1
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Lujan P, Garcia-Cabau C, Wakana Y, Vera Lillo J, Rodilla-Ramírez C, Sugiura H, Malhotra V, Salvatella X, Garcia-Parajo MF, Campelo F. Sorting of secretory proteins at the trans-Golgi network by human TGN46. eLife 2024; 12:RP91708. [PMID: 38466628 DOI: 10.7554/elife.91708] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Secretory proteins are sorted at the trans-Golgi network (TGN) for export into specific transport carriers. However, the molecular players involved in this fundamental process remain largely elusive. Here, we identified the human transmembrane protein TGN46 as a receptor for the export of secretory cargo protein PAUF in CARTS - a class of protein kinase D-dependent TGN-to-plasma membrane carriers. We show that TGN46 is necessary for cargo sorting and loading into nascent carriers at the TGN. By combining quantitative fluorescence microscopy and mutagenesis approaches, we further discovered that the lumenal domain of TGN46 encodes for its cargo sorting function. In summary, our results define a cellular function of TGN46 in sorting secretory proteins for export from the TGN.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yuichi Wakana
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Javier Vera Lillo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carmen Rodilla-Ramírez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hideaki Sugiura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vivek Malhotra
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
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2
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Basu S, Martínez-Cristóbal P, Frigolé-Vivas M, Pesarrodona M, Lewis M, Szulc E, Bañuelos CA, Sánchez-Zarzalejo C, Bielskutė S, Zhu J, Pombo-García K, Garcia-Cabau C, Zodi L, Dockx H, Smak J, Kaur H, Batlle C, Mateos B, Biesaga M, Escobedo A, Bardia L, Verdaguer X, Ruffoni A, Mawji NR, Wang J, Obst JK, Tam T, Brun-Heath I, Ventura S, Meierhofer D, García J, Robustelli P, Stracker TH, Sadar MD, Riera A, Hnisz D, Salvatella X. Rational optimization of a transcription factor activation domain inhibitor. Nat Struct Mol Biol 2023; 30:1958-1969. [PMID: 38049566 PMCID: PMC10716049 DOI: 10.1038/s41594-023-01159-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/23/2023] [Indexed: 12/06/2023]
Abstract
Transcription factors are among the most attractive therapeutic targets but are considered largely 'undruggable' in part due to the intrinsically disordered nature of their activation domains. Here we show that the aromatic character of the activation domain of the androgen receptor, a therapeutic target for castration-resistant prostate cancer, is key for its activity as transcription factor, allowing it to translocate to the nucleus and partition into transcriptional condensates upon activation by androgens. On the basis of our understanding of the interactions stabilizing such condensates and of the structure that the domain adopts upon condensation, we optimized the structure of a small-molecule inhibitor previously identified by phenotypic screening. The optimized compounds had more affinity for their target, inhibited androgen-receptor-dependent transcriptional programs, and had an antitumorigenic effect in models of castration-resistant prostate cancer in cells and in vivo. These results suggest that it is possible to rationally optimize, and potentially even to design, small molecules that target the activation domains of oncogenic transcription factors.
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Affiliation(s)
- Shaon Basu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paula Martínez-Cristóbal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Frigolé-Vivas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michael Lewis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - C Adriana Bañuelos
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Carolina Sánchez-Zarzalejo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stasė Bielskutė
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jiaqi Zhu
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Levente Zodi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Jordann Smak
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Harpreet Kaur
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Cristina Batlle
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Borja Mateos
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mateusz Biesaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Albert Escobedo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Verdaguer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain
| | - Alessandro Ruffoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nasrin R Mawji
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jun Wang
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jon K Obst
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Teresa Tam
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility, Berlin, Germany
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Travis H Stracker
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marianne D Sadar
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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3
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Sanfeliu-Cerdán N, Català-Castro F, Mateos B, Garcia-Cabau C, Ribera M, Ruider I, Porta-de-la-Riva M, Canals-Calderón A, Wieser S, Salvatella X, Krieg M. A MEC-2/stomatin condensate liquid-to-solid phase transition controls neuronal mechanotransduction during touch sensing. Nat Cell Biol 2023; 25:1590-1599. [PMID: 37857834 PMCID: PMC10635833 DOI: 10.1038/s41556-023-01247-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
A growing body of work suggests that the material properties of biomolecular condensates ensuing from liquid-liquid phase separation change with time. How this aging process is controlled and whether the condensates with distinct material properties can have different biological functions is currently unknown. Using Caenorhabditis elegans as a model, we show that MEC-2/stomatin undergoes a rigidity phase transition from fluid-like to solid-like condensates that facilitate transport and mechanotransduction, respectively. This switch is triggered by the interaction between the SH3 domain of UNC-89 (titin/obscurin) and MEC-2. We suggest that this rigidity phase transition has a physiological role in frequency-dependent force transmission in mechanosensitive neurons during body wall touch. Our data demonstrate a function for the liquid and solid phases of MEC-2/stomatin condensates in facilitating transport or mechanotransduction, and a previously unidentified role for titin homologues in neurons.
