1
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Tariq M, Ikeya T, Togashi N, Fairall L, Kamei S, Mayooramurugan S, Abbott LR, Hasan A, Bueno-Alejo C, Sukegawa S, Romartinez-Alonso B, Muro Campillo MA, Hudson AJ, Ito Y, Schwabe JW, Dominguez C, Tanaka K. Structural insights into the complex of oncogenic KRas4B G12V and Rgl2, a RalA/B activator. Life Sci Alliance 2024; 7:e202302080. [PMID: 37833074 PMCID: PMC10576006 DOI: 10.26508/lsa.202302080] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA, and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the switch I and switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.
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Affiliation(s)
- Mishal Tariq
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Teppei Ikeya
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoyuki Togashi
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Louise Fairall
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Shun Kamei
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Sannojah Mayooramurugan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Lauren R Abbott
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Anab Hasan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Carlos Bueno-Alejo
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Sakura Sukegawa
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Beatriz Romartinez-Alonso
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Miguel Angel Muro Campillo
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Andrew J Hudson
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Department of Chemistry, University of Leicester, Leicester, UK
| | - Yutaka Ito
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - John Wr Schwabe
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Cyril Dominguez
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Kayoko Tanaka
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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2
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Ferrari A, Whang E, Xiao X, Kennelly JP, Romartinez-Alonso B, Mack JJ, Weston T, Chen K, Kim Y, Tol MJ, Bideyan L, Nguyen A, Gao Y, Cui L, Bedard AH, Sandhu J, Lee SD, Fairall L, Williams KJ, Song W, Munguia P, Russell RA, Martin MG, Jung ME, Jiang H, Schwabe JWR, Young SG, Tontonoz P. Aster-dependent nonvesicular transport facilitates dietary cholesterol uptake. Science 2023; 382:eadf0966. [PMID: 37943936 DOI: 10.1126/science.adf0966] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/27/2023] [Indexed: 11/12/2023]
Abstract
Intestinal absorption is an important contributor to systemic cholesterol homeostasis. Niemann-Pick C1 Like 1 (NPC1L1) assists in the initial step of dietary cholesterol uptake, but how cholesterol moves downstream of NPC1L1 is unknown. We show that Aster-B and Aster-C are critical for nonvesicular cholesterol movement in enterocytes. Loss of NPC1L1 diminishes accessible plasma membrane (PM) cholesterol and abolishes Aster recruitment to the intestinal brush border. Enterocytes lacking Asters accumulate PM cholesterol and show endoplasmic reticulum cholesterol depletion. Aster-deficient mice have impaired cholesterol absorption and are protected against diet-induced hypercholesterolemia. Finally, the Aster pathway can be targeted with a small-molecule inhibitor to manipulate cholesterol uptake. These findings identify the Aster pathway as a physiologically important and pharmacologically tractable node in dietary lipid absorption.
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Affiliation(s)
- Alessandra Ferrari
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emily Whang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Pediatric Gastroenterology, Hepatology, and Nutrition, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xu Xiao
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John P Kennelly
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Julia J Mack
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Thomas Weston
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kai Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Youngjae Kim
- Department of Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marcus J Tol
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lara Bideyan
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Nguyen
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine
| | - Yajing Gao
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Liujuan Cui
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander H Bedard
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jaspreet Sandhu
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen D Lee
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Louise Fairall
- Institute for Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Kevin J Williams
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- UCLA Lipidomics Core, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wenxin Song
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Priscilla Munguia
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert A Russell
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Martin G Martin
- Pediatric Gastroenterology, Hepatology, and Nutrition, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael E Jung
- Department of Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Haibo Jiang
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - John W R Schwabe
- Institute for Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Stephen G Young
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Ferrari A, Whang E, Xiao X, Kennelly JP, Romartinez-Alonso B, Mack JJ, Weston T, Chen K, Kim Y, Tol MJ, Bideyan L, Nguyen A, Gao Y, Cui L, Bedard AH, Sandhu J, Lee SD, Fairall L, Williams KJ, Song W, Munguia P, Russell RA, Martin MG, Jung ME, Jiang H, Schwabe JWR, Young SG, Tontonoz P. Aster-dependent non-vesicular transport facilitates dietary cholesterol uptake. bioRxiv 2023:2023.07.07.548168. [PMID: 37503112 PMCID: PMC10369906 DOI: 10.1101/2023.07.07.548168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Intestinal cholesterol absorption is an important contributor to systemic cholesterol homeostasis. Niemann-Pick C1 Like 1 (NPC1L1), the target of the drug ezetimibe (EZ), assists in the initial step of dietary cholesterol uptake. However, how cholesterol moves downstream of NPC1L1 is unknown. Here we show that Aster-B and Aster-C are critical for non-vesicular cholesterol movement in enterocytes, bridging NPC1L1 at the plasma membrane (PM) and ACAT2 in the endoplasmic reticulum (ER). Loss of NPC1L1 diminishes accessible PM cholesterol in enterocytes and abolishes Aster recruitment to the intestinal brush border. Enterocytes lacking Asters accumulate cholesterol at the PM and display evidence of ER cholesterol depletion, including decreased cholesterol ester stores and activation of the SREBP-2 transcriptional pathway. Aster-deficient mice have impaired cholesterol absorption and are protected against diet-induced hypercholesterolemia. Finally, we show that the Aster pathway can be targeted with a small molecule inhibitor to manipulate dietary cholesterol uptake. These findings identify the Aster pathway as a physiologically important and pharmacologically tractable node in dietary lipid absorption. One-Sentence Summary Identification of a targetable pathway for regulation of dietary cholesterol absorption.
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4
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Wang S, Fairall L, Pham TK, Ragan TJ, Vashi D, Collins M, Dominguez C, Schwabe JR. A potential histone-chaperone activity for the MIER1 histone deacetylase complex. Nucleic Acids Res 2023; 51:6006-6019. [PMID: 37099381 PMCID: PMC10325919 DOI: 10.1093/nar/gkad294] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/10/2023] [Accepted: 04/19/2023] [Indexed: 04/27/2023] Open
Abstract
Histone deacetylases 1 and 2 (HDAC1/2) serve as the catalytic subunit of six distinct families of nuclear complexes. These complexes repress gene transcription through removing acetyl groups from lysine residues in histone tails. In addition to the deacetylase subunit, these complexes typically contain transcription factor and/or chromatin binding activities. The MIER:HDAC complex has hitherto been poorly characterized. Here, we show that MIER1 unexpectedly co-purifies with an H2A:H2B histone dimer. We show that MIER1 is also able to bind a complete histone octamer. Intriguingly, we found that a larger MIER1:HDAC1:BAHD1:C1QBP complex additionally co-purifies with an intact nucleosome on which H3K27 is either di- or tri-methylated. Together this suggests that the MIER1 complex acts downstream of PRC2 to expand regions of repressed chromatin and could potentially deposit histone octamer onto nucleosome-depleted regions of DNA.
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Affiliation(s)
- Siyu Wang
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Trong Khoa Pham
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Timothy J Ragan
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Dipti Vashi
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Cyril Dominguez
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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5
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Wang ZA, Whedon SD, Wu M, Wang S, Brown EA, Anmangandla A, Regan L, Lee K, Du J, Hong JY, Fairall L, Kay T, Lin H, Zhao Y, Schwabe JWR, Cole PA. Histone H2B Deacylation Selectivity: Exploring Chromatin's Dark Matter with an Engineered Sortase. J Am Chem Soc 2022; 144:3360-3364. [PMID: 35175758 PMCID: PMC8895396 DOI: 10.1021/jacs.1c13555] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a new method to produce histone H2B by semisynthesis with an engineered sortase transpeptidase. N-Terminal tail site-specifically modified acetylated, lactylated, and β-hydroxybutyrylated histone H2Bs were incorporated into nucleosomes and investigated as substrates of histone deacetylase (HDAC) complexes and sirtuins. A wide range of rates and site-specificities were observed by these enzyme forms suggesting distinct biological roles in regulating chromatin structure and epigenetics.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Siyu Wang
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Edward A Brown
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ananya Anmangandla
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Liam Regan
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jianfeng Du
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - Jun Young Hong
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Taylor Kay
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hening Lin
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yingming Zhao
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
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6
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Goga AE, Bekker LG, Garrett N, Takuva S, Sanne I, Odhiambo J, Mayat F, Fairall L, Brey Z, Bamford L, Tanna G, Grey G. Sisonke phase 3B open-label study: Lessons learnt for national and global vaccination scale-up during epidemics. S Afr Med J 2021; 112:13486. [PMID: 35140006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023] Open
Abstract
Sisonke is a multicentre, open-label, single-arm phase 3B vaccine implementation study of healthcare workers (HCWs) in South Africa, with prospective surveillance for 2 years. The primary endpoint is the rate of severe COVID‑19, including hospitalisations and deaths. The Sisonke study enrolled and vaccinated participants nationally at potential vaccination roll-out sites between 17 February and 26 May 2021. After May 2021, additional HCWs were vaccinated as part of a sub-study at selected clinical research sites. We discuss 10 lessons learnt to strengthen national and global vaccination strategies:(i) consistently advocate for vaccination to reduce public hesitancy; (ii) an electronic vaccination data system (EVDS) is critical; (iii) facilitate access to a choice of vaccination sites, such as religious and community centres, schools, shopping malls and drive-through centres; (iv) let digitally literate people help elderly and marginalised people to register for vaccination; (v) develop clear 'how to' guides for vaccine storage, pharmacy staff and vaccinators; (vi) leverage instant messaging platforms, such as WhatsApp, for quick communication among staff at vaccination centres; (vii) safety is paramount - rapid health assessments are needed at vaccination centres to identify people at high risk of serious adverse events, including anaphylaxis or thrombosis with thrombocytopenia syndrome. Be transparent about adverse events and contextualise vaccination benefits, while acknowledging the small risks; (viii) provide real-time, responsive support to vaccinees post vaccination and implement an accessible national vaccine adverse events surveillance system; (ix) develop efficient systems to monitor and investigate COVID‑19 breakthrough infections; and (x) flexibility and teamwork are essential in vaccination centres across national, provincial and district levels and between public and private sectors.
