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Estiar MA, Yu E, Haj Salem I, Ross JP, Mufti K, Akçimen F, Leveille E, Spiegelman D, Ruskey JA, Asayesh F, Dagher A, Yoon G, Tarnopolsky M, Boycott KM, Dupre N, Dion PA, Suchowersky O, Trempe JF, Rouleau GA, Gan-Or Z. Evidence for Non-Mendelian Inheritance in Spastic Paraplegia 7. Mov Disord 2021; 36:1664-1675. [PMID: 33598982 DOI: 10.1002/mds.28528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Although the typical inheritance of spastic paraplegia 7 is recessive, several reports have suggested that SPG7 variants may also cause autosomal dominant hereditary spastic paraplegia (HSP). OBJECTIVES We aimed to conduct an exome-wide genetic analysis on a large Canadian cohort of HSP patients and controls to examine the association of SPG7 and HSP. METHODS We analyzed 585 HSP patients from 372 families and 1175 controls, including 580 unrelated individuals. Whole-exome sequencing was performed on 400 HSP patients (291 index cases) and all 1175 controls. RESULTS The frequency of heterozygous pathogenic/likely pathogenic SPG7 variants (4.8%) among unrelated HSP patients was higher than among unrelated controls (1.7%; OR 2.88, 95% CI 1.24-6.66, P = 0.009). The heterozygous SPG7 p.(Ala510Val) variant was found in 3.7% of index patients versus 0.85% in unrelated controls (OR 4.42, 95% CI 1.49-13.07, P = 0.005). Similar results were obtained after including only genetically-undiagnosed patients. We identified four heterozygous SPG7 variant carriers with an additional pathogenic variant in known HSP genes, compared to zero in controls (OR 19.58, 95% CI 1.05-365.13, P = 0.0031), indicating potential digenic inheritance. We further identified four families with heterozygous variants in SPG7 and SPG7-interacting genes (CACNA1A, AFG3L2, and MORC2). Of these, there is especially compelling evidence for epistasis between SPG7 and AFG3L2. The p.(Ile705Thr) variant in AFG3L2 is located at the interface between hexamer subunits, in a hotspot of mutations associated with spinocerebellar ataxia type 28 that affect its proteolytic function. CONCLUSIONS Our results provide evidence for complex inheritance in SPG7-associated HSP, which may include recessive and possibly dominant and digenic/epistasis forms of inheritance. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Mehrdad A Estiar
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | | | - Jay P Ross
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Kheireddin Mufti
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Etienne Leveille
- Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Dan Spiegelman
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Jennifer A Ruskey
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Farnaz Asayesh
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Alain Dagher
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Grace Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Nicolas Dupre
- Neuroscience Axis, CHU de Québec, Université Laval, Québec City, Québec, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Québec City, Québec, Canada
| | - Patrick A Dion
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Oksana Suchowersky
- Departments of Medicine (Neurology) and Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Jean-Francois Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Québec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
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Laughlin TG, Bayne A, Trempe JF, Savage D, Davies K. Structure of the Cyanobacterial NAD(P)H Dehydrogenase-Like Complex of Oxygenic Photosynthesis. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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3
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Khalifa A, Ichikawa M, Dai D, Black C, Peri K, McAlear T, Kubo S, Veyron S, Kai Yang S, Basu K, Vargas J, Trempe JF, Bechstedt S, Huy Bui K. The Inner Junction Complex of the Cilia is an Interaction Hub that Involves Tubulin Post-translational Modifications. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Alcalay RN, Mallett V, Vanderperre B, Tavassoly O, Dauvilliers Y, Wu RY, Ruskey JA, Leblond CS, Ambalavanan A, Laurent SB, Spiegelman D, Dionne-Laporte A, Liong C, Levy OA, Fahn S, Waters C, Kuo SH, Chung WK, Ford B, Marder KS, Kang UJ, Hassin-Baer S, Greenbaum L, Trempe JF, Wolf P, Oliva P, Zhang XK, Clark LN, Langlois M, Dion PA, Fon EA, Dupre N, Rouleau GA, Gan-Or Z. SMPD1 mutations, activity, and α-synuclein accumulation in Parkinson's disease. Mov Disord 2019; 34:526-535. [PMID: 30788890 PMCID: PMC6469643 DOI: 10.1002/mds.27642] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [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: 02/14/2018] [Revised: 11/21/2018] [Accepted: 01/10/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND SMPD1 (acid-sphingomyelinase) variants have been associated with Parkinson's disease in recent studies. The objective of this study was to further investigate the role of SMPD1 mutations in PD. METHODS SMPD1 was sequenced in 3 cohorts (Israel Ashkenazi Jewish cohort, Montreal/Montpellier, and New York), including 1592 PD patients and 975 controls. Additional data were available for 10,709 Ashkenazi Jewish controls. Acid-sphingomyelinase activity was measured by a mass spectrometry-based assay in the New York cohort. α-Synuclein levels were measured in vitro following CRISPR/Cas9-mediated knockout and siRNA knockdown of SMPD1 in HeLa and BE(2)-M17 cells. Lysosomal localization of acid-sphingomyelinase with different mutations was studied, and in silico analysis of their effect on acid-sphingomyelinase structure was performed. RESULTS SMPD1 mutations were associated with PD in the Ashkenazi Jewish cohort, as 1.4% of PD patients carried the