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Gil-Martínez J, Bernardo-Seisdedos G, Mato JM, Millet O. The use of pharmacological chaperones in rare diseases caused by reduced protein stability. Proteomics 2022; 22:e2200222. [PMID: 36205620 DOI: 10.1002/pmic.202200222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
Rare diseases are most often caused by inherited genetic disorders that, after translation, will result in a protein with altered function. Decreased protein stability is the most frequent mechanism associated with a congenital pathogenic missense mutation and it implies the destabilization of the folded conformation in favour of unfolded or misfolded states. In the cellular context and when experimental data is available, a mutant protein with altered thermodynamic stability often also results in impaired homeostasis, with the deleterious accumulation of protein aggregates, metabolites and/or metabolic by-products. In the last decades, a significant effort has enabled the characterization of rare diseases associated to protein stability defects and triggered the development of innovative therapeutic intervention lines, say, the use of pharmacological chaperones to correct the intracellular impaired homeostasis. Here, we review the current knowledge on rare diseases caused by reduced protein stability, paying special attention to the thermodynamic aspects of the protein destabilization, also focusing on some examples where pharmacological chaperones are being tested.
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Affiliation(s)
- Jon Gil-Martínez
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain
| | | | - José M Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.,ATLAS Molecular Pharma, Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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2
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San Juan I, Pereira-Ortuzar T, Cendoya X, Laín A, To-Figueras J, Mateos B, Planes FJ, Bernardo-Seisdedos G, Mato JM, Millet O. ALAD Inhibition by Porphobilinogen Rationalizes the Accumulation of δ-Aminolevulinate in Acute Porphyrias. Biochemistry 2022; 61:2409-2416. [PMID: 36241173 DOI: 10.1021/acs.biochem.2c00434] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Patients with major forms of acute hepatic porphyria present acute neurological attacks with overproduction of porphobilinogen (PBG) and δ-aminolevulinic acid (ALA). Even if ALA is considered the most likely agent inducing the acute symptoms, the mechanism of its accumulation has not been experimentally demonstrated. In the most frequent form, acute intermittent porphyria (AIP), inherited gene mutations induce a deficiency in PBG deaminase; thus, accumulation of the substrate PBG is biochemically obligated but not that of ALA. A similar scenario is observed in other forms of acute hepatic porphyria (i.e., porphyria variegate, VP) in which PBG deaminase is inhibited by metabolic intermediates. Here, we have investigated the molecular basis of δ-aminolevulinate accumulation using in vitro fluxomics monitored by NMR spectroscopy and other biophysical techniques. Our results show that porphobilinogen, the natural product of δ-aminolevulinate deaminase, effectively inhibits its anabolic enzyme at abnormally low concentrations. Structurally, this high affinity can be explained by the interactions that porphobilinogen generates with the active site, most of them shared with the substrate. Enzymatically, our flux analysis of an altered heme pathway demonstrates that a minimum accumulation of porphobilinogen will immediately trigger the accumulation of δ-aminolevulinate, a long-lasting observation in patients suffering from acute porphyrias.
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Affiliation(s)
- Itxaso San Juan
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Tania Pereira-Ortuzar
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Xabier Cendoya
- , Universidad de Navarra, Tecnun Escuela de Ingeniería y Centro de Ingeniería Biomédica, San Sebastián 20009, Spain
| | - Ana Laín
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Jordi To-Figueras
- Biochemistry and Molecular Genetics Unit, Hospital Clinic, IDIBAPS, University of Barcelona, Villarroel 170, 08036 Barcelona, Spain
| | - Borja Mateos
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Francisco J Planes
- , Universidad de Navarra, Tecnun Escuela de Ingeniería y Centro de Ingeniería Biomédica, San Sebastián 20009, Spain.,Universidad de Navarra, DATAI Instituto de Ciencia de los Datos e Inteligencia Artificial, Pamplona 31009, Spain
| | - Ganeko Bernardo-Seisdedos
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain.,ATLAS Molecular Pharma, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - José M Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain.,Biomedical Research Network on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain.,ATLAS Molecular Pharma, Bizkaia Science and Technology Park, 48160 Derio, Spain.,Biomedical Research Network on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid 28029, Spain
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3
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Bernardo‐Seisdedos G, Bilbao J, Fernández‐Ramos D, Lopitz‐Otsoa F, Gutierrez de Juan V, Bizkarguenaga M, Mateos B, Fondevila MF, Abril‐Fornaguera J, Diercks T, Lu SC, Nogueiras R, Mato JM, Millet O. Metabolic Landscape of the Mouse Liver by Quantitative 31 P Nuclear Magnetic Resonance Analysis of the Phosphorome. Hepatology 2021; 74:148-163. [PMID: 33284502 PMCID: PMC8362057 DOI: 10.1002/hep.31676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/31/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS The liver plays a central role in all metabolic processes in the body. However, precise characterization of liver metabolism is often obscured by its inherent complexity. Phosphorylated metabolites occupy a prominent position in all anabolic and catabolic pathways. Here, we develop a 31 P nuclear magnetic resonance (NMR)-based method to study the liver "phosphorome" through the simultaneous identification and quantification of multiple hydrophilic and hydrophobic phosphorylated metabolites. APPROACH AND RESULTS We applied this technique to define the metabolic landscape in livers from a mouse model of the rare disease disorder congenital erythropoietic porphyria (CEP) as well as two well-known murine models of nonalcoholic steatohepatitis: one genetic, methionine adenosyltransferase 1A knockout mice, and the other dietary, mice fed a high-fat choline-deficient diet. We report alterations in the concentrations of phosphorylated metabolites that are readouts of the balance between glycolysis, gluconeogenesis, the pentose phosphate pathway, the tricarboxylic acid cycle, and oxidative phosphorylation and of phospholipid metabolism and apoptosis. Moreover, these changes correlate with the main histological features: steatosis, apoptosis, iron deposits, and fibrosis. Strikingly, treatment with the repurposed drug ciclopirox improves the phosphoromic profile of CEP mice, an effect that was mirrored by the normalization of liver histology. CONCLUSIONS In conclusion, these findings indicate that NMR-based phosphoromics may be used to unravel metabolic phenotypes of liver injury and to identify the mechanism of drug action.