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Affiliation(s)
- A E Goga
- South African Medical Research Council, South Africa; Department of Paediatrics and Child Health, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa.
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7
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Song Y, Dagil L, Fairall L, Robertson N, Wu M, Ragan TJ, Savva CG, Saleh A, Morone N, Kunze MBA, Jamieson AG, Cole PA, Hansen DF, Schwabe JWR. Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex. Cell Rep 2021; 30:2699-2711.e8. [PMID: 32101746 PMCID: PMC7043024 DOI: 10.1016/j.celrep.2020.01.091] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 09/13/2019] [Revised: 12/31/2019] [Accepted: 01/24/2020] [Indexed: 01/08/2023] Open
Abstract
The transcriptional corepressor complex CoREST is one of seven histone deacetylase complexes that regulate the genome through controlling chromatin acetylation. The CoREST complex is unique in containing both histone demethylase and deacetylase enzymes, LSD1 and HDAC1, held together by the RCOR1 scaffold protein. To date, it has been assumed that the enzymes function independently within the complex. Now, we report the assembly of the ternary complex. Using both structural and functional studies, we show that the activity of the two enzymes is closely coupled and that the complex can exist in at least two distinct states with different kinetics. Electron microscopy of the complex reveals a bi-lobed structure with LSD1 and HDAC1 enzymes at opposite ends of the complex. The structure of CoREST in complex with a nucleosome reveals a mode of chromatin engagement that contrasts with previous models. The activities of LSD1 and HDAC1 are closely coupled in the CoREST complex Both LSD1 and HDAC1 exist in two different kinetic states CoREST has a bi-lobed, flexible structure with the two enzymes located at opposite ends CoREST interacts with methylated nucleosomes via LSD1, but not HDAC1 or RCOR1
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Affiliation(s)
- Yun Song
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Lisbeth Dagil
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Louise Fairall
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Naomi Robertson
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - T J Ragan
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Christos G Savva
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Almutasem Saleh
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Nobuhiro Morone
- MRC-Toxicology Unit, University of Cambridge, University Road, Leicester LE1 7RH, UK
| | - Micha B A Kunze
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew G Jamieson
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
| | - John W R Schwabe
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK.
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8
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Millard CJ, Fairall L, Ragan TJ, Savva CG, Schwabe JWR. The topology of chromatin-binding domains in the NuRD deacetylase complex. Nucleic Acids Res 2020; 48:12972-12982. [PMID: 33264408 PMCID: PMC7736783 DOI: 10.1093/nar/gkaa1121] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 01/22/2023] Open
Abstract
Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate.
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Affiliation(s)
- Christopher J Millard
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Timothy J Ragan
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Christos G Savva
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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9
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Moran C, Seger C, Taylor K, Oddy S, Burling K, Rajanayagam O, Fairall L, McGowan A, Lyons G, Halsall D, Gurnell M, Schwabe J, Chatterjee K, Strey C. Hyperthyroxinemia and Hypercortisolemia due to Familial Dysalbuminemia. Thyroid 2020; 30:1681-1684. [PMID: 32669045 PMCID: PMC7692891 DOI: 10.1089/thy.2020.0315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A 23-year-old man and his grandmother with hyperthyroxinemia and hypercortisolemia were heterozygous for an ALB mutation (p. Arg218Pro), known to cause familial dysalbuminemic hyperthyroxinemia (FDH). However, serum-free cortisol levels in these individuals were normal and total cortisol concentrations fell markedly after depletion of albumin from their serum. We conclude that binding of steroid as well as iodothyronines to mutant albumin causes raised circulating cortisol as well as thyroid hormones in euthyroid euadrenal individuals with R218P FDH, with potential for misdiagnosis, unnecessary investigation, and inappropriate treatment.
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Affiliation(s)
- Carla Moran
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Christoph Seger
- Risch Laboratory Group, Lagerstrasse, Buchs, SG, Switzerland
| | - Kevin Taylor
- Department of Clinical Biochemistry, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Susan Oddy
- Department of Clinical Biochemistry, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Keith Burling
- Department of Clinical Biochemistry, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Odelia Rajanayagam
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Louise Fairall
- Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | - Anne McGowan
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Greta Lyons
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - David Halsall
- Department of Clinical Biochemistry, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Mark Gurnell
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - John Schwabe
- Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | - Krishna Chatterjee
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
- Address correspondence to: Krishna Chatterjee, MD, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
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10
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Zani B, Fairall L, Petersen I, Folb N, Bhana A, Thornicroft G, Hanass-Hancock J, Lund C, Bachmann M. Predictors of receiving a diagnosis, referral and treatment of depression in people on antiretroviral therapy in South African primary care: a secondary analysis of data from a randomised trial. Trop Med Int Health 2020; 25:1450-1466. [PMID: 32985080 PMCID: PMC7756779 DOI: 10.1111/tmi.13495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Objective To describe the receipt of a diagnosis, referral and treatment for depression in people receiving antiretroviral therapy (ART), with depressive symptoms and attending primary care clinics in South Africa, and investigate factors associated with receiving these components of care. Methods This is a secondary analysis of data from a randomised controlled trial of an intervention intended to improve detection and treatment of depression in primary care patients receiving ART. In this analysis, we combined cross‐sectional and longitudinal data from the intervention and control arms. Using regression models and adjusting for intra‐cluster correlation of outcomes, we investigated associations between socioeconomic characteristics, depressive symptoms, stress, disability and stigma, and receipt of a diagnosis, referral and treatment for depression. Results Of 2002 participants enrolled, 18% reported a previous diagnosis of depression by a healthcare worker and 10% reported having received counselling from a specialist mental health worker. Diagnosis, referral and counselling during the follow‐up period were appropriately targeted, being independently more frequent in participants with higher enrolment scores for depressive symptoms, stress or disability. Participants with higher stigma scores at enrolment were independently less likely to receive counselling. Severe socio‐economic deprivation was common but was not associated with treatment. Conclusion While the receipt of a diagnosis, referral and treatment for depression were uncommon, they seemed to be appropriately targeted. Socio‐economic deprivation was not associated with treatment.
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Affiliation(s)
- B Zani
- Knowledge Translation Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - L Fairall
- Knowledge Translation Unit, University of Cape Town Lung Institute, Cape Town, South Africa.,King's Global Health Institute, King's College London, London, UK.,Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - I Petersen
- Centre for Rural Health, University of KwaZulu-Natal, Durban, South Africa
| | - N Folb
- Knowledge Translation Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - A Bhana
- Centre for Rural Health, University of KwaZulu-Natal, Durban, South Africa.,Health Systems Research Unit, South African Medical Research Council, Durban, South Africa
| | - G Thornicroft
- Centre for Global Mental Health, King's College London, London, UK
| | - J Hanass-Hancock
- HIV Prevention Research Unit, South African Medical Research Council, Durban, South Africa.,School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - C Lund
- Centre for Global Mental Health, King's College London, London, UK.,Alan J Flisher Centre for Public Mental Health, University of Cape Town, Cape Town, South Africa
| | - M Bachmann
- Norwich Medical School, University of East Anglia, Norwich, UK
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11
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Turnbull RE, Fairall L, Saleh A, Kelsall E, Morris KL, Ragan TJ, Savva CG, Chandru A, Millard CJ, Makarova OV, Smith CJ, Roseman AM, Fry AM, Cowley SM, Schwabe JWR. The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Nat Commun 2020; 11:3252. [PMID: 32591534 PMCID: PMC7319964 DOI: 10.1038/s41467-020-17078-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/05/2020] [Indexed: 12/31/2022] Open
Abstract
MiDAC is one of seven distinct, large multi-protein complexes that recruit class I histone deacetylases to the genome to regulate gene expression. Despite implications of involvement in cell cycle regulation and in several cancers, surprisingly little is known about the function or structure of MiDAC. Here we show that MiDAC is important for chromosome alignment during mitosis in cancer cell lines. Mice lacking the MiDAC proteins, DNTTIP1 or MIDEAS, die with identical phenotypes during late embryogenesis due to perturbations in gene expression that result in heart malformation and haematopoietic failure. This suggests that MiDAC has an essential and unique function that cannot be compensated by other HDAC complexes. Consistent with this, the cryoEM structure of MiDAC reveals a unique and distinctive mode of assembly. Four copies of HDAC1 are positioned at the periphery with outward-facing active sites suggesting that the complex may target multiple nucleosomes implying a processive deacetylase function.
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Affiliation(s)
- Robert E Turnbull
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Almutasem Saleh
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Emma Kelsall
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- AstraZeneca, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Kyle L Morris
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- MRC London Institute of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - T J Ragan
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Christos G Savva
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Aditya Chandru
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Christopher J Millard
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Olga V Makarova
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Corinne J Smith
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Alan M Roseman
- Division of Molecular and Cellular Function, University of Manchester, Manchester, M13 9PL, UK
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Shaun M Cowley
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK.
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK.
