1
|
Gisladottir RS, Helgason A, Halldorsson BV, Helgason H, Borsky M, Chien YR, Gudnason J, Gudjonsson SA, Moisik S, Dediu D, Thorleifsson G, Tragante V, Bustamante M, Jonsdottir GA, Stefansdottir L, Rutsdottir G, Magnusson SH, Hardarson M, Ferkingstad E, Halldorsson GH, Rognvaldsson S, Skuladottir A, Ivarsdottir EV, Norddahl G, Thorgeirsson G, Jonsdottir I, Ulfarsson MO, Holm H, Stefansson H, Thorsteinsdottir U, Gudbjartsson DF, Sulem P, Stefansson K. Sequence variants affecting voice pitch in humans. Sci Adv 2023; 9:eabq2969. [PMID: 37294764 PMCID: PMC10256171 DOI: 10.1126/sciadv.abq2969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/04/2023] [Indexed: 06/11/2023]
Abstract
The genetic basis of the human vocal system is largely unknown, as are the sequence variants that give rise to individual differences in voice and speech. Here, we couple data on diversity in the sequence of the genome with voice and vowel acoustics in speech recordings from 12,901 Icelanders. We show how voice pitch and vowel acoustics vary across the life span and correlate with anthropometric, physiological, and cognitive traits. We found that voice pitch and vowel acoustics have a heritable component and discovered correlated common variants in ABCC9 that associate with voice pitch. The ABCC9 variants also associate with adrenal gene expression and cardiovascular traits. By showing that voice and vowel acoustics are influenced by genetics, we have taken important steps toward understanding the genetics and evolution of the human vocal system.
Collapse
Affiliation(s)
- Rosa S. Gisladottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- Department of Icelandic and Comparative Cultural Studies, University of Iceland, Saemundargata 2, 102 Reykjavik, Iceland
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Saemundargata 10, 102 Reykjavik, Iceland
| | - Bjarni V. Halldorsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- Department of Engineering, Reykjavik University, Menntavegur 1, 101 Reykjavik, Iceland
| | - Hannes Helgason
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Michal Borsky
- Department of Engineering, Reykjavik University, Menntavegur 1, 101 Reykjavik, Iceland
| | - Yu-Ren Chien
- Department of Engineering, Reykjavik University, Menntavegur 1, 101 Reykjavik, Iceland
| | - Jon Gudnason
- Department of Engineering, Reykjavik University, Menntavegur 1, 101 Reykjavik, Iceland
| | | | - Scott Moisik
- Division of Linguistics and Multilingual Studies, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Dan Dediu
- Department of Catalan Philology and General Linguistics, University of Barcelona, Gran Via 585, Barcelona 08007, Spain
- University of Barcelona Institute for Complex Systems (UBICS), Martí Franquès 1, Barcelona 08028, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| | | | | | | | | | | | | | | | | | - Egil Ferkingstad
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Gisli H. Halldorsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | | | | | | | | | - Gudmundur Thorgeirsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | - Magnus O. Ulfarsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | - Daniel F. Gudbjartsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Patrick Sulem
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| |
Collapse
|
2
|
Aegisdottir HM, Thorolfsdottir RB, Sveinbjornsson G, Stefansson OA, Gunnarsson B, Tragante V, Thorleifsson G, Stefansdottir L, Thorgeirsson TE, Ferkingstad E, Sulem P, Norddahl G, Rutsdottir G, Banasik K, Christensen AH, Mikkelsen C, Pedersen OB, Brunak S, Bruun MT, Erikstrup C, Jacobsen RL, Nielsen KR, Sørensen E, Frigge ML, Hjorleifsson KE, Ivarsdottir EV, Helgadottir A, Gretarsdottir S, Steinthorsdottir V, Oddsson A, Eggertsson HP, Halldorsson GH, Jones DA, Anderson JL, Knowlton KU, Nadauld LD, Haraldsson M, Thorgeirsson G, Bundgaard H, Arnar DO, Thorsteinsdottir U, Gudbjartsson DF, Ostrowski SR, Holm H, Stefansson K. Genetic variants associated with syncope implicate neural and autonomic processes. Eur Heart J 2023; 44:1070-1080. [PMID: 36747475 DOI: 10.1093/eurheartj/ehad016] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 11/22/2022] [Accepted: 01/05/2023] [Indexed: 02/08/2023] Open
