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Sambri I, Ferniani M, Campostrini G, Testa M, Meraviglia V, de Araujo MEG, Dokládal L, Vilardo C, Monfregola J, Zampelli N, Vecchio Blanco FD, Torella A, Ruosi C, Fecarotta S, Parenti G, Staiano L, Bellin M, Huber LA, De Virgilio C, Trepiccione F, Nigro V, Ballabio A. RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome. Nat Commun 2023; 14:2775. [PMID: 37188688 DOI: 10.1038/s41467-023-38428-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Heterozygous mutations in the gene encoding RagD GTPase were shown to cause a novel autosomal dominant condition characterized by kidney tubulopathy and cardiomyopathy. We previously demonstrated that RagD, and its paralogue RagC, mediate a non-canonical mTORC1 signaling pathway that inhibits the activity of TFEB and TFE3, transcription factors of the MiT/TFE family and master regulators of lysosomal biogenesis and autophagy. Here we show that RagD mutations causing kidney tubulopathy and cardiomyopathy are "auto- activating", even in the absence of Folliculin, the GAP responsible for RagC/D activation, and cause constitutive phosphorylation of TFEB and TFE3 by mTORC1, without affecting the phosphorylation of "canonical" mTORC1 substrates, such as S6K. By using HeLa and HK-2 cell lines, human induced pluripotent stem cell-derived cardiomyocytes and patient-derived primary fibroblasts, we show that RRAGD auto-activating mutations lead to inhibition of TFEB and TFE3 nuclear translocation and transcriptional activity, which impairs the response to lysosomal and mitochondrial injury. These data suggest that inhibition of MiT/TFE factors plays a key role in kidney tubulopathy and cardiomyopathy syndrome.
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Affiliation(s)
- Irene Sambri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Marco Ferniani
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | | | - Marialuisa Testa
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | | | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Ladislav Dokládal
- Department of Biology, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Claudia Vilardo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | - Jlenia Monfregola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | - Nicolina Zampelli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
| | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Carolina Ruosi
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Simona Fecarotta
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Giancarlo Parenti
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Institute for Genetic and Biomedical Research, National Research Council (CNR), Milan, Italy
| | - Milena Bellin
- Leiden University Medical Center, 2333ZC, Leiden, the Netherlands
- Department of Biology, University of Padua, 35131, Padua, Italy
- Veneto Institute of Molecular Medicine, 35129, Padua, Italy
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Francesco Trepiccione
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
- Biogem Research Institute Ariano Irpino, Ariano Irpino, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, (NA), Italy.
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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2
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Cui Z, Napolitano G, de Araujo MEG, Esposito A, Monfregola J, Huber LA, Ballabio A, Hurley JH. Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Nature 2023; 614:572-579. [PMID: 36697823 PMCID: PMC9931586 DOI: 10.1038/s41586-022-05652-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 12/13/2022] [Indexed: 01/26/2023]
Abstract
The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy1. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1)2-5 is unique in its mTORC1 substrate recruitment mechanism, which is strictly dependent on the amino acid-mediated activation of the RagC GTPase activating protein FLCN6,7. TFEB lacks the TOR signalling motif responsible for the recruitment of other mTORC1 substrates. We used cryogenic-electron microscopy to determine the structure of TFEB as presented to mTORC1 for phosphorylation, which we refer to as the 'megacomplex'. Two full Rag-Ragulator complexes present each molecule of TFEB to the mTOR active site. One Rag-Ragulator complex is bound to Raptor in the canonical mode seen previously in the absence of TFEB. A second Rag-Ragulator complex (non-canonical) docks onto the first through a RagC GDP-dependent contact with the second Ragulator complex. The non-canonical Rag dimer binds the first helix of TFEB with a RagCGDP-dependent aspartate clamp in the cleft between the Rag G domains. In cellulo mutation of the clamp drives TFEB constitutively into the nucleus while having no effect on mTORC1 localization. The remainder of the 108-amino acid TFEB docking domain winds around Raptor and then back to RagA. The double use of RagC GDP contacts in both Rag dimers explains the strong dependence of TFEB phosphorylation on FLCN and the RagC GDP state.
