1
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Clark NE, Schraut MR, Winters RA, Kearns K, Scanlon TC. An immuno-northern technique to measure the size of dsRNA byproducts in in vitro transcribed RNA. Electrophoresis 2024. [PMID: 38785136 DOI: 10.1002/elps.202400036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/01/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Double-stranded RNA is an immunogenic byproduct present in RNA synthesized with in vitro transcription. dsRNA byproducts engage virus-sensing innate immunity receptors and cause inflammation. Removing dsRNA from in vitro transcribed messenger RNA (mRNA) reduces immunogenicity and improves protein translation. Levels of dsRNA are typically 0.1%-0.5% of total transcribed RNA. Because they form such a minor fraction of the total RNA in transcription reactions, it is difficult to confidently identify discrete bands on agarose gels that correspond to the dsRNA byproducts. Thus, the sizes of dsRNA byproducts are largely unknown. Total levels of dsRNA are typically assayed with dsRNA-specific antibodies in ELISA and immuno dot-blot assays. Here we report a dsRNA-specific immuno-northern blot technique that provides a clear picture of the dsRNA size distributions in transcribed RNA. This technique could complement existing dsRNA analytical methods in studies of dsRNA byproduct synthesis, dsRNA removal, and characterization of therapeutic RNA drug substances.
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2
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Clark NE, Katolik A, Gallant P, Welch A, Murphy E, Buerer L, Schorl C, Naik N, Naik MT, Holloway SP, Cano K, Weintraub ST, Howard KM, Hart PJ, Jogl G, Damha MJ, Fairbrother WG. Activation of human RNA lariat debranching enzyme Dbr1 by binding protein TTDN1 occurs though an intrinsically disordered C-terminal domain. J Biol Chem 2023; 299:105100. [PMID: 37507019 PMCID: PMC10470207 DOI: 10.1016/j.jbc.2023.105100] [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: 04/26/2023] [Revised: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
In eukaryotic cells, the introns are excised from pre-mRNA by the spliceosome. These introns typically have a lariat configuration due to the 2'-5' phosphodiester bond between an internal branched residue and the 5' terminus of the RNA. The only enzyme known to selectively hydrolyze the 2'-5' linkage of these lariats is the RNA lariat debranching enzyme Dbr1. In humans, Dbr1 is involved in processes such as class-switch recombination of immunoglobulin genes, and its dysfunction is implicated in viral encephalitis, HIV, ALS, and cancer. However, mechanistic details of precisely how Dbr1 affects these processes are missing. Here we show that human Dbr1 contains a disordered C-terminal domain through sequence analysis and nuclear magnetic resonance. This domain stabilizes Dbr1 in vitro by reducing aggregation but is dispensable for debranching activity. We establish that Dbr1 requires Fe2+ for efficient catalysis and demonstrate that the noncatalytic protein Drn1 and the uncharacterized protein trichothiodystrophy nonphotosensitive 1 directly bind to Dbr1. We demonstrate addition of trichothiodystrophy nonphotosensitive 1 to in vitro debranching reactions increases the catalytic efficiency of human Dbr1 19-fold but has no effect on the activity of Dbr1 from the amoeba Entamoeba histolytica, which lacks a disordered C-terminal domain. Finally, we systematically examine how the identity of the branchpoint nucleotide affects debranching rates. These findings describe new aspects of Dbr1 function in humans and further clarify how Dbr1 contributes to human health and disease.
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Affiliation(s)
- Nathaniel E Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA.
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Pascal Gallant
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Eileen Murphy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Christoph Schorl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Nandita Naik
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Kristin Cano
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Katherine M Howard
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada-Las Vegas, Las Vegas, Nevada, USA
| | - P John Hart
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada.
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA.