Abstract
AIMS Syncope is a common and clinically challenging condition. In this study, the genetics of syncope were investigated to seek knowledge about its pathophysiology and prognostic implications. METHODS AND RESULTS This genome-wide association meta-analysis included 56 071 syncope cases and 890 790 controls from deCODE genetics (Iceland), UK Biobank (United Kingdom), and Copenhagen Hospital Biobank Cardiovascular Study/Danish Blood Donor Study (Denmark), with a follow-up assessment of variants in 22 412 cases and 286 003 controls from Intermountain (Utah, USA) and FinnGen (Finland). The study yielded 18 independent syncope variants, 17 of which were novel. One of the variants, p.Ser140Thr in PTPRN2, affected syncope only when maternally inherited. Another variant associated with a vasovagal reaction during blood donation and five others with heart rate and/or blood pressure regulation, with variable directions of effects. None of the 18 associations could be attributed to cardiovascular or other disorders. Annotation with regard to regulatory elements indicated that the syncope variants were preferentially located in neural-specific regulatory regions. Mendelian randomization analysis supported a causal effect of coronary artery disease on syncope. A polygenic score (PGS) for syncope captured genetic correlation with cardiovascular disorders, diabetes, depression, and shortened lifespan. However, a score based solely on the 18 syncope variants performed similarly to the PGS in detecting syncope risk but did not associate with other disorders. CONCLUSION The results demonstrate that syncope has a distinct genetic architecture that implicates neural regulatory processes and a complex relationship with heart rate and blood pressure regulation. A shared genetic background with poor cardiovascular health was observed, supporting the importance of a thorough assessment of individuals presenting with syncope.
Collapse
Affiliation(s)
- Hildur M Aegisdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | | | | | | | | | | | | | | | | | - Egil Ferkingstad
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Patrick Sulem
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Alex Hoerby Christensen
- The Unit for Inherited Cardiac Diseases, Department of Cardiology, The Heart Centre, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
- Department of Cardiology, Herlev-Gentofte Hospital, Copenhagen University Hospital, Borgmester Ib Juuls Vej 1, Herlev 2730, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Christina Mikkelsen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Ole Birger Pedersen
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
- Department of Clinical Immunology, Zealand University Hospital - Køge, Lykkebækvej 1, Køge 4600, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, J. B. Winsløws Vej 4, Odense 5000, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, Aarhus 8200, Denmark
- Department of Clinical Medicine, Aarhus University, Nordre Ringgade 1, Aarhus 8000, Denmark
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Urbansgade 32, Aalborg 9000, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Michael L Frigge
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - Anna Helgadottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - Asmundur Oddsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - David A Jones
- Precision Genomics, Intermountain Healthcare, 600 S. Medical Center Drive, Saint George, UT 84790, USA
| | - Jeffrey L Anderson
- Intermountain Medical Center, Intermountain Heart Institute, 5171 S. Cottonwood Street Building 1, Salt Lake City, UT 84107, USA
- Department of Internal Medicine, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA
| | - Kirk U Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, 5171 S. Cottonwood Street Building 1, Salt Lake City, UT 84107, USA
- School of Medicine, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA
| | - Lincoln D Nadauld
