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Bustad HJ, Christie MS, Laitaoja M, Aarsand AK, Martinez A, Jänis J, Kallio JP. One ring closer to a closure: the crystal structure of the ES 3 hydroxymethylbilane synthase intermediate. FEBS J 2024; 291:510-526. [PMID: 37863644 DOI: 10.1111/febs.16982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Hydroxymethylbilane synthase (HMBS), involved in haem biosynthesis, catalyses the head-to-tail coupling of four porphobilinogens (PBGs) via a dipyrromethane (DPM) cofactor. DPM is composed of two PBGs, and a hexapyrrole is built before the tetrapyrrolic 1-hydroxymethylbilane product is released. During this elongation, stable enzyme (E) intermediates are formed from the holoenzyme, with additional PBG substrates (S): ES, ES2 , ES3 and ES4 . Native PAGE and mass spectrometry of the acute intermittent porphyria (AIP)-associated HMBS variant p.Arg167Gln demonstrated an increased amount of ES3 . Kinetic parameters indicated catalytic dysfunction, however, the product release was not entirely prevented. Isolation and crystal structure analysis of the ES3 intermediate (PDB: 8PND) showed that a pentapyrrole was fully retained within the active site, revealing that polypyrrole elongation proceeds within the active site via a third interaction site, intermediate pyrrole site 3 (IPS3). The AIP-associated HMBS variant p.Arg195Cys, located on the opposite side to p.Arg167Gln in the active site, accumulated the ES4 intermediate in the presence of excess PBG, implying that product hydrolysis was obstructed. Arg167 is thus involved in all elongation steps and is a determinant for the rate of enzyme catalysis, whereas Arg195 is important for releasing the product. Moreover, by substituting residues in the vicinity of IPS3, our results indicate that a fully retained hexapyrrole could be hydrolysed in a novel site in proximity of the IPS3.
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Affiliation(s)
- Helene J Bustad
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Marthe S Christie
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Aasne K Aarsand
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
- Norwegian Organization for Quality Improvement of Laboratory Examinations, Haraldsplass Deaconess Hospital, Bergen, Norway
| | | | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Norway
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Wang X, Zhang H, Huang H, Wang W, Wen Y, Dai Z, Huang S, Zhou J, Zhou Y. Functional and structural analysis of a novel splice site HMBS variant in a Chinese AIP patient. Front Genet 2023; 14:1333111. [PMID: 38192441 PMCID: PMC10773753 DOI: 10.3389/fgene.2023.1333111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Background: Acute intermittent porphyria (AIP) is a rare metabolic disorder that results from mutations in the gene encoding hydroxymethylbilane synthase (HMBS), an enzyme involved in heme biosynthesis. AIP follows an autosomal dominant inheritance pattern, but most carriers are asymptomatic. The clinical manifestations of AIP include acute attacks of abdominal pain and neuropsychiatric disturbances. The pathogenicity of novel HMBS variants identified in Chinese patients has not been well established. Objective: The article aims to identify the pathogenic mutation in an AIP patient and prove its pathogenicity through in vitro experiments. Methods: A 22-year-old female diagnosed with AIP participated in the study. Variant screening of her HMBS gene was carried out through Sanger sequencing. To ascertain the consequences of the newly discovered variant, we conducted in vitro experimentation targeting HMBS gene expression and enzymatic function. Additionally, protein structure analysis was performed. Cycloheximide treatment and UPF1-specific siRNA knockdown were employed to assess the impact of the mutation on the mechanism of non-sense-mediated mRNA decay (NMD). Results: A novel splice site variant in the HMBS gene (c.648_651+1delCCAGG) was detected in the patient, which caused aberrant mRNA splicing. In vitro experiments demonstrated that this variant significantly decreased the expression of HMBS. Further investigation confirmed that this decrease was due to NMD. Additionally, structural analysis indicated that this variant would destabilize the HMBS protein and impair its catalytic activity. To gain a comprehensive understanding of HMBS mutations in the context of AIP, we conducted a literature search on PubMed using the keywords 'HMBS' and 'Acute intermittent porphyria' from 2013 to 2023. This search yielded 19 clinical case reports written in English, which collectively described 220 HMBS gene mutations worldwide. Conclusion: The study identified and proved the pathogenicity of a novel splice site HMBS variant for the first time. Our results elucidated the pathological mechanism by which this mutation causes AIP through reducing HMBS expression and activity. These findings provide theoretical guidance for the diagnosis, treatment and genetic counseling of AIP patients.
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Affiliation(s)
- Xiaoqing Wang
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
| | - Huifen Zhang
- Department of Endocrinology, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
| | - Huanhuan Huang
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
| | - Wenli Wang
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
| | - Yuping Wen
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
| | - Zhuojin Dai
- The First Clinical Medical College, Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Shuling Huang
- Department of Endocrinology, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
| | - Jingyi Zhou
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
| | - Yuqing Zhou
- Department of Endocrinology, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, Guangdong Province, China
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Balogun O, Nejak-Bowen K. The Hepatic Porphyrias: Revealing the Complexities of a Rare Disease. Semin Liver Dis 2023; 43:446-459. [PMID: 37973028 PMCID: PMC11256094 DOI: 10.1055/s-0043-1776760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The porphyrias are a group of metabolic disorders that are caused by defects in heme biosynthesis pathway enzymes. The result is accumulation of heme precursors, which can cause neurovisceral and/or cutaneous photosensitivity. Liver is commonly either a source or target of excess porphyrins, and porphyria-associated hepatic dysfunction ranges from minor abnormalities to liver failure. In this review, the first of a three-part series, we describe the defects commonly found in each of the eight enzymes involved in heme biosynthesis. We also discuss the pathophysiology of the hepatic porphyrias in detail, covering epidemiology, histopathology, diagnosis, and complications. Cellular consequences of porphyrin accumulation are discussed, with an emphasis on oxidative stress, protein aggregation, hepatocellular cancer, and endothelial dysfunction. Finally, we review current therapies to treat and manage symptoms of hepatic porphyria.
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Affiliation(s)
- Oluwashanu Balogun
- Department of Experimental Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Kari Nejak-Bowen
- Department of Experimental Pathology, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Institute, University of Pittsburgh, Pittsburgh, PA
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4
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van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Sheykhkarimli D, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. Am J Hum Genet 2023; 110:1769-1786. [PMID: 37729906 PMCID: PMC10577081 DOI: 10.1016/j.ajhg.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Defects in hydroxymethylbilane synthase (HMBS) can cause acute intermittent porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ∼⅓ of clinical HMBS variants are missense variants, and most clinically reported HMBS missense variants are designated as "variants of uncertain significance" (VUSs). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino acid substitutions. The resulting variant effect maps generally agreed with biochemical expectations and provide further evidence that HMBS can function as a monomer. Additionally, the maps implicated specific residues as having roles in active site dynamics, which was further supported by molecular dynamics simulations. Most importantly, these maps can help discriminate pathogenic from benign HMBS variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.
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Affiliation(s)
- Warren van Loggerenberg
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | | | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Rayna Hamilton
- Advanced Academic Programs, Johns Hopkins University, Washington, DC 20036, USA
| | - Aditya Chawla
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Dayag Sheykhkarimli
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | | | - Sami Mustajoki
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Elena Pischik
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Elena Di Pierro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Medicine and Metabolic Diseases, 20122 Milano, Italy
| | - Michela Barbaro
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Ylva Floderus
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Caroline Schmitt
- Centre français des porphyries, hôpital Louis-Mourier, Assistance Publique-Hopitaux de Paris, 92701 Colombes, France; Centre de recherche sur l'inflammation, Université Paris Cité, UMR1149 INSERM, 75018 Paris, France
| | - Laurent Gouya
- Centre français des porphyries, hôpital Louis-Mourier, Assistance Publique-Hopitaux de Paris, 92701 Colombes, France; Centre de recherche sur l'inflammation, Université Paris Cité, UMR1149 INSERM, 75018 Paris, France
| | | | | | - Edith C H Friesema
- Porphyria Expertcenter Rotterdam, Center for Lysosomal and Metabolic Diseases, Department of Internal Medicine, Erasmus MC, 3015 Rotterdam, the Netherlands
| | - Raili Kauppinen
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Jordi To-Figueras
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Aasne K Aarsand
- Norwegian Porphyria Centre, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Garton
- Institute Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada.
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5
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Liang L, Meng H, Wu H, Zhao J. Genetic analysis of acute intermittent porphyria caused by novel classical splicing variant in the insertion region of 29-residue specific to human HMBS protein. Front Mol Biosci 2023; 10:1230798. [PMID: 37635937 PMCID: PMC10448817 DOI: 10.3389/fmolb.2023.1230798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
Background: Acute intermittent porphyria (AIP; OMIM#176000) is a genetic disorder that is caused by mutations in the hydroxymethylbilane synthetase (HMBS) gene. This gene encodes the third enzyme in the heme biosynthesis pathway. Human HMBS (hHMBS) contains a 29-residue insert (residues 296-324) at the interface between domains 1 and 3. The function of this insert is currently unknown. In this study, a previously unidentified classical Splicing variant was discovered in the HMBS gene of a female AIP patient from China. The variant was validated through comparison with the patient's husband and daughter. Methods: Peripheral blood samples were obtained from the patient, the patient's husband, and their daughter. Gene expression was analyzed using whole exon sequencing and Sanger sequencing. To validate alternative splicing, RNA was extracted from the patient's peripheral blood and reverse transcribed into cDNA. Aberrant splicing caused by variants was predicted using I-TASSER and PyMOL software to simulate protein structures. Finally, molecular dynamics of the proteins were simulated using the AMBER14sb software. Results: The patient and her daughter have a classical Splicing variant c.912 + 1G>C of the HMBS gene. This variant was not found in the patient's husband and has not been previously reported in scientific literature. Analysis of the patient's peripheral blood transcripts revealed that c.912 + 1G>C retained intron 13 and resulted in an exon 13 skipping. Further analysis through homology modelling and molecular dynamics showed that this variant alters the secondary structure of the HMBS protein, leading to functional differences. Conclusion: This research has discovered a new classical Splicing variant c.912 + 1G>C in the HMBS gene that has been identified as pathogenic. This finding not only expands the molecular heterogeneity of AIP but also provides crucial information for genetic diagnosis.
