In this review, we discuss the importance of the GTPase domain for LRRK2-linked PD focusing in particular on its regulation, function, and contribution to neurotoxic mechanisms.
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Affiliation(s)
- An Phu Tran Nguyen
- Center for Neurodegenerative Science, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA
| | - Darren J Moore
- Center for Neurodegenerative Science, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.
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Guaitoli G, Raimondi F, Gilsbach BK, Gómez-Llorente Y, Deyaert E, Renzi F, Li X, Schaffner A, Jagtap PKA, Boldt K, von Zweydorf F, Gotthardt K, Lorimer DD, Yue Z, Burgin A, Janjic N, Sattler M, Versées W, Ueffing M, Ubarretxena-Belandia I, Kortholt A, Gloeckner CJ. Structural model of the dimeric Parkinson's protein LRRK2 reveals a compact architecture involving distant interdomain contacts. Proc Natl Acad Sci U S A 2016; 113:E4357-66. [PMID: 27357661 PMCID: PMC4968714 DOI: 10.1073/pnas.1523708113] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large, multidomain protein containing two catalytic domains: a Ras of complex proteins (Roc) G-domain and a kinase domain. Mutations associated with familial and sporadic Parkinson's disease (PD) have been identified in both catalytic domains, as well as in several of its multiple putative regulatory domains. Several of these mutations have been linked to increased kinase activity. Despite the role of LRRK2 in the pathogenesis of PD, little is known about its overall architecture and how PD-linked mutations alter its function and enzymatic activities. Here, we have modeled the 3D structure of dimeric, full-length LRRK2 by combining domain-based homology models with multiple experimental constraints provided by chemical cross-linking combined with mass spectrometry, negative-stain EM, and small-angle X-ray scattering. Our model reveals dimeric LRRK2 has a compact overall architecture with a tight, multidomain organization. Close contacts between the N-terminal ankyrin and C-terminal WD40 domains, and their proximity-together with the LRR domain-to the kinase domain suggest an intramolecular mechanism for LRRK2 kinase activity regulation. Overall, our studies provide, to our knowledge, the first structural framework for understanding the role of the different domains of full-length LRRK2 in the pathogenesis of PD.
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Affiliation(s)
- Giambattista Guaitoli
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Francesco Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; Cell Networks, University of Heidelberg, 69120 Heidelberg, Germany
| | - Bernd K Gilsbach
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, The Netherlands; Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Yacob Gómez-Llorente
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Egon Deyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Vlaams Instituut voor Biotechnologie, Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Fabiana Renzi
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Xianting Li
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adam Schaffner
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029; Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Pravin Kumar Ankush Jagtap
- Center for Integrated Protein Science Munich at Department of Chemistry, Technische Universität München, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Karsten Boldt
- Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Felix von Zweydorf
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Katja Gotthardt
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | | | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | | | - Michael Sattler
- Center for Integrated Protein Science Munich at Department of Chemistry, Technische Universität München, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Vlaams Instituut voor Biotechnologie, Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Iban Ubarretxena-Belandia
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, The Netherlands;
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany;
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Activation Mechanism of LRRK2 and Its Cellular Functions in Parkinson's Disease. PARKINSONS DISEASE 2016; 2016:7351985. [PMID: 27293958 PMCID: PMC4880697 DOI: 10.1155/2016/7351985] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/19/2016] [Indexed: 01/09/2023]
Abstract
Human LRRK2 (Leucine-Rich Repeat Kinase 2) has been associated with both familial and idiopathic Parkinson's disease (PD). Although several LRRK2 mediated pathways and interaction partners have been identified, the cellular functions of LRRK2 and LRRK2 mediated progression of PD are still only partially understood. LRRK2 belongs to the group of Roco proteins which are characterized by the presence of a Ras-like G-domain (Roc), a C-terminal of Roc domain (COR), a kinase, and several protein-protein interaction domains. Roco proteins exhibit a complex activation mechanism involving intramolecular signaling, dimerization, and substrate/effector binding. Importantly, PD mutations in LRRK2 have been linked to a decreased GTPase and impaired kinase activity, thus providing putative therapeutic targets. To fully explore these potential targets it will be crucial to understand the function and identify the pathways responsible for LRRK2-linked PD. Here, we review the recent progress in elucidating the complex LRRK2 activation mechanism, describe the accumulating evidence that link LRRK2-mediated PD to mitochondrial dysfunction and aberrant autophagy, and discuss possible ways for therapeutically targeting LRRK2.