p.L302P or p.fsP330 mutation, compared with 0.37% in 10,709 Ashkenazi Jewish controls (OR, 3.7; 95%CI, 1.6-8.2; P = 0.0025). In the Montreal/Montpellier cohort, the p.A487V variant was nominally associated with PD (1.5% versus 0.14%; P = 0.0065, not significant after correction for multiple comparisons). Among PD patients, reduced acid-sphingomyelinase activity was associated with a 3.5- to 5.8-year earlier onset of PD in the lowest quartile versus the highest quartile of acid-sphingomyelinase activity (P = 0.01-0.001). We further demonstrated that SMPD1 knockout and knockdown resulted in increased α-synuclein levels in HeLa and BE(2)-M17 dopaminergic cells and that the p.L302P and p.fsP330 mutations impair the traffic of acid-sphingomyelinase to the lysosome. CONCLUSIONS Our results support an association between SMPD1 variants, acid-sphingomyelinase activity, and PD. Furthermore, they suggest that reduced acid-sphingomyelinase activity may lead to α-synuclein accumulation. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Roy N. Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Victoria Mallett
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Benoît Vanderperre
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Omid Tavassoly
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Yves Dauvilliers
- Sleep Unit, National Reference Network for Narcolepsy, Department of Neurology Hôpital-Gui-de Chauliac, CHU Montpellier, INSERM U1061, France
| | - Richard Y.J. Wu
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
| | - Jennifer A. Ruskey
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Claire S. Leblond
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Amirthagowri Ambalavanan
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Sandra B. Laurent
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Alexandre Dionne-Laporte
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Christopher Liong
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Oren A. Levy
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Cheryl Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Sheng-Han Kuo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Wendy K. Chung
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Blair Ford
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Karen S. Marder
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Un Jung Kang
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Sharon Hassin-Baer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
- Movement Disorders Institute, Sheba Medical Center, Tel Hashomerf, Israel
| | - Lior Greenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Jean-Francois Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Québec, Canada
| | - Pavlina Wolf
- Translational Science, Sanofi, Framingham, MA, USA
| | - Petra Oliva
- Translational Science, Sanofi, Framingham, MA, USA
| | | | - Lorraine N. Clark
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Melanie Langlois
- Axe neurosciences du CHU de Québec - Université Laval, Québec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Québec, QC, Canada
| | - Patrick A. Dion
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Edward A. Fon
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Nicolas Dupre
- Axe neurosciences du CHU de Québec - Université Laval, Québec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Québec, QC, Canada
| | - Guy A. Rouleau
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Ziv Gan-Or
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
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5
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Seirafi M, Trempe JF, Sauve V, Kozlov G, Menade M, Nagar B, Gehring K. Structure of parkin reveals the mechanism of autoinhibition. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s205327331409161x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Mutations in the gene park2 that codes for a RING-In-Between-RING (RBR) E3 ubiquitin ligase are responsible for an autosomal recessive form of Parkinson's disease (PD). Compared to other ubiquitin ligases, the parkin protein exhibits low basal activity and requires activation both in vitro and in cells. Parkin is a 465-residue E3 ubiquitin ligase promoting mitophagy of damaged mitochondria. Parkin has two RING motifs RING1 and RING2 linked by a cysteine- rich in-between-RING (IBR) motif, a recently identified zinc-coordinating motif termed RING0, and an N-terminal ubiquitin-like domain (Ubl). It is believed that parkin may function as a RING/HECT hybrid, where ubiquitin is first transferred by the E2 enzyme onto parkin active cysteine and then to the substrate. Here, we report the crystal structure of full-length parkin at low resolution. This structure shows parkin in an auto-inhibited state and provides insight into how it is activated. In the structure RING0 occludes the ubiquitin acceptor site Cys431 in RING2 whereas a novel repressor element of parkin (REP) binds RING1 and blocks its E2-binding site. The ubiquitin-like domain (Ubl) binds adjacent to the REP through the hydrophobic surface centered around Ile44 and regulate parkin activity. Mutagenesis and NMR titrations verified interactions observed in the crystal. We also proposed the putative E2 binding site on RING1 and confirmed it by mutagenesis and NMR titrations. Importantly, mutations that disrupt these inhibitory interactions activate parkin both in vitro and in cells. The structure of the E3-ubiquitin ligase provides insights into how pathological mutations affect the protein integrity. Current work is directed towards obtaining high-resolution structure of full-length parkin in complex with E2 and substrates. The results will lead to new therapeutic strategies for treating and ultimately preventing PD.