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Affiliation(s)
- Lei Liang
- Center for Prenatal Diagnosis and Medical Genetics, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Haixia Meng
- Center for Prenatal Diagnosis and Medical Genetics, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Haotian Wu
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
| | - Jianrong Zhao
- Department of Nephrology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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6
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van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527353. [PMID: 36798224 PMCID: PMC9934555 DOI: 10.1101/2023.02.06.527353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~⅓ of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.
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Affiliation(s)
- Warren van Loggerenberg
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Rayna Hamilton
- Advanced Academic Programs, Johns Hopkins University, Washington, DC, USA
| | - Aditya Chawla
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | | | - Sami Mustajoki
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Elena Pischik
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Elena Di Pierro
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Unit of Medicine and Metabolic Diseases, Milan, Italy
| | - Michela Barbaro
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ylva Floderus
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Schmitt
- Centre Français des Porphyries, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes and Centre de Recherche sur l’Inflammation, UMR1149 INSERM, Université Paris Cité, Paris, France
| | - Laurent Gouya
- Centre Français des Porphyries, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes and Centre de Recherche sur l’Inflammation, UMR1149 INSERM, Université Paris Cité, Paris, France
| | | | | | - Edith C. H. Friesema
- Porphyria Expertcenter Rotterdam, Center for Lysosomal and Metabolic Diseases, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Raili Kauppinen
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Jordi To-Figueras
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Aasne K Aarsand
- Norwegian Porphyria Centre, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, ON, Canada
| | - Frederick P. Roth
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
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Christie MS, Laitaoja M, Aarsand AK, Kallio JP, Bustad HJ. Characterisation of a common hotspot variant in acute intermittent porphyria sheds light on the mechanism of hydroxymethylbilane synthase function. FEBS Open Bio 2022; 12:2136-2146. [PMID: 36115019 PMCID: PMC9714363 DOI: 10.1002/2211-5463.13490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 01/25/2023] Open
Abstract
Hydroxymethylbilane synthase (HMBS) is the third enzyme involved in haem biosynthesis, in which it catalyses the formation of tetrapyrrole 1-hydroxymethylbilane (HMB). In this process, HMBS binds four consecutive substrate molecules, creating the enzyme-intermediate complexes ES, ES2 , ES3 and ES4 . Pathogenic variants in the HMBS gene are associated with the dominantly inherited disorder acute intermittent porphyria. In this study, we have characterised the p.R26H variant to shed light on the role of Arg26 in the elongation mechanism of HMBS and to provide insights into its effect on the enzyme. With selected biophysical methods, we have been able to show that p.R26H forms a single enzyme-intermediate complex in the ES2 -state. We were also able to demonstrate that the p.R26H variant results in an inactive enzyme, which is unable to produce the HMB product.
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Affiliation(s)
- Marthe S. Christie
- Department of BiomedicineUniversity of BergenNorway,Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and PharmacologyHaukeland University HospitalBergenNorway
| | - Mikko Laitaoja
- Department of ChemistryUniversity of Eastern FinlandJoensuuFinland
| | - Aasne K. Aarsand
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and PharmacologyHaukeland University HospitalBergenNorway,Norwegian Organization for Quality Improvement of Laboratory ExaminationsHaraldsplass Deaconess HospitalBergenNorway
| | | | - Helene J. Bustad
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and PharmacologyHaukeland University HospitalBergenNorway
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Ricci A, Guida CC, Manzini P, Cuoghi C, Ventura P. Kidney Involvement in Acute Hepatic Porphyrias: Pathophysiology and Diagnostic Implications. Diagnostics (Basel) 2021; 11:2324. [PMID: 34943561 PMCID: PMC8700387 DOI: 10.3390/diagnostics11122324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 12/27/2022] Open
Abstract
Porphyrias are a group of rare disorders originating from an enzyme dysfunction in the pathway of heme biosynthesis. Depending on the specific enzyme involved, porphyrias manifest under drastically different clinical pictures. The most dramatic presentation of the four congenital acute hepatic porphyrias (AHPs: acute intermittent porphyria-AIP, ALAD deficiency, hereditary coproporphyria-HCP, and porphyria variegata-VP) consists of potentially life-threatening neurovisceral attacks, for which givosiran, a novel and effective siRNA-based therapeutic, has recently been licensed. Nonetheless, the clinical manifestations of acute porphyrias are multifaceted and do not limit themselves to acute attacks. In particular, porphyria-associated kidney disease (PAKD) is a distinct, long-term degenerating condition with specific pathological and clinical features, for which a satisfactory treatment is not available yet. In PAKD, chronic tubule-interstitial damage has been most commonly reported, though other pathologic features (e.g., chronic fibrous intimal hyperplasia) are consistent findings. Given the relevant role of the kidney in porphyrin metabolism, the mechanisms possibly intervening in causing renal damage in AHPs are different: among others, δ-aminolevulinic acid (ALA)-induced oxidative damage on mitochondria, intracellular toxic aggregation of porphyrins in proximal tubular cells, and derangements in the delicate microcirculatory balances of the kidney might be implicated. The presence of a variant of the human peptide transporter 2 (PEPT2), with a greater affinity to its substrates (including ALA), might confer a greater susceptibility to kidney damage in patients with AHPs. Furthermore, a possible effect of givosiran in worsening kidney function has been observed. In sum, the diagnostic workup of AHPs should always include a baseline evaluation of renal function, and periodic monitoring of the progression of kidney disease in patients with AHPs is strongly recommended. This review outlines the role of the kidney in porphyrin metabolism, the available evidence in support of the current etiologic and pathogenetic hypotheses, and the known clinical features of renal involvement in acute hepatic porphyrias.
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Affiliation(s)
- Andrea Ricci
- Internal Medicine Unit, Department of Medical and Surgical Science for Children and Adults, Regional Reference Centre for Diagnosing and Management of Porphyrias, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria Policlinico of Modena, Largo del Pozzo 71, 41124 Modena, Italy; (A.R.); (C.C.)
| | - Claudio Carmine Guida
- Interregional Reference Center for the Prevention, Surveillance, Diagnosis and Treatment of Porphyria, Nephrology and Dialysis Unit, Scientific Institute for Research and Health Care, Viale Cappuccini, San Giovanni Rotondo, 71013 Foggia, Italy;
| | - Paola Manzini
- Transfusion Medicine and Blood Establishment, Regional Reference Centre for Diagnosis and Management of Porphyrias, University Hospital City of Science and Health of Torino, 10126 Torino, Italy;
| | - Chiara Cuoghi
- Internal Medicine Unit, Department of Medical and Surgical Science for Children and Adults, Regional Reference Centre for Diagnosing and Management of Porphyrias, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria Policlinico of Modena, Largo del Pozzo 71, 41124 Modena, Italy; (A.R.); (C.C.)
| | - Paolo Ventura
- Internal Medicine Unit, Department of Medical and Surgical Science for Children and Adults, Regional Reference Centre for Diagnosing and Management of Porphyrias, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria Policlinico of Modena, Largo del Pozzo 71, 41124 Modena, Italy; (A.R.); (C.C.)
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Helliwell JR. The crystal structures of the enzyme hydroxymethylbilane synthase, also known as porphobilinogen deaminase. Acta Crystallogr F Struct Biol Commun 2021; 77:388-398. [PMID: 34726177 PMCID: PMC8561815 DOI: 10.1107/s2053230x2100964x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/16/2021] [Indexed: 12/03/2022] Open
Abstract
The enzyme hydroxymethylbilane synthase (HMBS; EC 4.3.1.8), also known as porphobilinogen deaminase, catalyses the stepwise addition of four molecules of porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane. Thirty years of crystal structures are surveyed in this topical review. These crystal structures aim at the elucidation of the structural basis of the complex reaction mechanism involving the formation of tetrapyrrole from individual porphobilinogen units. The consistency between the various structures is assessed. This includes an evaluation of the precision of each molecular model and what was not modelled. A survey is also made of the crystallization conditions used in the context of the operational pH of the enzyme. The combination of 3D structural techniques, seeking accuracy, has also been a feature of this research effort. Thus, SAXS, NMR and computational molecular dynamics have also been applied. The general framework is also a considerable chemistry research effort to understand the function of the enzyme and its medical pathologies in acute intermittent porphyria (AIP). Mutational studies and their impact on the catalytic reaction provide insight into the basis of AIP and are also invaluable for guiding the understanding of the crystal structure results. Future directions for research on HMBS are described, including the need to determine the protonation states of key amino-acid residues identified as being catalytically important. The question remains - what is the molecular engine for this complex reaction? Thermal fluctuations are the only suggestion thus far.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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10
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Two Novel Hydroxymethylbilane Synthase Splicing Mutations Predispose to Acute Intermittent Porphyria. Int J Mol Sci 2021; 22:ijms222011008. [PMID: 34681668 PMCID: PMC8541332 DOI: 10.3390/ijms222011008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Acute intermittent porphyria (AIP) is an autosomal dominant genetic disease caused by a lack or decrease in hydroxymethylbilane synthase (HMBS) activity. It is characterized by acute nerve and visceral attacks caused by factors in the process of heme synthesis. The penetrance rate of this disease is low, and the heterogeneity is strong. Here, we reported two novel HMBS mutations from two unrelated Chinese AIP patients and confirmed the pathogenicity of these two mutations. We found the HMBS c.760–771+2delCTGAGGCACCTGGTinsGCTGCATCGCTGAA and HMBS c.88-1G>C mutations by second-generation sequencing and Sanger sequencing. The in vitro expression analysis showed that these mutations caused abnormal HMBS mRNA splicing and premature termination or partial missing of HMBS protein. Homologous modeling analysis showed that the HMBS mutants lacked the amino acids which are crucial for the enzyme activity or the protein stability. Consistently, enzyme activity analysis confirmed that the HMBS mutants’ overexpression cells exhibited the reduced enzyme activity compared with the HMBS wildtype overexpression cells. Our study identified and confirmed two novel pathogenic HMBS mutations which will expand the molecular heterogeneity of AIP and provide further scientific basis for the clinical diagnosis of AIP.
