1
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Maneix L, Iakova P, Lee CG, Moree SE, Lu X, Datar GK, Hill CT, Spooner E, King JCK, Sykes DB, Saez B, Di Stefano B, Chen X, Krause DS, Sahin E, Tsai FTF, Goodell MA, Berk BC, Scadden DT, Catic A. Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing. Nat Cell Biol 2024; 26:593-603. [PMID: 38553595 PMCID: PMC11021199 DOI: 10.1038/s41556-024-01387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Loss of protein function is a driving force of ageing. We have identified peptidyl-prolyl isomerase A (PPIA or cyclophilin A) as a dominant chaperone in haematopoietic stem and progenitor cells. Depletion of PPIA accelerates stem cell ageing. We found that proteins with intrinsically disordered regions (IDRs) are frequent PPIA substrates. IDRs facilitate interactions with other proteins or nucleic acids and can trigger liquid-liquid phase separation. Over 20% of PPIA substrates are involved in the formation of supramolecular membrane-less organelles. PPIA affects regulators of stress granules (PABPC1), P-bodies (DDX6) and nucleoli (NPM1) to promote phase separation and increase cellular stress resistance. Haematopoietic stem cell ageing is associated with a post-transcriptional decrease in PPIA expression and reduced translation of IDR-rich proteins. Here we link the chaperone PPIA to the synthesis of intrinsically disordered proteins, which indicates that impaired protein interaction networks and macromolecular condensation may be potential determinants of haematopoietic stem cell ageing.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Polina Iakova
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Charles G Lee
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Shannon E Moree
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xuan Lu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gandhar K Datar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Cedric T Hill
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric Spooner
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Jordon C K King
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Borja Saez
- Center for Applied Medical Research, Hematology-Oncology Unit, Pamplona, Navarra, Spain
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Bradford C Berk
- Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA.
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA.
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2
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Zhang H, Murphy P, Yu J, Lee S, Tsai FTF, van Hoof A, Ling J. Coordination between aminoacylation and editing to protect against proteotoxicity. Nucleic Acids Res 2023; 51:10606-10618. [PMID: 37742077 PMCID: PMC10602869 DOI: 10.1093/nar/gkad778] [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: 06/16/2023] [Revised: 08/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that ligate amino acids to tRNAs, and often require editing to ensure accurate protein synthesis. Recessive mutations in aaRSs cause various neurological disorders in humans, yet the underlying mechanism remains poorly understood. Pathogenic aaRS mutations frequently cause protein destabilization and aminoacylation deficiency. In this study, we report that combined aminoacylation and editing defects cause severe proteotoxicity. We show that the ths1-C268A mutation in yeast threonyl-tRNA synthetase (ThrRS) abolishes editing and causes heat sensitivity. Surprisingly, experimental evolution of the mutant results in intragenic mutations that restore heat resistance but not editing. ths1-C268A destabilizes ThrRS and decreases overall Thr-tRNAThr synthesis, while the suppressor mutations in the evolved strains improve aminoacylation. We further show that deficiency in either ThrRS aminoacylation or editing is insufficient to cause heat sensitivity, and that ths1-C268A impairs ribosome-associated quality control. Our results suggest that aminoacylation deficiency predisposes cells to proteotoxic stress.
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Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jason Yu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Sukyeong Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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3
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Lee S, Lee SB, Sung N, Xu WW, Chang C, Kim HE, Catic A, Tsai FTF. Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria. Nat Commun 2023; 14:2028. [PMID: 37041140 PMCID: PMC10090083 DOI: 10.1038/s41467-023-37657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/23/2023] [Indexed: 04/13/2023] Open
Abstract
Mitochondria are critical to cellular and organismal health. To prevent damage, mitochondria have evolved protein quality control machines to survey and maintain the mitochondrial proteome. SKD3, also known as CLPB, is a ring-forming, ATP-fueled protein disaggregase essential for preserving mitochondrial integrity and structure. SKD3 deficiency causes 3-methylglutaconic aciduria type VII (MGCA7) and early death in infants, while mutations in the ATPase domain impair protein disaggregation with the observed loss-of-function correlating with disease severity. How mutations in the non-catalytic N-domain cause disease is unknown. Here, we show that the disease-associated N-domain mutation, Y272C, forms an intramolecular disulfide bond with Cys267 and severely impairs SKD3Y272C function under oxidizing conditions and in living cells. While Cys267 and Tyr272 are found in all SKD3 isoforms, isoform-1 features an additional α-helix that may compete with substrate-binding as suggested by crystal structure analyses and in silico modeling, underscoring the importance of the N-domain to SKD3 function.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sang Bum Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wendy W Xu
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
- Louisiana State University Health New Orleans School of Medicine, New Orleans, LA, 70112, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Hyun-Eui Kim
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Andre Catic
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
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4
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van Oosten-Hawle P, Backe SJ, Ben-Zvi A, Bourboulia D, Brancaccio M, Brodsky J, Clark M, Colombo G, Cox MB, De Los Rios P, Echtenkamp F, Edkins A, Freeman B, Goloubinoff P, Houry W, Johnson J, LaPointe P, Li W, Mezger V, Neckers L, Nillegoda NB, Prahlad V, Reitzel A, Scherz-Shouval R, Sistonen L, Tsai FTF, Woodford MR, Mollapour M, Truman AW. Second Virtual International Symposium on Cellular and Organismal Stress Responses, September 8-9, 2022. Cell Stress Chaperones 2023; 28:1-9. [PMID: 36602710 PMCID: PMC9877255 DOI: 10.1007/s12192-022-01318-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
The Second International Symposium on Cellular and Organismal Stress Responses took place virtually on September 8-9, 2022. This meeting was supported by the Cell Stress Society International (CSSI) and organized by Patricija Van Oosten-Hawle and Andrew Truman (University of North Carolina at Charlotte, USA) and Mehdi Mollapour (SUNY Upstate Medical University, USA). The goal of this symposium was to continue the theme from the initial meeting in 2020 by providing a platform for established researchers, new investigators, postdoctoral fellows, and students to present and exchange ideas on various topics on cellular stress and chaperones. We will summarize the highlights of the meeting here and recognize those that received recognition from the CSSI.