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Affiliation(s)
- Ganeko Bernardo‐Seisdedos
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain,ATLAS Molecular Pharma S. L.DerioSpain
| | - Jon Bilbao
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain
| | - David Fernández‐Ramos
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain,CIBERehdInstituto de Salud Carlos IIIMadridSpain
| | - Fernando Lopitz‐Otsoa
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain
| | - Virginia Gutierrez de Juan
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain
| | - Maider Bizkarguenaga
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain
| | - Borja Mateos
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain,Department of Structural and Computational BiologyUniversity of ViennaMax Perutz LabsVienna Biocenter Campus 5ViennaAustria
| | - Marcos F. Fondevila
- Department of PhysiologyCIMUSUniversity of Santiago de Compostela‐Instituto de Investigación SanitariaSantiago de CompostelaSpain,CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn)Santiago de CompostelaSpain
| | - Jordi Abril‐Fornaguera
- Liver Cancer Translational Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Hospital ClínicUniversitat de BarcelonaBarcelonaCataloniaSpain
| | - Tammo Diercks
- NMR PlatformCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaBizkaiaSpain
| | - Shelly C. Lu
- Division of Digestive and Liver DiseasesDepartment of MedicineCedars‐Sinai Medical CenterLos AngelesCA
| | - Rubén Nogueiras
- Department of PhysiologyCIMUSUniversity of Santiago de Compostela‐Instituto de Investigación SanitariaSantiago de CompostelaSpain,CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn)Santiago de CompostelaSpain
| | - José M. Mato
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain,CIBERehdInstituto de Salud Carlos IIIMadridSpain
| | - Oscar Millet
- Precision Medicine and Metabolism LaboratoryCIC bioGUNEBasque Research and Technology AllianceParque Tecnológico de BizkaiaDerioSpain,ATLAS Molecular Pharma S. L.DerioSpain
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4
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Bernardo-Seisdedos G, Charco JM, SanJuan I, García-Martínez S, Urquiza P, Eraña H, Castilla J, Millet O. Improving the Pharmacological Properties of Ciclopirox for Its Use in Congenital Erythropoietic Porphyria. J Pers Med 2021; 11:485. [PMID: 34071291 DOI: 10.3390/jpm11060485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
Congenital erythropoietic porphyria (CEP), also known as Günther's disease, results from a deficient activity in the fourth enzyme, uroporphyrinogen III synthase (UROIIIS), of the heme pathway. Ciclopirox (CPX) is an off-label drug, topically prescribed as an antifungal. It has been recently shown that it also acts as a pharmacological chaperone in CEP, presenting a specific activity in deleterious mutations in UROIIIS. Despite CPX is active at subtoxic concentrations, acute gastrointestinal (GI) toxicity was found due to the precipitation in the stomach of the active compound and subsequent accumulation in the intestine. To increase its systemic availability, we carried out pharmacokinetic (PK) and pharmacodynamic (PD) studies using alternative formulations for CPX. Such strategy effectively suppressed GI toxicity in WT mice and in a mouse model of the CEP disease (UROIIISP248Q/P248Q). In terms of activity, phosphorylation of CPX yielded good results in CEP cellular models but showed limited activity when administered to the CEP mouse model. These results highlight the need of a proper formulation for pharmacological chaperones used in the treatment of rare diseases.
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Pacheco-García JL, Cano-Muñoz M, Sánchez-Ramos I, Salido E, Pey AL. Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein. J Pers Med 2020; 10:E207. [PMID: 33153185 PMCID: PMC7711955 DOI: 10.3390/jpm10040207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 10/07/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022] Open
Abstract
The functional and pathological implications of the enormous genetic diversity of the human genome are mostly unknown, primarily due to our unability to predict pathogenicity in a high-throughput manner. In this work, we characterized the phenotypic consequences of eight naturally-occurring missense variants on the multifunctional and disease-associated NQO1 protein using biophysical and structural analyses on several protein traits. Mutations found in both exome-sequencing initiatives and in cancer cell lines cause mild to catastrophic effects on NQO1 stability and function. Importantly, some mutations perturb functional features located structurally far from the mutated site. These effects are well rationalized by considering the nature of the mutation, its location in protein structure and the local stability of its environment. Using a set of 22 experimentally characterized mutations in NQO1, we generated experimental scores for pathogenicity that correlate reasonably well with bioinformatic scores derived from a set of commonly used algorithms, although the latter fail to semiquantitatively predict the phenotypic alterations caused by a significant fraction of mutations individually. These results provide insight into the propagation of mutational effects on multifunctional proteins, the implementation of in silico approaches for establishing genotype-phenotype correlations and the molecular determinants underlying loss-of-function in genetic diseases.
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Affiliation(s)
- Juan Luis Pacheco-García
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Mario Cano-Muñoz
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Isabel Sánchez-Ramos
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, 38320 Tenerife, Spain;
| | - Angel L. Pey
- Departamento de Química Física y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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6
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Abstract
![]()
Evolutionary processes that led to the emergence of structured
protein domains left footprints in the sequences of modern proteins.
We searched for such hints employing state-of-the-art sequence analysis
and found evidence that the HemD-like fold emerged from the flavodoxin-like
fold through segment swap and gene duplication. To verify this hypothesis,
we reverted these evolutionary steps experimentally, constructing
a HemD-half that resulted in a protein with the canonical flavodoxin-like
architecture. These results of fold reconstruction from the sequence
of a different fold strongly support our hypothesis of common ancestry.
It further illustrates the plasticity of modern proteins to form new
folded proteins.
