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Yi SA, Sepic S, Schulman BA, Ordureau A, An H. mTORC1-CTLH E3 ligase regulates the degradation of HMG-CoA synthase 1 through the Pro/N-degron pathway. Mol Cell 2024; 84:2166-2184.e9. [PMID: 38788716 PMCID: PMC11186538 DOI: 10.1016/j.molcel.2024.04.026] [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: 11/27/2023] [Revised: 03/15/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024]
Abstract
Mammalian target of rapamycin (mTOR) senses changes in nutrient status and stimulates the autophagic process to recycle amino acids. However, the impact of nutrient stress on protein degradation beyond autophagic turnover is incompletely understood. We report that several metabolic enzymes are proteasomal targets regulated by mTOR activity based on comparative proteome degradation analysis. In particular, 3-hydroxy-3-methylglutaryl (HMG)-coenzyme A (CoA) synthase 1 (HMGCS1), the initial enzyme in the mevalonate pathway, exhibits the most significant half-life adaptation. Degradation of HMGCS1 is regulated by the C-terminal to LisH (CTLH) E3 ligase through the Pro/N-degron motif. HMGCS1 is ubiquitylated on two C-terminal lysines during mTORC1 inhibition, and efficient degradation of HMGCS1 in cells requires a muskelin adaptor. Importantly, modulating HMGCS1 abundance has a dose-dependent impact on cell proliferation, which is restored by adding a mevalonate intermediate. Overall, our unbiased degradomics study provides new insights into mTORC1 function in cellular metabolism: mTORC1 regulates the stability of limiting metabolic enzymes through the ubiquitin system.
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Affiliation(s)
- Sang Ah Yi
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sara Sepic
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany; Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany; Technical University of Munich, School of Natural Sciences, Munich, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Heeseon An
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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2
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Gross A, Müller J, Chrustowicz J, Strasser A, Gottemukkala KV, Sherpa D, Schulman BA, Murray PJ, Alpi AF. Skraban-Deardorff intellectual disability syndrome-associated mutations in WDR26 impair CTLH E3 complex assembly. FEBS Lett 2024; 598:978-994. [PMID: 38575527 DOI: 10.1002/1873-3468.14866] [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: 12/16/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
Patients with Skraban-Deardorff syndrome (SKDEAS), a neurodevelopmental syndrome associated with a spectrum of developmental and intellectual delays and disabilities, harbor diverse mutations in WDR26, encoding a subunit of the multiprotein CTLH E3 ubiquitin ligase complex. Structural studies revealed that homodimers of WDR26 bridge two core-CTLH E3 complexes to generate giant, hollow oval-shaped supramolecular CTLH E3 assemblies. Additionally, WDR26 mediates CTLH E3 complex binding to subunit YPEL5 and functions as substrate receptor for the transcriptional repressor HBP1. Here, we mapped SKDEAS-associated mutations on a WDR26 structural model and tested their functionality in complementation studies using genetically engineered human cells lacking CTLH E3 supramolecular assemblies. Despite the diversity of mutations, 15 of 16 tested mutants impaired at least one CTLH E3 complex function contributing to complex assembly and interactions, thus providing first mechanistic insights into SKDEAS pathology.
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Affiliation(s)
- Annette Gross
- Immunoregulation Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Judith Müller
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexander Strasser
- Immunoregulation Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karthik V Gottemukkala
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter J Murray
- Immunoregulation Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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3
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Leydon AR, Downing B, Sanchez JS, Loll-Krippleber R, Belliveau NM, Rodriguez-Mias RA, Bauer A, Watson IJ, Bae L, Villén J, Brown GW, Nemhauser JL. A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587599. [PMID: 38617365 PMCID: PMC11014602 DOI: 10.1101/2024.04.01.587599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast model Saccharomyces cerevisiae to localize repressive function to two distinct domains. Here, we employed two unbiased whole genome approaches to map the physical and genetic interactions of TPL at a repressed locus. We identified SPT4, SPT5 and SPT6 as necessary for repression with the SPT4 subunit acting as a bridge connecting TPL to SPT5 and SPT6. We also discovered the association of multiple additional constituents of the transcriptional preinitiation complex at TPL-repressed promoters, specifically those involved in early transcription initiation events. These findings were validated in yeast and plants through multiple assays, including a novel method to analyze conditional loss of function of essential genes in plants. Our findings support a model where TPL nucleates preassembly of the transcription activation machinery to facilitate rapid onset of transcription once repression is relieved.
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Affiliation(s)
| | - Benjamin Downing
- Department of Biology, University of Washington, Seattle, 98195, USA
| | | | | | | | | | - Andrew Bauer
- Department of Biology, University of Washington, Seattle, 98195, USA
| | | | - Lena Bae
- Department of Biology, University of Washington, Seattle, 98195, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, 98195, USA
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, CA
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4
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A single helix repression domain is functional across diverse eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2206986119. [PMID: 36191192 PMCID: PMC9564828 DOI: 10.1073/pnas.2206986119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The corepressor TOPLESS (TPL) and its paralogs coordinately regulate a large number of genes critical to plant development and immunity. As in many members of the larger pan-eukaryotic Tup1/TLE/Groucho corepressor family, TPL contains a Lis1 Homology domain (LisH), whose function is not well understood. We have previously found that the LisH in TPL-and specifically the N-terminal 18 amino acid alpha-helical region (TPL-H1)-can act as an autonomous repression domain. We hypothesized that homologous domains across diverse LisH-containing proteins could share the same function. To test that hypothesis, we built a library of H1s that broadly sampled the sequence and evolutionary space of LisH domains, and tested their activity in a synthetic transcriptional repression assay in Saccharomyces cerevisiae. Using this approach, we found that repression activity was highly conserved and likely the ancestral function of this motif. We also identified key residues that contribute to repressive function. We leveraged this new knowledge for two applications. First, we tested the role of mutations found in somatic cancers on repression function in two human LisH-containing proteins. Second, we validated function of many of our repression domains in plants, confirming that these sequences should be of use to synthetic biology applications across many eukaryotes.