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12
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Wang ZA, Millard CJ, Lin CL, Gurnett JE, Wu M, Lee K, Fairall L, Schwabe JWR, Cole PA. Diverse nucleosome Site-Selectivity among histone deacetylase complexes. eLife 2020; 9:e57663. [PMID: 32501215 PMCID: PMC7316510 DOI: 10.7554/elife.57663] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Histone acetylation regulates chromatin structure and gene expression and is removed by histone deacetylases (HDACs). HDACs are commonly found in various protein complexes to confer distinct cellular functions, but how the multi-subunit complexes influence deacetylase activities and site-selectivities in chromatin is poorly understood. Previously we reported the results of studies on the HDAC1 containing CoREST complex and acetylated nucleosome substrates which revealed a notable preference for deacetylation of histone H3 acetyl-Lys9 vs. acetyl-Lys14 (Wu et al, 2018). Here we analyze the enzymatic properties of five class I HDAC complexes: CoREST, NuRD, Sin3B, MiDAC and SMRT with site-specific acetylated nucleosome substrates. Our results demonstrate that these HDAC complexes show a wide variety of deacetylase rates in a site-selective manner. A Gly13 in the histone H3 tail is responsible for a sharp reduction in deacetylase activity of the CoREST complex for H3K14ac. These studies provide a framework for connecting enzymatic and biological functions of specific HDAC complexes.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Christopher J Millard
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Chia-Liang Lin
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Jennifer E Gurnett
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - John WR Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
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13
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Freeman SL, Kwon H, Portolano N, Parkin G, Venkatraman Girija U, Basran J, Fielding AJ, Fairall L, Svistunenko DA, Moody PCE, Schwabe JWR, Kyriacou CP, Raven EL. Heme binding to human CLOCK affects interactions with the E-box. Proc Natl Acad Sci U S A 2019; 116:19911-19916. [PMID: 31527239 PMCID: PMC6778266 DOI: 10.1073/pnas.1905216116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 12/16/2022] Open
Abstract
The circadian clock is an endogenous time-keeping system that is ubiquitous in animals and plants as well as some bacteria. In mammals, the clock regulates the sleep-wake cycle via 2 basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain proteins-CLOCK and BMAL1. There is emerging evidence to suggest that heme affects circadian control, through binding of heme to various circadian proteins, but the mechanisms of regulation are largely unknown. In this work we examine the interaction of heme with human CLOCK (hCLOCK). We present a crystal structure for the PAS-A domain of hCLOCK, and we examine heme binding to the PAS-A and PAS-B domains. UV-visible and electron paramagnetic resonance spectroscopies are consistent with a bis-histidine ligated heme species in solution in the oxidized (ferric) PAS-A protein, and by mutagenesis we identify His144 as a ligand to the heme. There is evidence for flexibility in the heme pocket, which may give rise to an additional Cys axial ligand at 20K (His/Cys coordination). Using DNA binding assays, we demonstrate that heme disrupts binding of CLOCK to its E-box DNA target. Evidence is presented for a conformationally mobile protein framework, which is linked to changes in heme ligation and which has the capacity to affect binding to the E-box. Within the hCLOCK structural framework, this would provide a mechanism for heme-dependent transcriptional regulation.
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Affiliation(s)
- Samuel L Freeman
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom
| | - Hanna Kwon
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom
| | - Nicola Portolano
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Gary Parkin
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Umakhanth Venkatraman Girija
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Jaswir Basran
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Alistair J Fielding
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, United Kingdom
| | - Peter C E Moody
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Charalambos P Kyriacou
- Department of Genetics and Genome Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Emma L Raven
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom;
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14
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Sandhu J, Li S, Fairall L, Pfisterer SG, Gurnett JE, Xiao X, Weston TA, Vashi D, Ferrari A, Orozco JL, Hartman CL, Strugatsky D, Lee SD, He C, Hong C, Jiang H, Bentolila LA, Gatta AT, Levine TP, Ferng A, Lee R, Ford DA, Young SG, Ikonen E, Schwabe JWR, Tontonoz P. Aster Proteins Facilitate Nonvesicular Plasma Membrane to ER Cholesterol Transport in Mammalian Cells. Cell 2018; 175:514-529.e20. [PMID: 30220461 DOI: 10.1016/j.cell.2018.08.033] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [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: 02/06/2018] [Revised: 06/08/2018] [Accepted: 08/15/2018] [Indexed: 11/28/2022]
Abstract
The mechanisms underlying sterol transport in mammalian cells are poorly understood. In particular, how cholesterol internalized from HDL is made available to the cell for storage or modification is unknown. Here, we describe three ER-resident proteins (Aster-A, -B, -C) that bind cholesterol and facilitate its removal from the plasma membrane. The crystal structure of the central domain of Aster-A broadly resembles the sterol-binding fold of mammalian StARD proteins, but sequence differences in the Aster pocket result in a distinct mode of ligand binding. The Aster N-terminal GRAM domain binds phosphatidylserine and mediates Aster recruitment to plasma membrane-ER contact sites in response to cholesterol accumulation in the plasma membrane. Mice lacking Aster-B are deficient in adrenal cholesterol ester storage and steroidogenesis because of an inability to transport cholesterol from SR-BI to the ER. These findings identify a nonvesicular pathway for plasma membrane to ER sterol trafficking in mammals.
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Affiliation(s)
- Jaspreet Sandhu
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shiqian Li
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland; Minerva Foundation Institute for Medical Research, Helsinki 00290, Finland
| | - Louise Fairall
- Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Simon G Pfisterer
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland; Minerva Foundation Institute for Medical Research, Helsinki 00290, Finland
| | - Jennifer E Gurnett
- Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Xu Xiao
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Thomas A Weston
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dipti Vashi
- Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Alessandra Ferrari
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jose L Orozco
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Celine L Hartman
- Edward A. Doisy Department of Biochemistry and Molecular Biology, and Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - David Strugatsky
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen D Lee
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cuiwen He
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cynthia Hong
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Haibo Jiang
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - Laurent A Bentolila
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Alberto T Gatta
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Tim P Levine
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Annie Ferng
- Ionis Pharmaceuticals, Carlsbad, CA 92008, USA
| | - Richard Lee
- Ionis Pharmaceuticals, Carlsbad, CA 92008, USA
| | - David A Ford
- Edward A. Doisy Department of Biochemistry and Molecular Biology, and Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Stephen G Young
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elina Ikonen
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland; Minerva Foundation Institute for Medical Research, Helsinki 00290, Finland
| | - John W R Schwabe
- Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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15
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Agostini M, Schoenmakers E, Beig J, Fairall L, Szatmari I, Rajanayagam O, Muskett FW, Adams C, Marais AD, O'Rahilly S, Semple RK, Nagy L, Majithia AR, Schwabe JWR, Blom DJ, Murphy R, Chatterjee K, Savage DB. A Pharmacogenetic Approach to the Treatment of Patients With PPARG Mutations. Diabetes 2018; 67:1086-1092. [PMID: 29622583 PMCID: PMC5967605 DOI: 10.2337/db17-1236] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/27/2018] [Indexed: 01/09/2023]
Abstract
Loss-of-function mutations in PPARG cause familial partial lipodystrophy type 3 (FPLD3) and severe metabolic disease in many patients. Missense mutations in PPARG are present in ∼1 in 500 people. Although mutations are often binarily classified as benign or deleterious, prospective functional classification of all missense PPARG variants suggests that their impact is graded. Furthermore, in testing novel mutations with both prototypic endogenous (e.g., prostaglandin J2 [PGJ2]) and synthetic ligands (thiazolidinediones, tyrosine agonists), we observed that synthetic agonists selectively rescue function of some peroxisome proliferator-activated receptor-γ (PPARγ) mutants. We report on patients with FPLD3 who harbor two such PPARγ mutations (R308P and A261E). Both PPARγ mutants exhibit negligible constitutive or PGJ2-induced transcriptional activity but respond readily to synthetic agonists in vitro, with structural modeling providing a basis for such differential ligand-dependent responsiveness. Concordant with this finding, dramatic clinical improvement was seen after pioglitazone treatment of a patient with R308P mutant PPARγ. A patient with A261E mutant PPARγ also responded beneficially to rosiglitazone, although cardiomyopathy precluded prolonged thiazolidinedione use. These observations indicate that detailed structural and functional classification can be used to inform therapeutic decisions in patients with PPARG mutations.
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Affiliation(s)
- Maura Agostini
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, U.K
| | - Erik Schoenmakers
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K
| | - Junaid Beig
- Greenlane Diabetes Centre, Auckland Hospital, Auckland, New Zealand
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, U.K
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Odelia Rajanayagam
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, U.K
| | - Frederick W Muskett
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, U.K
| | - Claire Adams
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, U.K
| | - A David Marais
- Division of Chemical Pathology, Department of Pathology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | - Stephen O'Rahilly
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, U.K
| | - Robert K Semple
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, U.K
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Amit R Majithia
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, U.K.
| | - Dirk J Blom
- Department of Medicine, University of Cape Town Health Science Faculty, Cape Town, South Africa
| | - Rinki Murphy
- Greenlane Diabetes Centre, Auckland Hospital, Auckland, New Zealand
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Krishna Chatterjee
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K.
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, U.K
| | - David B Savage
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, U.K.
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, U.K
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16
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Lin LY, Evans SE, Fairall L, Schwabe JWR, Wagner SD, Muskett FW. Backbone resonance assignment of the BCL6-BTB/POZ domain. Biomol NMR Assign 2018; 12:47-50. [PMID: 28929458 PMCID: PMC5869878 DOI: 10.1007/s12104-017-9778-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
BCL6 is a transcriptional repressor. Two domains of the protein, the N-terminal BTB-POZ domain and the RD2 domain are responsible for recruitment of co-repressor molecules and histone deacetylases. The BTB-POZ domain is found in a large and diverse range of proteins that play important roles in development, homeostasis and neoplasia. Crystal structures of several BTB-POZ domains, including BCL6 have been determined. The BTB-POZ domain of BCL6 not only mediates dimerisation but is also responsible for recruitment of co-repressors such as SMRT, NCOR and BCOR. Interestingly both SMRT and BCOR bind to the same site within the BCL6 BTB-POZ domain despite having very different primary sequences. Since both peptides and small molecules have been shown to bind to the co-repressor binding site it would suggest that the BTB_POZ domain is a suitable target for drug discovery. Here we report near complete backbone 15N, 13C and 1H assignments for the BTB-POZ domain of BCL6 to assist in the analysis of binding modes for small molecules.
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Affiliation(s)
- Li-Ying Lin
- Leicester Drug Discovery and Diagnostics Centre, Maurice Shock Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - S E Evans
- Leicester Drug Discovery and Diagnostics Centre, Maurice Shock Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - L Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK
| | - Simon D Wagner
- Department of Cancer Studies and Ernest and Helen Scott Haematological Research Institute, University of Leicester, Lancaster Road, Leicester, LE1 7HB, UK.
| | - Frederick W Muskett
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK.