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Affiliation(s)
- Patricija van Oosten-Hawle
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
| | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Jeff Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Melody Clark
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Marc B Cox
- Border Biomedical Research Center, Department of Pharmaceutical Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Paolo De Los Rios
- Institute of Physics & Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frank Echtenkamp
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Adrienne Edkins
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Brian Freeman
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pierre Goloubinoff
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel
| | - Walid Houry
- Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Jill Johnson
- Department of Biological Sciences and the Center for Reproductive Biology, University of Idaho, Moscow, ID, 83844, USA
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
| | - Wei Li
- The Department of Dermatology and the USC-Norris Comprehensive Cancer Center, Los Angeles, USA
- University of Southern California Keck Medical Center, Los Angeles, CA, 90089, USA
| | - Valerie Mezger
- CNRS, and Epigenetics and Cell Fate Center, Université Paris Cité, Paris, France
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Nadinath B Nillegoda
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Centre for Dementia and Brain Repair at the Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Veena Prahlad
- Department of Biology, Aging Mind and Brain Initiative, University of Iowa, Iowa City, IA, 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, 52242, USA
| | - Adam Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Francis T F Tsai
- Departments of Biochemistry and Molecular Biology, Molecular and Cellular Biology, and Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA.
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA.
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA.
| | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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5
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Mercado JM, Lee S, Chang C, Sung N, Soong L, Catic A, Tsai FTF. Atomic structure of the
Leishmania spp
. Hsp100
N‐domain. Proteins 2022; 90:1242-1246. [DOI: 10.1002/prot.26310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/14/2022] [Accepted: 02/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Jonathan M. Mercado
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston Texas USA
| | - Sukyeong Lee
- Advanced Technology Core for Macromolecular X‐ray Crystallography Baylor College of Medicine Houston Texas USA
- Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston Texas USA
| | - Changsoo Chang
- Structural Biology Center, X‐ray Science Division Argonne National Laboratory Argonne Illinois USA
| | - Nuri Sung
- Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston Texas USA
| | - Lynn Soong
- Department of Microbiology and Immunology, Institute of Human Infections and Immunity University of Texas Medical Branch Galveston Texas USA
| | - Andre Catic
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston Texas USA
- Huffington Center on Aging Baylor College of Medicine Houston Texas USA
| | - Francis T. F. Tsai
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston Texas USA
- Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston Texas USA
- Department of Molecular Virology and Microbiology Baylor College of Medicine Houston Texas USA
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6
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Maneix L, Sweeney MA, Lee S, Iakova P, Moree SE, Sahin E, Lulla P, Yellapragada SV, Tsai FTF, Catic A. The Mitochondrial Protease LonP1 Promotes Proteasome Inhibitor Resistance in Multiple Myeloma. Cancers (Basel) 2021; 13:843. [PMID: 33671345 PMCID: PMC7922145 DOI: 10.3390/cancers13040843] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/11/2021] [Indexed: 12/02/2022] Open
Abstract
Multiple myeloma and its precursor plasma cell dyscrasias affect 3% of the elderly population in the US. Proteasome inhibitors are an essential part of several standard drug combinations used to treat this incurable cancer. These drugs interfere with the main pathway of protein degradation and lead to the accumulation of damaged proteins inside cells. Despite promising initial responses, multiple myeloma cells eventually become drug resistant in most patients. The biology behind relapsed/refractory multiple myeloma is complex and poorly understood. Several studies provide evidence that in addition to the proteasome, mitochondrial proteases can also contribute to protein quality control outside of mitochondria. We therefore hypothesized that mitochondrial proteases might counterbalance protein degradation in cancer cells treated with proteasome inhibitors. Using clinical and experimental data, we found that overexpression of the mitochondrial matrix protease LonP1 (Lon Peptidase 1) reduces the efficacy of proteasome inhibitors. Some proteasome inhibitors partially crossinhibit LonP1. However, we show that the resistance effect of LonP1 also occurs when using drugs that do not block this protease, suggesting that LonP1 can compensate for loss of proteasome activity. These results indicate that targeting both the proteasome and mitochondrial proteases such as LonP1 could be beneficial for treatment of multiple myeloma.