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11
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Lin CN, Shiao MS, Cheng ML, Chen CM, Kuo HC. Profiling of Serum Metabolites of Acute Intermittent Porphyria and Asymptomatic HMBS Mutation Carriers. Cells 2021; 10:cells10102579. [PMID: 34685558 PMCID: PMC8533736 DOI: 10.3390/cells10102579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/25/2021] [Accepted: 09/25/2021] [Indexed: 11/16/2022] Open
Abstract
This study aims to present the serum metabolite profiles of patients with acute intermittent porphyria (AIP) and identify specific metabolites that could potentially discriminate between AIP, asymptomatic HMBS mutation carriers, and healthy individuals. The study cohort included 46 female participants: 21 AIP patients, 5 asymptomatic carriers, and 20 ‘normal’ participants (without HMBS gene mutation). Serum samples were analyzed for 157 selected metabolites or clinical variables using an assay combining liquid chromatography MS/MS and direct flow injection. AUC analysis was used to distinguish unique variables between the three groups. A total of 15 variables differed significantly between the AIP and normal control group (VIP score > 1.0 and p < 0.05 with FDR correction). In AIP patients, the levels tyrosine, valine, and eGFR were significantly lower, and the levels of sphingomyelin C16:0, C24:0, C24:1, phosphatidylcholine diacyl C32:1, C36:1, C36:3, ornithine, sarcosine, citrulline, blood urea nitrogen AST, and ALT were significantly higher. The AUC of these 15 variables in discriminating between normal and AIP patients ranged between 0.73 and 0.94 (p < 0.05). In conclusion, serum metabolic profiles differ between normal individuals and patients carrying the HMBS mutation. The unique metabolites associated with AIP identified in this study may be useful for monitoring the development of AIP symptoms.
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Affiliation(s)
- Chia-Ni Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Ming-Shi Shiao
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan; (M.-S.S.); (M.-L.C.)
| | - Mei-Ling Cheng
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan; (M.-S.S.); (M.-L.C.)
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Chiung-Mei Chen
- Linkou Medical Center, Department of Neurology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Hung-Chou Kuo
- Linkou Medical Center, Department of Neurology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Correspondence: ; Tel.: +886-3-3281200 (ext. 8340)
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12
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Xue Y, Li X, Mao M, He Y, Owusu Adjei M, Zhou X, Hu H, Liu J, Li X, Ma J. AbhemC encoding porphobilinogen deaminase plays an important role in chlorophyll biosynthesis and function in albino Ananas comosus var. bracteatus leaves. PeerJ 2021; 9:e11118. [PMID: 33850657 PMCID: PMC8018242 DOI: 10.7717/peerj.11118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022] Open
Abstract
Background The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts (Grs) and albino white parts (Whs). Although the underlying mechanism of albinism in A. comosus var. bracteatus leaves is not fully understood, it is likely associated with the chlorophyll (Chl) biosynthesis. In this biosynthetic process, porphobilinogen deaminase (PBGD) plays a crucial role by catalyzing the conversion of porphobilinogen (PBG) to uroporphyrinogen III (Urogen III). Therefore, its encoding gene AbhemC was investigated here in association with Chl biosynthesis and albinism in chimeric A. comosus var. bracteatus leaves. Methods The Chl content, main Chl biosynthesis precursor content, and main enzyme activity were determined and compared between the Whs and Grs of A. comosus var. bracteatus leaves. In addition, AbhemC was cloned and its transcriptional expression and prokaryotic protein expression were analyzed. Furthermore, RNAi-mediated silencing of AbhemC was produced and assessed in tobacco plants. Results The concentration of Chl a and Chl b in the Grs was significantly higher than that in the Whs, respectively. Additionally, the content of the Chl biosynthesis precursor Urogen III decreased significantly in the Whs compared with the Grs. Thus, the transition of PBG to Urogen III may be the first rate-limiting step leading to albinism in the chimeric leaves of A. comosus var. bracteatus. The gene AbhemC comprised 1,135 bp and was encoded into a protein with 371 amino acids; phylogenetically, AbhemC was most closely related to hemC of pineapple. Prokaryotic expression and in vitro enzyme activity analysis showed that the cloned mRNA sequence of AbhemC was successfully integrated and had PBGD activity. Compared with control plants, transgenic tobacco leaves with pFGC5941-AbhemC-RNAi vector were substantially less green with significantly reduced hemC expression and Chl content, as well as reduced PBGD enzyme activity and significantly decreased content of Chl biosynthesis precursors from Urogen III onwards. Our results suggest that the absence of hemC expression reduces the enzyme activity of PBGD, which blocks the transition of PBG to Urogen III, and in turn suppresses Chl synthesis leading to the pale-green leaf color. Therefore, we suggest that AbhemC plays an important role in Chl synthesis and may be an important factor in the albinism of A. comosus var. bracteatus leaves.
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Affiliation(s)
- Yanbin Xue
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China.,College of Biology and Food Engineering, Chongqing Three Gorges College, Chongqing, China
| | - Xia Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Meiqin Mao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yehua He
- South China Agricultural University, Guangzhou, China
| | - Mark Owusu Adjei
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xuzixin Zhou
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Hao Hu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiawen Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
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13
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Bustad HJ, Kallio JP, Laitaoja M, Toska K, Kursula I, Martinez A, Jänis J. Characterization of porphobilinogen deaminase mutants reveals that arginine-173 is crucial for polypyrrole elongation mechanism. iScience 2021; 24:102152. [PMID: 33665570 PMCID: PMC7907807 DOI: 10.1016/j.isci.2021.102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/03/2020] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
Porphobilinogen deaminase (PBGD), the third enzyme in the heme biosynthesis, catalyzes the sequential coupling of four porphobilinogen (PBG) molecules into a heme precursor. Mutations in PBGD are associated with acute intermittent porphyria (AIP), a rare metabolic disorder. We used Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to demonstrate that wild-type PBGD and AIP-associated mutant R167W both existed as holoenzymes (Eholo) covalently attached to the dipyrromethane cofactor, and three intermediate complexes, ES, ES2, and ES3, where S represents PBG. In contrast, only ES2 was detected in AIP-associated mutant R173W, indicating that the formation of ES3 is inhibited. The R173W crystal structure in the ES2-state revealed major rearrangements of the loops around the active site, compared to wild-type PBGD in the Eholo-state. These results contribute to elucidating the structural pathogenesis of two common AIP-associated mutations and reveal the important structural role of Arg173 in the polypyrrole elongation mechanism.
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Affiliation(s)
- Helene J Bustad
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, 80130 Joensuu, Finland
| | - Karen Toska
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, 80130 Joensuu, Finland
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14
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Sato H, Sugishima M, Tsukaguchi M, Masuko T, Iijima M, Takano M, Omata Y, Hirabayashi K, Wada K, Hisaeda Y, Yamamoto K. Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps. Biochem J 2021; 478:1023-1042. [PMID: 33600566 PMCID: PMC7959689 DOI: 10.1042/bcj20200996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 11/30/2022]
Abstract
Hydroxymethylbilane synthase (HMBS), which is involved in the heme biosynthesis pathway, has a dipyrromethane cofactor and combines four porphobilinogen (PBG) molecules to form a linear tetrapyrrole, hydroxymethylbilane. Enzyme kinetic study of human HMBS using a PBG-derivative, 2-iodoporphobilinogen (2-I-PBG), exhibited noncompetitive inhibition with the inhibition constant being 5.4 ± 0.3 µM. To elucidate the reaction mechanism of HMBS in detail, crystal structure analysis of 2-I-PBG-bound holo-HMBS and its reaction intermediate possessing two PBG molecules (ES2), and inhibitor-free ES2 was performed at 2.40, 2.31, and 1.79 Å resolution, respectively. Their overall structures are similar to that of inhibitor-free holo-HMBS, and the differences are limited near the active site. In both 2-I-PBG-bound structures, 2-I-PBG is located near the terminus of the cofactor or the tetrapyrrole chain. The propionate group of 2-I-PBG interacts with the side chain of Arg173, and its acetate group is associated with the side chains of Arg26 and Ser28. Furthermore, the aminomethyl group and pyrrole nitrogen of 2-I-PBG form hydrogen bonds with the side chains of Gln34 and Asp99, respectively. These amino acid residues form a single substrate-binding site, where each of the four PBG molecules covalently binds to the cofactor (or oligopyrrole chain) consecutively, ultimately forming a hexapyrrole chain. Molecular dynamics simulation of the ES2 intermediate suggested that the thermal fluctuation of the lid and cofactor-binding loops causes substrate recruitment and oligopyrrole chain shift needed for consecutive condensation. Finally, the hexapyrrole chain is hydrolyzed self-catalytically to produce hydroxymethylbilane.
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Affiliation(s)
- Hideaki Sato
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
| | - Mai Tsukaguchi
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
| | - Takahiro Masuko
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mikuru Iijima
- Department of Pure and Applied Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshiaki Omata
- Department of Molecular Biology, Faculty of Pharmaceutical Science, Yokohama University of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066, Japan
| | - Kei Hirabayashi
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yoshio Hisaeda
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
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15
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Prabantu VM, Naveenkumar N, Srinivasan N. Influence of Disease-Causing Mutations on Protein Structural Networks. Front Mol Biosci 2021; 7:620554. [PMID: 33778000 PMCID: PMC7987782 DOI: 10.3389/fmolb.2020.620554] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 01/18/2023] Open
Abstract
The interactions between residues in a protein tertiary structure can be studied effectively using the approach of protein structure network (PSN). A PSN is a node-edge representation of the structure with nodes representing residues and interactions between residues represented by edges. In this study, we have employed weighted PSNs to understand the influence of disease-causing mutations on proteins of known 3D structures. We have used manually curated information on disease mutations from UniProtKB/Swiss-Prot and their corresponding protein structures of wildtype and disease variant from the protein data bank. The PSNs of the wildtype and disease-causing mutant are compared to analyse variation of global and local dissimilarity in the overall network and at specific sites. We study how a mutation at a given site can affect the structural network at a distant site which may be involved in the function of the protein. We have discussed specific examples of the disease cases where the protein structure undergoes limited structural divergence in their backbone but have large dissimilarity in their all atom networks and vice versa, wherein large conformational alterations are observed while retaining overall network. We analyse the effect of variation of network parameters that characterize alteration of function or stability.