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Grishin AM, Ajamian E, Tao L, Bostina M, Zhang L, Trempe JF, Menard R, Rouiller I, Cygler M. Family of phenylacetyl-CoA monooxygenases differs in subunit organization from other monooxygenases. J Struct Biol 2013; 184:147-54. [PMID: 24055609 DOI: 10.1016/j.jsb.2013.09.012] [Citation(s) in RCA: 4] [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: 07/25/2013] [Revised: 09/12/2013] [Accepted: 09/14/2013] [Indexed: 11/25/2022]
Abstract
The phenylacetate degradation pathway is present in a wide range of microbes. A key component of this pathway is the four-subunit phenylacetyl-coenzyme A monooxygenase complex (PA-CoA MO, PaaACBE) that catalyzes the insertion of an oxygen in the aromatic ring of PA. This multicomponent enzyme represents a new family of monooxygenases. We have previously determined the structure of the PaaAC subcomplex of catalytic (A) and structural (C) subunits and shown that PaaACB form a stable complex. The PaaB subunit is unrelated to the small subunits of homologous monooxygenases and its role and organization of the PaaACB complex is unknown. From low-resolution crystal structure, electron microscopy and small angle X-ray scattering we show that the PaaACB complex forms heterohexamers, with a homodimer of PaaB bridging two PaaAC heterodimers. Modeling the interactions of reductase subunit PaaE with PaaACB suggested that a unique and conserved 'lysine bridge' constellation near the Fe-binding site in the PaaA subunit (Lys68, Glu49, Glu72 and Asp126) may form part of the electron transfer path from PaaE to the iron center. The crystal structure of the PaaA(K68Q/E49Q)-PaaC is very similar to the wild-type enzyme structure, but when combined with the PaaE subunit the mutant showed 20-50 times reduced activity, supporting the functional importance of the 'lysine bridge'.
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Affiliation(s)
- Andrey M Grishin
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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Riedinger C, Boehringer J, Trempe JF, Lowe ED, Brown NR, Gehring K, Noble MEM, Gordon C, Endicott JA. Structure of Rpn10 and its interactions with polyubiquitin chains and the proteasome subunit Rpn12. J Biol Chem 2010; 285:33992-4003. [PMID: 20739285 PMCID: PMC2962499 DOI: 10.1074/jbc.m110.134510] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [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: 04/15/2010] [Revised: 08/03/2010] [Indexed: 11/06/2022] Open
Abstract
Schizosaccharomyces pombe Rpn10 (SpRpn10) is a proteasomal ubiquitin (Ub) receptor located within the 19 S regulatory particle where it binds to subunits of both the base and lid subparticles. We have solved the structure of full-length SpRpn10 by determining the crystal structure of the von Willebrand factor type A domain and characterizing the full-length protein by NMR. We demonstrate that the single Ub-interacting motif (UIM) of SpRpn10 forms a 1:1 complex with Lys(48)-linked diUb, which it binds selectively over monoUb and Lys(63)-linked diUb. We further show that the SpRpn10 UIM binds to SpRpn12, a subunit of the lid subparticle, with an affinity comparable with Lys(48)-linked diUb. This is the first observation of a UIM binding other than a Ub fold and suggests that SpRpn12 could modulate the activity of SpRpn10 as a proteasomal Ub receptor.