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Affiliation(s)
- Neus Sanfeliu-Cerdán
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Frederic Català-Castro
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Borja Mateos
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Ribera
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Iris Ruider
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Montserrat Porta-de-la-Riva
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Adrià Canals-Calderón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stefan Wieser
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Michael Krieg
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain.
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4
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Christou-Kent M, Cuartero S, Garcia-Cabau C, Ruehle J, Naderi J, Erber J, Neguembor MV, Plana-Carmona M, Alcoverro-Bertran M, De Andres-Aguayo L, Klonizakis A, Julià-Vilella E, Lynch C, Serrano M, Hnisz D, Salvatella X, Graf T, Stik G. CEBPA phase separation links transcriptional activity and 3D chromatin hubs. Cell Rep 2023; 42:112897. [PMID: 37516962 DOI: 10.1016/j.celrep.2023.112897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Cell identity is orchestrated through an interplay between transcription factor (TF) action and genome architecture. The mechanisms used by TFs to shape three-dimensional (3D) genome organization remain incompletely understood. Here we present evidence that the lineage-instructive TF CEBPA drives extensive chromatin compartment switching and promotes the formation of long-range chromatin hubs during induced B cell-to-macrophage transdifferentiation. Mechanistically, we find that the intrinsically disordered region (IDR) of CEBPA undergoes in vitro phase separation (PS) dependent on aromatic residues. Both overexpressing B cells and native CEBPA-expressing cell types such as primary granulocyte-macrophage progenitors, liver cells, and trophectoderm cells reveal nuclear CEBPA foci and long-range 3D chromatin hubs at CEBPA-bound regions. In short, we show that CEBPA can undergo PS through its IDR, which may underlie in vivo foci formation and suggest a potential role of PS in regulating CEBPA function.
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Affiliation(s)
- Marie Christou-Kent
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Germans Trias I Pujol Research Institute (IGTP), Badalona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Julia Ruehle
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Julia Erber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marcos Plana-Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Luisa De Andres-Aguayo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Antonios Klonizakis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Cian Lynch
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Grégoire Stik
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.
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5
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Mensah MA, Niskanen H, Magalhaes AP, Basu S, Kircher M, Sczakiel HL, Reiter AMV, Elsner J, Meinecke P, Biskup S, Chung BHY, Dombrowsky G, Eckmann-Scholz C, Hitz MP, Hoischen A, Holterhus PM, Hülsemann W, Kahrizi K, Kalscheuer VM, Kan A, Krumbiegel M, Kurth I, Leubner J, Longardt AC, Moritz JD, Najmabadi H, Skipalova K, Snijders Blok L, Tzschach A, Wiedersberg E, Zenker M, Garcia-Cabau C, Buschow R, Salvatella X, Kraushar ML, Mundlos S, Caliebe A, Spielmann M, Horn D, Hnisz D. Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature 2023; 614:564-571. [PMID: 36755093 PMCID: PMC9931588 DOI: 10.1038/s41586-022-05682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/22/2022] [Indexed: 02/10/2023]
Abstract
Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.
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Affiliation(s)
- Martin A. Mensah
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Henri Niskanen
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandre P. Magalhaes
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Shaon Basu
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Kircher
- grid.484013.a0000 0004 6879 971XExploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Henrike L. Sczakiel
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alisa M. V. Reiter
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Elsner
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Meinecke
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Saskia Biskup
- grid.498061.20000 0004 6008 5552Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Brian H. Y. Chung
- grid.194645.b0000000121742757Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Gregor Dombrowsky
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Christel Eckmann-Scholz
- grid.412468.d0000 0004 0646 2097Department of Obstetrics and Gynecology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marc Phillip Hitz
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Alexander Hoischen
- grid.10417.330000 0004 0444 9382Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul-Martin Holterhus
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, Pediatric Endocrinology and Diabetes, University Hospital Schleswig-Holstein, Schleswig-Holstein, Germany
| | - Wiebke Hülsemann
- grid.440182.b0000 0004 0580 3398Handchirurgie, Katholisches Kinderkrankenhaus Wilhelmstift, Hamburg, Germany
| | - Kimia Kahrizi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Vera M. Kalscheuer
- grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anita Kan
- grid.415550.00000 0004 1764 4144Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Mandy Krumbiegel
- grid.5330.50000 0001 2107 3311Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingo Kurth
- grid.412301.50000 0000 8653 1507Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany
| | - Jonas Leubner
- grid.6363.00000 0001 2218 4662Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ann Carolin Longardt
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Center Schleswig‐Holstein, Kiel, Germany
| | - Jörg D. Moritz
- grid.412468.d0000 0004 0646 2097Department of Radiology and Neuroradiology, Pediatric Radiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hossein Najmabadi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Karolina Skipalova
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lot Snijders Blok
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andreas Tzschach
- grid.5963.9Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eberhard Wiedersberg
- grid.491868.a0000 0000 9601 2399Zentrum für Kinder-und Jugendmedizin, Helios Kliniken Schwerin, Schwerin, Germany
| | - Martin Zenker
- grid.5807.a0000 0001 1018 4307Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - René Buschow
- grid.419538.20000 0000 9071 0620Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, Barcelona, Spain
| | - Matthew L. Kraushar
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Mundlos
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany ,grid.506128.8BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Almuth Caliebe
- grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Malte Spielmann
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany.