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Affiliation(s)
| | - Nagarajan Naveenkumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,National Centre for Biological Sciences, TIFR, Bangalore, India.,Bharathidasan University, Tiruchirappalli, India
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16
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Bustad HJ, Kallio JP, Vorland M, Fiorentino V, Sandberg S, Schmitt C, Aarsand AK, Martinez A. Acute Intermittent Porphyria: An Overview of Therapy Developments and Future Perspectives Focusing on Stabilisation of HMBS and Proteostasis Regulators. Int J Mol Sci 2021; 22:E675. [PMID: 33445488 PMCID: PMC7827610 DOI: 10.3390/ijms22020675] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
Acute intermittent porphyria (AIP) is an autosomal dominant inherited disease with low clinical penetrance, caused by mutations in the hydroxymethylbilane synthase (HMBS) gene, which encodes the third enzyme in the haem biosynthesis pathway. In susceptible HMBS mutation carriers, triggering factors such as hormonal changes and commonly used drugs induce an overproduction and accumulation of toxic haem precursors in the liver. Clinically, this presents as acute attacks characterised by severe abdominal pain and a wide array of neurological and psychiatric symptoms, and, in the long-term setting, the development of primary liver cancer, hypertension and kidney failure. Treatment options are few, and therapies preventing the development of symptomatic disease and long-term complications are non-existent. Here, we provide an overview of the disorder and treatments already in use in clinical practice, in addition to other therapies under development or in the pipeline. We also introduce the pathomechanistic effects of HMBS mutations, and present and discuss emerging therapeutic options based on HMBS stabilisation and the regulation of proteostasis. These are novel mechanistic therapeutic approaches with the potential of prophylactic correction of the disease by totally or partially recovering the enzyme functionality. The present scenario appears promising for upcoming patient-tailored interventions in AIP.
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Affiliation(s)
- Helene J. Bustad
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; (H.J.B.); (J.P.K.)
| | - Juha P. Kallio
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; (H.J.B.); (J.P.K.)
| | - Marta Vorland
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway; (M.V.); (S.S.)
| | - Valeria Fiorentino
- INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018 Paris, France; (V.F.); (C.S.)
| | - Sverre Sandberg
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway; (M.V.); (S.S.)
- Norwegian Organization for Quality Improvement of Laboratory Examinations (Noklus), Haraldsplass Deaconess Hospital, 5009 Bergen, Norway
| | - Caroline Schmitt
- INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018 Paris, France; (V.F.); (C.S.)
- Assistance Publique Hôpitaux de Paris (AP-HP), Centre Français des Porphyries, Hôpital Louis Mourier, 92700 Colombes, France
| | - Aasne K. Aarsand
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway; (M.V.); (S.S.)
- Norwegian Organization for Quality Improvement of Laboratory Examinations (Noklus), Haraldsplass Deaconess Hospital, 5009 Bergen, Norway
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; (H.J.B.); (J.P.K.)
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17
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Ma L, Tian Y, Peng C, Zhang Y, Zhang S. Recent advances in the epidemiology and genetics of acute intermittent porphyria. Intractable Rare Dis Res 2020; 9:196-204. [PMID: 33139978 PMCID: PMC7586877 DOI: 10.5582/irdr.2020.03082] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Acute intermittent porphyria (AIP) is a dominant inherited disorder with a low penetrance that is caused by mutations in the gene coding for hydroxymethylbilane synthase (HMBS). Information about the epidemiology and molecular genetic features of this rare disorder is crucial to clinical research, and particularly to the evaluation of new treatments. Variations in the prevalence and penetrance of AIP in various studies may due to the different inclusion criteria and methods of assessment. Here, the prevalence and penetrance of AIP are analyzed systematically, and the genetic traits of different populations and findings regarding the genotype-phenotype correlation are summarized. In addition, quite a few studies have indicated that AIP susceptibility was affected by other factors, such as modifying genes. Findings regarding possible modifying genes are documented here, helping to reveal the pathogenesis of and treatments for AIP. The status of research on AIP in China reveals the lack of epidemiological and genetic studies of the Chinese population, a situation that needs to be promptly remedied.
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Affiliation(s)
- Liyan Ma
- Department of Endocrinology, The second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yu Tian
- Department of Endocrinology, The second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Chenxing Peng
- Department of Endocrinology, The second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yiran Zhang
- School of First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, China
| | - Songyun Zhang
- Department of Endocrinology, The second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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18
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Schnider CB, Yang H, Starrs L, Ehmann A, Rahimi F, Di Pierro E, Graziadei G, Matthews K, De Koning-Ward T, Bauer DC, Foote SJ, Burgio G, McMorran BJ. Host Porphobilinogen Deaminase Deficiency Confers Malaria Resistance in Plasmodium chabaudi but Not in Plasmodium berghei or Plasmodium falciparum During Intraerythrocytic Growth. Front Cell Infect Microbiol 2020; 10:464. [PMID: 33014890 PMCID: PMC7495142 DOI: 10.3389/fcimb.2020.00464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/28/2020] [Indexed: 11/17/2022] Open
Abstract
An important component in host resistance to malaria infection are inherited mutations that give rise to abnormalities and deficiencies in erythrocyte proteins and enzymes. Understanding how such mutations confer protection against the disease may be useful for developing new treatment strategies. A mouse ENU-induced mutagenesis screen for novel malaria resistance-conferring mutations identified a novel non-sense mutation in the gene encoding porphobilinogen deaminase (PBGD) in mice, denoted here as PbgdMRI58155. Heterozygote PbgdMRI58155 mice exhibited ~50% reduction in cellular PBGD activity in both mature erythrocytes and reticulocytes, although enzyme activity was ~10 times higher in reticulocytes than erythrocytes. When challenged with blood-stage P. chabaudi, which preferentially infects erythrocytes, heterozygote mice showed a modest but significant resistance to infection, including reduced parasite growth. A series of assays conducted to investigate the mechanism of resistance indicated that mutant erythrocyte invasion by P. chabaudi was normal, but that following intraerythrocytic establishment a significantly greater proportions of parasites died and therefore, affected their ability to propagate. The Plasmodium resistance phenotype was not recapitulated in Pbgd-deficient mice infected with P. berghei, which prefers reticulocytes, or when P. falciparum was cultured in erythrocytes from patients with acute intermittent porphyria (AIP), which had modest (20-50%) reduced levels of PBGD. Furthermore, the growth of Pbgd-null P. falciparum and Pbgd-null P. berghei parasites, which grew at the same rate as their wild-type counterparts in normal cells, were not affected by the PBGD-deficient background of the AIP erythrocytes or Pbgd-deficient mice. Our results confirm the dispensability of parasite PBGD for P. berghei infection and intraerythrocytic growth of P. falciparum, but for the first time identify a requirement for host erythrocyte PBGD by P. chabaudi during in vivo blood stage infection.
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Affiliation(s)
- Cilly Bernardette Schnider
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Hao Yang
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Lora Starrs
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Anna Ehmann
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Farid Rahimi
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Elena Di Pierro
- Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Internal Medicine Unit, Department of Medicine and Medical Specialties, Rare Diseases Center, Milan, Italy
| | - Giovanna Graziadei
- Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Internal Medicine Unit, Department of Medicine and Medical Specialties, Rare Diseases Center, Milan, Italy
| | | | | | | | - Simon J. Foote
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Brendan J. McMorran
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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19
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Morán-Jiménez MJ, Borrero-Corte MJ, Jara-Rubio F, García-Pastor I, Díaz-Díaz S, Castelbón-Fernandez FJ, Enríquez-de-Salamanca R, Méndez M. Molecular Analysis of 55 Spanish Patients with Acute Intermittent Porphyria. Genes (Basel) 2020; 11:genes11080924. [PMID: 32806544 PMCID: PMC7464722 DOI: 10.3390/genes11080924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
Acute intermittent porphyria (AIP) results from a decreased activity of hepatic hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway. AIP is an autosomal dominant disorder with incomplete penetrance, characterized by acute neurovisceral attacks precipitated by several factors that induce the hepatic 5-aminolevulinic acid synthase, the first enzyme in the heme biosynthesis. Thus, a deficiency in HMBS activity results in an overproduction of porphyrin precursors and the clinical manifestation of the disease. Early diagnosis and counselling are essential to prevent attacks, and mutation analysis is the most accurate method to identify asymptomatic carriers in AIP families. In the present study, we have investigated the molecular defects in 55 unrelated Spanish patients with AIP, identifying 32 HMBS gene mutations, of which six were novel and ten were found in more than one patient. The novel mutations included a missense, an insertion, two deletions, and two splice site variants. Prokaryotic expression studies demonstrated the detrimental effect for the missense mutation, whereas reverse transcription-PCR and sequencing showed aberrant splicing caused by each splice site mutation. These results will allow for an accurate diagnosis of carriers of the disease in these families. Furthermore, they increase the knowledge about the molecular heterogeneity of AIP in Spain.
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Affiliation(s)
- María-José Morán-Jiménez
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Centro de Investigación, Avenida de Córdoba s/n, 28041 Madrid, Spain; (M.-J.M.-J.); (M.-J.B.-C.); (F.J.-R.); (I.G.-P.); (R.E.-d.-S.)
| | - María-José Borrero-Corte
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Centro de Investigación, Avenida de Córdoba s/n, 28041 Madrid, Spain; (M.-J.M.-J.); (M.-J.B.-C.); (F.J.-R.); (I.G.-P.); (R.E.-d.-S.)
| | - Fátima Jara-Rubio
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Centro de Investigación, Avenida de Córdoba s/n, 28041 Madrid, Spain; (M.-J.M.-J.); (M.-J.B.-C.); (F.J.-R.); (I.G.-P.); (R.E.-d.-S.)
| | - Inmaculada García-Pastor
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Centro de Investigación, Avenida de Córdoba s/n, 28041 Madrid, Spain; (M.-J.M.-J.); (M.-J.B.-C.); (F.J.-R.); (I.G.-P.); (R.E.-d.-S.)
| | - Silvia Díaz-Díaz
- Servicio de Análisis Clínicos, Hospital 12 de Octubre, 28041 Madrid, Spain;
| | | | - Rafael Enríquez-de-Salamanca
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Centro de Investigación, Avenida de Córdoba s/n, 28041 Madrid, Spain; (M.-J.M.-J.); (M.-J.B.-C.); (F.J.-R.); (I.G.-P.); (R.E.-d.-S.)
| | - Manuel Méndez
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Centro de Investigación, Avenida de Córdoba s/n, 28041 Madrid, Spain; (M.-J.M.-J.); (M.-J.B.-C.); (F.J.-R.); (I.G.-P.); (R.E.-d.-S.)