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17
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Kalin JH, Wu M, Gomez AV, Song Y, Das J, Hayward D, Adejola N, Wu M, Panova I, Chung HJ, Kim E, Roberts HJ, Roberts JM, Prusevich P, Jeliazkov JR, Roy Burman SS, Fairall L, Milano C, Eroglu A, Proby CM, Dinkova-Kostova AT, Hancock WW, Gray JJ, Bradner JE, Valente S, Mai A, Anders NM, Rudek MA, Hu Y, Ryu B, Schwabe JWR, Mattevi A, Alani RM, Cole PA. Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors. Nat Commun 2018; 9:53. [PMID: 29302039 PMCID: PMC5754352 DOI: 10.1038/s41467-017-02242-4] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/14/2017] [Indexed: 01/08/2023] Open
Abstract
Here we report corin, a synthetic hybrid agent derived from the class I HDAC inhibitor (entinostat) and an LSD1 inhibitor (tranylcypromine analog). Enzymologic analysis reveals that corin potently targets the CoREST complex and shows more sustained inhibition of CoREST complex HDAC activity compared with entinostat. Cell-based experiments demonstrate that corin exhibits a superior anti-proliferative profile against several melanoma lines and cutaneous squamous cell carcinoma lines compared to its parent monofunctional inhibitors but is less toxic to melanocytes and keratinocytes. CoREST knockdown, gene expression, and ChIP studies suggest that corin's favorable pharmacologic effects may rely on an intact CoREST complex. Corin was also effective in slowing tumor growth in a melanoma mouse xenograft model. These studies highlight the promise of a new class of two-pronged hybrid agents that may show preferential targeting of particular epigenetic regulatory complexes and offer unique therapeutic opportunities.
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Affiliation(s)
- Jay H Kalin
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Muzhou Wu
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrea V Gomez
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Yun Song
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Jayanta Das
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dawn Hayward
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nkosi Adejola
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mingxuan Wu
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Izabela Panova
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hye Jin Chung
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Edward Kim
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Holly J Roberts
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Polina Prusevich
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Louise Fairall
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Charles Milano
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Abdulkerim Eroglu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Charlotte M Proby
- Division of Cancer Research, Jacqui Wood Cancer Centre, University of Dundee, Dundee, DD1 9SY, UK
| | - Albena T Dinkova-Kostova
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Division of Cancer Research, Jacqui Wood Cancer Centre, University of Dundee, Dundee, DD1 9SY, UK
| | - Wayne W Hancock
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sergio Valente
- Pasteur Institute, Cenci-Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Antonello Mai
- Pasteur Institute, Cenci-Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Nicole M Anders
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michelle A Rudek
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yong Hu
- Department of Oncology, BioDuro LLC, Shanghai, 200131, China
| | - Byungwoo Ryu
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - John W R Schwabe
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy.
| | - Rhoda M Alani
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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18
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Nigi I, Fairall L, Schwabe JWR. Expression and Purification of Protein Complexes Suitable for Structural Studies Using Mammalian HEK 293F Cells. ACTA ACUST UNITED AC 2017; 90:5.28.1-5.28.16. [PMID: 29091272 DOI: 10.1002/cpps.44] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Prokaryotic expression systems have been widely used to express proteins for structural studies. Such expression systems have the advantage of being economical, straightforward and fast. However, for many eukaryotic proteins and particularly protein complexes, bacterial expression systems do not produce significant yields of soluble protein. This may result from failure to efficiently transcribe/translate the required protein or may result from the formation of insoluble aggregates known as inclusion bodies. Mammalian expression systems can often produce natively folded proteins, sometimes with native post-translational modifications. However, such expression systems are underutilized due to the perception that they are costly, technically challenging and result in limited protein yields. In fact, HEK 293F cells are straightforward to grow, transfect with high efficiency and often produce significant yields of recombinant proteins. In this unit, we describe a method to express and purify milligram quantities of a human protein complex from HEK 293F cells grown in suspension transiently transfected with the appropriate plasmids. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Irene Nigi
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
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19
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Moran C, Agostini M, McGowan A, Schoenmakers E, Fairall L, Lyons G, Rajanayagam O, Watson L, Offiah A, Barton J, Price S, Schwabe J, Chatterjee K. Contrasting Phenotypes in Resistance to Thyroid Hormone Alpha Correlate with Divergent Properties of Thyroid Hormone Receptor α1 Mutant Proteins. Thyroid 2017; 27:973-982. [PMID: 28471274 PMCID: PMC5561448 DOI: 10.1089/thy.2017.0157] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Resistance to thyroid hormone alpha (RTHα), a disorder characterized by tissue-selective hypothyroidism and near-normal thyroid function tests due to thyroid receptor alpha gene mutations, is rare but probably under-recognized. This study sought to correlate the clinical characteristics and response to thyroxine (T4) therapy in two adolescent RTHα patients with the properties of the THRA mutation, affecting both TRα1 and TRα2 proteins, they harbored. METHODS Clinical, auxological, biochemical, and physiological parameters were assessed in each patient at baseline and after T4 therapy. RESULTS Heterozygous THRA mutations occurring de novo were identified in a 17-year-old male (patient P1; c.788C>T, p.A263V mutation) investigated for mild pubertal delay and in a 15-year-old male (patient P2; c.821T>C, p.L274P mutation) with short stature (0.4th centile), skeletal dysplasia, dysmorphic facies, and global developmental delay. Both individuals exhibited macrocephaly, delayed dentition, and constipation, together with a subnormal T4/triiodothyronine (T3) ratio, low reverse T3 levels, and mild anemia. When studied in vitro, A263V mutant TRα1 was transcriptionally impaired and inhibited the function of its wild-type counterpart at low (0.01-10 nM) T3 levels, with higher T3 concentrations (100 nM-1 μM) reversing dysfunction and such dominant negative inhibition. In contrast, L274P mutant TRα1 was transcriptionally inert, exerting significant dominant negative activity, only overcome with 10 μM of T3. Mirroring this, normal expression of KLF9, a TH-responsive target gene, was achieved in A263V mutation-containing peripheral blood mononuclear cells following 1 μM of T3 exposure, but with markedly reduced expression levels in L274P mutation-containing peripheral blood mononuclear cells, even with 10 μM of T3. Following T4 therapy, growth, body composition, dyspraxia, and constipation improved in P1, whereas growth retardation and constipation in P2 were unchanged. Neither A263V nor L274P mutations exhibited gain or loss of function in the TRα2 background, and no additional phenotype attributable to this was discerned. CONCLUSIONS This study correlates a milder clinical phenotype and favorable response to T4 therapy in a RTHα patient (P1) with heterozygosity for mutant TRα1 exhibiting partial, T3-reversible, loss of function. In contrast, a more severe clinical phenotype refractory to hormone therapy was evident in another case (P2) associated with severe, virtually irreversible, dysfunction of mutant TRα1.
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Affiliation(s)
- Carla Moran
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Maura Agostini
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Anne McGowan
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Erik Schoenmakers
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Greta Lyons
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Odelia Rajanayagam
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Laura Watson
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Amaka Offiah
- Academic Unit of Child Health, University of Sheffield, Sheffield, United Kingdom
| | - John Barton
- Department of Paediatric Endocrinology and Diabetes, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Susan Price
- Department of Clinical Genetics, Northampton General Hospital, Northampton, United Kingdom
| | - John Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Krishna Chatterjee
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
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20
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Abstract
Following the first isolation of nuclear receptor (NR) genes, genetic disorders caused by NR gene mutations were initially discovered by a candidate gene approach based on their known roles in endocrine pathways and physiologic processes. Subsequently, the identification of disorders has been informed by phenotypes associated with gene disruption in animal models or by genetic linkage studies. More recently, whole exome sequencing has associated pathogenic genetic variants with unexpected, often multisystem, human phenotypes. To date, defects in 20 of 48 human NR genes have been associated with human disorders, with different mutations mediating phenotypes of varying severity or several distinct conditions being associated with different changes in the same gene. Studies of individuals with deleterious genetic variants can elucidate novel roles of human NRs, validating them as targets for drug development or providing new insights into structure-function relationships. Importantly, human genetic discoveries enable definitive disease diagnosis and can provide opportunities to therapeutically manage affected individuals. Here we review germline changes in human NR genes associated with "monogenic" conditions, including a discussion of the structural basis of mutations that cause distinctive changes in NR function and the molecular mechanisms mediating pathogenesis.
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21
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Heinen CA, Losekoot M, Sun Y, Watson PJ, Fairall L, Joustra SD, Zwaveling-Soonawala N, Oostdijk W, van den Akker ELT, Alders M, Santen GWE, van Rijn RR, Dreschler WA, Surovtseva OV, Biermasz NR, Hennekam RC, Wit JM, Schwabe JWR, Boelen A, Fliers E, van Trotsenburg ASP. Mutations in TBL1X Are Associated With Central Hypothyroidism. J Clin Endocrinol Metab 2016; 101:4564-4573. [PMID: 27603907 PMCID: PMC5155687 DOI: 10.1210/jc.2016-2531] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
CONTEXT Isolated congenital central hypothyroidism (CeH) can result from mutations in TRHR, TSHB, and IGSF1, but its etiology often remains unexplained. We identified a missense mutation in the transducin β-like protein 1, X-linked (TBL1X) gene in three relatives diagnosed with isolated CeH. TBL1X is part of the thyroid hormone receptor-corepressor complex. OBJECTIVE The objectives of the study were the identification of TBL1X mutations in patients with unexplained isolated CeH, Sanger sequencing of relatives of affected individuals, and clinical and biochemical characterization; in vitro investigation of functional consequences of mutations; and mRNA expression in, and immunostaining of, human hypothalami and pituitary glands. DESIGN This was an observational study. SETTING The study was conducted at university medical centers. PATIENTS Nineteen individuals with and seven without a mutation participated in the study. MAIN OUTCOME MEASURES Outcome measures included sequencing results, clinical and biochemical characteristics of mutation carriers, and results of in vitro functional and expression studies. RESULTS Sanger sequencing yielded five additional mutations. All patients (n = 8; six males) were previously diagnosed with CeH (free T4 [FT4] concentration below the reference interval, normal thyrotropin). Eleven relatives (two males) also carried mutations. One female had CeH, whereas 10 others had low-normal FT4 concentrations. As a group, adult mutation carriers had 20%-25% lower FT4 concentrations than controls. Twelve of 19 evaluated carriers had hearing loss. Mutations are located in the highly conserved WD40-repeat domain of the protein, influencing its expression and thermal stability. TBL1X mRNA and protein are expressed in the human hypothalamus and pituitary. CONCLUSIONS TBL1X mutations are associated with CeH and hearing loss. FT4 concentrations in mutation carriers vary from low-normal to values compatible with CeH.