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Affiliation(s)
- Zhicheng Cui
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Alessandra Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Jlenia Monfregola
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- SSM School for Advanced Studies, Federico II University, Naples, Italy.
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
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3
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Nairz M, Bellmann-Weiler R, Ladstätter M, Schüllner F, Zimmermann M, Koller AM, Blunder S, Naschberger H, Klotz W, Herold M, Kerndler S, Jeske M, Haschka D, Petzer V, Schroll A, Sonnweber T, Tancevski I, Fritsche G, de Araujo MEG, Stasyk T, Huber LA, Griesmacher A, Theurl I, Weiss G. Overcoming limitations in the availability of swabs systems used for SARS-CoV-2 laboratory diagnostics. Sci Rep 2021; 11:2261. [PMID: 33500503 PMCID: PMC7838421 DOI: 10.1038/s41598-021-81782-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/03/2021] [Indexed: 01/21/2023] Open
Abstract
The diagnosis of COVID-19 relies on the direct detection of SARS-CoV-2 RNA in respiratory specimens by RT-PCR. The pandemic spread of the disease caused an imbalance between demand and supply of materials and reagents needed for diagnostic purposes including swab sets. In a comparative effectiveness study, we conducted serial follow-up swabs in hospitalized laboratory-confirmed COVID-19 patients. We assessed the diagnostic performance of an in-house system developed according to recommendations by the US CDC. In a total of 96 serial swabs, we found significant differences in the accuracy of the different swab systems to generate a positive result in SARS-CoV-2 RT-PCR, ranging from around 50 to 80%. Of note, an in-house swab system was superior to most commercially available sets as reflected by significantly lower Ct values of viral genes. Thus, a simple combination of broadly available materials may enable diagnostic laboratories to bypass global limitations in the supply of swab sets.
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Affiliation(s)
- Manfred Nairz
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria.
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Miriam Ladstätter
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - Falko Schüllner
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - Martina Zimmermann
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Anna-Maria Koller
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Silvia Blunder
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Helene Naschberger
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Werner Klotz
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Manfred Herold
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Sylvia Kerndler
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - Martina Jeske
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - David Haschka
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Verena Petzer
- Department of Internal Medicine V, Hematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Schroll
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Thomas Sonnweber
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Gernot Fritsche
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Taras Stasyk
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Griesmacher
- Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital of Innsbruck, Innsbruck, Austria
| | - Igor Theurl
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
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4
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Napolitano G, Di Malta C, Esposito A, de Araujo MEG, Pece S, Bertalot G, Matarese M, Benedetti V, Zampelli A, Stasyk T, Siciliano D, Venuta A, Cesana M, Vilardo C, Nusco E, Monfregola J, Calcagnì A, Di Fiore PP, Huber LA, Ballabio A. A substrate-specific mTORC1 pathway underlies Birt-Hogg-Dubé syndrome. Nature 2020; 585:597-602. [PMID: 32612235 PMCID: PMC7610377 DOI: 10.1038/s41586-020-2444-0] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/27/2020] [Indexed: 12/17/2022]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is a key metabolic hub that controls the cellular response to environmental cues by exerting its kinase activity on multiple substrates1–3. However, whether mTORC1 responds to diverse stimuli by differentially phosphorylating specific substrates is poorly understood. Here we show that Transcription Factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy4,5, is phosphorylated by mTORC1 via a substrate-specific mechanism mediated by RagGTPases. Thus, TFEB phosphorylation is strictly dependent on amino acid-mediated activation of RagC/D GTPase but, unlike other mTORC1 substrates such as S6K and 4E-BP1, insensitive to growth factor-induced Rheb activity. This mechanism plays a crucial role in Birt-Hogg-Dubé (BHD) syndrome, a disorder caused by mutations of the RagC/D activator folliculin (FLCN) and characterized by benign skin tumors, lung and kidney cysts and renal cell carcinoma6,7. We found that constitutive activation of TFEB is the main driver of the kidney abnormalities and paradoxical mTORC1 hyperactivity observed in BHD syndrome. Remarkably, depletion of TFEB in a kidney-specific mouse model of BHD syndrome fully rescued the disease phenotype and associated lethality and normalized mTORC1 activity. Together, these findings identify a substrate-specific control mechanism of mTORC1, whose dysregulation leads to kidney cysts and cancer.