- Correspondence:
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20
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Chakrabarty B, Das D, Bung N, Roy A, Bulusu G. Network analysis of hydroxymethylbilane synthase dynamics. J Mol Graph Model 2020; 99:107641. [PMID: 32619952 DOI: 10.1016/j.jmgm.2020.107641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/03/2020] [Accepted: 05/08/2020] [Indexed: 12/11/2022]
Abstract
Hydroxymethylbilane synthase (HMBS) is one of the key enzymes of the heme biosynthetic pathway that catalyzes porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane through four intermediate steps. Mutations in the human HMBS (hHMBS) can lead to acute intermittent porphyria (AIP), a lethal metabolic disorder. The molecular basis of importance of the amino acid residues at the catalytic site of hHMBS has been well studied. However, the role of non-active site residues toward the activity of the enzyme and hence the association of their mutations with AIP is not known. Network-based analyses of protein structures provide a systems approach to understand the correlations of the residues through a series of inter-residue interactions. We analyzed the dynamic network representation of HMBS protein derived from five molecular dynamics trajectories corresponding to the five steps of pyrrole polymerization. We analyzed the network clusters for each stage and identified the amino acid residues and interactions responsible for the structural stability and catalytic function of the protein. The analysis of high betweenness nodes and interaction paths from the active site help in understanding the molecular basis of the effect of non-active site AIP-causing mutations on the catalytic activity.
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Affiliation(s)
- Broto Chakrabarty
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Dibyajyoti Das
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Navneet Bung
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Arijit Roy
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India.
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21
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Yang Y, Chen X, Wu H, Peng H, Sun W, He B, Yuan Z. A novel heterozygous mutation in the HMBS gene in a patient with acute intermittent porphyria and posterior reversible encephalopathy syndrome. Mol Med Rep 2020; 22:516-524. [PMID: 32377710 PMCID: PMC7248523 DOI: 10.3892/mmr.2020.11117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Acute intermittent porphyria (AIP) is a rare inherited disorder, which is caused by the partial deficiency of hydroxymethylbilane synthase (HMBS), an enzyme of the heme biosynthetic pathway. Abdominal pain, neuropsychiatric disturbance and neuropathy are the typical manifestations of the disease. Complications such as posterior reversible encephalopathy syndrome (PRES), a rare type of brain lesion present on MRI, are also observed in patients with AIP. The present study reports on the case of a 36‑year‑old Chinese female patient with AIP and PRES. Genomic DNA were obtained from peripheral blood leukocytes and genomic regions of the HMBS gene were amplified as 2 fragments, which together contained all the exons and flanking intronic regions. Sanger sequencing of the amplified DNA fragments from the patient and the patient's family revealed a novel frameshift deletion (c.405‑406delAA) in exon 8 of the HMBS gene. This mutation leads to a subsequent truncated protein (p.Glu135AspfsX74). The recombinant mutant protein had 62% activity relative to the wild‑type protein but similar thermostability. It was confirmed that this novel mutation was the cause of AIP. Accumulation of D‑aminolevulinic acid (ALA) due to HMBS dysfunction is a potential mechanism of PRES. The manifestation of PRES may be associated with ALA‑induced cytotoxicity and the destruction of the blood‑brain barrier. In summary, in the present study, a novel pathogenic HMBS mutation was identified, expanding on the molecular heterogeneity of AIP.
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Affiliation(s)
- Yang Yang
- Department of Neurology, The Third Affiliated Hospital of The Second Military Medical University, Shanghai 200438, P.R. China
| | - Xiyun Chen
- Department of Hematology and Oncology, The Third Affiliated Hospital of The Second Military Medical University, Shanghai 200438, P.R. China
| | - Huijuan Wu
- Department of Neurology, The Second Affiliated Hospital of The Second Military Medical University, Shanghai 200003, P.R. China
| | - Hua Peng
- Department of Neurology, The Second Affiliated Hospital of The Second Military Medical University, Shanghai 200003, P.R. China
| | - Wenjing Sun
- Department of Neurology, The Third Affiliated Hospital of The Second Military Medical University, Shanghai 200438, P.R. China
| | - Bin He
- Department of Neurology, The Second Affiliated Hospital of The Second Military Medical University, Shanghai 200003, P.R. China
| | - Zhengang Yuan
- Department of Hematology and Oncology, The Third Affiliated Hospital of The Second Military Medical University, Shanghai 200438, P.R. China
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22
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Fu Y, Jia J, Yue L, Yang R, Guo Y, Ni X, Shi T. Systematically Analyzing the Pathogenic Variations for Acute Intermittent Porphyria. Front Pharmacol 2019; 10:1018. [PMID: 31572191 PMCID: PMC6753391 DOI: 10.3389/fphar.2019.01018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 08/09/2019] [Indexed: 12/18/2022] Open
Abstract
The rare autosomal dominant disorder acute intermittent porphyria (AIP) is caused by the deficient activity of hydroxymethylbilane synthase (HMBS). The symptoms of AIP are acute neurovisceral attacks which are induced by the dysfunction of heme biosynthesis. To better interpret the underlying mechanism of clinical phenotypes, we collected 117 HMBS gene mutations from reported individuals with AIP and evaluated the mutations' impacts on the corresponding protein structure and function. We found that several mutations with most severe clinical symptoms are located at dipyromethane cofactor (DPM) binding domain of HMBS. Mutations on these residues likely significantly influence the catalytic reaction. To infer new pathogenic mutations, we evaluated the pathogenicity for all the possible missense mutations of HMBS gene with different bioinformatic prediction algorithms, and identified 34 mutations with serious pathogenicity and low allele frequency. In addition, we found that gene PPARA may also play an important role in the mechanisms of AIP attacks. Our analysis about the distribution frequencies of the 23 variations revealed different distribution patterns among eight ethnic populations, which could help to explain the genetic basis that may contribute to population disparities in AIP prevalence. Our systematic analysis provides a better understanding for this disease and helps for the diagnosis and treatment of AIP.
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Affiliation(s)
- Yibao Fu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jinmeng Jia
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Lishu Yue
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Ruiying Yang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Biobank for Clinical Data and Samples in Pediatrics, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Xin Ni
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Biobank for Clinical Data and Samples in Pediatrics, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, China
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23
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Goncharova M, Pshenichnikova O, Luchinina Y, Pustovoit Y, Karpova I, Surin V. Molecular genetic study of acute intermittent porphyria in Russia: HMBS gene mutation spectrum and problem of penetrance. Clin Genet 2019; 96:91-97. [PMID: 31044425 DOI: 10.1111/cge.13558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/22/2019] [Accepted: 04/28/2019] [Indexed: 01/21/2023]
Abstract
Acute intermittent porphyria (AIP) is the most common and severe form of porphyrias. This is a dominant inherited disorder with low penetrance, caused by mutations in gene coding hydroxymethylbilane synthase (HMBS). We present the results of our long-term genetic study of AIP patients and their relatives (N = 153 and 302, respectively). We detected 88 HMBS gene mutations, 24 of which never described before. To identify additional factors conditioning AIP manifestation, we carried out whole exome sequencing on the group of AIP patients (N = 6). Mutation spectra of different patients virtually did not overlap. In 5 out of 6 patients, we found defects in genes regulating nervous system (UNC13A, ALG8, FBXO38, AGRN, DOK7, SCN4A). As usually acute AIP attacks have various neurological symptoms, we proposed a hypothesis of possible contribution of mutations in such genes in AIP manifestation.
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Affiliation(s)
- Maria Goncharova
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Olesya Pshenichnikova
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Yulia Luchinina
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Yaroslav Pustovoit
- Department of Chemotherapy of Hematological Diseases and Intensive Care, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Irina Karpova
- Biochemical Group of Centralised Clinical Diagnostic Laboratory, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Vadim Surin
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
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24
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Hassanpour H, Aghajani Z, Bahadoran S, Farhadi N, Nazari H, Kaewduangta W. Identification of reliable reference genes for quantitative real-time PCR in ovary and uterus of laying hens under heat stress. Stress 2019; 22:387-394. [PMID: 30806126 DOI: 10.1080/10253890.2019.1574294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The main stage in real-time quantitative PCR is a quantification of gene transcriptomes, in which suitable use of reliable reference genes is critical to normalize accurately. To determine the most stable reference genes in laying hens under heat stress, from a panel of nine typical candidate reference genes, the mRNA transcript of ACTB, HMBS, HPRT1, RPL13, RPL32, 18SrRNA, TBP, TFRC, and YWHAZ was evaluated in the ovary and uterus of both control and heat-stress groups of laying hens. Forty 23-week-old White Leghorn laying hens were housed in two rooms. The control (n = 20) and heat-stress (n = 20) groups were maintained at 21-23 °C and 36-38 °C for 8 weeks respectively. Analysis of this set of genes was done with BestKeeper, geNorm, and NormFinder software programs to find the most stable ones. Candidate reference genes ranked in the uterus of heat-stress and control groups of hens included YWHAZ, HPRT1, HMBS, RPL13, TFRC, ACTB, TBP, RPL32, and 18SrRNA; those in the ovary were YWHAZ, HPRT1, TFRC, HMBS, RPL13, TBP, RPL32, ACTB, and 18SrRNA. The overall results indicated that the most stable genes are YWHAZ, HPRT1, HMBS, RPL13, TFRC, TBP, ACTB, RPL32, and 18SrRNA respectively. In addition, the combination of YWHAZ, HPRT1, and HMBS is suggested as the most stable reference group of genes for more accurate quantitative data normalization in the ovarian and uterine tissues of laying hens under control and heat stress conditions. Lay summary Heat stress influences the expression of many genes in the reproductive tissues of birds. Accurate evaluation of these changes via real-time quantitative PCR depends on the determination of reliable reference genes. In this study, nine candidate housekeeping genes were evaluated, and the most stable were YWHAZ, HPRT1, HMBS, RPL13, TFRC, TBP, ACTB, RPL32, and 18SrRNA.