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Affiliation(s)
- Saacnicteh Toledo-Patiño
- Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany.,Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
| | - Manish Chaubey
- Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
| | - Murray Coles
- Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
| | - Birte Höcker
- Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany.,Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
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7
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Urquiza P, Laín A, Sanz-Parra A, Moreno J, Bernardo-Seisdedos G, Dubus P, González E, Gutiérrez-de-Juan V, García S, Eraña H, San Juan I, Macías I, Ben Bdira F, Pluta P, Ortega G, Oyarzábal J, González-Muñiz R, Rodríguez-Cuesta J, Anguita J, Díez E, Blouin JM, de Verneuil H, Mato JM, Richard E, Falcón-Pérez JM, Castilla J, Millet O. Repurposing ciclopirox as a pharmacological chaperone in a model of congenital erythropoietic porphyria. Sci Transl Med 2019; 10:10/459/eaat7467. [PMID: 30232228 DOI: 10.1126/scitranslmed.aat7467] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/04/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022]
Abstract
Congenital erythropoietic porphyria is a rare autosomal recessive disease produced by deficient activity of uroporphyrinogen III synthase, the fourth enzyme in the heme biosynthetic pathway. The disease affects many organs, can be life-threatening, and currently lacks curative treatments. Inherited mutations most commonly reduce the enzyme's stability, altering its homeostasis and ultimately blunting intracellular heme production. This results in uroporphyrin by-product accumulation in the body, aggravating associated pathological symptoms such as skin photosensitivity and disfiguring phototoxic cutaneous lesions. We demonstrated that the synthetic marketed antifungal ciclopirox binds to the enzyme, stabilizing it. Ciclopirox targeted the enzyme at an allosteric site distant from the active center and did not affect the enzyme's catalytic role. The drug restored enzymatic activity in vitro and ex vivo and was able to alleviate most clinical symptoms of congenital erythropoietic porphyria in a genetic mouse model of the disease at subtoxic concentrations. Our findings establish a possible line of therapeutic intervention against congenital erythropoietic porphyria, which is potentially applicable to most of deleterious missense mutations causing this devastating disease.
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Affiliation(s)
- Pedro Urquiza
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | - Ana Laín
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | - Arantza Sanz-Parra
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | - Jorge Moreno
- Prion Research Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | | | - Pierre Dubus
- Univerité de Bordeaux, Bordeaux Research in Translational Oncology, INSERM U1053, F-33000 Bordeaux, France.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, Bordeaux, France
| | | | | | | | - Hasier Eraña
- Atlas Molecular Pharma S. L., 48160 Derio, Spain
| | - Itxaso San Juan
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | - Iratxe Macías
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | - Fredj Ben Bdira
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain.,Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, 2300 RA Leiden, Netherlands
| | - Paula Pluta
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | - Gabriel Ortega
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Julen Oyarzábal
- Small Molecule Discovery Platform, Center for Applied Medical Research, University of Navarra, 31008 Pamplona, Spain
| | | | | | - Juan Anguita
- Animal Facility, CIC bioGUNE, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.,Macrophage and Tick Vaccine Laboratory, CIC bioGUNE, 48160 Derio, Spain
| | - Emilio Díez
- Atlas Molecular Pharma S. L., 48160 Derio, Spain
| | - Jean-Marc Blouin
- Université de Bordeaux, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France
| | - Hubert de Verneuil
- Université de Bordeaux, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France
| | - José M Mato
- Liver Metabolism Laboratory, CIC bioGUNE, 48160 Derio, Spain.,CIBERehd-ISCiii, 28029 Madrid, Spain
| | - Emmanuel Richard
- Université de Bordeaux, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France
| | - Juan M Falcón-Pérez
- Exosomes Laboratory, CIC bioGUNE, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.,CIBERehd-ISCiii, 28029 Madrid, Spain
| | - Joaquín Castilla
- Prion Research Laboratory, CIC bioGUNE, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, 48160 Derio, Spain.
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8
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Macias I, Laín A, Bernardo-Seisdedos G, Gil D, Gonzalez E, Falcon-Perez JM, Millet O. Hereditary tyrosinemia type I-associated mutations in fumarylacetoacetate hydrolase reduce the enzyme stability and increase its aggregation rate. J Biol Chem 2019; 294:13051-13060. [PMID: 31300554 PMCID: PMC6721957 DOI: 10.1074/jbc.ra119.009367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/15/2019] [Revised: 07/11/2019] [Indexed: 12/11/2022] Open
Abstract
More than 100 mutations in the gene encoding fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia type I (HT1), a metabolic disorder characterized by elevated blood levels of tyrosine. Some of these mutations are known to decrease FAH catalytic activity, but the mechanisms of FAH mutation–induced pathogenicity remain poorly understood. Here, using diffusion ordered NMR spectroscopy, cryo-EM, and CD analyses, along with site-directed mutagenesis, enzymatic assays, and molecular dynamics simulations, we investigated the putative role of thermodynamic and kinetic stability in WT FAH and a representative set of 19 missense mutations identified in individuals with HT1. We found that at physiological temperatures and concentrations, WT FAH is in equilibrium between a catalytically active dimer and a monomeric species, with the latter being inactive and prone to oligomerization and aggregation. We also found that the majority of the deleterious mutations reduce the kinetic stability of the enzyme and always accelerate the FAH aggregation pathway. Depending mainly on the position of the amino acid in the structure, pathogenic mutations either reduced the dimer population or decreased the energy barrier that separates the monomer from the aggregate. The mechanistic insights reported here pave the way for the development of pharmacological chaperones that target FAH to tackle the severe disease HT1.
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Affiliation(s)
- Iratxe Macias
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Ana Laín
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Ganeko Bernardo-Seisdedos
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - David Gil
- Electron Microscopy Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Esperanza Gonzalez
- Exosomes Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Juan M Falcon-Perez
- Exosomes Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, 48013 Spain
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain.
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9
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Serrano-Mendioroz I, Sampedro A, Serna N, de Salamanca RE, Sanz-Parra A, Corrales F, Berraondo P, Millet O, Fontanellas A. Bioengineered PBGD variant improves the therapeutic index of gene therapy vectors for acute intermittent porphyria. Hum Mol Genet 2019; 27:3688-3696. [PMID: 30085095 DOI: 10.1093/hmg/ddy283] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/24/2018] [Indexed: 12/15/2022] Open
Abstract
A first-in-human gene therapy trial using a recombinant adeno-associated viral (rAAV) vector for acute intermittent porphyria (AIP) reveals that higher doses would be required to reach therapeutic levels of the porphobilinogen deaminase (PBGD) transgene. We developed a hyperfunctional PBGD protein to improve the therapeutic index without increasing vector dose. A consensus protein sequence from 12 mammal species was compared to the human PBGD sequence, and eight amino acids were selected. I291M and N340S variants showed the highest increase in enzymatic activity when expressed in prokaryotic and eukaryotic systems. In silico analysis indicates that isoleucine 291 to methionine and asparagine 340 to serine variants did not affect the active site of the enzyme. In vitro analysis indicated a synergistic interaction between these two substitutions that improve kinetic stability. Finally, full protection against a phenobarbital-induced attack was achieved in AIP mice after the administration of 1 × 1011 gc/kg of rAAV2/8-PBGD-I291M/N340S vector; three times lower than the dose required to achieve full protection with the control rAAV2/8-hPBGD vector. In conclusion, we have developed and characterized a hyperfunctional PBGD protein. The inclusion of this variant sequence in a rAAV2/8 vector allows the effective dose to be lowered in AIP mice.