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Affiliation(s)
- Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | | | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Salvatore Pece
- IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Maria Matarese
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | | | - Angela Zampelli
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Taras Stasyk
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | | | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Claudia Vilardo
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | | | - Alessia Calcagnì
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Pier Paolo Di Fiore
- IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.,Austrian Drug Screening Institute (ADSI), Innsbruck, Austria
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy. .,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA. .,SSM School for Advanced Studies, Federico II University, Naples, Italy.
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5
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Abstract
Lysosomes are key cellular catabolic centers that also perform fundamental metabolic, signaling and quality control functions. Lysosomes are not static and they respond dynamically to intra‐ and extracellular stimuli triggering changes in organelle numbers, size and position. Such physical changes have a strong impact on lysosomal activity ultimately influencing cellular homeostasis. In this review, we summarize the current knowledge on lysosomal size regulation, on its physiological role(s) and association to several disease conditions.
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Affiliation(s)
- Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Gudrun Liebscher
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael W Hess
- Institute of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.,Austrian Drug Screening Institute, ADSI, Innsbruck, Austria
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6
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Hess MW, Vogel GF, Yordanov TE, Witting B, Gutleben K, Ebner HL, de Araujo MEG, Filipek PA, Huber LA. Combining high-pressure freezing with pre-embedding immunogold electron microscopy and tomography. Traffic 2018; 19:639-649. [PMID: 29673018 DOI: 10.1111/tra.12575] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 12/11/2022]
Abstract
Immunogold labeling of permeabilized whole-mount cells or thin-sectioned material is widely used for the subcellular localization of biomolecules at the high spatial resolution of electron microscopy (EM). Those approaches are well compatible with either 3-dimensional (3D) reconstruction of organelle morphology and antigen distribution or with rapid cryofixation-but not easily with both at once. We describe here a specimen preparation and labeling protocol for animal cell cultures, which represents a novel blend of specifically adapted versions of established techniques. It combines the virtues of reliably preserved organelle ultrastructure, as trapped by rapid freezing within milliseconds followed by freeze-substitution and specimen rehydration, with the advantages of robust labeling of intracellular constituents in 3D through means of pre-embedding NANOGOLD-silver immunocytochemistry. So obtained thin and semi-thick epoxy resin sections are suitable for transmission EM imaging, as well as tomographic reconstruction and modeling of labeling patterns in the 3D cellular context.
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Affiliation(s)
- Michael W Hess
- Division of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - Georg F Vogel
- Division of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria.,Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.,Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Teodor E Yordanov
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Barbara Witting
- Division of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - Karin Gutleben
- Division of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hannes L Ebner
- Division of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - Mariana E G de Araujo
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Przemyslaw A Filipek
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas A Huber
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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7
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Filipek PA, de Araujo MEG, Vogel GF, De Smet CH, Eberharter D, Rebsamen M, Rudashevskaya EL, Kremser L, Yordanov T, Tschaikner P, Fürnrohr BG, Lechner S, Dunzendorfer-Matt T, Scheffzek K, Bennett KL, Superti-Furga G, Lindner HH, Stasyk T, Huber LA. LAMTOR/Ragulator is a negative regulator of Arl8b- and BORC-dependent late endosomal positioning. J Cell Biol 2017; 216:4199-4215. [PMID: 28993467 PMCID: PMC5716276 DOI: 10.1083/jcb.201703061] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/28/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022] Open
Abstract
Signaling from lysosomes controls cellular clearance and energy metabolism. Lysosomal malfunction has been implicated in several pathologies, including neurodegeneration, cancer, infection, immunodeficiency, and obesity. Interestingly, many functions are dependent on the organelle position. Lysosomal motility requires the integration of extracellular and intracellular signals that converge on a competition between motor proteins that ultimately control lysosomal movement on microtubules. Here, we identify a novel upstream control mechanism of Arl8b-dependent lysosomal movement toward the periphery of the cell. We show that the C-terminal domain of lyspersin, a subunit of BLOC-1-related complex (BORC), is essential and sufficient for BORC-dependent recruitment of Arl8b to lysosomes. In addition, we establish lyspersin as the linker between BORC and late endosomal/lysosomal adaptor and mitogen activated protein kinase and mechanistic target of rapamycin activator (LAMTOR) complexes and show that epidermal growth factor stimulation decreases LAMTOR/BORC association, thereby promoting BORC- and Arl8b-dependent lysosomal centrifugal transport.