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5
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Structural and Functional Insights into GID/CTLH E3 Ligase Complexes. Int J Mol Sci 2022; 23:ijms23115863. [PMID: 35682545 PMCID: PMC9180843 DOI: 10.3390/ijms23115863] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Multi-subunit E3 ligases facilitate ubiquitin transfer by coordinating various substrate receptor subunits with a single catalytic center. Small molecules inducing targeted protein degradation have exploited such complexes, proving successful as therapeutics against previously undruggable targets. The C-terminal to LisH (CTLH) complex, also called the glucose-induced degradation deficient (GID) complex, is a multi-subunit E3 ligase complex highly conserved from Saccharomyces cerevisiae to humans, with roles in fundamental pathways controlling homeostasis and development in several species. However, we are only beginning to understand its mechanistic basis. Here, we review the literature of the CTLH complex from all organisms and place previous findings on individual subunits into context with recent breakthroughs on its structure and function.
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6
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Tehlan A, Bhowmick K, Kumar A, Subbarao N, Dhar SK. The tetrameric structure of Plasmodium falciparum phosphoglycerate mutase is critical for optimal enzymatic activity. J Biol Chem 2022; 298:101713. [PMID: 35150741 PMCID: PMC8913309 DOI: 10.1016/j.jbc.2022.101713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022] Open
Abstract
The glycolytic enzyme phosphoglycerate mutase (PGM) is of utmost importance for overall cellular metabolism and has emerged as a novel therapeutic target in cancer cells. This enzyme is also conserved in the rapidly proliferating malarial parasite Plasmodium falciparum, which have a similar metabolic framework as cancer cells and rely on glycolysis as the sole energy-yielding process during intraerythrocytic development. There is no redundancy among the annotated PGM enzymes in Plasmodium, and PfPGM1 is absolutely required for the parasite survival as evidenced by conditional knockdown in our study. A detailed comparison of PfPGM1 with its counterparts followed by in-depth structure-function analysis revealed unique attributes of this parasitic protein. Here, we report for the first time the importance of oligomerization for the optimal functioning of the enzyme in vivo, as earlier studies in eukaryotes only focused on the effects in vitro. We show that single point mutation of the amino acid residue W68 led to complete loss of tetramerization and diminished catalytic activity in vitro. Additionally, ectopic expression of the WT PfPGM1 protein enhanced parasite growth, whereas the monomeric form of PfPGM1 failed to provide growth advantage. Furthermore, mutation of the evolutionarily conserved residue K100 led to a drastic reduction in enzymatic activity. The indispensable nature of this parasite enzyme highlights the potential of PfPGM1 as a therapeutic target against malaria, and targeting the interfacial residues critical for oligomerization can serve as a focal point for promising drug development strategies that may not be restricted to malaria only.
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Affiliation(s)
- Ankita Tehlan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Krishanu Bhowmick
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Amarjeet Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Suman Kumar Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067.
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7
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Wang H, Noordam R, Cade BE, Schwander K, Winkler TW, Lee J, Sung YJ, Bentley AR, Manning AK, Aschard H, Kilpeläinen TO, Ilkov M, Brown MR, Horimoto AR, Richard M, Bartz TM, Vojinovic D, Lim E, Nierenberg JL, Liu Y, Chitrala K, Rankinen T, Musani SK, Franceschini N, Rauramaa R, Alver M, Zee PC, Harris SE, van der Most PJ, Nolte IM, Munroe PB, Palmer ND, Kühnel B, Weiss S, Wen W, Hall KA, Lyytikäinen LP, O'Connell J, Eiriksdottir G, Launer LJ, de Vries PS, Arking DE, Chen H, Boerwinkle E, Krieger JE, Schreiner PJ, Sidney S, Shikany JM, Rice K, Chen YDI, Gharib SA, Bis JC, Luik AI, Ikram MA, Uitterlinden AG, Amin N, Xu H, Levy D, He J, Lohman KK, Zonderman AB, Rice TK, Sims M, Wilson G, Sofer T, Rich SS, Palmas W, Yao J, Guo X, Rotter JI, Biermasz NR, Mook-Kanamori DO, Martin LW, Barac A, Wallace RB, Gottlieb DJ, Komulainen P, Heikkinen S, Mägi R, Milani L, Metspalu A, Starr JM, Milaneschi Y, Waken RJ, Gao C, Waldenberger M, Peters A, Strauch K, Meitinger T, Roenneberg T, Völker U, Dörr M, Shu XO, Mukherjee S, Hillman DR, Kähönen M, Wagenknecht LE, Gieger C, Grabe HJ, Zheng W, Palmer LJ, Lehtimäki T, Gudnason V, Morrison AC, Pereira AC, Fornage M, Psaty BM, van Duijn CM, Liu CT, Kelly TN, Evans MK, Bouchard C, Fox ER, Kooperberg C, Zhu X, Lakka TA, Esko T, North KE, Deary IJ, Snieder H, Penninx BWJH, Gauderman WJ, Rao DC, Redline S, van Heemst D. Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure. Mol Psychiatry 2021; 26:6293-6304. [PMID: 33859359 PMCID: PMC8517040 DOI: 10.1038/s41380-021-01087-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 03/18/2021] [Accepted: 03/29/2021] [Indexed: 02/02/2023]
Abstract