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3
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Buerer L, Clark NE, Welch A, Duan C, Taggart AJ, Townley BA, Wang J, Soemedi R, Rong S, Lin CL, Zeng Y, Katolik A, Staley JP, Damha MJ, Mosammaparast N, Fairbrother WG. The debranching enzyme Dbr1 regulates lariat turnover and intron splicing. Res Sq 2023:rs.3.rs-2931976. [PMID: 37398028 PMCID: PMC10312976 DOI: 10.21203/rs.3.rs-2931976/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of the first viable DBR1 knockout cell line, we find the predominantly nuclear Dbr1 enzyme to encode the sole debranching activity in human cells. Dbr1 preferentially debranches substrates that contain canonical U2 binding motifs, suggesting that branchsites discovered through sequencing do not necessarily represent those favored by the spliceosome. We find that Dbr1 also exhibits specificity for particular 5' splice site sequences. We identify Dbr1 interactors through co-immunoprecipitation mass spectroscopy. We present a mechanistic model for Dbr1 recruitment to the branchpoint through the intron-binding protein AQR. In addition to a 20-fold increase in lariats, Dbr1 depletion increases exon skipping. Using ADAR fusions to timestamp lariats, we demonstrate a defect in spliceosome recycling. In the absence of Dbr1, spliceosomal components remain associated with the lariat for a longer period of time. As splicing is co-transcriptional, slower recycling increases the likelihood that downstream exons will be available for exon skipping.
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Affiliation(s)
- Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Nathaniel E. Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Allison J. Taggart
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Brittany A. Townley
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jing Wang
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Rachel Soemedi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Stephen Rong
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Chien-Ling Lin
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Yi Zeng
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Jonathan P. Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - William G. Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
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4
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Clark NE, Katolik A, Welch A, Schorl C, Holloway SP, Schuermann JP, Hart PJ, Taylor AB, Damha MJ, Fairbrother WG. Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product. Biochemistry 2022; 61:2933-2939. [PMID: 36484984 DOI: 10.1021/acs.biochem.2c00590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RNA lariat debranching enzyme is the sole enzyme responsible for hydrolyzing the 2'-5' phosphodiester bond in RNA lariats produced by the spliceosome. Here, we test the ability of Dbr1 to hydrolyze branched RNAs (bRNAs) that contain a 2'-5'-phosphorothioate linkage, a modification commonly used to resist degradation. We attempted to cocrystallize a phosphorothioate-branched RNA (PS-bRNA) with wild-type Entamoeba histolytica Dbr1 (EhDbr1) but observed in-crystal hydrolysis of the phosphorothioate bond. The crystal structure revealed EhDbr1 in a product-bound state, with the hydrolyzed 2'-5' fragment of the PS-bRNA mimicking the binding mode of the native bRNA substrate. These findings suggest that product inhibition may contribute to the kinetic mechanism of Dbr1. We show that Dbr1 enzymes cleave phosphorothioate linkages at rates ∼10,000-fold more slowly than native phosphate linkages. This new product-bound crystal structure offers atomic details, which can aid inhibitor design. Dbr1 inhibitors could be therapeutic or investigative compounds for human diseases such as human immunodeficiency virus (HIV), amyotrophic lateral sclerosis (ALS), cancer, and viral encephalitis.
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Affiliation(s)
- Nathaniel E. Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
| | - Christoph Schorl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
| | - Stephen P. Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Jonathan P. Schuermann
- Northeastern Collaborative Access Team, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - P. John Hart
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Alexander B. Taylor
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - William G. Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
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5
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Clark NE, Katolik A, Taggart AJ, Buerer L, Holloway SP, Miller N, Phillips JD, Farrell CP, Damha MJ, Fairbrother WG. Metal content and kinetic properties of yeast RNA lariat debranching enzyme Dbr1. RNA 2022; 28:927-936. [PMID: 35459748 PMCID: PMC9202583 DOI: 10.1261/rna.079159.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
In eukaryotic cells, intron lariats produced by the spliceosome contain a 2'5' phosphodiester linkage. The RNA lariat debranching enzyme, Dbr1, is the only enzyme known to hydrolyze this bond. Dbr1 is a member of the metallophosphoesterase (MPE) family of enzymes, and recent X-ray crystal structures and biochemistry data demonstrate that Dbr1 from Entamoeba histolytica uses combinations of Mn2+, Zn2+, and Fe2+ as enzymatic cofactors. Here, we examine the kinetic properties and metal dependence of the Dbr1 homolog from Saccharomyces cerevisiae (yDbr1). Elemental analysis measured stoichiometric quantities of Fe and Zn in yDbr1 purified following heterologous expression E. coli We analyzed the ability of Fe2+, Zn2+, and Mn2+ to reconstitute activity in metal-free apoenzyme. Purified yDbr1 was highly active, turning over substrate at 5.6 sec-1, and apo-yDbr1 reconstituted with Fe2+ was the most active species, turning over at 9.2 sec-1 We treated human lymphoblastoid cells with the iron-chelator deferoxamine and measured a twofold increase in cellular lariats. These data suggest that Fe is an important biological cofactor for Dbr1 enzymes.