- Precision Genomics, Intermountain Healthcare, 600 S. Medical Center Drive, Saint George, UT 84790, USA
- School of Medicine, Stanford University, 291 Campus Drive, Stanford, CA 94305, USA
| | | | - Magnus Haraldsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
- Department of Psychiatry, Landspitali, The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
- Department of Medicine, Landspitali, The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Henning Bundgaard
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
- The Capital Regions Unit for Inherited Cardiac Diseases, Department of Cardiology, The Heart Centre, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - David O Arnar
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
- Department of Medicine, Landspitali, The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Hjardarhagi 4, Reykjavik 107, Iceland
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| |
Collapse
|
3
|
Saevarsdottir S, Stefansdottir L, Sulem P, Thorleifsson G, Ferkingstad E, Rutsdottir G, Glintborg B, Westerlind H, Grondal G, Loft IC, Sorensen SB, Lie BA, Brink M, Ärlestig L, Arnthorsson AO, Baecklund E, Banasik K, Bank S, Bjorkman LI, Ellingsen T, Erikstrup C, Frei O, Gjertsson I, Gudbjartsson DF, Gudjonsson SA, Halldorsson GH, Hendricks O, Hillert J, Hogdall E, Jacobsen S, Jensen DV, Jonsson H, Kastbom A, Kockum I, Kristensen S, Kristjansdottir H, Larsen MH, Linauskas A, Hauge EM, Loft AG, Ludviksson BR, Lund SH, Markusson T, Masson G, Melsted P, Moore KHS, Munk H, Nielsen KR, Norddahl GL, Oddsson A, Olafsdottir TA, Olason PI, Olsson T, Ostrowski SR, Hørslev-Petersen K, Rognvaldsson S, Sanner H, Silberberg GN, Stefansson H, Sørensen E, Sørensen IJ, Turesson C, Bergman T, Alfredsson L, Kvien TK, Brunak S, Steinsson K, Andersen V, Andreassen OA, Rantapää-Dahlqvist S, Hetland ML, Klareskog L, Askling J, Padyukov L, Pedersen OB, Thorsteinsdottir U, Jonsdottir I, Stefansson K. Multiomics analysis of rheumatoid arthritis yields sequence variants that have large effects on risk of the seropositive subset. Ann Rheum Dis 2022; 81:1085-1095. [PMID: 35470158 PMCID: PMC9279832 DOI: 10.1136/annrheumdis-2021-221754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/26/2021] [Accepted: 04/04/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To find causal genes for rheumatoid arthritis (RA) and its seropositive (RF and/or ACPA positive) and seronegative subsets. METHODS We performed a genome-wide association study (GWAS) of 31 313 RA cases (68% seropositive) and ~1 million controls from Northwestern Europe. We searched for causal genes outside the HLA-locus through effect on coding, mRNA expression in several tissues and/or levels of plasma proteins (SomaScan) and did network analysis (Qiagen). RESULTS We found 25 sequence variants for RA overall, 33 for seropositive and 2 for seronegative RA, altogether 37 sequence variants at 34 non-HLA loci, of which 15 are novel. Genomic, transcriptomic and proteomic analysis of these yielded 25 causal genes in seropositive RA and additional two overall. Most encode proteins in the network of interferon-alpha/beta and IL-12/23 that signal through the JAK/STAT-pathway. Highlighting those with largest effect on seropositive RA, a rare missense variant in STAT4 (rs140675301-A) that is independent of reported non-coding STAT4-variants, increases the risk of seropositive RA 2.27-fold (p=2.1×10-9), more than the rs2476601-A missense variant in PTPN22 (OR=1.59, p=1.3×10-160). STAT4 rs140675301-A replaces hydrophilic glutamic acid with hydrophobic valine (Glu128Val) in a conserved, surface-exposed loop. A stop-mutation (rs76428106-C) in FLT3 increases seropositive RA risk (OR=1.35, p=6.6×10-11). Independent missense variants in TYK2 (rs34536443-C, rs12720356-C, rs35018800-A, latter two novel) associate with decreased risk of seropositive RA (ORs=0.63-0.87, p=10-9-10-27) and decreased plasma levels of interferon-alpha/beta receptor 1 that signals through TYK2/JAK1/STAT4. CONCLUSION Sequence variants pointing to causal genes in the JAK/STAT pathway have largest effect on seropositive RA, while associations with seronegative RA remain scarce.