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Affiliation(s)
- Irantzu Serrano-Mendioroz
- Hepatology Program, CIMA-University of Navarra, Spain.,Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Ana Sampedro
- Hepatology Program, CIMA-University of Navarra, Spain.,Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193 Spain
| | | | - Arantza Sanz-Parra
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Spain
| | - Fernando Corrales
- Proteomics Unit, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - Pedro Berraondo
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain.,Program of Immunology and Immunotherapy, CIMA-University of Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Spain
| | - Antonio Fontanellas
- Hepatology Program, CIMA-University of Navarra, Spain.,Navarra Institute for Health Research (IDISNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Spain
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10
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Pey AL. Biophysical and functional perturbation analyses at cancer-associated P187 and K240 sites of the multifunctional NADP(H):quinone oxidoreductase 1. Int J Biol Macromol 2018; 118:1912-1923. [PMID: 30009918 DOI: 10.1016/j.ijbiomac.2018.07.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
Once whole-genome sequencing has reached the clinical practice, a main challenge ahead is the high-throughput and accurate prediction of the pathogenicity of genetic variants. However, current prediction tools do not consider explicitly a well-known property of disease-causing mutations: their ability to affect multiple functional sites distant in the protein structure. Here we carried out an extensive biophysical characterization of fourteen mutant variants at two cancer-associated sites of the enzyme NQO1, a paradigm of multi-functional protein. We showed that the magnitude of destabilizing effects, their molecular origins (structural vs. dynamic) and their efficient propagation through the protein structure gradually led to functional perturbations at different sites. Modulation of these structural perturbations also led to switches between molecular phenotypes. Our work supports that experimental and computational perturbation analyses would improve our understanding of the molecular basis of many loss-of-function genetic diseases as well as our ability to accurately predict the pathogenicity of genetic variants in a high-throughput fashion.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
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11
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Pluta P, Roversi P, Bernardo-Seisdedos G, Rojas AL, Cooper JB, Gu S, Pickersgill RW, Millet O. Structural basis of pyrrole polymerization in human porphobilinogen deaminase. Biochim Biophys Acta Gen Subj 2018; 1862:1948-1955. [PMID: 29908816 DOI: 10.1016/j.bbagen.2018.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 03/12/2018] [Revised: 05/17/2018] [Accepted: 06/13/2018] [Indexed: 01/27/2023]
Abstract
Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.
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Affiliation(s)
- Paula Pluta
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain
| | - Pietro Roversi
- Oxford Glycobiology Institute, Dept. of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, England, UK
| | | | - Adriana L Rojas
- Structural Biology Unit, CIC bioGUNE, Derio, Bizkaia 48160, Spain
| | - Jonathan B Cooper
- Department of Biological Sciences, Birkbeck, London WC1E 7HX, UK; Division of Medicine, University College London, London WC1E 6BT, UK
| | - Shuang Gu
- School of Biological and Chemical Sciences, Chemistry & Biochemistry Department, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Chemistry & Biochemistry Department, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain.
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12
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Blouin JM, Bernardo-Seisdedos G, Sasso E, Esteve J, Ged C, Lalanne M, Sanz-Parra A, Urquiza P, de Verneuil H, Millet O, Richard E. Missense UROS mutations causing congenital erythropoietic porphyria reduce UROS homeostasis that can be rescued by proteasome inhibition. Hum Mol Genet 2017; 26:1565-1576. [PMID: 28334762 DOI: 10.1093/hmg/ddx067] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
Abstract
Congenital erythropoietic porphyria (CEP) is an inborn error of heme biosynthesis characterized by uroporphyrinogen III synthase (UROS) deficiency resulting in deleterious porphyrin accumulation in blood cells responsible for hemolytic anemia and cutaneous photosensitivity. We analyzed here the molecular basis of UROS impairment associated with twenty nine UROS missense mutations actually described in CEP patients. Using a computational and biophysical joint approach we predicted that most disease-causing mutations would affect UROS folding and stability. Through the analysis of enhanced green fluorescent protein-tagged versions of UROS enzyme we experimentally confirmed these data and showed that thermodynamic instability and premature protein degradation is a major mechanism accounting for the enzymatic deficiency associated with twenty UROS mutants in human cells. Since the intracellular loss in protein homeostasis is in excellent agreement with the in vitro destabilization, we used molecular dynamic simulation to rely structural 3D modification with UROS disability. We found that destabilizing mutations could be clustered within three types of mechanism according to side chain rearrangements or contact alterations within the pathogenic UROS enzyme so that the severity degree correlated with cellular protein instability. Furthermore, proteasome inhibition using bortezomib, a clinically available drug, significantly enhanced proteostasis of each unstable UROS mutant. Finally, we show evidence that abnormal protein homeostasis is a prevalent mechanism responsible for UROS deficiency and that modulators of UROS proteolysis such as proteasome inhibitors or chemical chaperones may represent an attractive therapeutic option to reduce porphyrin accumulation and prevent skin photosensitivity in CEP patients when the genotype includes a missense variant.