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Affiliation(s)
- Nathaniel E Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Allison J Taggart
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, USA
| | - Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Nathaniel Miller
- Department of Geological Sciences, University of Texas Austin, Austin, Texas 78712, USA
| | - John D Phillips
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Colin P Farrell
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
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6
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Zhang SY, Clark NE, Freije CA, Pauwels E, Taggart A, Okada S, Mandel H, Garcia P, Ciancanelli MJ, Biran A, Lafaille FG, Tsumura M, Cobat A, Luo J, Volpi S, Zimmer B, Sakata S, Dinis A, Ohara O, Garcia Reino EJ, Dobbs K, Hasek M, Holloway SP, McCammon K, Hussong SA, DeRosa N, Van Skike CE, Katolik A, Lorenzo L, Hyodo M, Faria E, Halwani R, Fukuhara R, Smith GA, Galvan V, Damha MJ, Al-Muhsen S, Itan Y, Boeke JD, Notarangelo LD, Studer L, Kobayashi M, Diogo L, Fairbrother W, Abel L, Rosenberg B, Hart J, Etzioni A, Casanova JL. Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection. Cell 2018; 172:952-965.e18. [PMID: 29474921 PMCID: PMC5886375 DOI: 10.1016/j.cell.2018.02.019] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [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: 06/09/2017] [Revised: 12/03/2017] [Accepted: 02/07/2018] [Indexed: 01/05/2023]
Abstract
Viruses that are typically benign sometimes invade the brainstem in otherwise healthy children. We report bi-allelic DBR1 mutations in unrelated patients from different ethnicities, each of whom had brainstem infection due to herpes simplex virus 1 (HSV1), influenza virus, or norovirus. DBR1 encodes the only known RNA lariat debranching enzyme. We show that DBR1 expression is ubiquitous, but strongest in the spinal cord and brainstem. We also show that all DBR1 mutant alleles are severely hypomorphic, in terms of expression and function. The fibroblasts of DBR1-mutated patients contain higher RNA lariat levels than control cells, this difference becoming even more marked during HSV1 infection. Finally, we show that the patients' fibroblasts are highly susceptible to HSV1. RNA lariat accumulation and viral susceptibility are rescued by wild-type DBR1. Autosomal recessive, partial DBR1 deficiency underlies viral infection of the brainstem in humans through the disruption of tissue-specific and cell-intrinsic immunity to viruses.
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Affiliation(s)
- Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch,
INSERM U1163, Paris 75015, France,Paris Descartes University, Imagine Institute, Paris 75015,
France
| | - Nathaniel E. Clark
- Department of Biochemistry and Structural Biology, University of
Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Catherine A. Freije
- Program in Immunogenomics, The Rockefeller University, New York, NY
10065, USA
| | - Elodie Pauwels
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Allison Taggart
- Center for Computational Molecular Biology, Brown University,
Providence, RI 02912, USA
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of
Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Hanna Mandel
- Metabolic Unit, Ruth Children’s Hospital, Haifa 31096,
Israel,Rappaport Faculty of Medicine, Haifa 31096, Israel
| | - Paula Garcia
- Pediatric Hospital of Coimbra, Coimbra 3000-075, Portugal
| | - Michael J. Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Anat Biran
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Fabien G. Lafaille
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Miyuki Tsumura
- Center for Computational Molecular Biology, Brown University,
Providence, RI 02912, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch,
INSERM U1163, Paris 75015, France,Paris Descartes University, Imagine Institute, Paris 75015,
France
| | - Jingchuan Luo
- Department of Molecular Biology & Genetics, JHU School of
Medicine, Baltimore, MD 21205, USA,Institute for Systems Genetics, New York University Langone Medical
Center, New York 10016, NY, USA
| | - Stefano Volpi
- Department of Pediatrics, Giannina Gaslini Institute, Genoa 16100,
Italy
| | - Bastian Zimmer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for
Cancer Research, New York, NY 10065, USA
| | - Sonoko Sakata
- Department of Pediatrics, Hiroshima University Graduate School of
Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Alexandra Dinis
- Pediatric Intensive Care Unit, Hospital Pediátrico, Centro
Hospitalar e Universitário de Coimbra 3000-075, Portugal
| | - Osamu Ohara
- Department of Technology Development, Kazusa DNA Research
Institute, Chiba 292-0818, Japan,Laboratory for Integrative Genomics, RIKEN Center for Integrative
Medical Sciences, Yokohama 230-0045, Japan
| | - Eduardo J. Garcia Reino
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National
Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892-1456,
USA
| | - Mary Hasek
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Stephen P. Holloway
- Department of Biochemistry and Structural Biology, University of
Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karen McCammon
- Department of Biochemistry and Structural Biology, University of
Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Stacy A. Hussong
- Department of Cellular and Integrative Physiology and The Barshop