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Affiliation(s)
- Laure Maneix
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.); (M.A.S.); (P.I.); (S.E.M.); (F.T.F.T.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Melanie A. Sweeney
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.); (M.A.S.); (P.I.); (S.E.M.); (F.T.F.T.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Polina Iakova
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.); (M.A.S.); (P.I.); (S.E.M.); (F.T.F.T.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shannon E. Moree
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.); (M.A.S.); (P.I.); (S.E.M.); (F.T.F.T.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Premal Lulla
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarvari V. Yellapragada
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
| | - Francis T. F. Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.); (M.A.S.); (P.I.); (S.E.M.); (F.T.F.T.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andre Catic
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.); (M.A.S.); (P.I.); (S.E.M.); (F.T.F.T.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA;
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
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7
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Lee S, Roh SH, Lee J, Sung N, Liu J, Tsai FTF. Cryo-EM Structures of the Hsp104 Protein Disaggregase Captured in the ATP Conformation. Cell Rep 2020; 26:29-36.e3. [PMID: 30605683 PMCID: PMC6347426 DOI: 10.1016/j.celrep.2018.12.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/12/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022] Open
Abstract
Hsp104 is a ring-forming, ATP-driven molecular machine that recovers functional protein from both stress-denatured and amyloid-forming aggregates. Although Hsp104 shares a common architecture with Clp/Hsp100 protein unfoldases, different and seemingly conflicting 3D structures have been reported. Examining the structure of Hsp104 poses considerable challenges because Hsp104 readily hydrolyzes ATP, whereas ATP analogs can be slowly turned over and are often contaminated with other nucleotide species. Here, we present the single-particle electron cryo-microscopy (cryo-EM) structures of a catalytically inactive Hsp104 variant (Hsp104DWB) in the ATP-bound state determined between 7.7 Å and 9.3 Å resolution. Surprisingly, we observe that the Hsp104DWB hexamer adopts distinct ring conformations (closed, extended, and open) despite being in the same nucleotide state. The latter underscores the structural plasticity of Hsp104 in solution, with different conformations stabilized by nucleotide binding. Our findings suggest that, in addition to ATP hydrolysis-driven conformational changes, Hsp104 uses stochastic motions to translocate unfolded polypeptides. Hsp104 is a ring-forming ATPase that facilitates the disaggregation of amorphous and amyloid-forming protein aggregates. Lee et al. present three distinct cryo-EM structures of a catalytically inactive Hsp104-ATP variant, demonstrating that Hsp104 is a dynamic molecular machine and providing the structural basis for the passive threading of unfolded polypeptides.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Soung Hun Roh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jungsoon Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
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8
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Joshi A, Dai L, Liu Y, Lee J, Ghahhari NM, Segala G, Beebe K, Jenkins LM, Lyons GC, Bernasconi L, Tsai FTF, Agard DA, Neckers L, Picard D. The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis. BMC Biol 2020; 18:10. [PMID: 31987035 PMCID: PMC6986101 DOI: 10.1186/s12915-020-0740-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/16/2020] [Indexed: 01/01/2023] Open
Abstract
Background The molecular chaperone TRAP1, the mitochondrial isoform of cytosolic HSP90, remains poorly understood with respect to its pivotal role in the regulation of mitochondrial metabolism. Most studies have found it to be an inhibitor of mitochondrial oxidative phosphorylation (OXPHOS) and an inducer of the Warburg phenotype of cancer cells. However, others have reported the opposite, and there is no consensus on the relevant TRAP1 interactors. This calls for a more comprehensive analysis of the TRAP1 interactome and of how TRAP1 and mitochondrial metabolism mutually affect each other. Results We show that the disruption of the gene for TRAP1 in a panel of cell lines dysregulates OXPHOS by a metabolic rewiring that induces the anaplerotic utilization of glutamine metabolism to replenish TCA cycle intermediates. Restoration of wild-type levels of OXPHOS requires full-length TRAP1. Whereas the TRAP1 ATPase activity is dispensable for this function, it modulates the interactions of TRAP1 with various mitochondrial proteins. Quantitatively by far, the major interactors of TRAP1 are the mitochondrial chaperones mtHSP70 and HSP60. However, we find that the most stable stoichiometric TRAP1 complex is a TRAP1 tetramer, whose levels change in response to both a decline and an increase in OXPHOS. Conclusions Our work provides a roadmap for further investigations of how TRAP1 and its interactors such as the ATP synthase regulate cellular energy metabolism. Our results highlight that TRAP1 function in metabolism and cancer cannot be understood without a focus on TRAP1 tetramers as potentially the most relevant functional entity.
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Affiliation(s)
- Abhinav Joshi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland.,Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Li Dai
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Yanxin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA
| | - Jungsoon Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Pediatrics, Tropical Medicine, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nastaran Mohammadi Ghahhari
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Gregory Segala
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Kristin Beebe
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Gaelyn C Lyons
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Lilia Bernasconi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland.
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9
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Tsai JT, Sung N, Lee J, Chang C, Lee S, Tsai FTF. Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein. J Mol Biol 2019; 431:3179-3190. [PMID: 31202886 DOI: 10.1016/j.jmb.2019.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 02/17/2019] [Revised: 05/11/2019] [Accepted: 06/05/2019] [Indexed: 01/08/2023]
Abstract
Stress proteins promote cell survival by monitoring protein homeostasis in cells and organelles. YcjX is a conserved protein of unknown function, which is highly upregulated in response to acute and chronic stress. Notably, heat shock induction of ycjX exceeded even levels observed for major stress-induced chaperones, including GroEL, ClpB, and HtpG, which use ATP as energy source. YcjX features a Walker-type nucleotide-binding domain indicating that YcjX might function as a molecular chaperone. Here, we present the first crystal structure of YcjX from Shewanella oneidensis solved at 1.9-Å resolution by SAD phasing. We show that YcjX is a GTP-binding protein that shares at its core the canonical alpha-beta domain of p21ras (Ras). However, unlike Ras, YcjX features several unique insertions, including an entirely α-helical domain not previously observed in Ras-like GTPases. We note that this helical domain is reminiscent of a similar domain in the Gα subunit of heterotrimeric G proteins, supporting a potential role for YcjX as a signal transducer of stress responses. To elucidate the mechanism of GTP hydrolysis, we determined crystal structures of YcjX bound to GDP and GDPCP, respectively, which crystallized in three different nucleotide switch conformations. Supported by targeted mutagenesis experiments, we show that YcjX utilizes a non-canonical switch 2' motif not previously observed in Ras-like GTPases. Together, our structures provide atomic snapshots of YcjX in different functional states, illustrating the structural determinants for stress signaling.