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Affiliation(s)
- Jean-Marc Blouin
- Université de Bordeaux.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France.,Laboratory of excellence Gr-Ex, Paris, France
| | - Ganeko Bernardo-Seisdedos
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Emma Sasso
- Université de Bordeaux.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France.,Laboratory of excellence Gr-Ex, Paris, France
| | - Julie Esteve
- Université de Bordeaux.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France.,Laboratory of excellence Gr-Ex, Paris, France
| | - Cécile Ged
- Université de Bordeaux.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France.,Laboratory of excellence Gr-Ex, Paris, France
| | - Magalie Lalanne
- Université de Bordeaux.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France.,Laboratory of excellence Gr-Ex, Paris, France
| | - Arantza Sanz-Parra
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Pedro Urquiza
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Hubert de Verneuil
- Université de Bordeaux.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France.,Laboratory of excellence Gr-Ex, Paris, France
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Emmanuel Richard
- Université de Bordeaux.,INSERM, Biothérapie des Maladies Génétiques, Inflammatoires et Cancers, U1035, F-33000 Bordeaux, France.,Laboratory of excellence Gr-Ex, Paris, France
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13
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Szilágyi A, Györffy D, Závodszky P. Segment swapping aided the evolution of enzyme function: The case of uroporphyrinogen III synthase. Proteins 2016; 85:46-53. [PMID: 27756106 DOI: 10.1002/prot.25190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/22/2016] [Accepted: 10/10/2016] [Indexed: 11/10/2022]
Abstract
In an earlier study, we showed that two-domain segment-swapped proteins can evolve by domain swapping and fusion, resulting in a protein with two linkers connecting its domains. We proposed that a potential evolutionary advantage of this topology may be the restriction of interdomain motions, which may facilitate domain closure by a hinge-like movement, crucial for the function of many enzymes. Here, we test this hypothesis computationally on uroporphyrinogen III synthase, a two-domain segment-swapped enzyme essential in porphyrin metabolism. To compare the interdomain flexibility between the wild-type, segment-swapped enzyme (having two interdomain linkers) and circular permutants of the same enzyme having only one interdomain linker, we performed geometric and molecular dynamics simulations for these species in their ligand-free and ligand-bound forms. We find that in the ligand-free form, interdomain motions in the wild-type enzyme are significantly more restricted than they would be with only one interdomain linker, while the flexibility difference is negligible in the ligand-bound form. We also estimated the entropy costs of ligand binding associated with the interdomain motions, and find that the change in domain connectivity due to segment swapping results in a reduction of this entropy cost, corresponding to ∼20% of the total ligand binding free energy. In addition, the restriction of interdomain motions may also help the functional domain-closure motion required for catalysis. This suggests that the evolution of the segment-swapped topology facilitated the evolution of enzyme function for this protein by influencing its dynamic properties. Proteins 2016; 85:46-53. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- András Szilágyi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dániel Györffy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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14
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Abstract
Congenital erythropoietic porphyria (CEP) is a rare genetic disease resulting from the remarkable deficient activity of uroporphyrinogen III synthase, the fourth enzyme of the haem biosynthetic pathway. This enzyme defect results in overproduction of the non-physiological and pathogenic porphyrin isomers, uroporphyrin I and coproporphyrin I. The predominant clinical characteristics of CEP include bullous cutaneous photosensitivity to visible light from early infancy, progressive photomutilation and chronic haemolytic anaemia. The severity of clinical manifestations is markedly heterogeneous among patients; and interdependence between disease severity and porphyrin amount in the tissues has been pointed out. A more pronounced endogenous production of porphyrins concomitant to activation of ALAS2, the first and rate-limiting of the haem synthesis enzymes in erythroid cells, has also been reported. CEP is inherited as autosomal recessive or X-linked trait due to mutations in UROS or GATA1 genes; however an involvement of other causative or modifier genes cannot be ruled out.
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Affiliation(s)
- Elena Di Pierro
- U.O. di Medicina Interna, Fondazione IRCCS Cà Granda - Ospedale Maggiore Policlinico, Milano, Italy
| | - Valentina Brancaleoni
- U.O. di Medicina Interna, Fondazione IRCCS Cà Granda - Ospedale Maggiore Policlinico, Milano, Italy
| | - Francesca Granata
- U.O. di Medicina Interna, Fondazione IRCCS Cà Granda - Ospedale Maggiore Policlinico, Milano, Italy
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15
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Ortega G, Diercks T, Millet O. Halophilic Protein Adaptation Results from Synergistic Residue-Ion Interactions in the Folded and Unfolded States. ACTA ACUST UNITED AC 2015; 22:1597-607. [PMID: 26628359 DOI: 10.1016/j.chembiol.2015.10.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/25/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Halophilic organisms thrive in environments with extreme salt concentrations and have adapted by allowing molar quantities of cosolutes, mainly KCl, to accumulate in their cytoplasm. To cope with this high intracellular salinity, halophilic organisms modified the chemical composition of their proteins to enrich their surface with acidic and short polar side chains, while lysines and bulky hydrophobic residues got depleted. We have emulated the evolutionary process of haloadaptation with natural and designed halophilic polypeptides and applied novel nuclear magnetic resonance (NMR) methodology to study the different mechanisms contributing to protein haloadaptation at a per residue level. Our analysis of an extensive set of NMR observables, determined over several proteins, allowed us to disentangle the synergistic contributions of protein haloadaptation: cation exclusion and electrostatic repulsion between negatively charged residues destabilize the denatured state ensemble while cumulative weak cation-protein interactions stabilize the folded conformations.
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Affiliation(s)
- Gabriel Ortega
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Spain
| | - Tammo Diercks
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Spain
| | - Oscar Millet
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Spain.
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16
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ben Bdira F, González E, Pluta P, Laín A, Sanz-Parra A, Falcon-Perez JM, Millet O. Tuning intracellular homeostasis of human uroporphyrinogen III synthase by enzyme engineering at a single hotspot of congenital erythropoietic porphyria. Hum Mol Genet 2014; 23:5805-13. [PMID: 24925316 DOI: 10.1093/hmg/ddu298] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Congenital erythropoietic porphyria (CEP) results from a deficiency in uroporphyrinogen III synthase enzyme (UROIIIS) activity that ultimately stems from deleterious mutations in the uroS gene. C73 is a hotspot for these mutations and a C73R substitution, which drastically reduces the enzyme activity and stability, is found in almost one-third of all reported CEP cases. Here, we have studied the structural basis, by which mutations in this hotspot lead to UROIIIS destabilization. First, a strong interdependency is observed between the volume of the side chain at position 73 and the folded protein. Moreover, there is a correlation between the in vitro half-life of the mutated proteins and their expression levels in eukaryotic cell lines. Molecular modelling was used to rationalize the results, showing that the mutation site is coupled to the hinge region separating the two domains. Namely, mutations at position 73 modulate the inter-domain closure and ultimately affect protein stability. By incorporating residues capable of interacting with R73 to stabilize the hinge region, catalytic activity was fully restored and a moderate increase in the kinetic stability of the enzyme was observed. These results provide an unprecedented rationale for a destabilizing missense mutation and pave the way for the effective design of molecular chaperones as a therapy against CEP.