Institute for Longevity and Aging Studies, University of Texas Health Science Center
at San Antonio, TX 78229, USA
| | - Nicholas DeRosa
- Department of Cellular and Integrative Physiology and The Barshop
Institute for Longevity and Aging Studies, University of Texas Health Science Center
at San Antonio, TX 78229, USA
| | - Candice E. Van Skike
- Department of Cellular and Integrative Physiology and The Barshop
Institute for Longevity and Aging Studies, University of Texas Health Science Center
at San Antonio, TX 78229, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montréal
H3A0G4, Canada
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch,
INSERM U1163, Paris 75015, France,Paris Descartes University, Imagine Institute, Paris 75015,
France
| | - Maki Hyodo
- Department of Obstetrics and Gynecology, Hiroshima University
Graduate School of Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Emilia Faria
- Immuno-Allergy Department, Hospital and University of Coimbra,
3000-075 Portugal
| | - Rabih Halwani
- Immunology Research Laboratory, Department of Pediatrics, College
of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Rie Fukuhara
- Department of Neonatology, Hiroshima Prefectural Hospital,
Hiroshima 734-8551, Japan
| | - Gregory A. Smith
- Department of Microbiology-Immunology, Northwestern University
Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Veronica Galvan
- Department of Cellular and Integrative Physiology and The Barshop
Institute for Longevity and Aging Studies, University of Texas Health Science Center
at San Antonio, TX 78229, USA
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montréal
H3A0G4, Canada
| | - Saleh Al-Muhsen
- Immunology Research Laboratory, Department of Pediatrics, College
of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA,The Charles Bronfman Institute for Personalized Medicine, Icahn
School of Medicine at Mount Sinai, New York, NY 10029, USA,Department of Genetics and Genomics, Icahn School of Medicine at
Mount Sinai, New York, NY 10029, USA
| | - Jef D. Boeke
- Department of Molecular Biology & Genetics, JHU School of
Medicine, Baltimore, MD 21205, USA
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National
Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892-1456,
USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for
Cancer Research, New York, NY 10065, USA
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of
Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Luisa Diogo
- Pediatric Hospital of Coimbra, Coimbra 3000-075, Portugal
| | - William Fairbrother
- Center for Computational Molecular Biology, Brown University,
Providence, RI 02912, USA,Hassenfeld Child Health Innovation Institute, Brown University,
Providence, RI 02912, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch,
INSERM U1163, Paris 75015, France,Paris Descartes University, Imagine Institute, Paris 75015,
France
| | - Brad Rosenberg
- Program in Immunogenomics, The Rockefeller University, New York, NY
10065, USA,Department of Microbiology, Icahn School of Medicine at Mount
Sinai, New York, NY 10029, USA
| | - John Hart
- Department of Biochemistry and Structural Biology, University of
Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA,X-ray Crystallography Core Laboratory, University of Texas Health
Science Center at San Antonio, San Antonio, TX 78229, USA,Department of Veterans Affairs, South Texas Veterans Health Care
System, San Antonio, TX 78229, USA
| | - Amos Etzioni
- Metabolic Unit, Ruth Children’s Hospital, Haifa 31096,
Israel,Rappaport Faculty of Medicine, Haifa 31096, Israel
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases,
Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch,
INSERM U1163, Paris 75015, France,Paris Descartes University, Imagine Institute, Paris 75015,
France,Howard Hughes Medical Institute, New York, NY 10065, USA,Pediatric Immunology-Hematology Unit, Necker Hospital for Sick
Children, Paris 75015, France
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7
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Taylor AB, Roberts KM, Cao X, Clark NE, Holloway SP, Donati E, Polcaro CM, Pica-Mattoccia L, Tarpley RS, McHardy SF, Cioli D, LoVerde PT, Fitzpatrick PF, Hart PJ. Structural and enzymatic insights into species-specific resistance to schistosome parasite drug therapy. J Biol Chem 2017; 292:11154-11164. [PMID: 28536265 PMCID: PMC5500785 DOI: 10.1074/jbc.m116.766527] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 11/07/2016] [Revised: 05/17/2017] [Indexed: 02/05/2023] Open
Abstract
The antischistosomal prodrug oxamniquine is activated by a sulfotransferase (SULT) in the parasitic flatworm Schistosoma mansoni. Of the three main human schistosome species, only S. mansoni is sensitive to oxamniquine therapy despite the presence of SULT orthologs in Schistosoma hematobium and Schistosoma japonicum The reason for this species-specific drug action has remained a mystery for decades. Here we present the crystal structures of S. hematobium and S. japonicum SULTs, including S. hematobium SULT in complex with oxamniquine. We also examined the activity of the three enzymes in vitro; surprisingly, all three are active toward oxamniquine, yet we observed differences in catalytic efficiency that implicate kinetics as the determinant for species-specific toxicity. These results provide guidance for designing oxamniquine derivatives to treat infection caused by all species of schistosome to combat emerging resistance to current therapy.