Collapse
Affiliation(s)
- Saedis Saevarsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland .,Division of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Bente Glintborg
- The DANBIO registry, the Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (COPECARE), Centre for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helga Westerlind
- Division of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Gerdur Grondal
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland.,Center for Rheumatology Research, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Isabella C Loft
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Signe Bek Sorensen
- Molecular Diagnostics and Clinical Research Unit, IRS-Center Sonderjylland, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo, Oslo, Norway.,Oslo University Hospital, Oslo, Norway
| | - Mikael Brink
- Department of Public Health and Clinical Medicine, Rheumatology, Umeå University, Umeå, Sweden
| | - Lisbeth Ärlestig
- Department of Public Health and Clinical Medicine, Rheumatology, Umeå University, Umeå, Sweden
| | | | - Eva Baecklund
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steffen Bank
- Molecular Diagnostics and Clinical Research Unit, IRS-Center Sonderjylland, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Lena I Bjorkman
- Department of Rheumatology and Inflammation research, University of Gothenburg, Gothenburg, Sweden
| | - Torkell Ellingsen
- OPEN Explorative Network, University of Southern Denmark, Odense, Denmark.,Rheumatology Research Unit, Odense University Hospital and University of Southern Denmark, Odense, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Inger Gjertsson
- Department of Rheumatology and Inflammation Research, Gothenburg University, Gothenburg, Sweden
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Oliver Hendricks
- Danish Hospital for Rheumatic Diseases, University Hospital of Southern Denmark, Sønderborg, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Jan Hillert
- Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden
| | - Estrid Hogdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Søren Jacobsen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Lupus and Vasculitis Clinic, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Dorte Vendelbo Jensen
- Department of Rheumatology, Center for Rheumatology and Spine Diseases, Gentofte and Herlev Hospital, Rønne, Denmark
| | - Helgi Jonsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Alf Kastbom
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ingrid Kockum
- Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden
| | - Salome Kristensen
- Department of Rheumatology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Helga Kristjansdottir
- Center for Rheumatology Research, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Margit H Larsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Asta Linauskas
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Rheumatology, North Denmark Regional Hospital, Hjørring, Denmark
| | - Ellen-Margrethe Hauge
- Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Anne G Loft
- Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Bjorn R Ludviksson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Immunology, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Thorsteinn Markusson
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Pall Melsted
- deCODE genetics/Amgen, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Heidi Munk
- OPEN Explorative Network, University of Southern Denmark, Odense, Denmark.,Rheumatology Research Unit, Odense University Hospital and University of Southern Denmark, Odense, Denmark
| | - Kaspar R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | | | - Thorunn A Olafsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Tomas Olsson
- Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden
| | - Sisse Rye Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kim Hørslev-Petersen
- Danish Hospital for Rheumatic Diseases, University Hospital of Southern Denmark, Sønderborg, Denmark
| | | | - Helga Sanner
- Section of Rheumatology, Oslo University Hospital, Oslo, Norway.,Oslo New University College, Oslo, Norway
| | - Gilad N Silberberg
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | | | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Inge J Sørensen
- Copenhagen Lupus and Vasculitis Clinic, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Carl Turesson
- Rheumatology, Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| | - Thomas Bergman
- Division of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tore K Kvien
- University of Oslo, Oslo, Norway.,Diakonhjemmet Hospital, Oslo, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristján Steinsson
- Center for Rheumatology Research, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Vibeke Andersen
- Molecular Diagnostics and Clinical Research Unit, IRS-Center Sonderjylland, University Hospital of Southern Denmark, Aabenraa, Denmark.,OPEN Explorative Network, University of Southern Denmark, Odense, Denmark.,Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | | | - Merete Lund Hetland
- The DANBIO registry, the Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (COPECARE), Centre for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Johan Askling
- Division of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Bv Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Immunology, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland .,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | |
Collapse
|
4
|
Gisladottir RS, Ivarsdottir EV, Helgason A, Jonsson L, Hannesdottir NK, Rutsdottir G, Arnadottir GA, Skuladottir A, Jonsson BA, Norddahl GL, Ulfarsson MO, Helgason H, Halldorsson BV, Nawaz MS, Tragante V, Sveinbjornsson G, Thorgeirsson T, Oddsson A, Kristjansson RP, Bjornsdottir G, Thorgeirsson G, Jonsdottir I, Holm H, Gudbjartsson DF, Thorsteinsdottir U, Stefansson H, Sulem P, Stefansson K. Sequence Variants in TAAR5 and Other Loci Affect Human Odor Perception and Naming. Curr Biol 2020; 30:4643-4653.e3. [PMID: 33035477 DOI: 10.1016/j.cub.2020.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/04/2019] [Revised: 04/17/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022]
Abstract
Olfactory receptor (OR) genes in humans form a special class characterized by unusually high DNA sequence diversity, which should give rise to differences in perception and behavior. In the largest genome-wide association study to date based on olfactory testing, we investigated odor perception and naming with smell tasks performed by 9,122 Icelanders, with replication in a separate sample of 2,204 individuals. We discovered an association between a low-frequency missense variant in TAAR5 and reduced intensity rating of fish odor containing trimethylamine (p.Ser95Pro, pcombined = 5.6 × 10-15). We demonstrate that TAAR5 genotype affects aversion to fish odor, reflected by linguistic descriptions of the odor and pleasantness ratings. We also discovered common sequence variants in two canonical olfactory receptor loci that associate with increased intensity and naming of licorice odor (trans-anethole: lead variant p.Lys233Asn in OR6C70, pcombined = 8.8 × 10-16 and pcombined = 1.4 × 10-9) and enhanced naming of cinnamon (trans-cinnamaldehyde; intergenic variant rs317787-T, pcombined = 5.0 × 10-17). Together, our results show that TAAR5 genotype variation influences human odor responses and highlight that sequence diversity in canonical OR genes can lead to enhanced olfactory ability, in contrast to the view that greater tolerance for mutations in the human OR repertoire leads to diminished function.