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Affiliation(s)
- Fredj ben Bdira
- Structural Biology Unit and Metabolomics Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800-801A, Derio 48160, Spain and
| | - Esperanza González
- Structural Biology Unit and Metabolomics Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800-801A, Derio 48160, Spain and
| | - Paula Pluta
- Structural Biology Unit and Metabolomics Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800-801A, Derio 48160, Spain and
| | - Ana Laín
- Structural Biology Unit and Metabolomics Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800-801A, Derio 48160, Spain and
| | - Arantza Sanz-Parra
- Structural Biology Unit and Metabolomics Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800-801A, Derio 48160, Spain and
| | - Juan Manuel Falcon-Perez
- Structural Biology Unit and Metabolomics Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800-801A, Derio 48160, Spain and IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain
| | - Oscar Millet
- Structural Biology Unit and Metabolomics Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800-801A, Derio 48160, Spain and
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17
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Pey AL, Majtan T, Kraus JP. The role of surface electrostatics on the stability, function and regulation of human cystathionine β-synthase, a complex multidomain and oligomeric protein. Biochim Biophys Acta 2014; 1844:1453-62. [PMID: 24780582 DOI: 10.1016/j.bbapap.2014.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/06/2014] [Accepted: 04/21/2014] [Indexed: 11/25/2022]
Abstract
Human cystathionine β-synthase (hCBS) is a key enzyme of sulfur amino acid metabolism, controlling the commitment of homocysteine to the transsulfuration pathway and antioxidant defense. Mutations in hCBS cause inherited homocystinuria (HCU), a rare inborn error of metabolism characterized by accumulation of toxic homocysteine in blood and urine. hCBS is a complex multidomain and oligomeric protein whose activity and stability are independently regulated by the binding of S-adenosyl-methionine (SAM) to two different types of sites at its C-terminal regulatory domain. Here we study the role of surface electrostatics on the complex regulation and stability of hCBS using biophysical and biochemical procedures. We show that the kinetic stability of the catalytic and regulatory domains is significantly affected by the modulation of surface electrostatics through noticeable structural and energetic changes along their denaturation pathways. We also show that surface electrostatics strongly affect SAM binding properties to those sites responsible for either enzyme activation or kinetic stabilization. Our results provide new insight into the regulation of hCBS activity and stability in vivo with implications for understanding HCU as a conformational disease. We also lend experimental support to the role of electrostatic interactions in the recently proposed binding modes of SAM leading to hCBS activation and kinetic stabilization.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071 Granada, Spain.
| | - Tomas Majtan
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO 80045, USA
| | - Jan P Kraus
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO 80045, USA
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18
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Pey AL. pH-dependent relationship between thermodynamic and kinetic stability in the denaturation of human phosphoglycerate kinase 1. Biochimie 2014; 103:7-15. [PMID: 24721582 DOI: 10.1016/j.biochi.2014.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 03/27/2014] [Indexed: 12/14/2022]
Abstract
Human phosphoglycerate kinase 1 (hPGK1) is a glycolytic enzyme essential for ATP synthesis, and it is implicated in different pathological conditions such as inherited diseases, oncogenesis and activation of drugs for cancer and viral treatments. Particularly, mutations in hPGK1 cause human PGK1 deficiency, a rate metabolic conformational disease. We have recently found that most of these mutations cause protein kinetic destabilization by significant changes in the structure/energetics of the transition state for irreversible denaturation. In this work, we explore the relationships between protein conformation, thermodynamic and kinetic stability in hPGK1 by performing comprehensive analyses in a wide pH range (2.5-8). hPGK1 remains in a native conformation at pH 5-8, but undergoes a conformational transition to a molten globule-like state at acidic pH. Interestingly, hPGK1 kinetic stability remains essentially constant at pH 6-8, but is significantly reduced when pH is decreased from 6 to 5. We found that this decrease in kinetic stability is caused by significant changes in the energetic/structural balance of the denaturation transition state, which diverge from those found for disease-causing mutations. We also show that protein kinetic destabilization by acidic pH is strongly linked to lower thermodynamic stability, while in disease-causing mutations seems to be linked to lower unfolding cooperativity. These results highlight the plasticity of the hPGK1 denaturation mechanism that responds differently to changes in pH and in disease-causing mutations. New insight is presented into the different factors contributing to hPGK1 thermodynamic and kinetic stability and the role of denaturation mechanisms in hPGK1 deficiency.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av./Fuentenueva s/n, E-18071 Granada, Spain.
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19
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Blouin JM, Duchartre Y, Costet P, Lalanne M, Ged C, Lain A, Millet O, de Verneuil H, Richard E. Therapeutic potential of proteasome inhibitors in congenital erythropoietic porphyria. Proc Natl Acad Sci U S A 2013; 110:18238-43. [PMID: 24145442 DOI: 10.1073/pnas.1314177110] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Congenital erythropoietic porphyria (CEP) is a rare autosomal recessive disorder characterized by uroporphyrinogen III synthase (UROS) deficiency resulting in massive porphyrin accumulation in blood cells, which is responsible for hemolytic anemia and skin photosensitivity. Among the missense mutations actually described up to now in CEP patients, the C73R and the P248Q mutations lead to a profound UROS deficiency and are usually associated with a severe clinical phenotype. We previously demonstrated that the UROS(C73R) mutant protein conserves intrinsic enzymatic activity but triggers premature degradation in cellular systems that could be prevented by proteasome inhibitors. We show evidence that the reduced kinetic stability of the UROS(P248Q) mutant is also responsible for increased protein turnover in human erythroid cells. Through the analysis of EGFP-tagged versions of UROS enzyme, we demonstrate that both UROS(C73R) and UROS(P248Q) are equally destabilized in mammalian cells and targeted to the proteasomal pathway for degradation. We show that a treatment with proteasomal inhibitors, but not with lysosomal inhibitors, could rescue the expression of both EGFP-UROS mutants. Finally, in CEP mice (Uros(P248Q/P248Q)) treated with bortezomib (Velcade), a clinically approved proteasome inhibitor, we observed reduced porphyrin accumulation in circulating RBCs and urine, as well as reversion of skin photosensitivity on bortezomib treatment. These results of medical importance pave the way for pharmacologic treatment of CEP disease by preventing certain enzymatically active UROS mutants from early degradation by using proteasome inhibitors or chemical chaperones.