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Affiliation(s)
- Alexander B Taylor
- From the Departments of Biochemistry and Structural Biology and
- the X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Kenneth M Roberts
- Department of Chemistry and Physics, University of South Carolina, Aiken, South Carolina 29801
| | - Xiaohang Cao
- From the Departments of Biochemistry and Structural Biology and
| | | | | | - Enrica Donati
- Institute of Chemical Methodologies, Consiglio Nazionale delle Ricerche, Via Salaria Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Chiara M Polcaro
- Institute of Chemical Methodologies, Consiglio Nazionale delle Ricerche, Via Salaria Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Livia Pica-Mattoccia
- Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche, Via E. Ramarini 32, 00015 Monterotondo, Rome, Italy
| | - Reid S Tarpley
- Center for Innovative Drug Discovery, Department of Chemistry, University of Texas, San Antonio, Texas 78249, and
| | - Stanton F McHardy
- Center for Innovative Drug Discovery, Department of Chemistry, University of Texas, San Antonio, Texas 78249, and
| | - Donato Cioli
- Institute of Chemical Methodologies, Consiglio Nazionale delle Ricerche, Via Salaria Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Philip T LoVerde
- From the Departments of Biochemistry and Structural Biology and
- Pathology and
| | | | - P John Hart
- From the Departments of Biochemistry and Structural Biology and
- the X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, Texas 78229
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229
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8
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Katolik A, Clark NE, Tago N, Montemayor EJ, Hart PJ, Damha MJ. Fluorescent Branched RNAs for High-Throughput Analysis of Dbr1 Enzyme Kinetics and Inhibition. ACS Chem Biol 2017; 12:622-627. [PMID: 28055181 DOI: 10.1021/acschembio.6b00971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed fluorescent 2',5' branched RNAs (bRNA) that permit real time monitoring of RNA lariat (intron) debranching enzyme (Dbr1) kinetics. These compounds contain fluorescein (FAM) on the 5' arm of the bRNA that is quenched by a dabcyl moiety on the 2' arm. Dbr1-mediated hydrolysis of the 2',5' linkage induces a large increase in fluorescence, providing a convenient assay for Dbr1 hydrolysis. We show that unlabeled bRNAs with non-native 2',5'-phosphodiester linkages, such as phosphoramidate or phosphorothioate, can inhibit Dbr1-mediated debranching with IC50 values in the low nanomolar range. In addition to measuring kinetic parameters of the debranching enzyme, these probes can be used for high throughput screening (HTS) of chemical libraries with the aim of identifying Dbr1 inhibitors, compounds that may be useful in treating neurodegenerative diseases and retroviral infections.