Long and short sleep duration are associated with elevated blood pressure (BP), possibly through effects on molecular pathways that influence neuroendocrine and vascular systems. To gain new insights into the genetic basis of sleep-related BP variation, we performed genome-wide gene by short or long sleep duration interaction analyses on four BP traits (systolic BP, diastolic BP, mean arterial pressure, and pulse pressure) across five ancestry groups in two stages using 2 degree of freedom (df) joint test followed by 1df test of interaction effects. Primary multi-ancestry analysis in 62,969 individuals in stage 1 identified three novel gene by sleep interactions that were replicated in an additional 59,296 individuals in stage 2 (stage 1 + 2 Pjoint < 5 × 10-8), including rs7955964 (FIGNL2/ANKRD33) that increases BP among long sleepers, and rs73493041 (SNORA26/C9orf170) and rs10406644 (KCTD15/LSM14A) that increase BP among short sleepers (Pint < 5 × 10-8). Secondary ancestry-specific analysis identified another novel gene by long sleep interaction at rs111887471 (TRPC3/KIAA1109) in individuals of African ancestry (Pint = 2 × 10-6). Combined stage 1 and 2 analyses additionally identified significant gene by long sleep interactions at 10 loci including MKLN1 and RGL3/ELAVL3 previously associated with BP, and significant gene by short sleep interactions at 10 loci including C2orf43 previously associated with BP (Pint < 10-3). 2df test also identified novel loci for BP after modeling sleep that has known functions in sleep-wake regulation, nervous and cardiometabolic systems. This study indicates that sleep and primary mechanisms regulating BP may interact to elevate BP level, suggesting novel insights into sleep-related BP regulation.
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Affiliation(s)
- Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Karen Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alisa K Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Medicine and Public Health, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Andrea R Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Melissa Richard
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Elise Lim
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jovia L Nierenberg
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute Duke University School of Medicine, Durham, NC, USA
| | - Kumaraswamynaidu Chitrala
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Solomon K Musani
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Maris Alver
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Phyllis C Zee
- Division of Sleep Medicine, Department of Neurology, Northwestern University, Chicago, IL, USA
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- National Institute for Health Research Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, London, UK
| | | | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), partner site Greifswald, Greifswald, Germany
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelly A Hall
- School of Public Health, The University of Adelaide, Adelaide, SA, Australia
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jeff O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Public Health & School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jose E Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Pamela J Schreiner
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | | | - James M Shikany
- Division of Preventive Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Annemarie I Luik
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Daniel Levy
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Kurt K Lohman
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute Duke University School of Medicine, Durham, NC, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Treva K Rice
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Gregory Wilson
- JHS Graduate Training and Education Center, Jackson State University, Jackson, MS, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Walter Palmas
- Division of General Medicine, Department of Medicine, Columbia University, New York, NY, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nienke R Biermasz
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Lisa W Martin
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Ana Barac
- MedStar Heart and Vascular Institute, Washington, DC, USA
| | - Robert B Wallace
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
| | - Daniel J Gottlieb
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Pirjo Komulainen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Sami Heikkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - John M Starr
- Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh, UK
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, HJ, The Netherlands
| | - R J Waken
- Division of Cardiology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Till Roenneberg
- Institute and Polyclinic for Occupational-, Social- and Environmental Medicine, LMU Munich, Munich, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), partner site Greifswald, Greifswald, Germany
| | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sutapa Mukherjee
- Sleep Health Service, Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, SA, Australia
- Adelaide Institute for Sleep Health, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - David R Hillman
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lynne E Wagenknecht
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Hans J Grabe
- Department Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Lyle J Palmer
- School of Public Health, The University of Adelaide, Adelaide, SA, Australia
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Departments of Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Ervin R Fox
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Timo A Lakka
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Ian J Deary
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, HJ, The Netherlands
| | - W James Gauderman
- Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands.
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8
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Sherpa D, Chrustowicz J, Qiao S, Langlois CR, Hehl LA, Gottemukkala KV, Hansen FM, Karayel O, von Gronau S, Prabu JR, Mann M, Alpi AF, Schulman BA. GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme. Mol Cell 2021; 81:2445-2459.e13. [PMID: 33905682 PMCID: PMC8189437 DOI: 10.1016/j.molcel.2021.03.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 12/31/2022]
Abstract
How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GIDSR4, which resembles an organometallic supramolecular chelate. The Chelator-GIDSR4 assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.