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Affiliation(s)
- Joshua T Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jungsoon Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Changsoo Chang
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
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10
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Mok SA, Condello C, Freilich R, Gillies A, Arhar T, Oroz J, Kadavath H, Julien O, Assimon VA, Rauch JN, Dunyak BM, Lee J, Tsai FTF, Wilson MR, Zweckstetter M, Dickey CA, Gestwicki JE. Mapping interactions with the chaperone network reveals factors that protect against tau aggregation. Nat Struct Mol Biol 2018; 25:384-393. [PMID: 29728653 PMCID: PMC5942583 DOI: 10.1038/s41594-018-0057-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [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: 07/22/2017] [Accepted: 03/14/2018] [Indexed: 12/31/2022]
Abstract
A network of molecular chaperones is known to bind proteins ('clients') and balance their folding, function and turnover. However, it is often unclear which chaperones are critical for selective recognition of individual clients. It is also not clear why these key chaperones might fail in protein-aggregation diseases. Here, we utilized human microtubule-associated protein tau (MAPT or tau) as a model client to survey interactions between ~30 purified chaperones and ~20 disease-associated tau variants (~600 combinations). From this large-scale analysis, we identified human DnaJA2 as an unexpected, but potent, inhibitor of tau aggregation. DnaJA2 levels were correlated with tau pathology in human brains, supporting the idea that it is an important regulator of tau homeostasis. Of note, we found that some disease-associated tau variants were relatively immune to interactions with chaperones, suggesting a model in which avoiding physical recognition by chaperone networks may contribute to disease.
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Affiliation(s)
- Sue-Ann Mok
- Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - Carlo Condello
- Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - Rebecca Freilich
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Anne Gillies
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Taylor Arhar
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Javier Oroz
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen, Germany
| | | | - Olivier Julien
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Victoria A Assimon
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Jennifer N Rauch
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Bryan M Dunyak
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Jungsoon Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mark R Wilson
- llawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Markus Zweckstetter
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen, Germany
- Max-Planck-Institut für Biophysikalische Chemie, Goettingen, Germany
- Department of Neurology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Chad A Dickey
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, University of South Florida, Tampa, FL, USA
| | - Jason E Gestwicki
- Department of Neurology, University of California at San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.
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11
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Abstract
Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.
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Affiliation(s)
- Chiung-Wen Chang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA.,Departments of Molecular and Cellular Biology, and Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX, USA
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12
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Sung N, Lee J, Kim JH, Chang C, Tsai FTF, Lee S. 2.4 Å resolution crystal structure of human TRAP1NM, the Hsp90 paralog in the mitochondrial matrix. Acta Crystallogr D Struct Biol 2016; 72:904-11. [PMID: 27487821 PMCID: PMC4973209 DOI: 10.1107/s2059798316009906] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/17/2016] [Indexed: 11/10/2022] Open
Abstract
TRAP1 is an organelle-specific Hsp90 paralog that is essential for neoplastic growth. As a member of the Hsp90 family, TRAP1 is presumed to be a general chaperone facilitating the late-stage folding of Hsp90 client proteins in the mitochondrial matrix. Interestingly, TRAP1 cannot replace cytosolic Hsp90 in protein folding, and none of the known Hsp90 co-chaperones are found in mitochondria. Thus, the three-dimensional structure of TRAP1 must feature regulatory elements that are essential to the ATPase activity and chaperone function of TRAP1. Here, the crystal structure of a human TRAP1NM dimer is presented, featuring an intact N-domain and M-domain structure, bound to adenosine 5'-β,γ-imidotriphosphate (ADPNP). The crystal structure together with epitope-mapping results shows that the TRAP1 M-domain loop 1 contacts the neighboring subunit and forms a previously unobserved third dimer interface that mediates the specific interaction with mitochondrial Hsp70.
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Affiliation(s)
- Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jungsoon Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ji-Hyun Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Changsoo Chang
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Francis T. F. Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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13
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Saliba J, Zabriskie R, Ghosh R, Powell BC, Hicks S, Kimmel M, Meng Q, Ritter DI, Wheeler DA, Gibbs RA, Tsai FTF, Plon SE. Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs. Pharmacogenet Genomics 2016; 26:271-9. [PMID: 26906009 PMCID: PMC4853247 DOI: 10.1097/fpc.0000000000000208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 11/26/2022]
Abstract
BACKGROUND Mutations or alterations in expression of the 5' nucleotidase gene family can lead to altered responses to treatment with nucleoside analogs. While investigating leukemia susceptibility genes, we discovered a very rare p.L254P NT5C1A missense variant in the substrate recognition motif. Given the paucity of cellular drug response data from the NT5C1A germline variation, we characterized p.L254P and eight rare variants of NT5C1A from genomic databases. MATERIALS AND METHODS Through lentiviral infection, we created HEK293 cell lines that stably overexpress wild-type NT5C1A, p.L254P, or eight NT5C1A variants reported in the National Heart Lung and Blood Institute Exome Variant Server (one truncating and seven missense). IC50 values were determined by cytotoxicity assays after exposure to chemotherapeutic nucleoside analogs (cladribine, gemcitabine, 5-fluorouracil). In addition, we used structure-based homology modeling to generate a three-dimensional model for the C-terminal region of NT5C1A. RESULTS The p.R180X (truncating), p.A214T, and p.L254P missense changes were the only variants that significantly impaired protein function across all nucleotide analogs tested (>5-fold difference vs. wild-type; P<0.05). Several of the remaining variants individually showed differential effects (both more and less resistant) across the analogs tested. The homology model provided a structural framework to understand the impact of NT5C1A mutants on catalysis and drug processing. The model predicted active site residues within NT5C1A motif III and we experimentally confirmed that p.K314 (not p.K320) is required for NT5C1A activity. CONCLUSION We characterized germline variation and predicted protein structures of NT5C1A. Individual missense changes showed considerable variation in response to the different nucleoside analogs tested, which may impact patients' responses to treatment.