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Affiliation(s)
- Przemyslaw A Filipek
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Mariana E G de Araujo
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Georg F Vogel
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria.,Department of Pediatrics I, Innsbruck Medical University, Innsbruck, Austria
| | - Cedric H De Smet
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Daniela Eberharter
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Elena L Rudashevskaya
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Teodor Yordanov
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Philipp Tschaikner
- Institute for Molecular Biology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Barbara G Fürnrohr
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Stefan Lechner
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | | | - Klaus Scheffzek
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Herbert H Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Taras Stasyk
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Lukas A Huber
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
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8
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de Araujo MEG, Naschberger A, Fürnrohr BG, Stasyk T, Dunzendorfer-Matt T, Lechner S, Welti S, Kremser L, Shivalingaiah G, Offterdinger M, Lindner HH, Huber LA, Scheffzek K. Crystal structure of the human lysosomal mTORC1 scaffold complex and its impact on signaling. Science 2017; 358:377-381. [PMID: 28935770 DOI: 10.1126/science.aao1583] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/11/2017] [Indexed: 12/15/2022]
Abstract
The LAMTOR [late endosomal and lysosomal adaptor and MAPK (mitogen-activated protein kinase) and mTOR (mechanistic target of rapamycin) activator] complex, also known as "Ragulator," controls the activity of mTOR complex 1 (mTORC1) on the lysosome. The crystal structure of LAMTOR consists of two roadblock/LC7 domain-folded heterodimers wrapped and apparently held together by LAMTOR1, which assembles the complex on lysosomes. In addition, the Rag guanosine triphosphatases (GTPases) associated with the pentamer through their carboxyl-terminal domains, predefining the orientation for interaction with mTORC1. In vitro reconstitution and experiments with site-directed mutagenesis defined the physiological importance of LAMTOR1 in assembling the remaining components to ensure fidelity of mTORC1 signaling. Functional data validated the effect of two short LAMTOR1 amino acid regions in recruitment and stabilization of the Rag GTPases.
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Affiliation(s)
- Mariana E G de Araujo
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Andreas Naschberger
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Barbara G Fürnrohr
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Taras Stasyk
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | | | - Stefan Lechner
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Welti
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Giridhar Shivalingaiah
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin Offterdinger
- Division of Neurobiochemistry-Biooptics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Herbert H Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas A Huber
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria. .,Austrian Drug Screening Institute, 6020 Innsbruck, Austria
| | - Klaus Scheffzek
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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9
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Vogel GF, Ebner HL, de Araujo MEG, Schmiedinger T, Eiter O, Pircher H, Gutleben K, Witting B, Teis D, Huber LA, Hess MW. Ultrastructural Morphometry Points to a New Role for LAMTOR2 in Regulating the Endo/Lysosomal System. Traffic 2015; 16:617-34. [DOI: 10.1111/tra.12271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Georg F. Vogel
- Division of Histology and Embryology; Medical University of Innsbruck; Müllerstrasse 59 A-6020 Innsbruck Austria
- Division of Cell Biology, Biocenter; Medical University of Innsbruck; Innrain 80-82 A-6020 Innsbruck Austria
| | - Hannes L. Ebner
- Division of Histology and Embryology; Medical University of Innsbruck; Müllerstrasse 59 A-6020 Innsbruck Austria
- Current address: Department for Trauma Surgery; Medical University of Innsbruck; Anichstrasse 35 A-6020 Innsbruck Austria
| | - Mariana E. G. de Araujo
- Division of Cell Biology, Biocenter; Medical University of Innsbruck; Innrain 80-82 A-6020 Innsbruck Austria
| | - Thomas Schmiedinger
- Department of Therapeutic Radiology and Oncology; Medical University of Innsbruck; Anichstrasse 35 A-6020 Innsbruck Austria
| | - Oliver Eiter
- Department of Therapeutic Radiology and Oncology; Medical University of Innsbruck; Anichstrasse 35 A-6020 Innsbruck Austria