Collapse
Affiliation(s)
- Rosa S Gisladottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Humanities, University of Iceland, Saemundargata 2, 102 Reykjavik, Iceland.
| | - Erna V Ivarsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, Saemundargata 10, 102 Reykjavik, Iceland
| | - Lina Jonsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 13, SE-405 30, Gothenburg, Sweden; The Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Blå Stråket 15, 413 45, Gothenburg, Sweden
| | | | | | | | | | | | | | - Magnus O Ulfarsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Electrical and Computer Engineering, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Hannes Helgason
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Technology, Reykjavik University, Menntavegur 1, 101 Reykjavik, Iceland
| | - Muhammad S Nawaz
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | | | | | | | - Asmundur Oddsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | | | | | - Gudmundur Thorgeirsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland; Division of Cardiology, Department of Internal Medicine, Landspitali, The National University Hospital of Iceland, Hringbraut, 101 Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland; Department of Immunology, Landspitali, The National University Hospital of Iceland, Hringbraut, 101 Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | | | - Patrick Sulem
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland.
| |
Collapse
|
5
|
Söderberg CAG, Månsson C, Bernfur K, Rutsdottir G, Härmark J, Rajan S, Al-Karadaghi S, Rasmussen M, Höjrup P, Hebert H, Emanuelsson C. Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface. Sci Rep 2018; 8:5199. [PMID: 29581438 PMCID: PMC5979959 DOI: 10.1038/s41598-018-23035-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/05/2018] [Indexed: 12/28/2022] Open
Abstract
The remarkably efficient suppression of amyloid fibril formation by the DNAJB6 chaperone is dependent on a set of conserved S/T-residues and an oligomeric structure, features unusual among DNAJ chaperones. We explored the structure of DNAJB6 using a combination of structural methods. Lysine-specific crosslinking mass spectrometry provided distance constraints to select a homology model of the DNAJB6 monomer, which was subsequently used in crosslink-assisted docking to generate a dimer model. A peptide-binding cleft lined with S/T-residues is formed at the monomer-monomer interface. Mixed isotope crosslinking showed that the oligomers are dynamic entities that exchange subunits. The purified protein is well folded, soluble and composed of oligomers with a varying number of subunits according to small-angle X-ray scattering (SAXS). Elongated particles (160 × 120 Å) were detected by electron microscopy and single particle reconstruction resulted in a density map of 20 Å resolution into which the DNAJB6 dimers fit. The structure of the oligomer and the S/T-rich region is of great importance for the understanding of the function of DNAJB6 and how it can bind aggregation-prone peptides and prevent amyloid diseases.
Collapse
Affiliation(s)
| | - Cecilia Månsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Johan Härmark
- School of Technology and Health, KTH Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Salam Al-Karadaghi
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Morten Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Höjrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hans Hebert
- School of Technology and Health, KTH Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden.