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Affiliation(s)
- Hossein Hassanpour
- a Department of Basic Sciences Faculty of Veterinary Medicine , Shahrekord University , Shahrekord , Iran
- b Research Institute of Animal Embryo Technology , Shahrekord University , Shahrekord , Iran
| | - Zahra Aghajani
- a Department of Basic Sciences Faculty of Veterinary Medicine , Shahrekord University , Shahrekord , Iran
| | - Shahab Bahadoran
- c Department of Clinical Sciences Faculty of Veterinary Medicine , Shahrekord University , Shahrekord , Iran
| | - Navid Farhadi
- a Department of Basic Sciences Faculty of Veterinary Medicine , Shahrekord University , Shahrekord , Iran
| | - Hasan Nazari
- b Research Institute of Animal Embryo Technology , Shahrekord University , Shahrekord , Iran
| | - Waranyoo Kaewduangta
- d Department of Agricultural Technology Faculty of Technology , Mahasarakham University , Mahasarakham , Thailand
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25
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Lenglet H, Schmitt C, Grange T, Manceau H, Karboul N, Bouchet-Crivat F, Robreau AM, Nicolas G, Lamoril J, Simonin S, Mirmiran A, Karim Z, Casalino E, Deybach JC, Puy H, Peoc'h K, Gouya L. From a dominant to an oligogenic model of inheritance with environmental modifiers in acute intermittent porphyria. Hum Mol Genet 2019; 27:1164-1173. [PMID: 29360981 DOI: 10.1093/hmg/ddy030] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/09/2018] [Indexed: 01/02/2023] Open
Abstract
Acute intermittent porphyria (AIP) is a disease affecting the heme biosynthesis pathway caused by mutations of the hydroxymethylbilane synthase (HMBS) gene. AIP is thought to display autosomal dominant inheritance with incomplete penetrance. We evaluated the prevalence, penetrance and heritability of AIP, in families with the disease from the French reference center for porphyria (CFP) (602 overt patients; 1968 relatives) and the general population, using Exome Variant Server (EVS; 12 990 alleles) data. The pathogenicity of the 42 missense variants identified was assessed in silico, and in vitro, by measuring residual HMBS activity of the recombinant protein. The minimal estimated prevalence of AIP in the general population was 1/1299. Thus, 50 000 subjects would be expected to carry the AIP genetic trait in France. Penetrance was estimated at 22.9% in families with AIP, but at only 0.5-1% in the general population. Intrafamily correlation studies showed correlations to be strong overall and modulated by kinship and the area in which the person was living, demonstrating strong influences of genetic and environmental modifiers on inheritance. Null alleles were associated with a more severe phenotype and a higher penetrance than for other mutant alleles. In conclusion, the striking difference in the penetrance of HMBS mutations between the general population and the French AIP families suggests that AIP inheritance does not follow the classical autosomal dominant model, instead of being modulated by strong environmental and genetic factors independent from HMBS. An oligogenic inheritance model with environmental modifiers might better explain AIP penetrance and heritability.
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Affiliation(s)
- Hugo Lenglet
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Département des Urgences, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Bichat, F-75018 Paris, France
| | - Caroline Schmitt
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Université Paris Diderot, F-75018 Paris, France.,Centre Français des Porphyries, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Louis Mourier, F-92701 Colombes, France
| | - Thomas Grange
- INSERM UMR_S1048 Laboratory for Vascular Translational Science (LVTS) Université Paris Diderot, F-75018 Paris, France
| | - Hana Manceau
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Laboratoire de Biochimie, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Beaujon, 92110 Clichy, France and DHU Unity
| | - Narjesse Karboul
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France
| | - Florian Bouchet-Crivat
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France
| | - Anne-Marie Robreau
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Centre Français des Porphyries, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Louis Mourier, F-92701 Colombes, France
| | - Gael Nicolas
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France
| | - Jerôme Lamoril
- Département de Génétique, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Bichat, F-75018 Paris, France
| | - Sylvie Simonin
- Centre Français des Porphyries, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Louis Mourier, F-92701 Colombes, France
| | - Arienne Mirmiran
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France
| | - Zoubida Karim
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France
| | - Enrique Casalino
- Département des Urgences, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Bichat, F-75018 Paris, France.,Université Paris Diderot, F-75018 Paris, France
| | - Jean-Charles Deybach
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Université Paris Diderot, F-75018 Paris, France.,Centre Français des Porphyries, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Louis Mourier, F-92701 Colombes, France
| | - Hervé Puy
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Université Paris Diderot, F-75018 Paris, France.,Centre Français des Porphyries, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Louis Mourier, F-92701 Colombes, France.,Laboratory of Excellence GR-Ex, F-75015 Paris, France
| | - Katell Peoc'h
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Université Paris Diderot, F-75018 Paris, France.,Laboratoire de Biochimie, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Beaujon, 92110 Clichy, France and DHU Unity.,Laboratory of Excellence GR-Ex, F-75015 Paris, France
| | - Laurent Gouya
- UMRs 1149, Centre de Recherche sur l'Inflammation, Institut National de la Santé et de la Recherche Médicale, F-75018 Paris, France.,Université Paris Diderot, F-75018 Paris, France.,Centre Français des Porphyries, Assistance Publique-Hôpitaux de Paris, HUPNVS, Hôpital Louis Mourier, F-92701 Colombes, France.,Laboratory of Excellence GR-Ex, F-75015 Paris, France
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26
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Bung N, Roy A, Priyakumar UD, Bulusu G. Computational modeling of the catalytic mechanism of hydroxymethylbilane synthase. Phys Chem Chem Phys 2019; 21:7932-7940. [DOI: 10.1039/c9cp00196d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthesis pathway, catalyzes the formation of 1-hydroxymethylbilane (HMB) by a stepwise polymerization of four molecules of porphobilinogen (PBG) using the dipyrromethane (DPM) cofactor.
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Affiliation(s)
- Navneet Bung
- TCS Innovation Labs – Hyderabad (Life Sciences Division)
- Tata Consultancy Services Limited
- Hyderabad 500081
- India
- Center for Computational Natural Sciences and Bioinformatics
| | - Arijit Roy
- TCS Innovation Labs – Hyderabad (Life Sciences Division)
- Tata Consultancy Services Limited
- Hyderabad 500081
- India
| | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500032
- India
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs – Hyderabad (Life Sciences Division)
- Tata Consultancy Services Limited
- Hyderabad 500081
- India
- Center for Computational Natural Sciences and Bioinformatics
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27
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Sriretnakumar V, Harripaul R, Vincent JB, Kennedy JL, So J. Enrichment of pathogenic variants in genes associated with inborn errors of metabolism in psychiatric populations. Am J Med Genet B Neuropsychiatr Genet 2019; 180:46-54. [PMID: 30556376 DOI: 10.1002/ajmg.b.32702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/28/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
Abstract
Many genetic conditions can mimic mental health disorders, with psychiatric symptoms that are difficult to treat with standard psychotropic medications. This study tests the hypothesis that psychiatric populations are enriched for pathogenic variants associated with selected inborn errors of metabolism (IEMs). Using next-generation sequencing, 2046 psychiatric patients were screened for pathogenic variants in genes associated with four IEMs, Niemann-Pick disease type C (NPC), Wilson disease (WD), homocystinuria (HOM), and acute intermittent porphyria (AIP). Among the 2046 cases, carrier rates of 0.83, 0.98, and 0.20%, for NPC, WD and HOM, and affected rates of 0.10 and 0.24% for NPC and AIP were seen, respectively. An enrichment of known and predicted pathogenic variants in the genes associated with NPC and AIP was found in the psychiatric cohort and especially in schizophrenia patients. The results of this study support that pathogenic variants in genes associated with IEMs are enriched in psychiatric populations. Underlying undiagnosed IEMs could account for the psychiatric symptomatology in a subset of psychiatric patients. Further studies are warranted to investigate the possibility that carriers for IEMs may have an increased risk for psychiatric disorders, particularly in the context of poor treatment response.
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Affiliation(s)
- Venuja Sriretnakumar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ricardo Harripaul
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - John B Vincent
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - James L Kennedy
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Joyce So
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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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] [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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Bung N, Roy A, Chen B, Das D, Pradhan M, Yasuda M, New MI, Desnick RJ, Bulusu G. Human hydroxymethylbilane synthase: Molecular dynamics of the pyrrole chain elongation identifies step-specific residues that cause AIP. Proc Natl Acad Sci U S A 2018; 115:E4071-E4080. [PMID: 29632172 PMCID: PMC5924904 DOI: 10.1073/pnas.1719267115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway, catalyzes the head-to-tail condensation of four molecules of porphobilinogen (PBG) to form the linear tetrapyrrole 1-hydroxymethylbilane (HMB). Mutations in human HMBS (hHMBS) cause acute intermittent porphyria (AIP), an autosomal-dominant disorder characterized by life-threatening neurovisceral attacks. Although the 3D structure of hHMBS has been reported, the mechanism of the stepwise polymerization of four PBG molecules to form HMB remains unknown. Moreover, the specific roles of each of the critical active-site residues in the stepwise enzymatic mechanism and the dynamic behavior of hHMBS during catalysis have not been investigated. Here, we report atomistic studies of HMB stepwise synthesis by using molecular dynamics (MD) simulations, mutagenesis, and in vitro expression analyses. These studies revealed that the hHMBS active-site loop movement and cofactor turn created space for the elongating pyrrole chain. Twenty-seven residues around the active site and water molecules interacted to stabilize the large, negatively charged, elongating polypyrrole. Mutagenesis of these active-site residues altered the binding site, hindered cofactor binding, decreased catalysis, impaired ligand exit, and/or destabilized the enzyme. Based on intermediate stages of chain elongation, R26 and R167 were the strongest candidates for proton transfer to deaminate the incoming PBG molecules. Unbiased random acceleration MD simulations identified R167 as a gatekeeper and facilitator of HMB egress through the space between the enzyme's domains and the active-site loop. These studies identified the specific active-site residues involved in each step of pyrrole elongation, thereby providing the molecular bases of the active-site mutations causing AIP.