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Affiliation(s)
- Adam Katolik
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Nathaniel E. Clark
- Department
of Biochemistry and Structural Biology, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Nobuhiro Tago
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Eric J. Montemayor
- Departments
of Biochemistry and Biomolecular Chemistry, University Of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - P. John Hart
- Department
of Biochemistry and Structural Biology, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Department
of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, United States
| | - Masad J. Damha
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
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9
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Tago N, Katolik A, Clark NE, Montemayor EJ, Seio K, Sekine M, Hart PJ, Damha MJ. Design, Synthesis, and Properties of Phosphoramidate 2',5'-Linked Branched RNA: Toward the Rational Design of Inhibitors of the RNA Lariat Debranching Enzyme. J Org Chem 2015; 80:10108-18. [PMID: 26378468 PMCID: PMC4749351 DOI: 10.1021/acs.joc.5b01719] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Two RNA fragments linked by means of a 2',5' phosphodiester bridge (2' hydroxyl of one fragment connected to the 5' hydroxyl of the other) constitute a class of nucleic acids known as 2'-5' branched RNAs (bRNAs). In this report we show that bRNA analogues containing 2'-5' phosphoramidate linkages (bN-RNAs) inhibit the lariat debranching enzyme, a 2',5'-phosphodiesterase that has recently been implicated in neurodegenerative diseases associated with aging. bN-RNAs were efficiently generated using automated solid-phase synthesis and suitably protected branchpoint building blocks. Two orthogonally removable groups, namely the 4-monomethoxytrityl (MMTr) group and the fluorenylmethyl-oxycarbonyl (Fmoc) groups, were evaluated as protecting groups of the 2' amino functionality. The 2'-N-Fmoc methodology was found to successfully produce bN-RNAs on solid-phase oligonucleotide synthesis. The synthesized bN-RNAs resisted hydrolysis by the lariat debranching enzyme (Dbr1) and, in addition, were shown to attenuate the Dbr1-mediated hydrolysis of native bRNA.
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Affiliation(s)
- Nobuhiro Tago
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama, Kanagawa, 226-8501, Japan
| | - Adam Katolik
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Nathaniel E. Clark
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, United States
| | - Eric J. Montemayor
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, United States
- Departments of Biochemistry and Biomolecular Chemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, United States
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama, Kanagawa, 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama, Kanagawa, 226-8501, Japan
| | - P. John Hart
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, United States
- Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, United States
| | - Masad J. Damha
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
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10
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Montemayor EJ, Katolik A, Clark NE, Taylor AB, Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens SW, Damha MJ, Hart PJ. Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1. Nucleic Acids Res 2014; 42:10845-55. [PMID: 25123664 PMCID: PMC4176325 DOI: 10.1093/nar/gku725] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The enzymatic processing of cellular RNA molecules requires selective recognition of unique chemical and topological features. The unusual 2',5'-phosphodiester linkages in RNA lariats produced by the spliceosome must be hydrolyzed by the intron debranching enzyme (Dbr1) before they can be metabolized or processed into essential cellular factors, such as snoRNA and miRNA. Dbr1 is also involved in the propagation of retrotransposons and retroviruses, although the precise role played by the enzyme in these processes is poorly understood. Here, we report the first structures of Dbr1 alone and in complex with several synthetic RNA compounds that mimic the branchpoint in lariat RNA. The structures, together with functional data on Dbr1 variants, reveal the molecular basis for 2',5'-phosphodiester recognition and explain why the enzyme lacks activity toward 3',5'-phosphodiester linkages. The findings illuminate structure/function relationships in a unique enzyme that is central to eukaryotic RNA metabolism and set the stage for the rational design of inhibitors that may represent novel therapeutic agents to treat retroviral infections and neurodegenerative disease.
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Affiliation(s)
- Eric J Montemayor
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA X-ray Crystallography Core Laboratory, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Nathaniel E Clark
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA X-ray Crystallography Core Laboratory, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Alexander B Taylor
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA X-ray Crystallography Core Laboratory, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jonathan P Schuermann
- Northeastern Collaborative Access Team, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - D Joshua Combs
- Program in Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78212, USA
| | - Richard Johnsson
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Stephen P Holloway
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Scott W Stevens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - P John Hart
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA X-ray Crystallography Core Laboratory, The University of Texas Health Science Center, San Antonio, TX 78229, USA Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, USA
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11
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Rood KL, Clark NE, Stoddard PR, Garman SC, Chien P. Adaptor-dependent degradation of a cell-cycle regulator uses a unique substrate architecture. Structure 2012; 20:1223-32. [PMID: 22682744 DOI: 10.1016/j.str.2012.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 03/15/2012] [Accepted: 04/25/2012] [Indexed: 01/31/2023]
Abstract
In Caulobacter crescentus, the ClpXP protease degrades several crucial cell-cycle regulators, including the phosphodiesterase PdeA. Degradation of PdeA requires the response regulator CpdR and signals a morphological transition in concert with initiation of DNA replication. Here, we report the structure of a Per-Arnt-Sim (PAS) domain of PdeA and show that it is necessary for CpdR-dependent degradation in vivo and in vitro. CpdR acts as an adaptor, tethering the amino-terminal PAS domain to ClpXP and promoting recognition of the weak carboxyl-terminal degron of PdeA, a combination that ensures processive proteolysis. We identify sites on the PAS domain needed for CpdR recognition and find that one subunit of the PdeA dimer can be delivered to ClpXP by its partner. Finally, we show that improper stabilization of PdeA in vivo alters cellular behavior. These results introduce an adaptor/substrate pair for ClpXP and reveal broad diversity in adaptor-mediated proteolysis.