| | - Haymo Pircher
- Research Institute for Biomedical Aging Research; University of Innsbruck; Rennweg 10 A-6020 Innsbruck Austria
| | - Karin Gutleben
- Division of Histology and Embryology; Medical University of Innsbruck; Müllerstrasse 59 A-6020 Innsbruck Austria
| | - Barbara Witting
- Division of Histology and Embryology; Medical University of Innsbruck; Müllerstrasse 59 A-6020 Innsbruck Austria
| | - David Teis
- Division of Cell Biology, Biocenter; Medical University of Innsbruck; Innrain 80-82 A-6020 Innsbruck Austria
| | - Lukas A. Huber
- Division of Cell Biology, Biocenter; Medical University of Innsbruck; Innrain 80-82 A-6020 Innsbruck Austria
| | - Michael W. Hess
- Division of Histology and Embryology; Medical University of Innsbruck; Müllerstrasse 59 A-6020 Innsbruck Austria
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10
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Schiefermeier N, Scheffler JM, de Araujo MEG, Stasyk T, Yordanov T, Ebner HL, Offterdinger M, Munck S, Hess MW, Wickström SA, Lange A, Wunderlich W, Fässler R, Teis D, Huber LA. The late endosomal p14-MP1 (LAMTOR2/3) complex regulates focal adhesion dynamics during cell migration. ACTA ACUST UNITED AC 2014; 205:525-40. [PMID: 24841562 PMCID: PMC4033770 DOI: 10.1083/jcb.201310043] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Late endosomes locally regulate cell migration by transporting the p14–MP1 scaffold complex to the vicinity of focal adhesions. Cell migration is mediated by the dynamic remodeling of focal adhesions (FAs). Recently, an important role of endosomal signaling in regulation of cell migration was recognized. Here, we show an essential function for late endosomes carrying the p14–MP1 (LAMTOR2/3) complex in FA dynamics. p14–MP1-positive endosomes move to the cell periphery along microtubules (MTs) in a kinesin1- and Arl8b-dependent manner. There they specifically target FAs to regulate FA turnover, which is required for cell migration. Using genetically modified fibroblasts from p14-deficient mice and Arl8b-depleted cells, we demonstrate that MT plus end–directed traffic of p14–MP1-positive endosomes triggered IQGAP1 disassociation from FAs. The release of IQGAP was required for FA dynamics. Taken together, our results suggest that late endosomes contribute to the regulation of cell migration by transporting the p14–MP1 scaffold complex to the vicinity of FAs.
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Affiliation(s)
- Natalia Schiefermeier
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, AustriaDivision of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Julia M Scheffler
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Mariana E G de Araujo
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Taras Stasyk
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Teodor Yordanov
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Hannes L Ebner
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, AustriaDivision of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Martin Offterdinger
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Sebastian Munck
- VIB Center for the Biology of Disease, KU Leuven, 3000 Leuven, Belgium
| | - Michael W Hess
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Sara A Wickström
- Paul Gerson Unna group "Skin Homeostasis and Ageing", Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany Department of Molecular Medicine, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Anika Lange
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Winfried Wunderlich
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria Oncotyrol, 6020 Innsbruck, Austria
| | - Reinhard Fässler
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - David Teis
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Lukas A Huber
- Division of Cell Biology and Division of Neurobiochemistry/Biooptics, Biocenter, Department of Physiology and Medical Physics, Division of Physiology, Department of Traumatology, Center of Operative Medicine, and Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
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11
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Thauerer B, Voegele P, Hermann-Kleiter N, Thuille N, de Araujo MEG, Offterdinger M, Baier G, Huber LA, Baier-Bitterlich G. LAMTOR2-mediated modulation of NGF/MAPK activation kinetics during differentiation of PC12 cells. PLoS One 2014; 9:e95863. [PMID: 24752675 PMCID: PMC3994133 DOI: 10.1371/journal.pone.0095863] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 03/31/2014] [Indexed: 12/26/2022] Open
Abstract