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Affiliation(s)
- Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Shuai Qiao
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Laura A Hehl
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Karthik Varma Gottemukkala
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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9
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Leydon AR, Wang W, Gala HP, Gilmour S, Juarez-Solis S, Zahler ML, Zemke JE, Zheng N, Nemhauser JL. Repression by the Arabidopsis TOPLESS corepressor requires association with the core mediator complex. eLife 2021; 10:66739. [PMID: 34075876 PMCID: PMC8203292 DOI: 10.7554/elife.66739] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/31/2021] [Indexed: 02/06/2023] Open
Abstract
The plant corepressor TOPLESS (TPL) is recruited to a large number of loci that are selectively induced in response to developmental or environmental cues, yet the mechanisms by which it inhibits expression in the absence of these stimuli are poorly understood. Previously, we had used the N-terminus of Arabidopsis thaliana TPL to enable repression of a synthetic auxin response circuit in Saccharomyces cerevisiae (yeast). Here, we leveraged the yeast system to interrogate the relationship between TPL structure and function, specifically scanning for repression domains. We identified a potent repression domain in Helix 8 located within the CRA domain, which directly interacted with the Mediator middle module subunits Med21 and Med10. Interactions between TPL and Mediator were required to fully repress transcription in both yeast and plants. In contrast, we found that multimer formation, a conserved feature of many corepressors, had minimal influence on the repression strength of TPL.
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Affiliation(s)
| | - Wei Wang
- Department of Pharmacology, Seattle, United States
| | - Hardik P Gala
- Department of Biology, University of Washington, Seattle, United States
| | - Sabrina Gilmour
- Department of Biology, University of Washington, Seattle, United States
| | | | - Mollye L Zahler
- Department of Biology, University of Washington, Seattle, United States
| | - Joseph E Zemke
- Department of Biology, University of Washington, Seattle, United States
| | - Ning Zheng
- Department of Pharmacology, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
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10
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Kneussel M, Sánchez-Rodríguez N, Mischak M, Heisler FF. Dynein and muskelin control myosin VI delivery towards the neuronal nucleus. iScience 2021; 24:102416. [PMID: 33997696 PMCID: PMC8099778 DOI: 10.1016/j.isci.2021.102416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/15/2021] [Accepted: 04/07/2021] [Indexed: 11/30/2022] Open
Abstract
Protein transport toward the nucleus is important for translating molecular signals into gene expression changes. Interestingly, the unconventional motor protein myosin VI regulates RNA polymerase II-dependent gene transcription. Whether actin-filament-dependent myosins are actively transported to nuclear compartments remains unknown. Here, we report that neurons also contain myosin VI inside their nucleus. Notably, nuclear appearance of this actin-dependent motor depends on functional cytoplasmic dynein, a minus end-directed microtubule motor. We find that the trafficking factor muskelin assists in the formation of dynein-myosin VI interactions and further localizes to nuclear foci, enriched in the myosin. Impairment of dynein, but not myosin VI function, reduces nuclear muskelin levels. In turn, muskelin represents a critical determinant in regulating myosin VI nuclear targeting. Our data reveal that minus end-directed microtubule transport determines myosin VI subcellular localization. They suggest a pathway of cytoplasm-to-nucleus trafficking that requires muskelin and is based on dynein-myosin cross talk.
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Affiliation(s)
- Matthias Kneussel
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Noelia Sánchez-Rodríguez
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Michaela Mischak
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Frank F. Heisler
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
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11
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Dindo M, Ambrosini G, Oppici E, Pey AL, O’Toole PJ, Marrison JL, Morrison IEG, Butturini E, Grottelli S, Costantini C, Cellini B. Dimerization Drives Proper Folding of Human Alanine:Glyoxylate Aminotransferase But Is Dispensable for Peroxisomal Targeting. J Pers Med 2021; 11:jpm11040273. [PMID: 33917320 PMCID: PMC8067440 DOI: 10.3390/jpm11040273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022] Open
Abstract
Peroxisomal matrix proteins are transported into peroxisomes in a fully-folded state, but whether multimeric proteins are imported as monomers or oligomers is still disputed. Here, we used alanine:glyoxylate aminotransferase (AGT), a homodimeric pyridoxal 5′-phosphate (PLP)-dependent enzyme, whose deficit causes primary hyperoxaluria type I (PH1), as a model protein and compared the intracellular behavior and peroxisomal import of native dimeric and artificial monomeric forms. Monomerization strongly reduces AGT intracellular stability and increases its aggregation/degradation propensity. In addition, monomers are partly retained in the cytosol. To assess possible differences in import kinetics, we engineered AGT to allow binding of a membrane-permeable dye and followed its intracellular trafficking without interfering with its biochemical properties. By fluorescence recovery after photobleaching, we measured the import rate in live cells. Dimeric and monomeric AGT displayed a similar import rate, suggesting that the oligomeric state per se does not influence import kinetics. However, when dimerization is compromised, monomers are prone to misfolding events that can prevent peroxisomal import, a finding crucial to predicting the consequences of PH1-causing mutations that destabilize the dimer. Treatment with pyridoxine of cells expressing monomeric AGT promotes dimerization and folding, thus, demonstrating the chaperone role of PLP. Our data support a model in which dimerization represents a potential key checkpoint in the cytosol at the crossroad between misfolding and correct targeting, a possible general mechanism for other oligomeric peroxisomal proteins.