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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6
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Escobedo A, Piccirillo J, Aranda J, Diercks T, Mateos B, Garcia-Cabau C, Sánchez-Navarro M, Topal B, Biesaga M, Staby L, Kragelund BB, García J, Millet O, Orozco M, Coles M, Crehuet R, Salvatella X. A glutamine-based single α-helix scaffold to target globular proteins. Nat Commun 2022; 13:7073. [PMID: 36400768 PMCID: PMC9674830 DOI: 10.1038/s41467-022-34793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.
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Affiliation(s)
- Albert Escobedo
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.473715.30000 0004 6475 7299Present Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan Piccirillo
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.428469.50000 0004 1794 1018Present Address: Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Juan Aranda
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Tammo Diercks
- grid.420161.0CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Borja Mateos
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Macarena Sánchez-Navarro
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Armilla, Granada Spain
| | - Busra Topal
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mateusz Biesaga
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lasse Staby
- grid.5254.60000 0001 0674 042XREPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- grid.5254.60000 0001 0674 042XREPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jesús García
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Oscar Millet
- grid.420161.0CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Modesto Orozco
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Department of Biochemistry and Biomedicine, University of Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
| | - Murray Coles
- grid.419580.10000 0001 0942 1125Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tubingen, Germany
| | - Ramon Crehuet
- grid.4711.30000 0001 2183 4846Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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7
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Bielskutė S, Garcia-Cabau C, Frigolé-Vivas M, Szulc E, De Mol E, Pesarrodona M, García J, Salvatella X. Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain. Protein Sci 2021; 30:1427-1437. [PMID: 33978290 DOI: 10.1002/pro.4110] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 04/19/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023]
Abstract
The phase equilibria of intrinsically disordered proteins are exquisitely sensitive to changes in solution conditions and this can be used to investigate the driving forces of phase separation in vitro as well as the biological roles of phase transitions in live cells. Here we investigate how using D2 O as co-solvent in an aqueous buffer changes the phase equilibrium of a fragment of the activation domain of the androgen receptor, a transcription factor that plays a role in the development of the male phenotype and is a therapeutic target for castration resistant prostate cancer. We show how replacing even small fractions of H2 O with D2 O increases the propensity of this fragment to undergo liquid-liquid phase separation, likely reflecting a stabilization of the hydrophobic interactions that drive condensation. Our results indicate that it is necessary to take this effect into consideration when studying phase separation phenomena with biophysical methods that require using D2 O as a co-solvent. In addition, they suggest that additions of D2 O may be used to enhance phase separation phenomena in cells, facilitating their observation.
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Affiliation(s)
- Stasė Bielskutė
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Marta Frigolé-Vivas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Eva De Mol
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain.,ICREA, Barcelona, Spain
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8
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Garcia-Cabau C, Salvatella X. Regulation of biomolecular condensate dynamics by signaling. Curr Opin Cell Biol 2021; 69:111-119. [PMID: 33578289 DOI: 10.1016/j.ceb.2021.01.002] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022]
Abstract
Biomolecular condensates are mesoscopic biomolecular assemblies devoid of long range order that contribute to important cellular functions. They form reversibly, are stabilized by numerous but relatively weak intermolecular interactions, and their formation can be regulated by various cellular signals including changes in local concentration, post-translational modifications, energy-consuming processes, and biomolecular interactions. Condensates formed by liquid-liquid phase separation are initially liquid but are metastable relative to hydrogels or irreversible solids that have been associated with protein aggregation diseases and are stabilized by stronger, more permanent interactions. As a consequence of this, a series of cellular mechanisms are available to regulate not only biomolecular condensation but also the physical properties of the condensates.
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Affiliation(s)
- Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028, Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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