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Affiliation(s)
- Navneet Bung
- Life Sciences Division, TCS Innovation Labs-Hyderabad, Tata Consultancy Services Limited, Hyderabad 500081, India
| | - Arijit Roy
- Life Sciences Division, TCS Innovation Labs-Hyderabad, Tata Consultancy Services Limited, Hyderabad 500081, India
| | - Brenden Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Dibyajyoti Das
- Life Sciences Division, TCS Innovation Labs-Hyderabad, Tata Consultancy Services Limited, Hyderabad 500081, India
| | - Meenakshi Pradhan
- Life Sciences Division, TCS Innovation Labs-Hyderabad, Tata Consultancy Services Limited, Hyderabad 500081, India
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Maria I New
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Gopalakrishnan Bulusu
- Life Sciences Division, TCS Innovation Labs-Hyderabad, Tata Consultancy Services Limited, Hyderabad 500081, India;
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Mienda BS, Salihu R, Adamu A, Idris S. Genome-scale metabolic models as platforms for identification of novel genes as antimicrobial drug targets. Future Microbiol 2018; 13:455-467. [PMID: 29469596 DOI: 10.2217/fmb-2017-0195] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The growing number of multidrug-resistant pathogenic bacteria is becoming a world leading challenge for the scientific community and for public health. However, advances in high-throughput technologies and whole-genome sequencing of bacterial pathogens make the construction of bacterial genome-scale metabolic models (GEMs) increasingly realistic. The use of GEMs as an alternative platforms will expedite identification of novel unconditionally essential genes and enzymes of target organisms with existing and forthcoming GEMs. This approach will follow the existing protocol for construction of high-quality GEMs, which could ultimately reduce the time, cost and labor-intensive processes involved in identification of novel antimicrobial drug targets in drug discovery pipelines. We discuss the current impact of existing GEMs of selected multidrug-resistant pathogenic bacteria for identification of novel antimicrobial drug targets and the challenges of closing the gap between genome-scale metabolic modeling and conventional experimental trial-and-error approaches in drug discovery pipelines.
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Affiliation(s)
- Bashir Sajo Mienda
- Department of Microbiology & Biotechnology, Faculty of Science, Federal University Dutse, PMB 7156 Ibrahim Aliyu Bypass, Dutse, Jigawa State, Nigeria
| | - Rabiu Salihu
- Department of Microbiology & Biotechnology, Faculty of Science, Federal University Dutse, PMB 7156 Ibrahim Aliyu Bypass, Dutse, Jigawa State, Nigeria
| | - Aliyu Adamu
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences & Medical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
| | - Shehu Idris
- Department of Microbiology, Faculty of Science, Kaduna State University, Tafawa Balewa Way, PMB 2339 Kaduna State, Nigeria
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Guo J, Erskine P, Coker AR, Wood SP, Cooper JB. Structural studies of domain movement in active-site mutants of porphobilinogen deaminase from Bacillus megaterium. Acta Crystallogr F Struct Biol Commun 2017; 73:612-620. [PMID: 29095155 PMCID: PMC5683031 DOI: 10.1107/s2053230x17015436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/23/2017] [Indexed: 11/10/2022] Open
Abstract
The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. The substrate molecules are linked to the cofactor in a stepwise head-to-tail manner during the reaction, which is catalysed by a conserved aspartate residue: Asp82 in the B. megaterium enzyme. Three mutations have been made affecting Asp82 (D82A, D82E and D82N) and their crystal structures have been determined at resolutions of 2.7, 1.8 and 1.9 Å, respectively. These structures reveal that whilst the D82E mutant possesses the DPM cofactor, in the D82N and D82A mutants the cofactor is likely to be missing, incompletely assembled or disordered. Comparison of the mutant PBGD structures with that of the wild-type enzyme shows that there are significant domain movements and suggests that the enzyme adopts `open' and `closed' conformations, potentially in response to substrate binding.
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Affiliation(s)
- Jingxu Guo
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Peter Erskine
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
| | - Alun R. Coker
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Steve P. Wood
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Jonathan B. Cooper
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
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Dailey HA, Dailey TA, Gerdes S, Jahn D, Jahn M, O'Brian MR, Warren MJ. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product. Microbiol Mol Biol Rev 2017; 81:e00048-16. [PMID: 28123057 PMCID: PMC5312243 DOI: 10.1128/mmbr.00048-16] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
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Affiliation(s)
- Harry A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Tamara A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Svetlana Gerdes
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Mark R O'Brian
- Department of Biochemistry, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Martin J Warren
- Department of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
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Abstract
INTRODUCTION Mitochondria are cellular organelles that perform numerous bioenergetic, biosynthetic, and regulatory functions and play a central role in iron metabolism. Extracellular iron is taken up by cells and transported to the mitochondria, where it is utilized for synthesis of cofactors essential to the function of enzymes involved in oxidation-reduction reactions, DNA synthesis and repair, and a variety of other cellular processes. Areas covered: This article reviews the trafficking of iron to the mitochondria and normal mitochondrial iron metabolism, including heme synthesis and iron-sulfur cluster biogenesis. Much of our understanding of mitochondrial iron metabolism has been revealed by pathologies that disrupt normal iron metabolism. These conditions affect not only iron metabolism but mitochondrial function and systemic health. Therefore, this article also discusses these pathologies, including conditions of systemic and mitochondrial iron dysregulation as well as cancer. Literature covering these areas was identified via PubMed searches using keywords: Iron, mitochondria, Heme Synthesis, Iron-sulfur Cluster, and Cancer. References cited by publications retrieved using this search strategy were also consulted. Expert commentary: While much has been learned about mitochondrial and its iron, key questions remain. Developing a better understanding of mitochondrial iron and its regulation will be paramount in developing therapies for syndromes that affect mitochondrial iron.
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Affiliation(s)
- Bibbin T. Paul
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut
| | - David H. Manz
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut
- School of Dental Medicine, University of Connecticut Health, Farmington, Connecticut
| | - Frank M. Torti
- Department of Medicine, University of Connecticut Health, Farmington, Connecticut
| | - Suzy V. Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut
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Chen B, Solis-Villa C, Hakenberg J, Qiao W, Srinivasan RR, Yasuda M, Balwani M, Doheny D, Peter I, Chen R, Desnick RJ. Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease. Hum Mutat 2016; 37:1215-1222. [PMID: 27539938 DOI: 10.1002/humu.23067] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/12/2016] [Indexed: 12/17/2022]
Abstract
Acute intermittent porphyria results from hydroxymethylbilane synthase (HMBS) mutations that markedly decrease HMBS enzymatic activity. This dominant disease is diagnosed when heterozygotes have life-threatening acute attacks, while most heterozygotes remain asymptomatic and undiagnosed. Although >400 HMBS mutations have been reported, the prevalence of pathogenic HMBS mutations in genomic/exomic databases, and the actual disease penetrance are unknown. Thus, we interrogated genomic/exomic databases, identified non-synonymous variants (NSVs) and consensus splice-site variants (CSSVs) in various demographic/racial groups, and determined the NSV's pathogenicity by prediction algorithms and in vitro expression assays. Caucasians had the most: 58 NSVs and two CSSVs among ∼92,000 alleles, a 0.00575 combined allele frequency. In silico algorithms predicted 14 out of 58 NSVs as "likely-pathogenic." In vitro expression identified 10 out of 58 NSVs as likely-pathogenic (seven predicted in silico), which together with two CSSVs had a combined allele frequency of 0.00056. Notably, six presumably pathogenic mutations/NSVs in the Human Gene Mutation Database were benign. Compared with the recent prevalence estimate of symptomatic European heterozygotes (∼0.000005), the prevalence of likely-pathogenic HMBS mutations among Caucasians was >100 times more frequent. Thus, the estimated penetrance of acute attacks was ∼1% of heterozygotes with likely-pathogenic mutations, highlighting the importance of predisposing/protective genes and environmental modifiers that precipitate/prevent the attacks.
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Affiliation(s)
- Brenden Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Constanza Solis-Villa
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Jörg Hakenberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Wanqiong Qiao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Ramakrishnan R Srinivasan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Manisha Balwani
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Dana Doheny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Rong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.
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Grussendorf KA, Trezza CJ, Salem AT, Al-Hashimi H, Mattingly BC, Kampmeyer DE, Khan LA, Hall DH, Göbel V, Ackley BD, Buechner M. Facilitation of Endosomal Recycling by an IRG Protein Homolog Maintains Apical Tubule Structure in Caenorhabditis elegans. Genetics 2016; 203:1789-806. [PMID: 27334269 PMCID: PMC4981278 DOI: 10.1534/genetics.116.192559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 06/15/2016] [Indexed: 02/08/2023] Open
Abstract
Determination of luminal diameter is critical to the function of small single-celled tubes. A series of EXC proteins, including EXC-1, prevent swelling of the tubular excretory canals in Caenorhabditis elegans In this study, cloning of exc-1 reveals it to encode a homolog of mammalian IRG proteins, which play roles in immune response and autophagy and are associated with Crohn's disease. Mutants in exc-1 accumulate early endosomes, lack recycling endosomes, and exhibit abnormal apical cytoskeletal structure in regions of enlarged tubules. EXC-1 interacts genetically with two other EXC proteins that also affect endosomal trafficking. In yeast two-hybrid assays, wild-type and putative constitutively active EXC-1 binds to the LIM-domain protein EXC-9, whose homolog, cysteine-rich intestinal protein, is enriched in mammalian intestine. These results suggest a model for IRG function in forming and maintaining apical tubule structure via regulation of endosomal recycling.
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Affiliation(s)
- Kelly A Grussendorf
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 Department of Biological Sciences, Minnesota State University, Mankato, Minnesota 56001
| | - Christopher J Trezza
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Alexander T Salem
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Hikmat Al-Hashimi
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Brendan C Mattingly
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Drew E Kampmeyer
- Department of Biological Sciences, Minnesota State University, Mankato, Minnesota 56001
| | - Liakot A Khan
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - David H Hall
- Department of Neuroscience, Center for Caenorhabditis elegans Anatomy, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Verena Göbel
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Brian D Ackley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Matthew Buechner
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
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Medlock AE, Shiferaw MT, Marcero JR, Vashisht AA, Wohlschlegel JA, Phillips JD, Dailey HA. Identification of the Mitochondrial Heme Metabolism Complex. PLoS One 2015; 10:e0135896. [PMID: 26287972 PMCID: PMC4545792 DOI: 10.1371/journal.pone.0135896] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/28/2015] [Indexed: 11/21/2022] Open
Abstract
Heme is an essential cofactor for most organisms and all metazoans. While the individual enzymes involved in synthesis and utilization of heme are fairly well known, less is known about the intracellular trafficking of porphyrins and heme, or regulation of heme biosynthesis via protein complexes. To better understand this process we have undertaken a study of macromolecular assemblies associated with heme synthesis. Herein we have utilized mass spectrometry with coimmunoprecipitation of tagged enzymes of the heme biosynthetic pathway in a developing erythroid cell culture model to identify putative protein partners. The validity of these data obtained in the tagged protein system is confirmed by normal porphyrin/heme production by the engineered cells. Data obtained are consistent with the presence of a mitochondrial heme metabolism complex which minimally consists of ferrochelatase, protoporphyrinogen oxidase and aminolevulinic acid synthase-2. Additional proteins involved in iron and intermediary metabolism as well as mitochondrial transporters were identified as potential partners in this complex. The data are consistent with the known location of protein components and support a model of transient protein-protein interactions within a dynamic protein complex.