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Affiliation(s)
- Keith L Rood
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA
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12
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Guce AI, Clark NE, Rogich JJ, Garman SC. The molecular basis of pharmacological chaperoning in human α-galactosidase. ACTA ACUST UNITED AC 2012; 18:1521-6. [PMID: 22195554 DOI: 10.1016/j.chembiol.2011.10.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 10/14/2022]
Abstract
Fabry disease patients show a deficiency in the activity of the lysosomal enzyme α-galactosidase (α-GAL or α-Gal A). One proposed treatment for Fabry disease is pharmacological chaperone therapy, where a small molecule stabilizes the α-GAL protein, leading to increased enzymatic activity. Using enzyme kinetics, tryptophan fluorescence, circular dichroism, and proteolysis assays, we show that the pharmacological chaperones 1-deoxygalactonojirimycin (DGJ) and galactose stabilize the human α-GAL glycoprotein. Crystal structures of complexes of α-GAL and chaperones explain the molecular basis for the higher potency of DGJ over galactose. Using site-directed mutagenesis, we show the higher potency of DGJ results from an ionic interaction with D170. We propose that protonation of D170 in acidic conditions leads to weaker binding of DGJ. The results establish a biochemical basis for pharmacological chaperone therapy applicable to other protein misfolding diseases.
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Affiliation(s)
- Abigail I Guce
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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13
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Tomasic IB, Metcalf MC, Guce AI, Clark NE, Garman SC. Interconversion of the specificities of human lysosomal enzymes associated with Fabry and Schindler diseases. J Biol Chem 2010; 285:21560-6. [PMID: 20444686 PMCID: PMC2898384 DOI: 10.1074/jbc.m110.118588] [Citation(s) in RCA: 23] [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: 02/26/2010] [Revised: 04/23/2010] [Indexed: 11/06/2022] Open
Abstract
The human lysosomal enzymes alpha-galactosidase (alpha-GAL, EC 3.2.1.22) and alpha-N-acetylgalactosaminidase (alpha-NAGAL, EC 3.2.1.49) share 46% amino acid sequence identity and have similar folds. The active sites of the two enzymes share 11 of 13 amino acids, differing only where they interact with the 2-position of the substrates. Using a rational protein engineering approach, we interconverted the enzymatic specificity of alpha- GAL and alpha-NAGAL. The engineered alpha-GAL (which we call alpha-GAL(SA)) retains the antigenicity of alpha-GAL but has acquired the enzymatic specificity of alpha-NAGAL. Conversely, the engineered alpha-NAGAL (which we call alpha-NAGAL(EL)) retains the antigenicity of alpha-NAGAL but has acquired the enzymatic specificity of the alpha-GAL enzyme. Comparison of the crystal structures of the designed enzyme alpha-GAL(SA) to the wild-type enzymes shows that active sites of alpha-GAL(SA) and alpha-NAGAL superimpose well, indicating success of the rational design. The designed enzymes might be useful as non-immunogenic alternatives in enzyme replacement therapy for treatment of lysosomal storage disorders such as Fabry disease.