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20
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Pey AL, Mesa-Torres N, Chiarelli LR, Valentini G. Structural and energetic basis of protein kinetic destabilization in human phosphoglycerate kinase 1 deficiency. Biochemistry 2013; 52:1160-70. [PMID: 23336698 DOI: 10.1021/bi301565m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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
Protein kinetic destabilization is a common feature of many human genetic diseases. Human phosphoglycerate kinase 1 (PGK1) deficiency is a rare genetic disease caused by mutations in the PGK1 protein, which often shows reduced kinetic stability. In this work, we have performed an in-depth characterization of the thermal stability of the wild type and four disease-causing mutants (I47N, L89P, E252A, and T378P) of human PGK1. PGK1 thermal denaturation is a process under kinetic control, and it is described well by a two-state irreversible denaturation model. Kinetic analysis of differential scanning calorimetry profiles shows that the disease-causing mutations decrease PGK1 kinetic stability from ~5-fold (E252A) to ~100000-fold (L89P) compared to that of wild-type PGK1, and in some cases, mutant enzymes are denatured on a time scale of a few minutes at physiological temperature. We show that changes in protein kinetic stability are associated with large differences in enthalpic and entropic contributions to denaturation free energy barriers. It is also shown that the denaturation transition state becomes more nativelike in terms of solvent exposure as the protein is destabilized by mutations (Hammond effect). Unfolding experiments with urea further suggest a scenario in which the thermodynamic stability of PGK1 at least partly determines its kinetic stability. ATP and ADP kinetically stabilize PGK1 enzymes, and kinetic stabilization is nucleotide- and mutant-selective. Overall, our data provide insight into the structural and energetic basis underlying the low kinetic stability displayed by some mutants causing human PGK1 deficiency, which may have important implications for the development of native state kinetic stabilizers for the treatment of this disease.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain.
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21
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Maakaron J, Abdel Malak O, Itani S, Cappellini M, Di Pierro E, Brancaleoni V, Granata F, Taher A. A puzzling mutation in congenital erythropoietic porphyria and an association with β-thalassaemia trait. Br J Dermatol 2012; 167:697-9. [DOI: 10.1111/j.1365-2133.2012.10954.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Fortian A, Castaño D, Gonzalez E, Laín A, Falcon-Perez JM, Millet O. Structural, thermodynamic, and mechanistical studies in uroporphyrinogen III synthase: molecular basis of congenital erythropoietic porphyria. Adv Protein Chem Struct Biol 2012; 83:43-74. [PMID: 21570665 DOI: 10.1016/b978-0-12-381262-9.00002-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Congenital erythropoietic porphyria (CEP) is a rare autosomal disease ultimately related to deleterious mutations in uroporphyrinogen III synthase (UROIIIS), the fourth enzyme of the biosynthetic route of the heme group. UROIIIS catalyzes the cyclization of the linear tetrapyrrol hydroxymethylbilane (HMB), inverting the configuration in one of the aromatic rings. In the absence of the enzyme (or when ill-functioning), HMB spontaneously degrades to the by-product uroporphyrinogen I, which cannot lead to the heme group and accumulates in the body, producing some of the symptoms observed in CEP patients. In the present chapter, clinical, biochemical, and biophysical information has been compiled to provide an integrative view on the molecular basis of CEP. The high-resolution structure of UROIIIS sheds light on the enzyme reaction mechanism while thermodynamic analysis revealed that the protein is thermolabile. Pathogenic missense mutations are found throughout the primary sequence of the enzyme. All but one of these is rarely found in patients, whereas C73R is responsible for more than one-third of the reported cases. Most of the mutant proteins (C73R included) retain partial catalytic activity but the mutations often reduce the enzyme's stability. The stabilization of the protein in vivo is discussed in the context of a new line of intervention to complement existing treatments such as bone marrow transplantation and gene therapy.
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Abstract
Congenital erythropoietic porphyria (CEP) is one of the rarest of porphyrias occurring worldwide. CEP is a very rare genetic autosomal recessive disease, with mutation in the gene that codifies uroporphyrinogen-III synthase, leading to porphyrin accumulation in many tissues, with marked skin photosensitivity, hemolytic anemia with splenomegaly and a decreased life expectancy. We report a case of Gü;nther's disease in view of its rarity along with a description of this interesting condition. An 18-month-old female baby with clinical, hematological and biochemical profile of CEP was reported with marked skin photosensitivity over face and hands. She had erythrodontia with delayed eruption of teeth. When evaluating erythrodontia of uncertain cause, we advocate maintaining a high degree of awareness for porphyria, especially for CEP as it is the rarest among porphyria and is a life-threatening condition.
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Affiliation(s)
- Rashmi Bhavasar
- Department of Oral Pathology and Microbiology, Kamineni Institute of Dental Sciences, Narketpalli, Andhra Pradesh, India
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To-Figueras J, Ducamp S, Clayton J, Badenas C, Delaby C, Ged C, Lyoumi S, Gouya L, de Verneuil H, Beaumont C, Ferreira GC, Deybach JC, Herrero C, Puy H. ALAS2 acts as a modifier gene in patients with congenital erythropoietic porphyria. Blood 2011; 118:1443-51. [PMID: 21653323 DOI: 10.1182/blood-2011-03-342873] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in the uroporphyrinogen III synthase (UROS) gene cause congenital erythropoietic porphyria (CEP), an autosomal-recessive inborn error of erythroid heme biosynthesis. Clinical features of CEP include dermatologic and hematologic abnormalities of variable severity. The discovery of a new type of erythroid porphyria, X-linked dominant protoporphyria (XLDPP), which results from increased activity of 5-aminolevulinate synthase 2 (ALAS2), the rate-controlling enzyme of erythroid heme synthesis, led us to hypothesize that the CEP phenotype may be modulated by sequence variations in the ALAS2 gene. We genotyped ALAS2 in 4 unrelated CEP patients exhibiting the same C73R/P248Q UROS genotype. The most severe of the CEP patients, a young girl, proved to be heterozygous for a novel ALAS2 mutation: c.1757 A > T in exon 11. This mutation is predicted to affect the highly conserved and penultimate C-terminal amino acid of ALAS2 (Y586). The rate of 5-aminolevulinate release from Y586F was significantly increased over that of wild-type ALAS2. The contribution of the ALAS2 gain-of-function mutation to the CEP phenotype underscores the importance of modifier genes underlying CEP. We propose that ALAS2 gene mutations should be considered not only as causative of X-linked sideroblastic anemia (XLSA) and XLDPP but may also modulate gene function in other erythropoietic disorders.