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Affiliation(s)
- Christiane Riedinger
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jonas Boehringer
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jean-Francois Trempe
- the Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada, and
| | - Edward D. Lowe
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicholas R. Brown
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Kalle Gehring
- the Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada, and
| | - Martin E. M. Noble
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Colin Gordon
- the Medical Research Council Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, United Kingdom
| | - Jane A. Endicott
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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Boehringer J, Riedinger C, Trempe JF, Endicott J. S. pombeRpn12 and ubiquitin compete for binding to Rpn10. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310099575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Trempe JF, Grenier K, Xiuqing C, Camacho E, Kozlov G, Fon EA, Gehring K. Interaction Of The Parkin UBL Domain With SH3-containing Proteins Involved In Synaptic Vesicle Endocytosis: Structure And Role In Protein Ubiquitination. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.2875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Denisov AY, Noronha AM, Wilds CJ, Trempe JF, Pon RT, Gehring K, Damha MJ. Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids. Nucleic Acids Res 2001; 29:4284-93. [PMID: 11691916 PMCID: PMC60200 DOI: 10.1093/nar/29.21.4284] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, knowledge of the structure of ANA/RNA hybrids may prove helpful in the design of future antisense oligonucleotide analogs. In this study, we have determined the NMR solution structures of ANA/RNA and DNA/RNA hairpin duplexes and compared them to the recently published structure of a 2'F-ANA/RNA hairpin duplex. We demonstrate here that the sugars of RNA nucleotides of the ANA/RNA hairpin stem adopt the C3'-endo (north, A-form) conformation, whereas those of the ANA strand adopt a 'rigid' O4'-endo (east) sugar pucker. The DNA strand of the DNA/RNA hairpin stem is flexible, but the average DNA/RNA hairpin structural parameters are close to the ANA/RNA and 2'F-ANA/RNA hairpin parameters. The minor groove width of ANA/RNA, 2'F-ANA/RNA and DNA/RNA helices is 9.0 +/- 0.5 A, a value that is intermediate between that of A- and B-form duplexes. These results rationalize the ability of ANA/RNA and 2'F-ANA/RNA hybrids to elicit RNase H activity.
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Affiliation(s)
- A Y Denisov
- Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, Montreal, QC H3G 1Y6, Canada
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Trempe JF, Wilds CJ, Denisov AY, Pon RT, Damha MJ, Gehring K. NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes. J Am Chem Soc 2001; 123:4896-903. [PMID: 11457316 DOI: 10.1021/ja003859p] [Citation(s) in RCA: 59] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.
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Affiliation(s)
- J F Trempe
- Department of Biochemistry and Montreal Joint Center for Structural Biology, McGill University, Montreal, Canada
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Kozlov G, Trempe JF, Khaleghpour K, Kahvejian A, Ekiel I, Gehring K. Structure and function of the C-terminal PABC domain of human poly(A)-binding protein. Proc Natl Acad Sci U S A 2001; 98:4409-13. [PMID: 11287632 PMCID: PMC31848 DOI: 10.1073/pnas.071024998] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have determined the solution structure of the C-terminal quarter of human poly(A)-binding protein (hPABP). The protein fragment contains a protein domain, PABC [for poly(A)-binding protein C-terminal domain], which is also found associated with the HECT family of ubiquitin ligases. By using peptides derived from PABP interacting protein (Paip) 1, Paip2, and eRF3, we show that PABC functions as a peptide binding domain. We use chemical shift perturbation analysis to identify the peptide binding site in PABC and the major elements involved in peptide recognition. From comparative sequence analysis of PABC-binding peptides, we formulate a preliminary PABC consensus sequence and identify human ataxin-2, the protein responsible for type 2 spinocerebellar ataxia (SCA2), as a potential PABC ligand.
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Affiliation(s)
- G Kozlov
- Department of Biochemistry, McGill University and Montreal Joint Center for Structural Biology, 3655 Promenade Sir William Osler, Montreal, QC, Canada H3G 1Y6
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Damha MJ, Noronha AM, Wilds CJ, Trempe JF, Denisov A, Pon RT, Gehring K. Properties of arabinonucleic acids (ANA & 20'F-ANA): implications for the design of antisense therapeutics that invoke RNase H cleavage of RNA. Nucleosides Nucleotides Nucleic Acids 2001; 20:429-40. [PMID: 11563058 DOI: 10.1081/ncn-100002317] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Inversion of configuration of the C2' position of RNA leads to a very unique nucleic acid structure: arabinonucleic acid (ANA). ANA, and its 2'-fluoro derivative (2'F-ANA) from hybrids with RNA that are capable of activating RNase H, resulting in cleavage of the RNA strand. In this paper, we review the properties of duplexes formed between ANA (or 2'F-ANA) and its RNA complement. These studies support the notion that RNase H is sensitive to the minor groove dimensions of the hybrid substrate.
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Affiliation(s)
- M J Damha
- Department of Chemistry, McGill University, Montreal, QC, Canada
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