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Affiliation(s)
- Ivan B. Tomasic
- From the Departments of Biochemistry & Molecular Biology and
| | | | - Abigail I. Guce
- Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | | | - Scott C. Garman
- From the Departments of Biochemistry & Molecular Biology and
- Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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14
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Guce AI, Clark NE, Salgado EN, Ivanen DR, Kulminskaya AA, Brumer H, Garman SC. Catalytic mechanism of human alpha-galactosidase. J Biol Chem 2010; 285:3625-3632. [PMID: 19940122 PMCID: PMC2823503 DOI: 10.1074/jbc.m109.060145] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 11/06/2009] [Indexed: 11/06/2022] Open
Abstract
The enzyme alpha-galactosidase (alpha-GAL, also known as alpha-GAL A; E.C. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. Defects in human alpha-GAL lead to the development of Fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-GAL is an active target of clinical research: there are currently two treatment options for Fabry disease, recombinant enzyme replacement therapy (approved in the United States in 2003) and pharmacological chaperone therapy (currently in clinical trials). Previously, we have reported the structure of human alpha-GAL, which revealed the overall structure of the enzyme and established the locations of hundreds of mutations that lead to the development of Fabry disease. Here, we describe the catalytic mechanism of the enzyme derived from x-ray crystal structures of each of the four stages of the double displacement reaction mechanism. Use of a difluoro-alpha-galactopyranoside allowed trapping of a covalent intermediate. The ensemble of structures reveals distortion of the ligand into a (1)S(3) skew (or twist) boat conformation in the middle of the reaction cycle. The high resolution structures of each step in the catalytic cycle will allow for improved drug design efforts on alpha-GAL and other glycoside hydrolase family 27 enzymes by developing ligands that specifically target different states of the catalytic cycle. Additionally, the structures revealed a second ligand-binding site suitable for targeting by novel pharmacological chaperones.
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Affiliation(s)
- Abigail I Guce
- Departments of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Nathaniel E Clark
- From the Departments of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Eric N Salgado
- From the Departments of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Dina R Ivanen
- the Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute, Russian Academy of Science, Orlova Roscha, Gatchina 188300, Leningrad District, Russia, and
| | - Anna A Kulminskaya
- the Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute, Russian Academy of Science, Orlova Roscha, Gatchina 188300, Leningrad District, Russia, and
| | - Harry Brumer
- the Department of Biotechnology, Royal Insitute of Technology (KTH), 10691 Stockholm, Sweden
| | - Scott C Garman
- Departments of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003; From the Departments of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003.
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15
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Clark NE, Garman SC. The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases. J Mol Biol 2009; 393:435-47. [PMID: 19683538 PMCID: PMC2771859 DOI: 10.1016/j.jmb.2009.08.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/30/2009] [Accepted: 08/04/2009] [Indexed: 01/07/2023]
Abstract
alpha-N-acetylgalactosaminidase (alpha-NAGAL; E.C. 3.2.1.49) is a lysosomal exoglycosidase that cleaves terminal alpha-N-acetylgalactosamine residues from glycopeptides and glycolipids. In humans, a deficiency of alpha-NAGAL activity results in the lysosomal storage disorders Schindler disease and Kanzaki disease. To better understand the molecular defects in the diseases, we determined the crystal structure of human alpha-NAGAL after expressing wild-type and glycosylation-deficient glycoproteins in recombinant insect cell expression systems. We measured the enzymatic parameters of our purified wild-type and mutant enzymes, establishing their enzymatic equivalence. To investigate the binding specificity and catalytic mechanism of the human alpha-NAGAL enzyme, we determined three crystallographic complexes with different catalytic products bound in the active site of the enzyme. To better understand how individual defects in the alpha-NAGAL glycoprotein lead to Schindler disease, we analyzed the effect of disease-causing mutations on the three-dimensional structure.
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Affiliation(s)
- Nathaniel E Clark
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, 01003, USA
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16
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Abstract
Talonavicular coalition is a rare entity and is often discovered as a secondary radiographic finding. Today, orthoses are as varied as the patients for whom they are prescribed; however, in cases of symptomatic talonavicular fusion, the use of a shallow U-shaped dispersion within the high medial flange of an orthosis can prove beneficial to the pediatric patient. This article encourages podiatric physicians to return to utilizing basic diagnostic tools (gait analysis, biomechanical examination, and radiographs) to detect and treat talonavicular coalition, a significant but rare anomaly of the foot.
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Affiliation(s)
- D R David
- Department of Pediatrics, New York College of Podiatric Medicine, NY 10035, USA
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17
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Abstract
A case of a rare genetic disorder with typical lower extremity and gait alterations as the chief concern was presented. A description of the characteristic lower extremity and gait manifestations of this syndrome has been developed. The major and minor diagnostic criteria, which have been published to identify this syndrome, were reviewed with respect to this case. The practitioner who has the opportunity to evaluate patients for gait and lower extremity complaints should be aware of these correlations to aid in timely diagnosis of this condition. Management of compensations from these lower extremity pathologies may improve stability and prognosis for normal function. Management may also include surgical correlation of deformities found in association with this syndrome.
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Affiliation(s)
- R G Volpe
- New York College of Podiatric Medicine, New York, USA
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