| |
Collapse
|
6
|
Rutsdottir G, I Rasmussen M, Hojrup P, Bernfur K, Emanuelsson C, Söderberg CAG. Chaperone-client interactions between Hsp21 and client proteins monitored in solution by small angle X-ray scattering and captured by crosslinking mass spectrometry. Proteins 2017; 86:110-123. [PMID: 29082555 DOI: 10.1002/prot.25413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 06/03/2017] [Revised: 10/13/2017] [Accepted: 10/27/2017] [Indexed: 11/07/2022]
Abstract
The small heat shock protein (sHsp) chaperones are important for stress survival, yet the molecular details of how they interact with client proteins are not understood. All sHsps share a folded middle domain to which is appended flexible N- and C-terminal regions varying in length and sequence between different sHsps which, in different ways for different sHsps, mediate recognition of client proteins. In plants there is a chloroplast-localized sHsp, Hsp21, and a structural model suggests that Hsp21 has a dodecameric arrangement with six N-terminal arms located on the outside of the dodecamer and six inwardly-facing. Here, we investigated the interactions between Hsp21 and thermosensitive model substrate client proteins in solution, by small-angle X-ray scattering (SAXS) and crosslinking mass spectrometry. The chaperone-client complexes were monitored and the Rg -values were found to increase continuously during 20 min at 45°, which could reflect binding of partially unfolded clients to the flexible N-terminal arms of the Hsp21 dodecamer. No such increase in Rg -values was observed with a mutational variant of Hsp21, which is mainly dimeric and has reduced chaperone activity. Crosslinking data suggest that the chaperone-client interactions involve the N-terminal region in Hsp21 and only certain parts in the client proteins. These parts are peripheral structural elements presumably the first to unfold under destabilizing conditions. We propose that the flexible and hydrophobic N-terminal arms of Hsp21 can trap and refold early-unfolding intermediates with or without dodecamer dissociation.
Collapse
Affiliation(s)
- Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Morten I Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Hojrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | | | | |
Collapse
|
7
|
Bernfur K, Rutsdottir G, Emanuelsson C. The chloroplast-localized small heat shock protein Hsp21 associates with the thylakoid membranes in heat-stressed plants. Protein Sci 2017; 26:1773-1784. [PMID: 28608391 PMCID: PMC5563132 DOI: 10.1002/pro.3213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 03/21/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022]
Abstract
The small heat shock protein (sHsp) chaperones are crucial for cell survival and can prevent aggregation of client proteins that partially unfold under destabilizing conditions. Most investigations on the chaperone activity of sHsps are based on a limited set of thermosensitive model substrate client proteins since the endogenous targets are often not known. There is a high diversity among sHsps with a single conserved β‐sandwich fold domain defining the family, the α‐crystallin domain, whereas the N‐terminal and C‐terminal regions are highly variable in length and sequence among various sHsps and conserved only within orthologues. The endogenous targets are probably also varying among various sHsps, cellular compartments, cell type and organism. Here we have investigated Hsp21, a non‐metazoan sHsp expressed in the chloroplasts in green plants which experience huge environmental fluctuations not least in temperature. We describe how Hsp21 can also interact with the chloroplast thylakoid membranes, both when isolated thylakoid membranes are incubated with Hsp21 protein and when plants are heat‐stressed. The amount of Hsp21 associated with the thylakoid membranes was precisely determined by quantitative mass spectrometry after metabolic 15N‐isotope labeling of either recombinantly expressed and purified Hsp21 protein or intact Arabidopsis thaliana plants. We found that Hsp21 is among few proteins that become associated with the thylakoid membranes in heat‐stressed plants, and that approximately two thirds of the pool of chloroplast Hsp21 is affected. We conclude that for a complete picture of the role of sHsps in plant stress resistance also their association with the membranes should be considered.
Collapse
Affiliation(s)
- Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| |
Collapse
|
8
|
Rutsdottir G, Härmark J, Weide Y, Hebert H, Rasmussen MI, Wernersson S, Respondek M, Akke M, Højrup P, Koeck PJB, Söderberg CAG, Emanuelsson C. Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity. J Biol Chem 2017; 292:8103-8121. [PMID: 28325834 PMCID: PMC5427286 DOI: 10.1074/jbc.m116.766816] [Citation(s) in RCA: 21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/16/2017] [Indexed: 01/14/2023] Open
Abstract
Small heat-shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have been hard to define due to limited structural information; currently, there is only one high-resolution structure of a plant sHsp published, that of the cytosolic Hsp16.9. We took interest in Hsp21, a chloroplast-localized sHsp crucial for plant stress resistance, which has even longer N-terminal arms than Hsp16.9, with a functionally important and conserved methionine-rich motif. To provide a framework for investigating structure-function relationships of Hsp21 and understanding these sequence variations, we developed a structural model of Hsp21 based on homology modeling, cryo-EM, cross-linking mass spectrometry, NMR, and small-angle X-ray scattering. Our data suggest a dodecameric arrangement of two trimer-of-dimer discs stabilized by the C-terminal tails, possibly through tail-to-tail interactions between the discs, mediated through extended IXVXI motifs. Our model further suggests that six N-terminal arms are located on the outside of the dodecamer, accessible for interaction with client proteins, and distinct from previous undefined or inwardly facing arms. To test the importance of the IXVXI motif, we created the point mutant V181A, which, as expected, disrupts the Hsp21 dodecamer and decreases chaperone activity. Finally, our data emphasize that sHsp chaperone efficiency depends on oligomerization and that client interactions can occur both with and without oligomer dissociation. These results provide a generalizable workflow to explore sHsps, expand our understanding of sHsp structural motifs, and provide a testable Hsp21 structure model to inform future investigations.