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Affiliation(s)
- Mirco Dindo
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Giulia Ambrosini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Peter J. O’Toole
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Joanne L. Marrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Ian E. G. Morrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Elena Butturini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Silvia Grottelli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
- Correspondence: ; Tel.: +39-075-585-8339
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12
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He D, Wu D, Muller S, Wang L, Saha P, Ahanger SH, Liu SJ, Cui M, Hong SJ, Jain M, Olson HE, Akeson M, Costello JF, Diaz A, Lim DA. miRNA-independent function of long noncoding pri-miRNA loci. Proc Natl Acad Sci U S A 2021; 118:e2017562118. [PMID: 33758101 PMCID: PMC8020771 DOI: 10.1073/pnas.2017562118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Among the large, diverse set of mammalian long noncoding RNAs (lncRNAs), long noncoding primary microRNAs (lnc-pri-miRNAs) are those that host miRNAs. Whether lnc-pri-miRNA loci have important biological function independent of their cognate miRNAs is poorly understood. From a genome-scale lncRNA screen, lnc-pri-miRNA loci were enriched for function in cell proliferation, and in glioblastoma (i.e., GBM) cells with DGCR8 or DROSHA knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied LOC646329 (also known as MIR29HG), which hosts the miR-29a/b1 cluster. In GBM cells, LOC646329 knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster (LOC646329-miR29Δ) did not decrease cell growth, while knockdown of LOC646329-miR29Δ transcripts reduced cell proliferation. The miR-29a/b1-independent activity of LOC646329 corresponded to enhancer-like activation of a neighboring oncogene (MKLN1), regulating cell propagation. The LOC646329 locus interacts with the MKLN1 promoter, and antisense oligonucleotide knockdown of the lncRNA disrupts these interactions and reduces the enhancer-like activity. More broadly, analysis of genome-wide data from multiple human cell types showed that lnc-pri-miRNA loci are significantly enriched for DNA looping interactions with gene promoters as well as genomic and epigenetic characteristics of transcriptional enhancers. Functional studies of additional lnc-pri-miRNA loci demonstrated cognate miRNA-independent enhancer-like activity. Together, these data demonstrate that lnc-pri-miRNA loci can regulate cell biology via both miRNA-dependent and miRNA-independent mechanisms.
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Affiliation(s)
- Daniel He
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Developmental and Stem Cell Biology Graduate Program, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - David Wu
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Soren Muller
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Lin Wang
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Parna Saha
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Department of Surgery, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121
| | - Sajad Hamid Ahanger
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Department of Surgery, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121
| | - Siyuan John Liu
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Miao Cui
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Sung Jun Hong
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Developmental and Stem Cell Biology Graduate Program, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Miten Jain
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064
| | - Hugh E Olson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064
| | - Mark Akeson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064
| | - Joseph F Costello
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Aaron Diaz
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
| | - Daniel A Lim
- Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143;
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Department of Surgery, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121
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13
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Ryu H, Lee H, Lee J, Noh H, Shin M, Kumar V, Hong S, Kim J, Park S. The molecular dynamics of subdistal appendages in multi-ciliated cells. Nat Commun 2021; 12:612. [PMID: 33504787 PMCID: PMC7840914 DOI: 10.1038/s41467-021-20902-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 12/24/2020] [Indexed: 11/09/2022] Open
Abstract
The motile cilia of ependymal cells coordinate their beats to facilitate a forceful and directed flow of cerebrospinal fluid (CSF). Each cilium originates from a basal body with a basal foot protruding from one side. A uniform alignment of these basal feet is crucial for the coordination of ciliary beating. The process by which the basal foot originates from subdistal appendages of the basal body, however, is unresolved. Here, we show FGFR1 Oncogene Partner (FOP) is a useful marker for delineating the transformation of a circular, unpolarized subdistal appendage into a polarized structure with a basal foot. Ankyrin repeat and SAM domain-containing protein 1A (ANKS1A) interacts with FOP to assemble region I of the basal foot. Importantly, disruption of ANKS1A reduces the size of region I. This produces an unstable basal foot, which disrupts rotational polarity and the coordinated beating of cilia in young adult mice. ANKS1A deficiency also leads to severe degeneration of the basal foot in aged mice and the detachment of cilia from their basal bodies. This role of ANKS1A in the polarization of the basal foot is evolutionarily conserved in vertebrates. Thus, ANKS1A regulates FOP to build and maintain the polarity of subdistal appendages.
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Affiliation(s)
- Hyunchul Ryu
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Korea
- Department of Life Science, University of Seoul, Seoul, 02504, Korea
| | - Haeryung Lee
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Jiyeon Lee
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Hyuna Noh
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Miram Shin
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Vijay Kumar
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Sejeong Hong
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Jaebong Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Soochul Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Korea.
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14
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Joachimiak E, Waclawek E, Niziolek M, Osinka A, Fabczak H, Gaertig J, Wloga D. The LisH Domain-Containing N-Terminal Fragment is Important for the Localization, Dimerization, and Stability of Katnal2 in Tetrahymena. Cells 2020; 9:cells9020292. [PMID: 31991798 PMCID: PMC7072489 DOI: 10.3390/cells9020292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/14/2020] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
Katanin-like 2 protein (Katnal2) orthologs have a tripartite domain organization. Two highly conserved regions, an N-terminal LisH (Lis-homology) domain and a C-terminal AAA catalytic domain, are separated by a less conserved linker. The AAA domain of Katnal2 shares the highest amino acid sequence homology with the AAA domain of the canonical katanin p60. Katnal2 orthologs are present in a wide range of eukaryotes, from protists to humans. In the ciliate Tetrahymena thermophila, a Katnal2 ortholog, Kat2, co-localizes with the microtubular structures, including basal bodies and ciliary outer doublets, and this co-localization is sensitive to levels of microtubule glutamylation. The functional analysis of Kat2 domains suggests that an N-terminal fragment containing a LisH domain plays a role in the subcellular localization, dimerization, and stability of Kat2.