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Affiliation(s)
- Jason Saliba
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ryan Zabriskie
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Rajarshi Ghosh
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Bradford C Powell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | | | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX
| | - Qingchang Meng
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Deborah I Ritter
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Francis T F Tsai
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Sharon E Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
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14
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Biter AB, Lee J, Sung N, Tsai FTF, Lee S. Functional analysis of conserved cis- and trans-elements in the Hsp104 protein disaggregating machine. J Struct Biol 2012; 179:172-80. [PMID: 22634726 DOI: 10.1016/j.jsb.2012.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [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: 01/09/2012] [Revised: 04/24/2012] [Accepted: 05/16/2012] [Indexed: 11/17/2022]
Abstract
Hsp104 is a double ring-forming AAA+ ATPase, which harnesses the energy of ATP binding and hydrolysis to rescue proteins from a previously aggregated state. Like other AAA+ machines, Hsp104 features conserved cis- and trans-acting elements, which are hallmarks of AAA+ members and are essential to Hsp104 function. Despite these similarities, it was recently proposed that Hsp104 is an atypical AAA+ ATPase, which markedly differs in 3D structure from other AAA+ machines. Consequently, it was proposed that arginines found in the non-conserved M-domain, but not the predicted Arg-fingers, serve the role of the critical trans-acting element in Hsp104. While the structural discrepancy has been resolved, the role of the Arg-finger residues in Hsp104 remains controversial. Here, we exploited the ability of Hsp104 variants featuring mutations in one ring to retain ATPase and chaperone activities, to elucidate the functional role of the predicted Arg-finger residues. We found that the evolutionarily conserved Arg-fingers are absolutely essential for ATP hydrolysis but are dispensable for hexamer assembly in Hsp104. On the other hand, M-domain arginines are not strictly required for ATP hydrolysis and affect the ATPase and chaperone activities in a complex manner. Our results confirm that Hsp104 is not an atypical AAA+ ATPase, and uses conserved structural elements common to diverse AAA+ machines to drive the mechanical unfolding of aggregated proteins.
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Affiliation(s)
- Amadeo B Biter
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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15
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Sielaff B, Lee S, Tsai FTF. The M‐domain controls the Hsp104 protein disaggregating activity. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.907.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bernhard Sielaff
- Verna and Marss McLean Department of Biochemistry and Molecular BiologyBaylor College of MedicineHoustonTX
| | - Sukyeong Lee
- Verna and Marss McLean Department of Biochemistry and Molecular BiologyBaylor College of MedicineHoustonTX
| | - Francis T. F. Tsai
- Verna and Marss McLean Department of Biochemistry and Molecular BiologyBaylor College of MedicineHoustonTX
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16
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Lee S, Augustin S, Tatsuta T, Gerdes F, Langer T, Tsai FTF. Electron cryomicroscopy structure of a membrane-anchored mitochondrial AAA protease. J Biol Chem 2010; 286:4404-11. [PMID: 21147776 DOI: 10.1074/jbc.m110.158741] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FtsH-related AAA proteases are conserved membrane-anchored, ATP-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. Homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an ATPase domain of the AAA family and an H41 metallopeptidase domain. Mutations in subunits of mitochondrial m-AAA proteases have been associated with different neurodegenerative disorders in human, raising questions on the functional differences between homo- and hetero-oligomeric AAA proteases. Here, we have analyzed the hetero-oligomeric yeast m-AAA protease composed of homologous Yta10 and Yta12 subunits. We combined genetic and structural approaches to define the molecular determinants for oligomer assembly and to assess functional similarities between Yta10 and Yta12. We demonstrate that replacement of only two amino acid residues within the metallopeptidase domain of Yta12 allows its assembly into homo-oligomeric complexes. To provide a molecular explanation, we determined the 12 Å resolution structure of the intact yeast m-AAA protease with its transmembrane domains by electron cryomicroscopy (cryo-EM) and atomic structure fitting. The full-length m-AAA protease has a bipartite structure and is a hexamer in solution. We found that residues in Yta12, which facilitate homo-oligomerization when mutated, are located at the interface between neighboring protomers in the hexamer ring. Notably, the transmembrane and intermembrane space domains are separated from the main body, creating a passage on the matrix side, which is wide enough to accommodate unfolded but not folded polypeptides. These results suggest a mechanism regarding how proteins are recognized and degraded by m-AAA proteases.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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17
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Sielaff B, Lee KS, Tsai FTF. Structural and functional conservation of Mycobacterium tuberculosis GroEL paralogs suggests that GroEL1 Is a chaperonin. J Mol Biol 2010; 405:831-9. [PMID: 21094166 DOI: 10.1016/j.jmb.2010.11.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 11/09/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
Abstract
GroEL is a group I chaperonin that facilitates protein folding and prevents protein aggregation in the bacterial cytosol. Mycobacteria are unusual in encoding two or more copies of GroEL in their genome. While GroEL2 is essential for viability and likely functions as the general housekeeping chaperonin, GroEL1 is dispensable, but its structure and function remain unclear. Here, we present the 2.2-Å resolution crystal structure of a 23-kDa fragment of Mycobacterium tuberculosis GroEL1 consisting of an extended apical domain. Our X-ray structure of the GroEL1 apical domain closely resembles those of Escherichia coli GroEL and M. tuberculosis GroEL2, thus highlighting the remarkable structural conservation of bacterial chaperonins. Notably, in our structure, the proposed substrate-binding site of GroEL1 interacts with the N-terminal region of a symmetry-related neighboring GroEL1 molecule. The latter is consistent with the known GroEL apical domain function in substrate binding and is supported by results obtained from using peptide array technology. Taken together, these data show that the apical domains of M. tuberculosis GroEL paralogs are conserved in three-dimensional structure, suggesting that GroEL1, like GroEL2, is a chaperonin.