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Affiliation(s)
- Charlotte A Heinen
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Monique Losekoot
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Yu Sun
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Peter J Watson
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Louise Fairall
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Sjoerd D Joustra
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Nitash Zwaveling-Soonawala
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Wilma Oostdijk
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Erica L T van den Akker
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Mariëlle Alders
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Gijs W E Santen
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Rick R van Rijn
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Wouter A Dreschler
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Olga V Surovtseva
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Nienke R Biermasz
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Raoul C Hennekam
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Jan M Wit
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - John W R Schwabe
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Anita Boelen
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - Eric Fliers
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
| | - A S Paul van Trotsenburg
- Department of Endocrinology and Metabolism (C.A.H., O.V.S., A.B., E.F.), Clinical Genetics (M.A.), and Clinical and Experimental Audiology (W.A.D.), Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Paediatric Endocrinology (C.A.H., N.Z.-S., A.S.P.v.T.), Radiology (R.R.v.R.), and Paediatrics (R.C.H.), Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands; Departments of Clinical Genetics (M.L., Y.S., G.W.E.S.), Paediatrics (S.D.J., W.O., J.M.W.), and Endocrinology and Metabolism (S.D.J., N.R.B.), Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Henry Wellcome Laboratories of Structural Biology (P.J.W., L.F., J.W.R.S.), Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and Department of Paediatric Endocrinology (E.L.T.v.d.A.), Erasmus Medical Centre, 3000 CB Rotterdam, The Netherlands
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22
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Hughes MA, Powley IR, Jukes-Jones R, Horn S, Feoktistova M, Fairall L, Schwabe JWR, Leverkus M, Cain K, MacFarlane M. Co-operative and Hierarchical Binding of c-FLIP and Caspase-8: A Unified Model Defines How c-FLIP Isoforms Differentially Control Cell Fate. Mol Cell 2016; 61:834-49. [PMID: 26990987 PMCID: PMC4819448 DOI: 10.1016/j.molcel.2016.02.023] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/22/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
The death-inducing signaling complex (DISC) initiates death receptor-induced apoptosis. DISC assembly and activation are controlled by c-FLIP isoforms, which function as pro-apoptotic (c-FLIPL only) or anti-apoptotic (c-FLIPL/c-FLIPS) regulators of procaspase-8 activation. Current models assume that c-FLIP directly competes with procaspase-8 for recruitment to FADD. Using a functional reconstituted DISC, structure-guided mutagenesis, and quantitative LC-MS/MS, we show that c-FLIPL/S binding to the DISC is instead a co-operative procaspase-8-dependent process. FADD initially recruits procaspase-8, which in turn recruits and heterodimerizes with c-FLIPL/S via a hierarchical binding mechanism. Procaspase-8 activation is regulated by the ratio of unbound c-FLIPL/S to procaspase-8, which determines composition of the procaspase-8:c-FLIPL/S heterodimer. Thus, procaspase-8:c-FLIPL exhibits localized enzymatic activity and is preferentially an activator, promoting DED-mediated procaspase-8 oligomer assembly, whereas procaspase-8:c-FLIPS lacks activity and potently blocks procaspase-8 activation. This co-operative hierarchical binding model explains the dual role of c-FLIPL and crucially defines how c-FLIP isoforms differentially control cell fate.
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Affiliation(s)
- Michelle A Hughes
- MRC Toxicology Unit, Hodgkin Building, P.O. Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Ian R Powley
- MRC Toxicology Unit, Hodgkin Building, P.O. Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Rebekah Jukes-Jones
- MRC Toxicology Unit, Hodgkin Building, P.O. Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Sebastian Horn
- Department of Dermatology, Venereology and Allergology, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Maria Feoktistova
- Department of Dermatology and Allergology, Medical Faculty of the RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - John W R Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Martin Leverkus
- Department of Dermatology and Allergology, Medical Faculty of the RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Kelvin Cain
- MRC Toxicology Unit, Hodgkin Building, P.O. Box 138, Lancaster Road, Leicester LE1 9HN, UK.
| | - Marion MacFarlane
- MRC Toxicology Unit, Hodgkin Building, P.O. Box 138, Lancaster Road, Leicester LE1 9HN, UK.
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23
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Millard CJ, Varma N, Saleh A, Morris K, Watson PJ, Bottrill AR, Fairall L, Smith CJ, Schwabe JWR. The structure of the core NuRD repression complex provides insights into its interaction with chromatin. eLife 2016; 5:e13941. [PMID: 27098840 PMCID: PMC4841774 DOI: 10.7554/elife.13941] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/24/2016] [Indexed: 12/14/2022] Open
Abstract
The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.
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Affiliation(s)
- Christopher J Millard
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Niranjan Varma
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Almutasem Saleh
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Kyle Morris
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Peter J Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Andrew R Bottrill
- Protein and Nucleic Acid Chemistry Laboratory, Core Biotechnology Services, University of Leicester, Leicester, United Kingdom
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Corinne J Smith
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - John WR Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
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24
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Hudson GM, Watson PJ, Fairall L, Jamieson AG, Schwabe JWR. Insights into the Recruitment of Class IIa Histone Deacetylases (HDACs) to the SMRT/NCoR Transcriptional Repression Complex. J Biol Chem 2015; 290:18237-18244. [PMID: 26055705 PMCID: PMC4505066 DOI: 10.1074/jbc.m115.661058] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/27/2015] [Indexed: 11/06/2022] Open
Abstract
Class IIa histone deacetylases repress transcription of target genes. However, their mechanism of action is poorly understood because they exhibit very low levels of deacetylase activity. The class IIa HDACs are associated with the SMRT/NCoR repression complexes and this may, at least in part, account for their repressive activity. However, the molecular mechanism of recruitment to co-repressor proteins has yet to be established. Here we show that a repeated peptide motif present in both SMRT and NCoR is sufficient to mediate specific interaction, with micromolar affinity, with all the class IIa HDACs (HDACs 4, 5, 7, and 9). Mutations in the consensus motif abrogate binding. Mutational analysis of HDAC4 suggests that the peptide interacts in the vicinity of the active site of the enzyme and requires the "closed" conformation of the zinc-binding loop on the surface of the enzyme. Together these findings represent the first insights into the molecular mechanism of recruitment of class IIa HDACs to the SMRT/NCoR repression complexes.
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Affiliation(s)
- Gregg M Hudson
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester LE1 9HN
| | - Peter J Watson
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester LE1 9HN
| | - Louise Fairall
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester LE1 9HN
| | - Andrew G Jamieson
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - John W R Schwabe
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester LE1 9HN.
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25
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Itoh T, Fairall L, Muskett FW, Milano CP, Watson PJ, Arnaudo N, Saleh A, Millard CJ, El-Mezgueldi M, Martino F, Schwabe JWR. Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting. Nucleic Acids Res 2015; 43:2033-44. [PMID: 25653165 PMCID: PMC4344507 DOI: 10.1093/nar/gkv068] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [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] [Indexed: 01/24/2023] Open
Abstract
Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex.
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Affiliation(s)
- Toshimasa Itoh
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Frederick W Muskett
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Charles P Milano
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Peter J Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Nadia Arnaudo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Almutasem Saleh
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Christopher J Millard
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Mohammed El-Mezgueldi
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Fabrizio Martino
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - John W R Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
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26
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Nettleship JE, Watson PJ, Rahman-Huq N, Fairall L, Posner MG, Upadhyay A, Reddivari Y, Chamberlain JMG, Kolstoe SE, Bagby S, Schwabe JWR, Owens RJ. Transient expression in HEK 293 cells: an alternative to E. coli for the production of secreted and intracellular mammalian proteins. Methods Mol Biol 2015; 1258:209-22. [PMID: 25447866 DOI: 10.1007/978-1-4939-2205-5_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Transient transfection of human embryonic kidney cells (HEK 293) enables the rapid and affordable lab-scale production of recombinant proteins. In this chapter protocols for the expression and purification of both secreted and intracellular proteins using transient expression in HEK 293 cells are described.
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Affiliation(s)
- Joanne E Nettleship
- OPPF-UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell Oxford, Didcot, OX11 0FA, UK,
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27
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Abstract
Gene expression is controlled through the recruitment of large coregulator complexes to specific gene loci to regulate chromatin structure by modifying epigenetic marks on DNA and histones. Metastasis-associated protein 1 (MTA1) is an essential component of the nucleosome remodelling and deacetylase (NuRD) complex that acts as a scaffold protein to assemble enzymatic activity and nucleosome targeting proteins. MTA1 consists of four characterised domains, a number of interaction motifs, and regions that are predicted to be intrinsically disordered. The ELM2-SANT domain is one of the best-characterised regions of MTA1, which recruits histone deacetylase 1 (HDAC1) and activates the enzyme in the presence of inositol phosphate. MTA1 is highly upregulated in several types of aggressive tumours and is therefore a possible target for cancer therapy. In this review, we summarise the structure and function of the four domains of MTA1 and discuss the possible functions of less well-characterised regions of the protein.