Collapse
Affiliation(s)
| | - Johan Härmark
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Yoran Weide
- From the Departments of Biochemistry and Structural Biology and
| | - Hans Hebert
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Morten I Rasmussen
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | | | | | | | - Peter Højrup
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Philip J B Koeck
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | | | | |
Collapse
|
9
|
Lambert W, Rutsdottir G, Hussein R, Bernfur K, Kjellström S, Emanuelsson C. Probing the transient interaction between the small heat-shock protein Hsp21 and a model substrate protein using crosslinking mass spectrometry. Cell Stress Chaperones 2013; 18:75-85. [PMID: 22851138 PMCID: PMC3508123 DOI: 10.1007/s12192-012-0360-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/15/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022] Open
Abstract
Small heat-shock protein chaperones are important players in the protein quality control system of the cell, because they can immediately respond to partially unfolded proteins, thereby protecting the cell from harmful aggregates. The small heat-shock proteins can form large polydisperse oligomers that are exceptionally dynamic, which is implicated in their function of protecting substrate proteins from aggregation. Yet the mechanism of substrate recognition remains poorly understood, and little is known about what parts of the small heat-shock proteins interact with substrates and what parts of a partially unfolded substrate protein interact with the small heat-shock proteins. The transient nature of the interactions that prevent substrate aggregation rationalize probing this interaction by crosslinking mass spectrometry. Here, we used a workflow with lysine-specific crosslinking and offline nano-liquid chromatography matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry to explore the interaction between the plant small heat-shock protein Hsp21 and a thermosensitive model substrate protein, malate dehydrogenase. The identified crosslinks point at an interaction between the disordered N-terminal region of Hsp21 and the C-terminal presumably unfolding part of the substrate protein.
Collapse
Affiliation(s)
- Wietske Lambert
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Rasha Hussein
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Sven Kjellström
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
10
|
Söderberg CAG, Lambert W, Kjellström S, Wiegandt A, Wulff RP, Månsson C, Rutsdottir G, Emanuelsson C. Detection of crosslinks within and between proteins by LC-MALDI-TOFTOF and the software FINDX to reduce the MSMS-data to acquire for validation. PLoS One 2012; 7:e38927. [PMID: 22723907 PMCID: PMC3377668 DOI: 10.1371/journal.pone.0038927] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/14/2012] [Indexed: 11/19/2022] Open
Abstract
Lysine-specific chemical crosslinking in combination with mass spectrometry is emerging as a tool for the structural characterization of protein complexes and protein-protein interactions. After tryptic digestion of crosslinked proteins there are thousands of peptides amenable to MSMS, of which only very few are crosslinked peptides of interest. Here we describe how the advantage offered by off-line LC-MALDI-TOF/TOF mass spectrometry is exploited in a two-step workflow to focus the MSMS-acquisition on crosslinks mainly. In a first step, MS-data are acquired and all the peak list files from the LC-separated fractions are merged by the FINDX software and screened for presence of crosslinks which are recognized as isotope-labeled doublet peaks. Information on the isotope doublet peak mass and intensity can be used as search constraints to reduce the number of false positives that match randomly to the observed peak masses. Based on the MS-data a precursor ion inclusion list is generated and used in a second step, where a restricted number of MSMS-spectra are acquired for crosslink validation. The decoupling of MS and MSMS and the peptide sorting with FINDX based on MS-data has the advantage that MSMS can be restricted to and focused on crosslinks of Type 2, which are of highest biological interest but often lowest in abundance. The LC-MALDI TOF/TOF workflow here described is applicable to protein multisubunit complexes and using (14)N/(15)N mixed isotope strategy for the detection of inter-protein crosslinks within protein oligomers.