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Abstract
Mutations in LRRK2 are associated with inherited Parkinson's disease (PD) in a large number of families, and the genetic locus containing the LRRK2 gene contains a risk factor for sporadic PD. The LRRK2 protein contains several domains that suggest a role in cellular signaling, including a kinase domain. It is also clear that LRRK2 interacts, either physically or genetically, with several other important proteins implicated in PD, suggesting that LRRK2 may be a central player in the pathways that underlie parkinsonism. As such, LRRK2 has been proposed to be a plausible target for therapeutic intervention, with kinase inhibition being pursued most actively. However, there are still several fundamental aspects of LRRK2 biology and function that remain unresolved at this time. This review will focus on the key questions of normal function of LRRK2 and how this might be related to the pathophysiology of PD.
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Langston RG, Rudenko IN, Cookson MR. The function of orthologues of the human Parkinson's disease gene LRRK2 across species: implications for disease modelling in preclinical research. Biochem J 2016; 473:221-32. [PMID: 26811536 PMCID: PMC5165698 DOI: 10.1042/bj20150985] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the period since LRRK2 (leucine-rich repeat kinase 2) was identified as a causal gene for late-onset autosomal dominant parkinsonism, a great deal of work has been aimed at understanding whether the LRRK2 protein might be a druggable target for Parkinson's disease (PD). As part of this effort, animal models have been developed to explore both the normal and the pathophysiological roles of LRRK2. However, LRRK2 is part of a wider family of proteins whose functions in different organisms remain poorly understood. In this review, we compare the information available on biochemical properties of LRRK2 homologues and orthologues from different species from invertebrates (e.g. Caenorhabditis elegans and Drosophila melanogaster) to mammals. We particularly discuss the mammalian LRRK2 homologue, LRRK1, and those species where there is only a single LRRK homologue, discussing examples where each of the LRRK family of proteins has distinct properties as well as those cases where there appear to be functional redundancy. We conclude that uncovering the function of LRRK2 orthologues will help to elucidate the key properties of human LRRK2 as well as to improve understanding of the suitability of different animal models for investigation of LRRK2-related PD.
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Affiliation(s)
- Rebekah G. Langston
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, 20892
| | - Iakov N. Rudenko
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, 20892
| | - Mark R. Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, 20892
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Rho Signaling in Dictyostelium discoideum. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 322:61-181. [DOI: 10.1016/bs.ircmb.2015.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Imai Y, Kobayashi Y, Inoshita T, Meng H, Arano T, Uemura K, Asano T, Yoshimi K, Zhang CL, Matsumoto G, Ohtsuka T, Kageyama R, Kiyonari H, Shioi G, Nukina N, Hattori N, Takahashi R. The Parkinson's Disease-Associated Protein Kinase LRRK2 Modulates Notch Signaling through the Endosomal Pathway. PLoS Genet 2015; 11:e1005503. [PMID: 26355680 PMCID: PMC4565672 DOI: 10.1371/journal.pgen.1005503] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/14/2015] [Indexed: 12/03/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a key molecule in the pathogenesis of familial and idiopathic Parkinson’s disease (PD). We have identified two novel LRRK2-associated proteins, a HECT-type ubiquitin ligase, HERC2, and an adaptor-like protein with six repeated Neuralized domains, NEURL4. LRRK2 binds to NEURL4 and HERC2 via the LRRK2 Ras of complex proteins (ROC) domain and NEURL4, respectively. HERC2 and NEURL4 link LRRK2 to the cellular vesicle transport pathway and Notch signaling, through which the LRRK2 complex promotes the recycling of the Notch ligand Delta-like 1 (Dll1)/Delta (Dl) through the modulation of endosomal trafficking. This process negatively regulates Notch signaling through cis-inhibition by stabilizing Dll1/Dl, which accelerates neural stem cell differentiation and modulates the function and survival of differentiated dopaminergic neurons. These effects are strengthened by the R1441G ROC domain-mutant of LRRK2. These findings suggest that the alteration of Notch signaling in mature neurons is a component of PD etiology linked to LRRK2. LRRK2 is linked to autosomal dominant late-onset Parkinson’s disease, suggesting that LRRK2 gain-of-function mutations lead to age-dependent degeneration of the midbrain dopaminergic neurons. In this study, we describe two novel LRRK2-associated proteins HERC2 and NEURL4, which are a ubiquitin ligase and an adaptor-like protein, respectively. HERC2 and NEURL4 direct LRRK2 to Notch signaling pathway, in which the LRRK2-NEURL4-HERC2 complex promotes the recycling of the Notch ligand Delta-like 1 (Dll1)/Delta (Dl) through the modulation of endosomal trafficking. As a result, the amounts of Dll1/D1 on the plasma membrane are increased, which affects negatively Notch signaling through cis-inhibition. The effect is enhanced by a Parkinson’s-disease associated mutation of LRRK2. Inhibition of Notch signaling in adult dopaminergic neurons impairs its functions and survival. These findings indicate a possible link between Notch pathway and Parkinson’s disease.