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Affiliation(s)
- Christopher J. Millard
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN UK
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN UK
| | - John W. R. Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN UK
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28
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Portolano N, Watson PJ, Fairall L, Millard CJ, Milano CP, Song Y, Cowley SM, Schwabe JWR. Recombinant protein expression for structural biology in HEK 293F suspension cells: a novel and accessible approach. J Vis Exp 2014:e51897. [PMID: 25349981 PMCID: PMC4420617 DOI: 10.3791/51897] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The expression and purification of large amounts of recombinant protein complexes is an essential requirement for structural biology studies. For over two decades, prokaryotic expression systems such as E. coli have dominated the scientific literature over costly and less efficient eukaryotic cell lines. Despite the clear advantage in terms of yields and costs of expressing recombinant proteins in bacteria, the absence of specific co-factors, chaperones and post-translational modifications may cause loss of function, mis-folding and can disrupt protein-protein interactions of certain eukaryotic multi-subunit complexes, surface receptors and secreted proteins. The use of mammalian cell expression systems can address these drawbacks since they provide a eukaryotic expression environment. However, low protein yields and high costs of such methods have until recently limited their use for structural biology. Here we describe a simple and accessible method for expressing and purifying milligram quantities of protein by performing transient transfections of suspension grown HEK (Human Embryonic Kidney) 293 F cells.
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Affiliation(s)
| | | | | | | | | | - Yun Song
- Department of Biochemistry, University of Leicester
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Evans SE, Goult BT, Fairall L, Jamieson AG, Ko Ferrigno P, Ford R, Schwabe JWR, Wagner SD. The ansamycin antibiotic, rifamycin SV, inhibits BCL6 transcriptional repression and forms a complex with the BCL6-BTB/POZ domain. PLoS One 2014; 9:e90889. [PMID: 24595451 PMCID: PMC3942486 DOI: 10.1371/journal.pone.0090889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/05/2014] [Indexed: 11/22/2022] Open
Abstract
BCL6 is a transcriptional repressor that is over-expressed due to chromosomal translocations, or other abnormalities, in ∼40% of diffuse large B-cell lymphoma. BCL6 interacts with co-repressor, SMRT, and this is essential for its role in lymphomas. Peptide or small molecule inhibitors, which prevent the association of SMRT with BCL6, inhibit transcriptional repression and cause apoptosis of lymphoma cells in vitro and in vivo. In order to discover compounds, which have the potential to be developed into BCL6 inhibitors, we screened a natural product library. The ansamycin antibiotic, rifamycin SV, inhibited BCL6 transcriptional repression and NMR spectroscopy confirmed a direct interaction between rifamycin SV and BCL6. To further determine the characteristics of compounds binding to BCL6-POZ we analyzed four other members of this family and showed that rifabutin, bound most strongly. An X-ray crystal structure of the rifabutin-BCL6 complex revealed that rifabutin occupies a partly non-polar pocket making interactions with tyrosine58, asparagine21 and arginine24 of the BCL6-POZ domain. Importantly these residues are also important for the interaction of BLC6 with SMRT. This work demonstrates a unique approach to developing a structure activity relationship for a compound that will form the basis of a therapeutically useful BCL6 inhibitor.
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Affiliation(s)
- Sian E. Evans
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
- Department of Cancer Studies and Molecular Medicine and MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Benjamin T. Goult
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Louise Fairall
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Andrew G. Jamieson
- Department of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Paul Ko Ferrigno
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Robert Ford
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - John W. R. Schwabe
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Simon D. Wagner
- Department of Cancer Studies and Molecular Medicine and MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Abstract
Nuclear receptors are transcription factors that regulate gene expression through the ligand-controlled recruitment of a diverse group of proteins known as coregulators. Most nuclear receptor coregulators function in large multi-protein complexes that modify chromatin and thereby regulate the transcription of target genes. Structural and functional studies are beginning to reveal how these complexes are assembled bringing together multiple functionalities that mediate: recruitment to specific genomic loci through interaction with transcription factors; recruitment of enzymatic activities that either modify or remodel chromatin and targeting the complexes to their chromatin substrate. These activities are regulated by post-translational modifications, alternative splicing and small signalling molecules. This review focuses on our current understanding of coregulator complexes and aims to highlight the common principles that are beginning to emerge.
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Affiliation(s)
- Christopher J. Millard
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN. UK
| | - Peter J. Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN. UK
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN. UK
| | - John W.R. Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN. UK
- Correspondence to:
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Millard C, Watson P, Celardo I, Gordiyenko Y, Cowley S, Robinson C, Fairall L, Schwabe J. Class I HDACs share a common mechanism of regulation by inositol phosphates. Mol Cell 2013; 51:57-67. [PMID: 23791785 PMCID: PMC3710971 DOI: 10.1016/j.molcel.2013.05.020] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/23/2013] [Accepted: 05/16/2013] [Indexed: 01/06/2023]
Abstract
Class I histone deacetylases (HDAC1, HDAC2, and HDAC3) are recruited by cognate corepressor proteins into specific transcriptional repression complexes that target HDAC activity to chromatin resulting in chromatin condensation and transcriptional silencing. We previously reported the structure of HDAC3 in complex with the SMRT corepressor. This structure revealed the presence of inositol-tetraphosphate [Ins(1,4,5,6)P4] at the interface of the two proteins. It was previously unclear whether the role of Ins(1,4,5,6)P4 is to act as a structural cofactor or a regulator of HDAC3 activity. Here we report the structure of HDAC1 in complex with MTA1 from the NuRD complex. The ELM2-SANT domains from MTA1 wrap completely around HDAC1 occupying both sides of the active site such that the adjacent BAH domain is ideally positioned to recruit nucleosomes to the active site of the enzyme. Functional assays of both the HDAC1 and HDAC3 complexes reveal that Ins(1,4,5,6)P4 is a bona fide conserved regulator of class I HDAC complexes.
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Affiliation(s)
- Christopher J. Millard
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Peter J. Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Ivana Celardo
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Yuliya Gordiyenko
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Shaun M. Cowley
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Carol V. Robinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - John W.R. Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
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Dickens LS, Boyd RS, Jukes-Jones R, Hughes MA, Robinson GL, Fairall L, Schwabe JWR, Cain K, Macfarlane M. A death effector domain chain DISC model reveals a crucial role for caspase-8 chain assembly in mediating apoptotic cell death. Mol Cell 2012; 47:291-305. [PMID: 22683266 PMCID: PMC3477315 DOI: 10.1016/j.molcel.2012.05.004] [Citation(s) in RCA: 245] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 03/24/2012] [Accepted: 05/04/2012] [Indexed: 11/17/2022]
Abstract
Formation of the death-inducing signaling complex (DISC) is a critical step in death receptor-mediated apoptosis, yet the mechanisms underlying assembly of this key multiprotein complex remain unclear. Using quantitative mass spectrometry, we have delineated the stoichiometry of the native TRAIL DISC. While current models suggest that core DISC components are present at a ratio of 1:1, our data indicate that FADD is substoichiometric relative to TRAIL-Rs or DED-only proteins; strikingly, there is up to 9-fold more caspase-8 than FADD in the DISC. Using structural modeling, we propose an alternative DISC model in which procaspase-8 molecules interact sequentially, via their DED domains, to form a caspase-activating chain. Mutating key interacting residues in procaspase-8 DED2 abrogates DED chain formation in cells and disrupts TRAIL/CD95 DISC-mediated procaspase-8 activation in a functional DISC reconstitution model. This provides direct experimental evidence for a DISC model in which DED chain assembly drives caspase-8 dimerization/activation, thereby triggering cell death.
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Affiliation(s)
- Laura S Dickens
- MRC Toxicology Unit, Hodgkin Building, P.O. Box 138, Lancaster Road, Leicester LE1 9HN, UK
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Abstract
Co-repressor proteins, such as SMRT and NCoR, mediate the repressive activity of unliganded nuclear receptors and other transcription factors. They appear to act as intrinsically disordered "hub proteins" that integrate the activities of a range of transcription factors with a number of histone modifying enzymes. Although these co-repressor proteins are challenging targets for structural studies due to their largely unstructured character, a number of structures have recently been determined of co-repressor interaction regions in complex with their interacting partners. These have yielded considerable insight into the mechanism of assembly of these complexes, the structural basis for the specificity of the interactions and also open opportunities for targeting these interactions therapeutically.
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Watson PJ, Fairall L, Santos GM, Schwabe JWR. Structure of HDAC3 bound to co-repressor and inositol tetraphosphate. Nature 2012; 481:335-40. [PMID: 22230954 PMCID: PMC3272448 DOI: 10.1038/nature10728] [Citation(s) in RCA: 356] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/23/2011] [Indexed: 01/08/2023]
Abstract
Histone deacetylase enzymes (HDACs) are emerging cancer drug targets. They regulate gene expression by removing acetyl groups from lysine residues in histone tails resulting in chromatin condensation. The enzymatic activity of most class I HDACs requires recruitment to corepressor complexes. We report the first structure of an HDAC:corepressor complex - HDAC3 with the deacetylase-activation-domain (DAD) from the SMRT corepressor. The structure reveals two remarkable features. First the SMRT-DAD undergoes a large structural rearrangement on forming the complex. Second there is an essential inositol tetraphosphate molecule, Ins(1,4,5,6)P4, acting as an ‘intermolecular glue’ between the two proteins. Assembly of the complex is clearly dependent on the Ins(1,4,5,6)P4, which may act as a regulator – potentially explaining why inositol phosphates and their kinases have been found to act as transcriptional regulators. This mechanism for the activation of HDAC3 appears to be conserved in class I HDACs from yeast to man and opens novel therapeutic opportunities.