LAMTOR2 (p14), a part of the larger LAMTOR/Ragulator complex, plays a crucial role in EGF-dependent activation of p42/44 mitogen-activated protein kinases (MAPK, ERK1/2). In this study, we investigated the role of LAMTOR2 in nerve growth factor (NGF)-mediated neuronal differentiation. Stimulation of PC12 (rat adrenal pheochromocytoma) cells with NGF is known to activate the MAPK. Pharmacological inhibition of MEK1 as well as siRNA–mediated knockdown of both p42 and p44 MAPK resulted in inhibition of neurite outgrowth. Contrary to expectations, siRNA–mediated knockdown of LAMTOR2 effectively augmented neurite formation and neurite length of PC12 cells. Ectopic expression of a siRNA-resistant LAMTOR2 ortholog reversed this phenotype back to wildtype levels, ruling out nonspecific off-target effects of this LAMTOR2 siRNA approach. Mechanistically, LAMTOR2 siRNA treatment significantly enhanced NGF-dependent MAPK activity, and this effect again was reversed upon expression of the siRNA-resistant LAMTOR2 ortholog. Studies of intracellular trafficking of the NGF receptor TrkA revealed a rapid colocalization with early endosomes, which was modulated by LAMTOR2 siRNA. Inhibition of LAMTOR2 and concomitant destabilization of the remaining members of the LAMTOR complex apparently leads to a faster release of the TrkA/MAPK signaling module and nuclear increase of activated MAPK. These results suggest a modulatory role of the MEK1 adapter protein LAMTOR2 in NGF-mediated MAPK activation required for induction of neurite outgrowth in PC12 cells.
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Affiliation(s)
- Bettina Thauerer
- Division of Neurobiochemistry, CCB-Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Paul Voegele
- Division of Neurobiochemistry, CCB-Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- Division of Cell Genetics, Department for Pharmacology and Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Natascha Hermann-Kleiter
- Division of Cell Genetics, Department for Pharmacology and Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Nikolaus Thuille
- Division of Cell Genetics, Department for Pharmacology and Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Mariana E. G. de Araujo
- Division of Cell Biology, CCB-Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Offterdinger
- Division of Neurobiochemistry, CCB-Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Gottfried Baier
- Division of Cell Genetics, Department for Pharmacology and Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas A. Huber
- Division of Cell Biology, CCB-Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriele Baier-Bitterlich
- Division of Neurobiochemistry, CCB-Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- * E-mail:
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12
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Kurzbauer R, Teis D, de Araujo MEG, Maurer-Stroh S, Eisenhaber F, Bourenkov GP, Bartunik HD, Hekman M, Rapp UR, Huber LA, Clausen T. Crystal structure of the p14/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes. Proc Natl Acad Sci U S A 2004; 101:10984-9. [PMID: 15263099 PMCID: PMC503730 DOI: 10.1073/pnas.0403435101] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Signaling pathways in eukaryotic cells are often controlled by the formation of specific signaling complexes, which are coordinated by scaffold and adaptor proteins. Elucidating their molecular architecture is essential to understand the spatial and temporal regulation of cellular signaling. p14 and MP1 form a tight (K(d) = 12.8 nM) endosomal adaptor/scaffold complex, which regulates mitogen-activated protein kinase (MAPK) signaling. Here, we present the 1.9-A crystal structure of a biologically functional p14/MP1 complex. The overall topology of the individual MP1 and p14 proteins is almost identical, having a central five-stranded beta-sheet sandwiched between a two-helix and a one-helix layer. Formation of the p14/MP1 heterodimer proceeds by beta-sheet augmentation and yields a unique, almost symmetrical, complex with several potential protein-binding sites on its surface. Mutational analysis allowed identification of the p14 endosomal adaptor motif, which seems to orient the complex relative to the endosomal membrane. Two highly conserved and hydrophobic protein-binding sites are located on the opposite "cytoplasmic" face of the p14/MP1 heterodimer and might therefore function as docking sites for the target proteins extracellular regulated kinase (ERK) 1 and MAPK/ERK kinase 1. Furthermore, detailed sequence analyses revealed that MP1/p14, together with profilins, define a protein superfamily of small subcellular adaptor proteins, named ProflAP. Taken together, the presented work provides insight into the spatial regulation of MAPK signaling, illustrating how p14 and MP1 collaborate as an endosomal adaptor/scaffold complex.
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Affiliation(s)
- Robert Kurzbauer
- Institute for Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
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