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Affiliation(s)
- Yuzuru Imai
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
- * E-mail: (YI); (NH); (RT)
| | - Yoshito Kobayashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- CREST (Core Research for Evolutionary Science and Technology), Japan Science and Technology Agency, Saitama, Japan
| | - Tsuyoshi Inoshita
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hongrui Meng
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Taku Arano
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kengo Uemura
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Asano
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenji Yoshimi
- Department of Neurophysiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Chang-Liang Zhang
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- CREST (Core Research for Evolutionary Science and Technology), Japan Science and Technology Agency, Saitama, Japan
| | - Gen Matsumoto
- Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshiyuki Ohtsuka
- Department of Cell Biology, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Ryoichiro Kageyama
- Department of Cell Biology, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Go Shioi
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Nobuyuki Nukina
- Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobutaka Hattori
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
- CREST (Core Research for Evolutionary Science and Technology), Japan Science and Technology Agency, Saitama, Japan
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- * E-mail: (YI); (NH); (RT)
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- CREST (Core Research for Evolutionary Science and Technology), Japan Science and Technology Agency, Saitama, Japan
- * E-mail: (YI); (NH); (RT)
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40
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Conformational heterogeneity of the Roc domains in C. tepidum Roc-COR and implications for human LRRK2 Parkinson mutations. Biosci Rep 2015; 35:BSR20150128. [PMID: 26310572 PMCID: PMC4721548 DOI: 10.1042/bsr20150128] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/10/2015] [Indexed: 12/30/2022] Open
Abstract
Ras of complex proteins (Roc) is a Ras-like GTP-binding domain that always occurs in tandem with the C-terminal of Roc (COR) domain and is found in bacteria, plants and animals. Recently, it has been shown that Roco proteins belong to the family of G-proteins activated by nucleotide (nt)-dependent dimerization (GADs). We investigated the RocCOR tandem from the bacteria Chlorobium tepidum with site-directed spin labelling and pulse EPR distance measurements to follow conformational changes during the Roco G-protein cycle. Our results confirm that the COR domains are a stable dimerization device serving as a scaffold for the Roc domains that, in contrast, are structurally heterogeneous and dynamic entities. Contrary to other GAD proteins, we observed only minor structural alterations upon binding and hydrolysis of GTP, indicating significant mechanistic variations within this protein class. Mutations in the most prominent member of the Roco family of proteins, leucine-rich repeat (LRR) kinase 2 (LRRK2), are the most frequent cause of late-onset Parkinson's disease (PD). Using a stable recombinant LRRK2 Roc-COR-kinase fragment we obtained detailed kinetic data for the G-protein cycle. Our data confirmed that dimerization is essential for efficient GTP hydrolysis and PD mutations in the Roc domain result in decreased GTPase activity. Previous data have shown that these LRRK2 PD-mutations are located in the interface between Roc and COR. Importantly, analogous mutations in the conserved C. tepidum Roc/COR interface significantly influence the structure and nt-induced conformational changes of the Roc domains.