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Affiliation(s)
- Peter J Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester LE1 9HN, UK
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Zhang L, Fairall L, Goult BT, Calkin AC, Hong C, Millard CJ, Tontonoz P, Schwabe JWR. The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor. Genes Dev 2011; 25:1262-74. [PMID: 21685362 DOI: 10.1101/gad.2056211] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We previously identified the E3 ubiquitin ligase IDOL as a sterol-dependent regulator of the LDL receptor (LDLR). The molecular pathway underlying IDOL action, however, remains to be determined. Here we report the identification and biochemical and structural characterization of an E2-E3 ubiquitin ligase complex for LDLR degradation. We identified the UBE2D family (UBE2D1-4) as E2 partners for IDOL that support both autoubiquitination and IDOL-dependent ubiquitination of the LDLR in a cell-free system. NMR chemical shift mapping and a 2.1 Å crystal structure of the IDOL RING domain-UBE2D1 complex revealed key interactions between the dimeric IDOL protein and the E2 enzyme. Analysis of the IDOL-UBE2D1 interface also defined the stereochemical basis for the selectivity of IDOL for UBE2Ds over other E2 ligases. Structure-based mutations that inhibit IDOL dimerization or IDOL-UBE2D interaction block IDOL-dependent LDLR ubiquitination and degradation. Furthermore, expression of a dominant-negative UBE2D enzyme inhibits the ability of IDOL to degrade the LDLR in cells. These results identify the IDOL-UBE2D complex as an important determinant of LDLR activity, and provide insight into molecular mechanisms underlying the regulation of cholesterol uptake.
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Affiliation(s)
- Li Zhang
- Howard Hughes Medical Institute, University of California at Los Angeles School of Medicine, USA
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Santos GM, Fairall L, Schwabe JW. Negative regulation by nuclear receptors: a plethora of mechanisms. Trends Endocrinol Metab 2011; 22:87-93. [PMID: 21196123 PMCID: PMC3053446 DOI: 10.1016/j.tem.2010.11.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/29/2010] [Accepted: 11/30/2010] [Indexed: 10/30/2022]
Abstract
Nuclear receptors are arguably the best understood transcriptional regulators. We know a great deal about the mechanisms through which they activate transcription in response to ligand binding and about the mechanisms through which they repress transcription in the absence of ligand. However, endocrine regulation often requires that ligand-bound receptors repress transcription of a subset of genes. An understanding of the mechanism for ligand-induced repression and how this differs from activation has proven elusive. A number of recent studies have directly or indirectly addressed this problem. Yet it seems the more evidence that accumulates, the more complex the mystery becomes.
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Affiliation(s)
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester, LE1 9HN, UK
| | - John W.R. Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester, LE1 9HN, UK
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Stein J, Lewin S, Fairall L, Mayers P, English R, Bheekie A, Bateman E, Zwarenstein M. Building capacity for antiretroviral delivery in South Africa: a qualitative evaluation of the PALSA PLUS nurse training programme. BMC Health Serv Res 2008; 8:240. [PMID: 19017394 PMCID: PMC2613903 DOI: 10.1186/1472-6963-8-240] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 11/18/2008] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND South Africa recently launched a national antiretroviral treatment programme. This has created an urgent need for nurse-training in antiretroviral treatment (ART) delivery. The PALSA PLUS programme provides guidelines and training for primary health care (PHC) nurses in the management of adult lung diseases and HIV/AIDS, including ART. A process evaluation was undertaken to document the training, explore perceptions regarding the value of the training, and compare the PALSA PLUS training approach (used at intervention sites) with the provincial training model. The evaluation was conducted alongside a randomized controlled trial measuring the effects of the PALSA PLUS nurse-training (Trial reference number ISRCTN24820584). METHODS Qualitative methods were utilized, including participant observation of training sessions, focus group discussions and interviews. Data were analyzed thematically. RESULTS Nurse uptake of PALSA PLUS training, with regard not only to ART specific components but also lung health, was high. The ongoing on-site training of all PHC nurses, as opposed to the once-off centralized training provided for ART nurses only at non-intervention clinics, enhanced nurses' experience of support for their work by allowing, not only for ongoing experiential learning, supervision and emotional support, but also for the ongoing managerial review of all those infrastructural and system-level changes required to facilitate health provider behaviour change and guideline implementation. The training of all PHC nurses in PALSA PLUS guideline use, as opposed to ART nurses only, was also perceived to better facilitate the integration of AIDS care within the clinic context. CONCLUSION PALSA PLUS training successfully engaged all PHC nurses in a comprehensive approach to a range of illnesses affecting both HIV positive and negative patients. PHC nurse-training for integrated systems-based interventions should be prioritized on the ART funding agenda. Training for individual provider behaviour change is nonetheless only one aspect of the ongoing system-wide interventions required to effect lasting improvements in patient care in the context of an over-burdened and under-resourced PHC system.
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Affiliation(s)
- J Stein
- University of Cape Town Lung Institute, George St, Mowbray 7700, Cape Town, South Africa
| | - S Lewin
- Department of Public Health and Policy, London School of Hygiene and Tropical Medicine, UK
- Health Systems Research Unit, Medical Research Council of South Africa, PO Box 19070, Tygerberg 7505, Cape Town, South Africa
| | - L Fairall
- University of Cape Town Lung Institute, George St, Mowbray 7700, Cape Town, South Africa
| | - P Mayers
- School of Health and Rehabilitation Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
- University of Cape Town Lung Institute, George St, Mowbray 7700, Cape Town, South Africa
| | - R English
- University of Cape Town Lung Institute, George St, Mowbray 7700, Cape Town, South Africa
| | - A Bheekie
- School of Pharmacy, University of the Western Cape, P/Bag X17, Bellville 7535, Cape Town, South Africa
| | - E Bateman
- Department of Medicine, University of Cape Town Lung Institute, George St, Mowbray, Cape Town, South Africa
| | - M Zwarenstein
- Centre for Health Services Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
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Bheekie A, Buskens I, Allen S, English R, Mayers P, Fairall L, Majara B, Bateman ED, Zwarenstein M, Bachmann M. The Practical Approach to Lung Health in South Africa (PALSA) intervention: respiratory guideline implementation for nurse trainers. Int Nurs Rev 2007; 53:261-8. [PMID: 17083414 DOI: 10.1111/j.1466-7657.2006.00520.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM This paper describes the design, facilitation and preliminary assessment of a 1-week cascade training programme for nurse trainers in preparation for implementation of the Practical Approach to Lung Health in South Africa (PALSA) intervention, tested within the context of a pragmatic cluster randomized controlled trial in the Free State province. PALSA combines evidence-based syndromic guidelines on the management of respiratory disease in adults with group educational outreach to nurse practitioners. BACKGROUND Evidence-based strategies to facilitate the implementation of primary care guidelines in low- to middle-income countries are limited. In South Africa, where the burden of respiratory diseases is high and growing, documentation and evaluation of training programmes in chronic conditions for health professionals is limited. METHOD The PALSA training design aimed for coherence between the content of the guidelines and the facilitation process that underpins adult learning. Content facilitation involved the use of key management principles (key messages) highlighted in nurse-centred guidelines manual and supplemented by illustrated material and reminders. Process facilitation entailed reflective and experiential learning, role-playing and non-judgemental feedback. DISCUSSION AND RESULTS Preliminary feedback showed an increase in trainers' self-awareness and self-confidence. Process and content facilitators agreed that the integrated training approach was balanced. All participants found that the training was motivational, minimally prescriptive, highly nurse-centred and offered personal growth. CONCLUSION In addition to tailored guideline recommendations, training programmes should consider individual learning styles and adult learning processes.
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Affiliation(s)
- A Bheekie
- School of Pharmacy, Discipline of Pharmacology, University of the Western Cape, Cape Town, South Africa
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Robinson PJJ, Fairall L, Huynh VAT, Rhodes D. EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure. Proc Natl Acad Sci U S A 2006; 103:6506-11. [PMID: 16617109 PMCID: PMC1436021 DOI: 10.1073/pnas.0601212103] [Citation(s) in RCA: 378] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin structure plays a fundamental role in the regulation of nuclear processes such as DNA transcription, replication, recombination, and repair. Despite considerable efforts during three decades, the structure of the 30-nm chromatin fiber remains controversial. To define fiber dimensions accurately, we have produced very long and regularly folded 30-nm fibers from in vitro reconstituted nucleosome arrays containing the linker histone and with increasing nucleosome repeat lengths (10 to 70 bp of linker DNA). EM measurements show that the dimensions of these fully folded fibers do not increase linearly with increasing linker length, a finding that is inconsistent with two-start helix models. Instead, we find that there are two distinct classes of fiber structure, both with unexpectedly high nucleosome density: arrays with 10 to 40 bp of linker DNA all produce fibers with a diameter of 33 nm and 11 nucleosomes per 11 nm, whereas arrays with 50 to 70 bp of linker DNA all produce 44-nm-wide fibers with 15 nucleosomes per 11 nm. Using the physical constraints imposed by these measurements, we have built a model in which tight nucleosome packing is achieved through the interdigitation of nucleosomes from adjacent helical gyres. Importantly, the model closely matches raw image projections of folded chromatin arrays recorded in the solution state by using electron cryo-microscopy.
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Affiliation(s)
- Philip J. J. Robinson
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - Louise Fairall
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - Van A. T. Huynh
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - Daniela Rhodes
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
- To whom correspondence should be addressed. E-mail:
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Bateman ED, Fairall L, Lombardi DM, English R. Budesonide/formoterol and formoterol provide similar rapid relief in patients with acute asthma showing refractoriness to salbutamol. Respir Res 2006; 7:13. [PMID: 16433920 PMCID: PMC1386666 DOI: 10.1186/1465-9921-7-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [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: 09/01/2005] [Accepted: 01/24/2006] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND To compare the efficacy and safety of budesonide/formoterol (Symbicort) with formoterol (Oxis) in the treatment of patients with acute asthma who showed evidence of refractoriness to short-acting beta2-agonist therapy. METHODS In a 3 hour, randomized, double-blind study, a total of 115 patients with acute asthma (mean FEV1 40% of predicted normal) and a refractory response to salbutamol (mean reversibility 2% of predicted normal after inhalation of 400 microg), were randomized to receive either budesonide/formoterol (320/9 microg, 2 inhalations at t = -5 minutes and 2 inhalations at 0 minutes [total dose 1280/36 microg]) or formoterol (9 microg, 2 inhalations at t = -5 minutes and 2 inhalations at 0 minutes [total dose 36 microg]). The primary efficacy variable was the average FEV1 from the first intake of study medication to the measurement at 90 minutes. Secondary endpoints included changes in FEV1 at other timepoints and change in respiratory rate at 180 minutes. Treatment success, treatment failure and patient assessment of the effectiveness of the study medication were also measured. RESULTS FEV1 increased after administration of the study medication in both treatment groups. No statistically significant difference between the treatment groups was apparent for the primary outcome variable, or for any of the other efficacy endpoints. There were no statistically significant between-group differences for treatment success, treatment failure or patient assessment of medication effectiveness. Both treatments were well tolerated. CONCLUSION Budesonide/formoterol and formoterol provided similarly rapid relief of acute bronchoconstriction in patients with asthma who showed evidence of refractoriness to a short-acting beta2-agonist.