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Affiliation(s)
- Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur, 02-093 Warsaw, Poland; (E.J.); (E.W.); (M.N.); (A.O.); (H.F.)
| | - Ewa Waclawek
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur, 02-093 Warsaw, Poland; (E.J.); (E.W.); (M.N.); (A.O.); (H.F.)
| | - Michal Niziolek
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur, 02-093 Warsaw, Poland; (E.J.); (E.W.); (M.N.); (A.O.); (H.F.)
| | - Anna Osinka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur, 02-093 Warsaw, Poland; (E.J.); (E.W.); (M.N.); (A.O.); (H.F.)
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur, 02-093 Warsaw, Poland; (E.J.); (E.W.); (M.N.); (A.O.); (H.F.)
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA;
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur, 02-093 Warsaw, Poland; (E.J.); (E.W.); (M.N.); (A.O.); (H.F.)
- Correspondence: ; Tel.: +48-(22)-5892338
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15
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Käshammer L, Saathoff JH, Lammens K, Gut F, Bartho J, Alt A, Kessler B, Hopfner KP. Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex. Mol Cell 2019; 76:382-394.e6. [DOI: 10.1016/j.molcel.2019.07.035] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/17/2019] [Accepted: 07/25/2019] [Indexed: 02/01/2023]
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16
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The mammalian CTLH complex is an E3 ubiquitin ligase that targets its subunit muskelin for degradation. Sci Rep 2019; 9:9864. [PMID: 31285494 PMCID: PMC6614414 DOI: 10.1038/s41598-019-46279-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022] Open
Abstract
The multi-subunit C-terminal to LisH (CTLH) complex is the mammalian homologue of the yeast Gid E3 ubiquitin ligase complex. In this study, we investigated the human CTLH complex and characterized its E3 ligase activity. We confirm that the complex immunoprecipitated from human cells comprises RanBPM, ARMC8 α/β, muskelin, WDR26, GID4 and the RING domain proteins RMND5A and MAEA. We find that loss of expression of individual subunits compromises the stability of other complex members and that MAEA and RMND5A protein levels are interdependent. Using in vitro ubiquitination assays, we demonstrate that the CTLH complex has E3 ligase activity which is dependent on RMND5A and MAEA. We report that the complex can pair with UBE2D1, UBE2D2 and UBE2D3 E2 enzymes and that recombinant RMND5A mediates K48 and K63 poly-ubiquitin chains. Finally, we show a proteasome-dependent increase in the protein levels of CTLH complex member muskelin in RMND5A KO cells. Furthermore, muskelin ubiquitination is dependent on RMND5A, suggesting that it may be a target of the complex. Overall, we further the characterization of the CTLH complex as an E3 ubiquitin ligase complex in human cells and reveal a potential autoregulation mechanism.
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17
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Salemi LM, Maitland MER, McTavish CJ, Schild-Poulter C. Cell signalling pathway regulation by RanBPM: molecular insights and disease implications. Open Biol 2018; 7:rsob.170081. [PMID: 28659384 PMCID: PMC5493780 DOI: 10.1098/rsob.170081] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 06/01/2017] [Indexed: 12/25/2022] Open
Abstract
RanBPM (Ran-binding protein M, also called RanBP9) is an evolutionarily conserved, ubiquitous protein which localizes to both nucleus and cytoplasm. RanBPM has been implicated in the regulation of a number of signalling pathways to regulate several cellular processes such as apoptosis, cell adhesion, migration as well as transcription, and plays a critical role during development. In addition, RanBPM has been shown to regulate pathways implicated in cancer and Alzheimer's disease, implying that RanBPM has important functions in both normal and pathological development. While its functions in these processes are still poorly understood, RanBPM has been identified as a component of a large complex, termed the CTLH (C-terminal to LisH) complex. The yeast homologue of this complex functions as an E3 ubiquitin ligase that targets enzymes of the gluconeogenesis pathway. While the CTLH complex E3 ubiquitin ligase activity and substrates still remain to be characterized, the high level of conservation between the complexes in yeast and mammals infers that the CTLH complex could also serve to promote the degradation of specific substrates through ubiquitination, therefore suggesting the possibility that RanBPM's various functions may be mediated through the activity of the CTLH complex.
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Affiliation(s)
- Louisa M Salemi
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
| | - Matthew E R Maitland
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
| | - Christina J McTavish
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
| | - Caroline Schild-Poulter
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
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18
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Muskelin Coordinates PrP C Lysosome versus Exosome Targeting and Impacts Prion Disease Progression. Neuron 2018; 99:1155-1169.e9. [PMID: 30174115 DOI: 10.1016/j.neuron.2018.08.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/04/2018] [Accepted: 08/06/2018] [Indexed: 01/01/2023]
Abstract
Cellular prion protein (PrPC) modulates cell adhesion and signaling in the brain. Conversion to its infectious isoform causes neurodegeneration, including Creutzfeldt-Jakob disease in humans. PrPC undergoes rapid plasma membrane turnover and extracellular release via exosomes. However, the intracellular transport of PrPC and its potential impact on prion disease progression is barely understood. Here we identify critical components of PrPC trafficking that also link intracellular and extracellular PrPC turnover. PrPC associates with muskelin, dynein, and KIF5C at transport vesicles. Notably, muskelin coordinates bidirectional PrPC transport and facilitates lysosomal degradation over exosomal PrPC release. Muskelin gene knockout consequently causes PrPC accumulation at the neuronal surface and on secreted exosomes. Moreover, prion disease onset is accelerated following injection of pathogenic prions into muskelin knockout mice. Our data identify an essential checkpoint in PrPC turnover. They propose a novel connection between neuronal intracellular lysosome targeting and extracellular exosome trafficking, relevant to the pathogenesis of neurodegenerative conditions.