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41
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Ye N, Zhang X, Miao M, Fan X, Zheng Y, Xu D, Wang J, Zhou L, Wang D, Gao Y, Wang Y, Shi W, Ji P, Li D, Guan Z, Shao C, Zhuang Z, Gao Z, Qi J, Zhao F. Saccharina genomes provide novel insight into kelp biology. Nat Commun 2015; 6:6986. [PMID: 25908475 PMCID: PMC4421812 DOI: 10.1038/ncomms7986] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/20/2015] [Indexed: 01/28/2023] Open
Abstract
Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome of Saccharina japonica, one of the most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98.5% of the estimated genome, and 18,733 protein-coding genes are predicted and annotated. Gene families related to cell wall synthesis, halogen concentration, development and defence systems were expanded. Functional diversification of the mannuronan C-5-epimerase and haloperoxidase gene families provides insight into the evolutionary adaptation of polysaccharide biosynthesis and iodine antioxidation. Additional sequencing of seven cultivars and nine wild individuals reveal that the genetic diversity within wild populations is greater than among cultivars. All of the cultivars are descendants of a wild S. japonica accession showing limited admixture with S. longissima. This study represents an important advance toward improving yields and economic traits in Saccharina and provides an invaluable resource for plant genome studies.
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Affiliation(s)
- Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Miao Miao
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yi Zheng
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Zhou
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongsheng Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yuan Gao
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Wenyu Shi
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peifeng Ji
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biosystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zheng Guan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhimeng Zhuang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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Garcia-Miralles M, Coomaraswamy J, Häbig K, Herzig MC, Funk N, Gillardon F, Maisel M, Jucker M, Gasser T, Galter D, Biskup S. No dopamine cell loss or changes in cytoskeleton function in transgenic mice expressing physiological levels of wild type or G2019S mutant LRRK2 and in human fibroblasts. PLoS One 2015; 10:e0118947. [PMID: 25830304 PMCID: PMC4382199 DOI: 10.1371/journal.pone.0118947] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 01/14/2015] [Indexed: 11/25/2022] Open
Abstract
Mutations within the LRRK2 gene have been identified in Parkinson’s disease (PD) patients and have been implicated in the dysfunction of several cellular pathways. Here, we explore how pathogenic mutations and the inhibition of LRRK2 kinase activity affect cytoskeleton dynamics in mouse and human cell systems. We generated and characterized a novel transgenic mouse model expressing physiological levels of human wild type and G2019S-mutant LRRK2. No neuronal loss or neurodegeneration was detected in midbrain dopamine neurons at the age of 12 months. Postnatal hippocampal neurons derived from transgenic mice showed no alterations in the seven parameters examined concerning neurite outgrowth sampled automatically on several hundred neurons using high content imaging. Treatment with the kinase inhibitor LRRK2-IN-1 resulted in no significant changes in the neurite outgrowth. In human fibroblasts we analyzed whether pathogenic LRRK2 mutations change cytoskeleton functions such as cell adhesion. To this end we compared the adhesion characteristics of human skin fibroblasts derived from six PD patients carrying one of three different pathogenic LRRK2 mutations and from four age-matched control individuals. The mutant LRRK2 variants as well as the inhibition of LRRK2 kinase activity did not reveal any significant cell adhesion differences in cultured fibroblasts. In summary, our results in both human and mouse cell systems suggest that neither the expression of wild type or mutant LRRK2, nor the inhibition of LRRK2 kinase activity affect neurite complexity and cellular adhesion.