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Affiliation(s)
- ED Bateman
- University of Cape Town Lung Institute, Cape Town, South Africa
| | - L Fairall
- University of Cape Town Lung Institute, Cape Town, South Africa
| | - DM Lombardi
- Hospital Municipal de Rehabilitación Respiratoria 'María Ferrer', Buenos Aires, Argentina
| | - R English
- University of Cape Town Lung Institute, Cape Town, South Africa
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Court R, Chapman L, Fairall L, Rhodes D. How the human telomeric proteins TRF1 and TRF2 recognize telomeric DNA: a view from high-resolution crystal structures. EMBO Rep 2005; 6:39-45. [PMID: 15608617 PMCID: PMC1299224 DOI: 10.1038/sj.embor.7400314] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Revised: 11/04/2004] [Accepted: 11/10/2004] [Indexed: 12/13/2022] Open
Abstract
Human telomeres consist of tandem arrays of TTAGGG sequence repeats that are specifically bound by two proteins, TRF1 and TRF2. They bind to DNA as preformed homodimers and have the same architecture in which the DNA-binding domains (Dbds) form independent structural units. Despite these similarities, TRF1 and TRF2 have different functions at telomeres. The X-ray crystal structures of both TRF1- and TRF2-Dbds in complex with telomeric DNA (2.0 and 1.8 angstroms resolution, respectively) show that they recognize the same TAGGGTT binding site by means of homeodomains, as does the yeast telomeric protein Rap1p. Two of the three G-C base pairs that characterize telomeric repeats are recognized specifically and an unusually large number of water molecules mediate protein-DNA interactions. The binding of the TRF2-Dbd to the DNA double helix shows no distortions that would account for the promotion of t-loops in which TRF2 has been implicated.
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Affiliation(s)
- Robert Court
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | - Lynda Chapman
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | - Louise Fairall
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | - Daniela Rhodes
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
- Tel: +44 1223 248011; Fax: +44 1223 213556; E-mail:
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Court R, Chapman L, Fairall L, Rhodes D. Erratum: How the human telomeric proteins TRF1 and TRF2 recognize telomeric DNA: a view from high‐resolution crystal structures. EMBO Rep 2005. [DOI: 10.1038/sj.embor.7400348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Abstract
Telomeres are protein-DNA complexes that cap chromosome ends and protect them from being recognized and processed as DNA breaks. Loss of capping function results in genetic instability and loss of cellular viability. The emerging view is that maintenance of an appropriate telomere structure is essential for function. Structural information on telomeric proteins that bind to double and single-stranded telomeric DNA shows that, despite a lack of extensive amino-acid sequence conservation, telomeric DNA recognition occurs via conserved DNA-binding domains. Furthermore, telomeric proteins have multidomain structures and hence are conformationally flexible. A possibility is that telomeric proteins take up different conformations when bound to different partners, providing a simple mechanism for modulating telomere architecture.
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Affiliation(s)
- Daniela Rhodes
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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44
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Abstract
TRF1 and TRF2 are key components of vertebrate telomeres. They bind to double-stranded telomeric DNA as homodimers. Dimerization involves the TRF homology (TRFH) domain, which also mediates interactions with other telomeric proteins. The crystal structures of the dimerization domains from human TRF1 and TRF2 were determined at 2.9 and 2.2 A resolution, respectively. Despite a modest sequence identity, the two TRFH domains have the same entirely alpha-helical architecture, resembling a twisted horseshoe. The dimerization interfaces feature unique interactions that prevent heterodimerization. Mutational analysis of TRF1 corroborates the structural data and underscores the importance of the TRFH domain in dimerization, DNA binding, and telomere localization. A possible structural homology between the TRFH domain of fission yeast telomeric protein Taz1 with those of the vertebrate TRFs is suggested.
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Affiliation(s)
- L Fairall
- MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom
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45
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Abstract
TRF1 is a key player in telomere length regulation. Because length control was proposed to depend on the architecture of telomeres, we studied how TRF1 binds telomeric TTAGGG repeat DNA and alters its conformation. Although the single Myb-type helix-turn-helix motif of a TRF1 monomer can interact with telomeric DNA, TRF1 predominantly binds as a homodimer. Systematic Evolution of Ligands by Exponential enrichment (SELEX) with dimeric TRF1 revealed a bipartite telomeric recognition site with extreme spatial variability. Optimal sites have two copies of a 5'-YTAGGGTTR-3' half-site positioned without constraint on distance or orientation. Analysis of binding affinities and DNase I footprinting showed that both half-sites are simultaneously contacted by the TRF1 dimer, and electron microscopy revealed looping of the intervening DNA. We propose that a flexible segment in TRF1 allows the two Myb domains of the homodimer to interact independently with variably positioned half-sites. This unusual DNA binding mode is directly relevant to the proposed architectural role of TRF1.
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Affiliation(s)
- A Bianchi
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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46
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König P, Fairall L, Rhodes D. Sequence-specific DNA recognition by the myb-like domain of the human telomere binding protein TRF1: a model for the protein-DNA complex. Nucleic Acids Res 1998; 26:1731-40. [PMID: 9512546 PMCID: PMC147458 DOI: 10.1093/nar/26.7.1731] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Telomeres consist of tandem arrays of short G-rich sequence motifs packaged by specific DNA binding proteins. In humans the double-stranded telomeric TTAGGG repeats are specifically bound by TRF1 and TRF2. Although telomere binding proteins from evolutionarily distant species are not sequence homologues, they share a Myb-like DNA binding motif. Here we have used gel retardation, primer extension and DNase I footprinting analyses to define the binding site of the isolated Myb-like domain of TRF1 and present a three-dimensional model for its interaction with human telomeric DNA. Our results suggest that the Myb-like domain of TRF1 recognizes a binding site centred on the sequence GGGTTA and that its DNA binding mode is similar to that of the homeodomain-like motifs of the yeast telomere binding protein RAP1. The implications of these findings for recognition of telomeric DNA in general are discussed.
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Affiliation(s)
- P König
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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47
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Abstract
Understanding how proteins recognize DNA in a sequence-specific manner is central to our understanding of the regulation of transcription and other cellular processes. In this article we review the principles of DNA recognition that have emerged from the large number of high-resolution crystal structures determined over the last 10 years. The DNA-binding domains of transcription factors exhibit surprisingly diverse protein architectures, yet all achieve a precise complementarity of shape facilitating specific chemical recognition of their particular DNA targets. Although general rules for recognition can be derived, the complex nature of the recognition mechanism precludes a simple recognition code. In particular, it has become evident that the structure and flexibility of DNA and contacts mediated by water molecules contribute to the recognition process. Nevertheless, based on known structures it has proven possible to design proteins with novel recognition specificities. Despite this considerable practical success, the thermodynamic and kinetic properties of protein/DNA recognition remain poorly understood.
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Affiliation(s)
- D Rhodes
- MRC Laboratory of Molecular Biology, Cambridge, U.K
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48
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Fairall L, Schwabe JW, Chapman L, Finch JT, Rhodes D. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature 1993; 366:483-7. [PMID: 8247159 DOI: 10.1038/366483a0] [Citation(s) in RCA: 304] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Cys2-His2 zinc-finger is the most widely occurring DNA-binding motif. The first structure of a zinc-finger/DNA complex revealed a fairly simple mechanism for DNA recognition suggesting that the zinc-finger might represent a candidate template for designing proteins to recognize DNA. Residues at three key positions in an alpha-helical 'reading head' play a dominant role in base-recognition and have been targets for mutagenesis experiments aimed at deriving a recognition code. Here we report the structure of a two zinc-finger DNA-binding domain from the protein Tramtrack complexed with DNA. The amino-terminal zinc-finger and its interaction with DNA illustrate several novel features. These include the use of a serine residue, which is semi-conserved and located outside the three key positions, to make a base contact. Its role in base-recognition correlates with a large, local, protein-induced deformation of the DNA helix at a flexible A-T-A sequence and may give insight into previous mutagenesis experiments. It is apparent from this structure that zinc-finger/DNA recognition is more complex than was originally perceived.
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Affiliation(s)
- L Fairall
- MRC Laboratory of Molecular Biology, Cambridge, UK
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49
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Schwabe JW, Fairall L, Chapman L, Finch JT, Dutnall RN, Rhodes D. The cocrystal structures of two zinc-stabilized DNA-binding domains illustrate different ways of achieving sequence-specific DNA recognition. Cold Spring Harb Symp Quant Biol 1993; 58:141-7. [PMID: 7956024 DOI: 10.1101/sqb.1993.058.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- J W Schwabe
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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50
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Abstract
We have re-examined DNase I footprinting data for the binding of transcription factor IIIA (TFIIIA) to the 5S RNA gene, taking into account the protein-DNA contacts observed in the crystal structure of the DNase I/DNA complex (1, 2). This structure was not available when many of the original footprinting experiments on the TFIIIA/DNA complex were performed. In this way the pattern of DNase I cleavage can be interpreted to map out with greater precision the regions on the 5S DNA occupied by TFIIIA. Then, assuming the binding site for a zinc-finger may be the same as that found in the structure of the zinc-finger protein Zif268/DNA complex (3), and taking into account footprinting data for truncated forms of TFIIIA, the TFIIIA zinc-fingers were fitted within the permitted regions. On the basis of this, an alignment of the zinc-fingers of TFIIIA with its DNA binding site is proposed, which combines features of earlier models (4).
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Affiliation(s)
- L Fairall
- MRC Laboratory of Molecular Biology, Cambridge, UK
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