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Lampert F, Stafa D, Goga A, Soste MV, Gilberto S, Olieric N, Picotti P, Stoffel M, Peter M. The multi-subunit GID/CTLH E3 ubiquitin ligase promotes cell proliferation and targets the transcription factor Hbp1 for degradation. eLife 2018; 7:35528. [PMID: 29911972 PMCID: PMC6037477 DOI: 10.7554/elife.35528] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/16/2018] [Indexed: 12/17/2022] Open
Abstract
In yeast, the glucose-induced degradation-deficient (GID) E3 ligase selectively degrades superfluous gluconeogenic enzymes. Here, we identified all subunits of the mammalian GID/CTLH complex and provide a comprehensive map of its hierarchical organization and step-wise assembly. Biochemical reconstitution demonstrates that the mammalian complex possesses inherent E3 ubiquitin ligase activity, using Ube2H as its cognate E2. Deletions of multiple GID subunits compromise cell proliferation, and this defect is accompanied by deregulation of critical cell cycle markers such as the retinoblastoma (Rb) tumor suppressor, phospho-Histone H3 and Cyclin A. We identify the negative regulator of pro-proliferative genes Hbp1 as a bonafide GID/CTLH proteolytic substrate. Indeed, Hbp1 accumulates in cells lacking GID/CTLH activity, and Hbp1 physically interacts and is ubiquitinated in vitro by reconstituted GID/CTLH complexes. Our biochemical and cellular analysis thus demonstrates that the GID/CTLH complex prevents cell cycle exit in G1, at least in part by degrading Hbp1.
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Affiliation(s)
| | - Diana Stafa
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Algera Goga
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | | | | | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
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20
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Bauer A, Jagannathan V, Högler S, Richter B, McEwan NA, Thomas A, Cadieu E, André C, Hytönen MK, Lohi H, Welle MM, Roosje P, Mellersh C, Casal ML, Leeb T. MKLN1 splicing defect in dogs with lethal acrodermatitis. PLoS Genet 2018; 14:e1007264. [PMID: 29565995 PMCID: PMC5863938 DOI: 10.1371/journal.pgen.1007264] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
Lethal acrodermatitis (LAD) is a genodermatosis with monogenic autosomal recessive inheritance in Bull Terriers and Miniature Bull Terriers. The LAD phenotype is characterized by poor growth, immune deficiency, and skin lesions, especially at the paws. Utilizing a combination of genome wide association study and haplotype analysis, we mapped the LAD locus to a critical interval of ~1.11 Mb on chromosome 14. Whole genome sequencing of an LAD affected dog revealed a splice region variant in the MKLN1 gene that was not present in 191 control genomes (chr14:5,731,405T>G or MKLN1:c.400+3A>C). This variant showed perfect association in a larger combined Bull Terrier/Miniature Bull Terrier cohort of 46 cases and 294 controls. The variant was absent from 462 genetically diverse control dogs of 62 other dog breeds. RT-PCR analysis of skin RNA from an affected and a control dog demonstrated skipping of exon 4 in the MKLN1 transcripts of the LAD affected dog, which leads to a shift in the MKLN1 reading frame. MKLN1 encodes the widely expressed intracellular protein muskelin 1, for which diverse functions in cell adhesion, morphology, spreading, and intracellular transport processes are discussed. While the pathogenesis of LAD remains unclear, our data facilitate genetic testing of Bull Terriers and Miniature Bull Terriers to prevent the unintentional production of LAD affected dogs. This study may provide a starting point to further clarify the elusive physiological role of muskelin 1 in vivo. Lethal acrodermatitis (LAD) is an autosomal recessive hereditary disease in dogs. It is characterized by poor growth, immune deficiency and characteristic skin lesions of the paws and of the face. We mapped the LAD locus to a ~1.11 Mb segment on canine chromosome 14. Whole genome sequence data of an LAD affected dog and 191 controls revealed a candidate causative variant in the MKLN1 gene, encoding muskelin 1. The identified variant, a single nucleotide substitution, MKLN1:c.400+3A>C, altered the 5’-splice site at the beginning of intron 4. We experimentally confirmed that this variant leads to complete skipping of exon 4 in the MKLN1 mRNA in skin. Various cellular functions have been postulated for muskelin 1 including roles in intracellular transport processes, cell morphology, cell spreading, and cell adhesion. Our data from dogs reveal a novel in vivo role for muskelin 1 that is related to the immune system and skin. MKLN1 thus represents a novel candidate gene for human patients with unsolved acrodermatitis and/or immune deficiency phenotypes. LAD affected dogs may serve as models to gain more insights into the function of muskelin 1.