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Affiliation(s)
- Marta Garcia-Miralles
- Department of Neurodegeneration, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
| | - Janaky Coomaraswamy
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
| | - Karina Häbig
- Department of Medical Genetics and Applied Genomics, Institute of Human Genetics, University of Tuebingen, 72076 Tuebingen, Germany
| | - Martin C. Herzig
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
| | - Natalja Funk
- Department of Neurodegeneration, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
| | - Frank Gillardon
- Boehringer Ingelheim Pharma GmbH & Co. KG, CNS Research, 88397 Biberach an der Riss, Germany
| | - Martina Maisel
- Department of Neurodegeneration, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
| | - Mathias Jucker
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
| | - Thomas Gasser
- Department of Neurodegeneration, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
| | - Dagmar Galter
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Saskia Biskup
- Department of Neurodegeneration, Hertie-Institute for Clinical Brain Research and DZNE, German Center for Neurodegenerative Diseases, 72076 Tuebingen, Germany
- * E-mail:
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43
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Abstract
DAP-kinase (DAPK) is a Ca(2+)/calmodulin regulated Ser/Thr kinase that activates a diverse range of cellular activities. It is subject to multiple layers of regulation involving both intramolecular signaling, and interactions with additional proteins, including other kinases and phosphatases. Its protein stability is modulated by at least three distinct ubiquitin-dependent systems. Like many kinases, DAPK participates in several signaling cascades, by phosphorylating additional kinases such as ZIP-kinase and protein kinase D (PKD), or Pin1, a phospho-directed peptidyl-prolyl isomerase that regulates the function of many phosphorylated proteins. Other substrate targets have more direct cellular effects; for example, phosphorylation of the myosin II regulatory chain and tropomyosin mediate some of DAPK's cytoskeletal functions, including membrane blebbing during cell death and cell motility. DAPK induces distinct death pathways of apoptosis, autophagy and programmed necrosis. Among the substrates implicated in these processes, phosphorylation of PKD, Beclin 1, and the NMDA receptor has been reported. Interestingly, not all cellular effects are mediated by DAPK's catalytic activity. For example, by virtue of protein-protein interactions alone, DAPK activates pyruvate kinase isoform M2, the microtubule affinity regulating kinases and inflammasome protein NLRP3, to promote glycolysis, influence microtubule dynamics, and enhance interleukin-1β production, respectively. In addition, a number of other substrates and interacting proteins have been identified, the physiological significance of which has not yet been established. All of these substrates, effectors and regulators together comprise the DAPK interactome. By presenting the components of the interactome network, this review will clarify both the mechanisms by which DAPK function is regulated, and by which it mediates its various cellular effects.
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Affiliation(s)
- Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, 76100, Rehovot, Israel
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44
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Reyniers L, Del Giudice MG, Civiero L, Belluzzi E, Lobbestael E, Beilina A, Arrigoni G, Derua R, Waelkens E, Li Y, Crosio C, Iaccarino C, Cookson MR, Baekelandt V, Greggio E, Taymans JM. Differential protein-protein interactions of LRRK1 and LRRK2 indicate roles in distinct cellular signaling pathways. J Neurochem 2014; 131:239-50. [PMID: 24947832 PMCID: PMC4272680 DOI: 10.1111/jnc.12798] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/30/2014] [Accepted: 06/17/2014] [Indexed: 02/07/2023]
Abstract
Genetic studies show that LRRK2, and not its closest paralogue LRRK1, is linked to Parkinson's disease. To gain insight into the molecular and cellular basis of this discrepancy, we searched for LRRK1- and LRRK2-specific cellular processes by identifying their distinct interacting proteins. A protein microarray-based interaction screen was performed with recombinant 3xFlag-LRRK1 and 3xFlag-LRRK2 and, in parallel, co-immunoprecipitation followed by mass spectrometry was performed from SH-SY5Y neuroblastoma cell lines stably expressing 3xFlag-LRRK1 or 3xFlag-LRRK2. We identified a set of LRRK1- and LRRK2-specific as well as common interactors. One of our most prominent findings was that both screens pointed to epidermal growth factor receptor (EGF-R) as a LRRK1-specific interactor, while 14-3-3 proteins were LRRK2-specific. This is consistent with phosphosite mapping of LRRK1, revealing phosphosites outside of 14-3-3 consensus binding motifs. To assess the functional relevance of these interactions, SH-SY5Y-LRRK1 and -LRRK2 cell lines were treated with LRRK2 kinase inhibitors that disrupt 14-3-3 binding, or with EGF, an EGF-R agonist. Redistribution of LRRK2, not LRRK1, from diffuse cytoplasmic to filamentous aggregates was observed after inhibitor treatment. Similarly, EGF induced translocation of LRRK1, but not of LRRK2, to endosomes. Our study confirms that LRRK1 and LRRK2 can carry out distinct functions by interacting with different cellular proteins. LRRK1 and LRRK2 (leucine-rich repeat kinase) interaction partners were identified by two different protein-protein interaction screens. These confirmed epidermal growth factor receptor (EGR-R) as a LRRK1-specific interactor, while 14-3-3 proteins were LRRK2-specific. Functional analysis of these interactions and the pathways they mediate shows that LRRK1 and LRRK2 signaling do not intersect, reflective of the differential role of both LRRKs in Parkinson's disease.