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Affiliation(s)
- Bernhard Sielaff
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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18
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Sielaff B, Tsai FTF. The M-domain controls Hsp104 protein remodeling activity in an Hsp70/Hsp40-dependent manner. J Mol Biol 2010; 402:30-7. [PMID: 20654624 DOI: 10.1016/j.jmb.2010.07.030] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 07/09/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
Abstract
Yeast Hsp104 is a ring-forming ATP-dependent protein disaggregase that, together with the cognate Hsp70 chaperone system, has the remarkable ability to rescue stress-damaged proteins from a previously aggregated state. Both upstream and downstream functions for the Hsp70 system have been reported, but it remains unclear how Hsp70/Hsp40 is coupled to Hsp104 protein remodeling activity. Hsp104 is a multidomain protein that possesses an N-terminal domain, an M-domain, and two tandem AAA(+) domains. The M-domain forms an 85-A long coiled coil and is a hallmark of the Hsp104 chaperone family. While the three-dimensional structure of Hsp104 has been determined, the function of the M-domain is unclear. Here, we demonstrate that the M-domain is essential for protein disaggregation, but dispensable for Hsp104 ATPase- and substrate-translocating activities. Remarkably, replacing the Hsp104 M-domain with that of bacterial ClpB, and vice versa, switches species specificity so that our chimeras now cooperate with the noncognate Hsp70/DnaK chaperone system. Our results demonstrate that the M-domain controls Hsp104 protein remodeling activities in an Hsp70/Hsp40-dependent manner, which is required to unleash Hsp104 protein disaggregating activity.
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Affiliation(s)
- Bernhard Sielaff
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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19
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Sielaff B, Lee KS, Tsai FTF. Crystallization and preliminary X-ray crystallographic analysis of a GroEL1 fragment from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:418-20. [PMID: 20383012 PMCID: PMC2852334 DOI: 10.1107/s1744309110004409] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 02/03/2010] [Indexed: 12/31/2022]
Abstract
Full-length GroEL1 from Mycobacterium tuberculosis H37Rv was cloned, overexpressed and purified. Crystals were obtained by the hanging-drop vapor-diffusion method and contained a 23 kDa GroEL1 fragment. A complete native data set was collected from a single frozen crystal that belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 75.47, b = 78.67, c = 34.89 A, alpha = beta = gamma = 90 degrees , and diffracted to 2.2 A resolution on a home X-ray source.
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Affiliation(s)
- Bernhard Sielaff
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston TX 77030, USA
| | - Ki Seog Lee
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston TX 77030, USA
| | - Francis T. F. Tsai
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston TX 77030, USA
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20
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Augustin S, Gerdes F, Lee S, Tsai FTF, Langer T, Tatsuta T. An intersubunit signaling network coordinates ATP hydrolysis by m-AAA proteases. Mol Cell 2009; 35:574-85. [PMID: 19748354 DOI: 10.1016/j.molcel.2009.07.018] [Citation(s) in RCA: 82] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 05/08/2009] [Accepted: 07/10/2009] [Indexed: 11/17/2022]
Abstract
Ring-shaped AAA+ ATPases control a variety of cellular processes by substrate unfolding and remodeling of macromolecular structures. However, how ATP hydrolysis within AAA+ rings is regulated and coupled to mechanical work is poorly understood. Here we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes, conserved AAA+ machines in the inner membrane of mitochondria. ATP binding to one AAA subunit inhibits ATP hydrolysis by the neighboring subunit, leading to coordinated rather than stochastic ATP hydrolysis within the AAA ring. Unbiased genetic screens define an intersubunit signaling pathway involving conserved AAA motifs and reveal an intimate coupling of ATPase activities to central AAA pore loops. Coordinated ATP hydrolysis between adjacent subunits is required for membrane dislocation of substrates, but not for substrate processing. These findings provide insight into how AAA+ proteins convert energy derived from ATP hydrolysis into mechanical work.
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Affiliation(s)
- Steffen Augustin
- Institute for Genetics, Center for Molecular Medicine Cologne, University of Cologne, Germany
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21
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Lee S, Tsai FTF. Crystallization and preliminary X-ray crystallographic analysis of a 40 kDa N-terminal fragment of the yeast prion-remodeling factor Hsp104. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:784-6. [PMID: 17768355 PMCID: PMC2376311 DOI: 10.1107/s1744309107038328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 08/03/2007] [Indexed: 11/10/2022]
Abstract
A 40 kDa N-terminal fragment of Saccharomyces cerevisiae Hsp104 was crystallized in two different crystal forms. Native 1 diffracted to 2.6 A resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 66.6, b = 75.8, c = 235.7 A. Native 2 diffracted to 2.9 A resolution and belonged to space group P6(1)22 or P6(5)22, with unit-cell parameters a = 179.1, b = 179.1, c = 69.7 A. This is the first report of the crystallization of a eukaryotic member of the Hsp100 family of molecular chaperones.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francis T. F. Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Lee S, Choi JM, Tsai FTF. Visualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB. Mol Cell 2007; 25:261-71. [PMID: 17244533 PMCID: PMC1855157 DOI: 10.1016/j.molcel.2007.01.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [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: 07/27/2006] [Revised: 10/10/2006] [Accepted: 01/03/2007] [Indexed: 11/17/2022]
Abstract
ClpB is a ring-shaped molecular chaperone that has the remarkable ability to disaggregate stress-damaged proteins. Here we present the electron cryomicroscopy reconstruction of an ATP-activated ClpB trap mutant, along with reconstructions of ClpB in the AMPPNP, ADP, and in the nucleotide-free state. We show that motif 2 of the ClpB M domain is positioned between the D1-large domains of neighboring subunits and could facilitate a concerted, ATP-driven conformational change in the AAA-1 ring. We further demonstrate biochemically that ATP is essential for high-affinity substrate binding to ClpB and cannot be substituted with AMPPNP. Our structures show that in the ATP-activated state, the D1 loops are stabilized at the central pore, providing the structural basis for high-affinity substrate binding. Taken together, our results support a mechanism by which ClpB captures substrates on the upper surface of the AAA-1 ring before threading them through the ClpB hexamer in an ATP hydrolysis-driven step.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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23
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Haslberger T, Weibezahn J, Zahn R, Lee S, Tsai FTF, Bukau B, Mogk A. M domains couple the ClpB threading motor with the DnaK chaperone activity. Mol Cell 2007; 25:247-60. [PMID: 17244532 DOI: 10.1016/j.molcel.2006.11.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 10/10/2006] [Accepted: 11/08/2006] [Indexed: 11/17/2022]
Abstract
The AAA(+) chaperone ClpB mediates the reactivation of aggregated proteins in cooperation with the DnaK chaperone system. ClpB consists of two AAA domains that drive the ATP-dependent threading of substrates through a central translocation channel. Its unique middle (M) domain forms a coiled-coil structure that laterally protrudes from the ClpB ring and is essential for aggregate solubilization. Here, we demonstrate that the conserved helix 3 of the M domain is specifically required for the DnaK-dependent shuffling of aggregated proteins, but not of soluble denatured substrates, to the pore entrance of the ClpB translocation channel. Helix 3 exhibits nucleotide-driven conformational changes possibly involving a transition between folded and unfolded states. This molecular switch controls the ClpB ATPase cycle by contacting the first ATPase domain and establishes the M domain as a regulatory device that acts in the disaggregation process by coupling the threading motor of ClpB with the DnaK chaperone activity.