Collapse
Affiliation(s)
- Christopher A. G. Söderberg
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Wietske Lambert
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Sven Kjellström
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Alena Wiegandt
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Ragna Peterson Wulff
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Cecilia Månsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
- * E-mail:
| |
Collapse
|
11
|
Lambert W, Söderberg CAG, Rutsdottir G, Boelens WC, Emanuelsson C. Thiol-exchange in DTSSP crosslinked peptides is proportional to cysteine content and precisely controlled in crosslink detection by two-step LC-MALDI MSMS. Protein Sci 2011; 20:1682-91. [PMID: 21780214 DOI: 10.1002/pro.699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/04/2011] [Accepted: 07/07/2011] [Indexed: 11/06/2022]
Abstract
The lysine-specific crosslinker 3,3'-dithiobis(sulfosuccinimidylpropionate) (DTSSP) is commonly used in the structural characterization of proteins by chemical crosslinking and mass spectrometry and we here describe an efficient two-step LC-MALDI-TOF/TOF procedure to detect crosslinked peptides. First MS data are acquired, and the properties of isotope-labeled DTSSP are used in data analysis to identify candidate crosslinks. MSMS data are then acquired for a restricted number of precursor ions per spot for final crosslink identification. We show that the thiol-catalyzed exchange between crosslinked peptides, which is due to the disulfide bond in DTSSP and known to possibly obscure data, can be precisely quantified using isotope-labeled DTSSP. Crosslinked peptides are recognized as 8 Da doublet peaks and a new isotopic peak with twice the intensity appears in the middle of the doublet as a consequence of the thiol-exchange. False-positive crosslinks, formed exclusively by thiol-exchange, yield a 1:2:1 isotope pattern, whereas true crosslinks, formed by two lysine residues within crosslinkable distance in the native protein structure, yield a 1:0:1 isotope pattern. Peaks with a 1:X:1 isotope pattern, where 0 < X < 2, can be trusted as true crosslinks, with a defined proportion of the signal [2X/(2 + X)] being noise from the thiol-exchange. The thiol-exchange was correlated with the protein cysteine content and was minimized by shortening the trypsin incubation time, and for two molecular chaperone proteins with known structure all crosslinks fitted well to the structure data. The thiol-exchange can thus be controlled and isotope-labeled DTSSP safely used to detect true crosslinks between lysine residues in proteins.
Collapse
Affiliation(s)
- Wietske Lambert
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden.
| | | | | | | | | |
Collapse
|
12
|
Wulff RP, Lundqvist J, Rutsdottir G, Hansson A, Stenbaek A, Elmlund D, Elmlund H, Jensen PE, Hansson M. The activity of barley NADPH-dependent thioredoxin reductase C is independent of the oligomeric state of the protein: tetrameric structure determined by cryo-electron microscopy. Biochemistry 2011; 50:3713-23. [PMID: 21456578 DOI: 10.1021/bi200058a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thioredoxin and thioredoxin reductase can regulate cell metabolism through redox regulation of disulfide bridges or through removal of H(2)O(2). These two enzymatic functions are combined in NADPH-dependent thioredoxin reductase C (NTRC), which contains an N-terminal thioredoxin reductase domain fused with a C-terminal thioredoxin domain. Rice NTRC exists in different oligomeric states, depending on the absence or presence of its NADPH cofactor. It has been suggested that the different oligomeric states may have diverse activity. Thus, the redox status of the chloroplast could influence the oligomeric state of NTRC and thereby its activity. We have characterized the oligomeric states of NTRC from barley (Hordeum vulgare L.). This also includes a structural model of the tetrameric NTRC derived from cryo-electron microscopy and single-particle reconstruction. We conclude that the tetrameric NTRC is a dimeric arrangement of two NTRC homodimers. Unlike that of rice NTRC, the quaternary structure of barley NTRC complexes is unaffected by addition of NADPH. The activity of NTRC was tested with two different enzyme assays. The N-terminal part of NTRC was tested in a thioredoxin reductase assay. A peroxide sensitive Mg-protoporphyrin IX monomethyl ester (MPE) cyclase enzyme system of the chlorophyll biosynthetic pathway was used to test the catalytic ability of both the N- and C-terminal parts of NTRC. The different oligomeric assembly states do not exhibit significantly different activities. Thus, it appears that the activities are independent of the oligomeric state of barley NTRC.
Collapse
|