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Affiliation(s)
- Lauran Reyniers
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | | | - Laura Civiero
- Department of Biology, University of Padova, Padova, Italy
| | - Elisa Belluzzi
- Department of Biology, University of Padova, Padova, Italy
| | - Evy Lobbestael
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Alexandra Beilina
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, USA
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Proteomics Center of Padova University, Padova, Italy
| | - Rita Derua
- Department of Cellular and Molecular Medicine, KU Leuven, Laboratory of protein phosphorylation and proteomics, Leuven, Belgium
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, KU Leuven, Laboratory of protein phosphorylation and proteomics, Leuven, Belgium
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, USA
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Elisa Greggio
- Department of Biology, University of Padova, Padova, Italy
| | - Jean-Marc Taymans
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
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Abstract
Parkinson’s disease (PD) is a progressively debilitating neurodegenerative syndrome. Although best described as a movement disorder, the condition has prominent autonomic, cognitive, psychiatric, sensory and sleep components. Striatal dopaminergic innervation and nigral neurons are progressively lost, with associated Lewy pathology readily apparent on autopsy. Nevertheless, knowledge of the molecular events leading to this pathophysiology is limited. Current therapies offer symptomatic benefit but they fail to slow progression and patients continue to deteriorate. Recent discoveries in sporadic, Mendelian and more complex forms of parkinsonism provide novel insight into disease etiology; 28 genes, including those encoding alpha-synuclein (SNCA), leucine-rich repeat kinase 2 (LRRK2) and microtubule-associated protein tau (MAPT), have been linked and/or associated with PD. A consensus regarding the affected biological pathways and molecular processes has also started to emerge. In early-onset and more a typical PD, deficits in mitophagy pathways and lysosomal function appear to be prominent. By contrast, in more typical late-onset PD, chronic, albeit subtle, dysfunction in synaptic transmission, early endosomal trafficking and receptor recycling, as well as chaperone-mediated autophagy, provide a unifying synthesis of the molecular pathways involved. Disease-modification (neuroprotection) is no longer such an elusive goal given the unparalleled opportunity for diagnosis, translational neuroscience and therapeutic development provided by genetic discovery.
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Affiliation(s)
- Michelle K Lin
- Djavad Mowafaghian Centre for Brain Health, Centre for Applied Neurogenetics, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Matthew J Farrer
- Djavad Mowafaghian Centre for Brain Health, Centre for Applied Neurogenetics, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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Pfannes EKB, Anielski A, Gerhardt M, Beta C. Intracellular photoactivation of caged cGMP induces myosin II and actin responses in motile cells. Integr Biol (Camb) 2014; 5:1456-63. [PMID: 24136144 DOI: 10.1039/c3ib40109j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Cyclic GMP (cGMP) is a ubiquitous second messenger in eukaryotic cells. It is assumed to regulate the association of myosin II with the cytoskeleton of motile cells. When cells of the social amoeba Dictyostelium discoideum are exposed to chemoattractants or to increased osmotic stress, intracellular cGMP levels rise, preceding the accumulation of myosin II in the cell cortex. To directly investigate the impact of intracellular cGMP on cytoskeletal dynamics in a living cell, we released cGMP inside the cell by laser-induced photo-cleavage of a caged precursor. With this approach, we could directly show in a live cell experiment that an increase in intracellular cGMP indeed induces myosin II to accumulate in the cortex. Unexpectedly, we observed for the first time that also the amount of filamentous actin in the cell cortex increases upon a rise in the cGMP concentration, independently of cAMP receptor activation and signaling. We discuss our results in the light of recent work on the cGMP signaling pathway and suggest possible links between cGMP signaling and the actin system.
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Affiliation(s)
- Eva K B Pfannes
- Biological Physics, Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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47
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Genetic, structural, and molecular insights into the function of ras of complex proteins domains. ACTA ACUST UNITED AC 2014; 21:809-18. [PMID: 24981771 PMCID: PMC4104024 DOI: 10.1016/j.chembiol.2014.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/13/2014] [Accepted: 05/28/2014] [Indexed: 11/22/2022]
Abstract
Ras of complex proteins (ROC) domains were identified in 2003 as GTP binding modules in large multidomain proteins from Dictyostelium discoideum. Research into the function of these domains exploded with their identification in a number of proteins linked to human disease, including leucine-rich repeat kinase 2 (LRRK2) and death-associated protein kinase 1 (DAPK1) in Parkinson’s disease and cancer, respectively. This surge in research has resulted in a growing body of data revealing the role that ROC domains play in regulating protein function and signaling pathways. In this review, recent advances in the structural information available for proteins containing ROC domains, along with insights into enzymatic function and the integration of ROC domains as molecular switches in a cellular and organismal context, are explored.