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Affiliation(s)
- Tobias Haslberger
- ZMBH, Universität Heidelberg, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
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24
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Abstract
Steroid hormone receptor antagonists are widely used in clinical medicine, but their use is often complicated by the lack of receptor specificity to presently available drugs. We previously demonstrated an important role of a widely conserved helix 3 (H3)-helix 5 (H5) interaction in determining the sensitivity and specificity of steroid hormone receptors to receptor agonists. Intriguingly, the same H3 residues also play a crucial role in receptor antagonism; mutation of these residues alters the response of these receptors to antagonists. Given the close interaction of H3 and H5 residues at this site, we asked whether H5 residues might also play a role in the sensitivity of these receptors to antagonists. We demonstrate here that modification of H5 residues produces marked changes in the sensitivities of the glucocorticoid and progesterone receptor (PR) to RU486 antagonism. Moreover, while we confirm previous reports that alteration of the H3 residue, Gly 722 prevents RU486-mediated inhibition of the PR, we show that the corresponding substitution in the glucocorticoid receptor does not inhibit RU486-mediated receptor antagonism. Taken together, our data support the notion that RU486 binds differently to these two receptors, providing a potential target for the design of more specific antiglucocorticoid and antiprogestin drugs.
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MESH Headings
- Animals
- COS Cells
- Chlorocebus aethiops
- Genes, Reporter
- Hormone Antagonists/metabolism
- Humans
- Mifepristone/metabolism
- Models, Molecular
- Protein Structure, Secondary
- Receptors, Glucocorticoid/chemistry
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/metabolism
- Receptors, Mineralocorticoid/chemistry
- Receptors, Mineralocorticoid/genetics
- Receptors, Mineralocorticoid/metabolism
- Receptors, Progesterone/chemistry
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
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Affiliation(s)
- Junhui Zhang
- Section of Nephrology, Yale University School of Medicine, PO Box 208029, New Haven, CT 06520-8029, USA
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25
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Rees I, Lee S, Kim H, Tsai FTF. The E3 ubiquitin ligase CHIP binds the androgen receptor in a phosphorylation-dependent manner. Biochim Biophys Acta 2006; 1764:1073-9. [PMID: 16725394 DOI: 10.1016/j.bbapap.2006.03.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 03/09/2006] [Accepted: 03/27/2006] [Indexed: 11/17/2022]
Abstract
In Eukarya, the 26S proteasome is primarily responsible for intracellular protein degradation. To be degraded, proteins must be ubiquitinated. The latter requires a multi-enzyme cascade consisting of an E1, an E2, and an E3 enzyme. While there is only a single E1 and a few E2s, there are many different E3s that target substrates by recognizing specific sequence motifs, known as degrons. Here, we have used the peptide array technology to identify binding motifs in the human androgen receptor (AR), which are recognized by the Carboxyl-terminus of Hsc70-Interacting Protein (CHIP), a U-box E3 and Hsp70/Hsp90 co-chaperone. We show that CHIP recognizes AR in a highly specific, phosphorylation- and sequence-dependent manner, and propose that this interaction could provide a mechanism that regulates the degradation of CHIP substrates.
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Affiliation(s)
- Ian Rees
- Program in Structural and Computational Biology and Molecular Biophysics, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
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26
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Abstract
Proteins must fold into their correct three-dimensional conformation in order to attain their biological function. Conversely, protein aggregation and misfolding are primary contributors to many devastating human diseases, such as prion-mediated infections, Alzheimer's disease, type II diabetes and cystic fibrosis. While the native conformation of a polypeptide is encoded within its primary amino acid sequence and is sufficient for protein folding in vitro, the situation in vivo is more complex. Inside the cell, proteins are synthesized or folded continuously; a process that is greatly assisted by molecular chaperones. Molecular chaperones are a group of structurally diverse and mechanistically distinct proteins that either promote folding or prevent the aggregation of other proteins. With our increasing understanding of the proteome, it is becoming clear that the number of proteins that can be classified as molecular chaperones is increasing steadily. Many of these proteins have novel but essential cellular functions that differ from that of more "conventional" chaperones, such as Hsp70 and the GroE system. This review focuses on the emerging role of molecular chaperones in protein quality control, i.e. the mechanism that rids the cell of misfolded or incompletely synthesized polypeptides that otherwise would interfere with normal cellular function.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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27
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Abstract
The ligand-binding domains of steroid hormone receptors possess a conserved structure with 12 alpha-helices surrounding a central hydrophobic core. On agonist binding, a repositioned helix 12 forms a pocket with helix 3 (H3) and helix 5 (H5), where transcriptional coactivators bind. The precise molecular interactions responsible for activation of these receptors remain to be elucidated. We previously identified a H3-H5 interaction that permits progesterone-mediated activation of a mutant mineralocorticoid receptor. We were intrigued to note that the potential for such interaction is widely conserved in the nuclear receptor family, indicating a possible functional significance. Here, we demonstrate via transcriptional activation studies in cell culture that alteration of residues involved in H3-H5 interaction consistently produces a gain of function in steroid hormone receptors. These data suggest that H3-H5 interaction may function as a molecular switch regulating the activity of nuclear receptors and suggest this site as a general target for pharmacologic intervention. Furthermore, they reveal a general mechanism for the creation of nuclear receptors bearing increased activity, providing a potentially powerful tool for the study of physiologic pathways in vivo.