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Affiliation(s)
- Anina Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Sandra Högler
- Department of Pathobiology, Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Barbara Richter
- Department of Pathobiology, Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Neil A. McEwan
- Department of Small Animal Clinical Sciences, The University of Liverpool, Leahurst Campus, Neston, Cheshire, United Kingdom
| | - Anne Thomas
- Antagene, Animal Genetics Laboratory, La Tour de Salvagny, France
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes (IGDR), CNRS-UMR6290, Université Rennes1, Rennes, France
| | - Catherine André
- Institut de Génétique et Développement de Rennes (IGDR), CNRS-UMR6290, Université Rennes1, Rennes, France
| | - Marjo K. Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
| | - Monika M. Welle
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Petra Roosje
- DermFocus, University of Bern, Bern, Switzerland
- Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern,Bern, Switzerland
| | - Cathryn Mellersh
- Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Margret L. Casal
- Section of Medical Genetics, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
- * E-mail:
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21
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Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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22
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Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression. Proc Natl Acad Sci U S A 2017; 114:8107-8112. [PMID: 28698367 DOI: 10.1073/pnas.1703054114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as Arabidopsis thaliana, the most prominent corepressor is TOPLESS (TPL), which plays a key role in hormone signaling and development. Here we present the crystallographic structure of the Arabidopsis TPL N-terminal region comprising the LisH and CTLH (C-terminal to LisH) domains and a newly identified third region, which corresponds to a CRA domain. Comparing the structure of TPL with the mammalian TBL1, which shares a similar domain structure and performs a parallel corepressor function, revealed that the plant TPLs have evolved a new tetramerization interface and unique and highly conserved surface for interaction with repressors. Using site-directed mutagenesis, we validated those surfaces in vitro and in vivo and showed that TPL tetramerization and repressor binding are interdependent. Our results illustrate how evolution used a common set of protein domains to create a diversity of corepressors, achieving similar properties with different molecular solutions.
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Van De Weghe JC, Rusterholz TD, Latour B, Grout ME, Aldinger KA, Shaheen R, Dempsey JC, Maddirevula S, Cheng YHH, Phelps IG, Gesemann M, Goel H, Birk OS, Alanzi T, Rawashdeh R, Khan AO, Bamshad MJ, Nickerson DA, Neuhauss SC, Dobyns WB, Alkuraya FS, Roepman R, Bachmann-Gagescu R, Doherty D, Doherty D. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish. Am J Hum Genet 2017. [PMID: 28625504 DOI: 10.1016/j.ajhg.2017.05.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown. All of the gene products localize in and around the primary cilium, making JS a canonical ciliopathy. Ciliopathies are unified by their overlapping clinical features and underlying mechanisms involving ciliary dysfunction. In this work, we identify biallelic rare, predicted-deleterious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals with JS from 8 families, accounting for approximately 1% of the disorder. The associated phenotypes range from isolated neurological involvement to JS with retinal dystrophy, additional brain abnormalities (e.g., heterotopia, Dandy-Walker malformation), pituitary insufficiency, and/or synpolydactyly. We show that ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. Typical ciliopathy phenotypes (curved body shape, retinal dystrophy, coloboma, and decreased cilia) in a CRISPR/Cas9-engineered zebrafish mutant model provide additional support for ARMC9 as a ciliopathy-associated gene. Identifying ARMC9 mutations as a cause of JS takes us one step closer to a full genetic understanding of this important disorder and enables future functional work to define the central biological mechanisms underlying JS and other ciliopathies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
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Studies of recombinant TWA1 reveal constitutive dimerization. Biosci Rep 2017; 37:BSR20160401. [PMID: 27920276 PMCID: PMC5234100 DOI: 10.1042/bsr20160401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/06/2023] Open
Abstract
The mammalian muskelin/RanBP9/C-terminal to LisH (CTLH) complex and the Saccharomyces cerevisiae glucose-induced degradation (GID) complex are large, multi-protein complexes that each contain a RING E3 ubiquitin ligase. The yeast GID complex acts to degrade a key enzyme of gluconeogenesis, fructose 1,6-bisphosphatase, under conditions of abundant fermentable carbon sources. However, the assembly and functions of the mammalian complex remain poorly understood. A striking feature of these complexes is the presence of multiple proteins that contain contiguous lissencephaly-1 homology (LisH), CTLH and C-terminal CT11-RanBP9 (CRA) domains. TWA1/Gid8, the smallest constituent protein of these complexes, consists only of LisH, CTLH and CRA domains and is highly conserved in eukaryotes. Towards better knowledge of the role of TWA1 in these multi-protein complexes, we established a method for bacterial expression and purification of mouse TWA1 that yields tag-free, recombinant TWA1 in quantities suitable for biophysical and biochemical studies. CD spectroscopy of recombinant TWA1 indicated a predominantly α-helical protein. Gel filtration chromatography, size-exclusion chromatography (SEC) with multi-angle light scattering (SEC-MALS) and native PAGE demonstrated a propensity of untagged TWA1 to form stable dimers and, to a lesser extent, higher order oligomers. TWA1 has a single cysteine residue, Cys139, yet the dimeric form was preserved when TWA1 was purified in the presence of the reducing agent tris(2-carboxyethyl)phosphine (TCEP). These findings have implications for understanding the molecular role of TWA1 in the yeast GID complex and related multi-protein E3 ubiquitin ligases identified in other eukaryotes.
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