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48
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Gilsbach BK, Kortholt A. Structural biology of the LRRK2 GTPase and kinase domains: implications for regulation. Front Mol Neurosci 2014; 7:32. [PMID: 24847205 PMCID: PMC4017136 DOI: 10.3389/fnmol.2014.00032] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/07/2014] [Indexed: 12/20/2022] Open
Abstract
Human leucine rich repeat kinase 2 (LRRK2) belongs to the Roco family of proteins, which are characterized by the presence of a Ras-like G-domain (Roc), a C-terminal of Roc domain (COR), and a kinase domain. Mutations in LRRK2 have been found to be thus far the most frequent cause of late-onset Parkinson’s disease (PD). Several of the pathogenic mutations in LRRK2 result in decreased GTPase activity and enhanced kinase activity, suggesting a possible PD-related gain of abnormal function. Important progress in the structural understanding of LRRK2 has come from our work with related Roco proteins from lower organisms. Atomic structures of Roco proteins from prokaryotes revealed that Roco proteins belong to the GAD class of molecular switches (G proteins activated by nucleotide dependent dimerization). As in LRRK2, PD-analogous mutations in Roco proteins from bacteria decrease the GTPase reaction. Studies with Roco proteins from the model organism Dictyostelium discoideum revealed that PD mutants have different effects and most importantly they explained the G2019S-related increased LRRK2 kinase activity. Furthermore, the structure of Dictyostelium Roco4 kinase in complex with the LRRK2 inhibitor H1152 showed that Roco4 and other Roco family proteins can be important for the optimization of the current, and identification of new, LRRK2 kinase inhibitors. In this review we highlight the recent progress in structural and biochemical characterization of Roco proteins and discuss its implication for the understanding of the complex regulatory mechanism of LRRK2.
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Affiliation(s)
- Bernd K Gilsbach
- Department of Cell Biochemistry, University of Groningen Groningen, Netherlands
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen Groningen, Netherlands
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Prokaryotic Ancestry of Eukaryotic Protein Networks Mediating Innate Immunity and Apoptosis. J Mol Biol 2014; 426:1568-82. [DOI: 10.1016/j.jmb.2013.11.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/21/2013] [Accepted: 11/27/2013] [Indexed: 12/22/2022]
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50
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Sobczyk GJ, Wang J, Weijer CJ. SILAC-based proteomic quantification of chemoattractant-induced cytoskeleton dynamics on a second to minute timescale. Nat Commun 2014; 5:3319. [PMID: 24569529 PMCID: PMC3971484 DOI: 10.1038/ncomms4319] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/25/2014] [Indexed: 01/14/2023] Open
Abstract
Cytoskeletal dynamics during cell behaviours ranging from endocytosis and exocytosis to cell division and movement is controlled by a complex network of signalling pathways, the full details of which are as yet unresolved. Here we show that SILAC-based proteomic methods can be used to characterize the rapid chemoattractant-induced dynamic changes in the actin–myosin cytoskeleton and regulatory elements on a proteome-wide scale with a second to minute timescale resolution. This approach provides novel insights in the ensemble kinetics of key cytoskeletal constituents and association of known and novel identified binding proteins. We validate the proteomic data by detailed microscopy-based analysis of in vivo translocation dynamics for key signalling factors. This rapid large-scale proteomic approach may be applied to other situations where highly dynamic changes in complex cellular compartments are expected to play a key role. Actin-dependent motility is driven by the rapid changes in the recruitment of many different structural and regulatory proteins at the cell’s cortex. Sobczyk et al. characterize these changes in the cytoskeletal proteome on a second to minute timescale during chemotactic response in Dictyostelium using SILAC-based proteomics.
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Affiliation(s)
- Grzegorz J Sobczyk
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jun Wang
- 1] Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK [2]
| | - Cornelis J Weijer
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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