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Affiliation(s)
- Junhui Zhang
- Section of Nephrology, Yale University School of Medicine, New Haven, CT 06520, USA
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28
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Lee S, Sowa ME, Choi JM, Tsai FTF. The ClpB/Hsp104 molecular chaperone-a protein disaggregating machine. J Struct Biol 2004; 146:99-105. [PMID: 15037241 DOI: 10.1016/j.jsb.2003.11.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2003] [Revised: 11/06/2003] [Indexed: 11/16/2022]
Abstract
ClpB and Hsp104 (ClpB/Hsp104) are essential proteins of the heat-shock response and belong to the class 1 family of Clp/Hsp100 AAA+ ATPases. Members of this family form large ring structures and contain two AAA+ modules, which consist of a RecA-like nucleotide-binding domain (NBD) and an alpha-helical domain. Furthermore, ClpB/Hsp104 has a longer middle region, the ClpB/Hsp104-linker, which is essential for chaperone activity. Unlike other Clp/Hsp100 proteins, however, ClpB/Hsp104 neither associates with a cellular protease nor directs the degradation of its substrate proteins. Rather, ClpB/Hsp104 is a bona fide molecular chaperone, which has the remarkable ability to rescue proteins from an aggregated state. The full recovery of these proteins requires the assistance of the cognate DnaK/Hsp70 chaperone system. The mechanism of this "bi-chaperone" network, however, remains elusive. Here we review the current understanding of the structure-function relationship of the ClpB/Hsp104 molecular chaperone and its role in protein disaggregation.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston TX, 77030, USA
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29
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Weibezahn J, Tessarz P, Schlieker C, Zahn R, Maglica Z, Lee S, Zentgraf H, Weber-Ban EU, Dougan DA, Tsai FTF, Mogk A, Bukau B. Thermotolerance Requires Refolding of Aggregated Proteins by Substrate Translocation through the Central Pore of ClpB. Cell 2004; 119:653-65. [PMID: 15550247 DOI: 10.1016/j.cell.2004.11.027] [Citation(s) in RCA: 341] [Impact Index Per Article: 17.1] [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: 05/30/2004] [Revised: 08/20/2004] [Accepted: 10/06/2004] [Indexed: 10/26/2022]
Abstract
Cell survival under severe thermal stress requires the activity of the ClpB (Hsp104) AAA+ chaperone that solubilizes and reactivates aggregated proteins in concert with the DnaK (Hsp70) chaperone system. How protein disaggregation is achieved and whether survival is solely dependent on ClpB-mediated elimination of aggregates or also on reactivation of aggregated proteins has been unclear. We engineered a ClpB variant, BAP, which associates with the ClpP peptidase and thereby is converted into a degrading disaggregase. BAP translocates substrates through its central pore directly into ClpP for degradation. ClpB-dependent translocation is demonstrated to be an integral part of the disaggregation mechanism. Protein disaggregation by the BAP/ClpP complex remains dependent on DnaK, defining a role for DnaK at early stages of the disaggregation reaction. The activity switch of BAP to a degrading disaggregase does not support thermotolerance development, demonstrating that cell survival during severe thermal stress requires reactivation of aggregated proteins.
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Affiliation(s)
- Jimena Weibezahn
- Zentrum für Molekulare Biologie der Universität Heidelberg, Universität Heidelberg, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
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30
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Lee S, Hisayoshi M, Yoshida M, Tsai FTF. Crystallization and preliminary X-ray crystallographic analysis of the Hsp100 chaperone ClpB fromThermus thermophilus. Acta Crystallogr D Biol Crystallogr 2003; 59:2334-6. [PMID: 14646112 DOI: 10.1107/s0907444903023266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Accepted: 10/15/2003] [Indexed: 11/10/2022]
Abstract
ClpB from Thermus thermophilus (TClpB) has been crystallized by the vapour-diffusion method in the presence of adenosine 5'-(beta,gamma-imido)triphosphate (AMPPNP) and adenosine 5'-(gamma-thio)triphosphate (ATPgammaS), respectively. Complete native data sets have been collected from frozen crystals, which belonged to the primitive orthorhombic space group P2(1)2(1)2(1) with unit-cell parameters a = 109.2, b = 139.6, c = 213.0 A, alpha = beta = gamma = 90 degrees.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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31
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Abstract
Molecular chaperones assist protein folding by facilitating their "forward" folding and preventing aggregation. However, once aggregates have formed, these chaperones cannot facilitate protein disaggregation. Bacterial ClpB and its eukaryotic homolog Hsp104 are essential proteins of the heat-shock response, which have the remarkable capacity to rescue stress-damaged proteins from an aggregated state. We have determined the structure of Thermus thermophilus ClpB (TClpB) using a combination of X-ray crystallography and cryo-electron microscopy (cryo-EM). Our single-particle reconstruction shows that TClpB forms a two-tiered hexameric ring. The ClpB/Hsp104-linker consists of an 85 A long and mobile coiled coil that is located on the outside of the hexamer. Our mutagenesis and biochemical data show that both the relative position and motion of this coiled coil are critical for chaperone function. Taken together, we propose a mechanism by which an ATP-driven conformational change is coupled to a large coiled-coil motion, which is indispensable for protein disaggregation.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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