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Bishop DF, Clavero S, Mohandas N, Desnick RJ. Congenital erythropoietic porphyria: characterization of murine models of the severe common (C73R/C73R) and later-onset genotypes. Mol Med 2011; 17:748-56. [PMID: 21365124 DOI: 10.2119/molmed.2010.00258] [Citation(s) in RCA: 9] [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] [Received: 12/10/2010] [Accepted: 02/24/2011] [Indexed: 11/06/2022] Open
Abstract
Congenital erythropoietic porphyria (CEP) is an autosomal recessive disorder due to the deficient activity of uroporphyrinogen III synthase (UROS). Knock-in mouse models were generated for the common, hematologically severe human genotype, C73R/C73R, and milder genotypes (C73R/V99L and V99L/V99L). The specific activities of the UROS enzyme in the livers and erythrocytes of these mice averaged approximately 1.2%, 11% and 19% of normal, respectively. C73R/C73R mice that survived fetal life to weaning age (~12%) had a severe microcytic hypochromic anemia (hemoglobin 7.9 g/dL, mean cellular volume 26.6 fL, mean cellular hemoglobin content 27.4 g/dL, red cell distribution width 37.7%, reticulocytes 19%) and massively accumulated isomer I porphyrins (95, 183 and 44 μmol/L in erythrocytes, spleen and liver, respectively), but a nearly normal lifespan. In adult C73R/C73R mice, spleen and liver weights were 8.2- and 1.5-fold increased, respectively. C73R/V99L mice were mildly anemic (hemoglobin was 14.0 g/dL and mean cellular hemoglobin was 13.3), with minimally accumulated porphyrins (0.10, 5.54 and 0.58 μmol/L in erythrocytes, spleen and liver, respectively), whereas adult V99L/V99L mice were normal. Of note, even the mildest genotype, V99L/V99L, exhibited porphyria in utero, which disappeared by 2 months of age. These severe and mild mouse models inform therapeutic interventions and permit further investigation of the porphyrin-induced hematopathology, which leads to photo-induced cutaneous lesions. Of significance for therapeutic intervention, these mouse models suggest that only 11% of wild-type activity might be needed to reverse the pathology in CEP patients.
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Affiliation(s)
- David F Bishop
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, USA.
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Fortian A, González E, Castaño D, Falcon-Perez JM, Millet O. Intracellular rescue of the uroporphyrinogen III synthase activity in enzymes carrying the hotspot mutation C73R. J Biol Chem 2011; 286:13127-33. [PMID: 21343304 DOI: 10.1074/jbc.m110.205849] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A single mutation (C73R) in the enzyme uroporphyrinogen III synthase (UROIIIS) is responsible for more than one-third of all of the reported cases of the rare autosomal disease congenital erythropoietic porphyria (CEP). CEP patients carrying this hotspot mutation develop a severe phenotype of the disease, including reduced life expectancy. Here, we have investigated the molecular basis for the functional deficit in the mutant enzyme both in vitro and in cellular systems. We show that a Cys in position 73 is not essential for the catalytic activity of the enzyme but its mutation to Arg speeds up the process of irreversible unfolding and aggregation. In the mammalian cell milieu, the mutant protein levels decrease to below the detection limit, whereas wild type UROIIIS can be detected easily. The disparate response is not produced by differences at the level of transcription, and the results with cultured cells and in vitro are consistent with a model where the protein becomes very unstable upon mutation and triggers a degradation mechanism via the proteasome. Mutant protein levels can be restored upon cell treatment with the proteasome inhibitor MG132. The intracellularly recovered C73R-UROIIIS protein shows enzymatic activity, paving the way for a new line of therapeutic intervention in CEP patients.
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Affiliation(s)
- Arola Fortian
- Structural Biology Unit, Centro de Investigacion Cooperativa en Biociencias, Derio, Vizcaya 48160, Spain.
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Clavero S, Bishop DF, Giger U, Haskins ME, Desnick RJ. Feline congenital erythropoietic porphyria: two homozygous UROS missense mutations cause the enzyme deficiency and porphyrin accumulation. Mol Med 2010; 16:381-8. [PMID: 20485863 DOI: 10.2119/molmed.2010.00038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 05/11/2010] [Indexed: 02/02/2023] Open
Abstract
The first feline model of human congenital erythropoietic porphyria (CEP) due to deficient uroporphyrinogen III synthase (URO-synthase) activity was identified by its characteristic clinical phenotype, and confirmed by biochemical and molecular genetic studies. The proband, an adult domestic shorthair cat, had dark-red urine and brownish discolored teeth with red fluorescence under ultraviolet light. Biochemical studies demonstrated markedly increased uroporphyrinogen I in urine and plasma (2,650- and 10,700-fold greater than wild type, respectively), whereas urinary 5-aminolevulinic acid and porphobilinogen were lower than normal. Erythrocytic URO-synthase activity was <1% of mean wild-type activity, confirming the diagnosis and distinguishing it from feline phenocopies having acute intermittent porphyria. Sequencing of the affected cat's UROS gene revealed two missense mutations, c.140C>T (p.S47F) in exon 3 and c.331G>A (p.G111S) in exon 6, both of which were homozygous, presumably owing to parental consanguinity. Neither was present in 100 normal cat alleles. Prokaryotic expression and thermostability studies of the purified monomeric wild-type, p.S47F, p.G111S, and p.S47F/G111S enzymes showed that the p.S47F enzyme had 100% of wild-type specific activity but ~50% decreased thermostability, whereas the p.G111S and p.S47F/G111S enzymes had about 60% and 20% of wild-type specific activity, respectively, and both were markedly thermolabile. Molecular modeling results indicated that the less active/less stable p.G111S enzyme was further functionally impaired by a structural interaction induced by the presence of the S47F substitution. Thus, the synergistic interaction of two rare amino acid substitutions in the URO-synthase polypeptide caused the feline model of human CEP.
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Affiliation(s)
- Sonia Clavero
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, USA
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