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Affiliation(s)
- Amy E. Medlock
- Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- GRU-UGA Medical Partnership, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Mesafint T. Shiferaw
- Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- GRU-UGA Medical Partnership, University of Georgia, Athens, Georgia, United States of America
| | - Jason R. Marcero
- Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Ajay A. Vashisht
- Department of Biological Chemistry and the Institute of Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - James A. Wohlschlegel
- Department of Biological Chemistry and the Institute of Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - John D. Phillips
- Division of Hematology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Harry A. Dailey
- Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
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Acute intermittent porphyria in Argentina: an update. BIOMED RESEARCH INTERNATIONAL 2015; 2015:946387. [PMID: 26075277 PMCID: PMC4449928 DOI: 10.1155/2015/946387] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/20/2014] [Indexed: 12/05/2022]
Abstract
Porphyrias are a group of metabolic diseases that arise from deficiencies in the heme biosynthetic pathway. A partial deficiency in hydroxymethylbilane synthase (HMBS) produces a hepatic disorder named Acute Intermittent Porphyria (AIP); the acute porphyria is more frequent in Argentina. In this paper we review the results obtained for 101 Argentinean AIP families and 6 AIP families from foreign neighbour countries studied at molecular level at Centro de Investigaciones sobre Porfirinas y Porfirias (CIPYP). Thirty-five different mutations were found, of which 14 were described for the first time in our population. The most prevalent type of mutations was the missense mutations (43%) followed by splice defects (26%) and small deletions (20%). An odd case of a double heterozygous presentation of AIP in a foreign family from Paraguay is discussed. Moreover, it can be noted that 38 new families were found carrying the most frequent mutation in Argentina (p.G111R), increasing to 55.66% the prevalence of this genetic change in our population and adding further support to our previous hypothesis of a founder effect for this mutation in Argentina. Identification of patients with an overt AIP is important because treatment depends on an accurate diagnosis, but more critical is the identification of asymptomatic relatives to avoid acute attacks which may progress to death.
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Li Y, Qu H, Wang H, Deng H, Liu Z. Novel A219P mutation of hydroxymethylbilane synthase identified in a Chinese woman with acute intermittent porphyria and syndrome of inappropriate antidiuretic hormone. Ann Hum Genet 2015; 79:310-2. [PMID: 25787008 DOI: 10.1111/ahg.12107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/11/2014] [Indexed: 11/30/2022]
Abstract
Acute intermittent porphyria (AIP) is an autosomal dominant metabolic disorder caused by deficiency of the heme biosynthetic enzyme hydroxymethylbilane synthase (approved gene symbol HMBS), also known as porphobilinogen deaminase (PBGD). AIP is characterised by intermittent attacks of abdominal pain, vomiting, and neurological complaints. The highly variable symptomatic presentation of AIP causes confusion with other diseases and results in a high misdiagnosis rate (68% in China) and delayed effective treatments. Based on biochemical and genetic analysis of two Chinese families, a new and a previously reported HMBS mutation were identified in patients with AIP and syndrome of inappropriate antidiuretic hormone (SIADH). The novel HMBS mutation is the 655G>C point mutation (A219P). In addition, the 973C>T point mutation (R325X), which had been previously reported in two Danish families, was identified.
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Affiliation(s)
- Yingjie Li
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University
| | - Hua Qu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University
| | - Hang Wang
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University
| | - Huacong Deng
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University
| | - Ziyan Liu
- Clinical Laboratory, Guiyang Provincial People's Hospital, 55002, Guiyang, Guizhou Province, China
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Abstract
Acute intermittent porphyria (AIP), variegate porphyria (VP), and hereditary coproporphyria (HCP) are caused by mutations in the hydroxymethylbilane synthase (HMBS), protoporphyrinogen oxidase (PPOX), and coproporphyrinogen oxidase (CPOX) genes, respectively. This study aimed to identify mutations in seven Bulgarian families with AIP, six with VP, and one with HCP. A total of 33 subjects, both symptomatic (n = 21) and asymptomatic (n = 12), were included in this study. The identification of mutations was performed by direct sequencing of all the coding exons of the corresponding enzymes in the probands. The available relatives were screened for the possible mutations. A total of six different mutations in HMBS were detected in all seven families with AIP, three of which were previously described: c.76C>T [p.R26C] in exon 3, c.287C>T [p.S96F] in exon 7, and c.445C>T [p.R149X] in exon 9. The following three novel HMBS mutations were found: c.345-2A>C in intron 7-8, c.279-280insAT in exon 7, and c.887delC in exon 15. A total of three different novel mutations were identified in the PPOX gene in the VP families: c.441-442delCA in exon 5, c.917T>C [p.L306P] in exon 9, and c.1252T>C [p.C418R] in exon 12. A novel nonsense mutation, c.364G>T [p.E122X], in exon 1 of the CPOX gene was identified in the HCP family. This study, which identified mutations in Bulgarian families with AHP for the first time, established seven novel mutation sites. Seven latent carriers were also diagnosed and, therefore, were able to receive crucial counseling to prevent attacks.
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Bung N, Pradhan M, Srinivasan H, Bulusu G. Structural insights into E. coli porphobilinogen deaminase during synthesis and exit of 1-hydroxymethylbilane. PLoS Comput Biol 2014; 10:e1003484. [PMID: 24603363 PMCID: PMC3945110 DOI: 10.1371/journal.pcbi.1003484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/08/2014] [Indexed: 11/19/2022] Open
Abstract
Porphobilinogen deaminase (PBGD) catalyzes the formation of 1-hydroxymethylbilane (HMB), a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen (PBG), using a unique dipyrromethane (DPM) cofactor. Structural and biochemical studies have suggested residues with catalytic importance, but their specific role in the mechanism and the dynamic behavior of the protein with respect to the growing pyrrole chain remains unknown. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation suggested that the compactness of the overall protein decreases progressively with addition of each pyrrole ring. Essential dynamics showed that domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. Steered molecular dynamics was performed to predict the exit mechanism of HMB from PBGD at the end of the catalytic cycle. Based on the force profile and minimal structural changes the proposed path for the exit of HMB is through the space between the domains flanking the active site loop. Residues reported as catalytically important, also play an important role in the exit of HMB. Further, upon removal of HMB, the structure of PBGD gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle. Heme is the prosthetic group at the core of the oxygen carrier metalloprotein hemoglobin. Heme consists of a tetrapyrrole called porphyrin bound to an iron ion. It is synthesized by the heme biosynthetic pathway, which is common to all eukaryotes and most prokaryotes. Porphobilinogen deaminase, an enzyme in the heme biosynthetic pathway, catalyzes the formation of a linear tetrapyrrole product, 1-hydroxymethylbilane, from four units of porphobilinogen. In this study we carried out molecular dynamics simulations to understand the structural changes that the enzyme undergoes while catalyzing this reaction. There are three segments to the study: 1) understanding the changes in the enzyme when the porphobilinogen units get attached to the dipyrromethane cofactor, thereby forming a polypyrrole chain; 2) exit of the product from the active site of the enzyme via steered molecular dynamics; and 3) the relaxation of the enzyme to the initial stage to resume its catalytic cycle. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation gives insight into the motions of domains, active site loop and role of conserved active site residues in facilitating the accommodation of the polypyrrole chain. In addition to this, we propose a possible exit path for the product and demonstrate the relaxation of the enzyme after the exit of the product to resume the catalytic cycle.
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Affiliation(s)
- Navneet Bung
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Meenakshi Pradhan
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Harini Srinivasan
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
- * E-mail:
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Azim N, Deery E, Warren MJ, Wolfenden BAA, Erskine P, Cooper JB, Coker A, Wood SP, Akhtar M. Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:744-51. [PMID: 24598743 PMCID: PMC3949521 DOI: 10.1107/s139900471303294x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022]
Abstract
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.
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Affiliation(s)
- N. Azim
- School of Biological Sciences, University of Punjab, New Campus, Lahore-54590, Pakistan
| | - E. Deery
- School of Biosciences, University of Kent, Stacey Building, Canterbury CT2 7NJ, England
| | - M. J. Warren
- School of Biosciences, University of Kent, Stacey Building, Canterbury CT2 7NJ, England
| | - B. A. A. Wolfenden
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - P. Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J. B. Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - A. Coker
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - S. P. Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - M. Akhtar
- School of Biological Sciences, University of Punjab, New Campus, Lahore-54590, Pakistan
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Conformational stability and activity analysis of two hydroxymethylbilane synthase mutants, K132N and V215E, with different phenotypic association with acute intermittent porphyria. Biosci Rep 2013; 33:BSR20130045. [PMID: 23815679 PMCID: PMC3738108 DOI: 10.1042/bsr20130045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The autosomal dominantly inherited disease AIP (acute intermittent porphyria) is caused by mutations in HMBS [hydroxymethylbilane synthase; also known as PBG (porphobilinogen) deaminase], the third enzyme in the haem biosynthesis pathway. Enzyme-intermediates with increasing number of PBG molecules are formed during the catalysis of HMBS. In this work, we studied the two uncharacterized mutants K132N and V215E comparative with wt (wild-type) HMBS and to the previously reported AIP-associated mutants R116W, R167W and R173W. These mainly present defects in conformational stability (R116W), enzyme kinetics (R167W) or both (R173W). A combination of native PAGE, CD, DSF (differential scanning fluorimetry) and ion-exchange chromatography was used to study conformational stability and activity of the recombinant enzymes. We also investigated the distribution of intermediates corresponding to specific elongation stages. It is well known that the thermostability of HMBS increases when the DPM (dipyrromethane) cofactor binds to the apoenzyme and the holoenzyme is formed. Interestingly, a decrease in thermal stability was measured concomitant to elongation of the pyrrole chain, indicating a loosening of the structure prior to product release. No conformational or kinetic defect was observed for the K132N mutant, whereas V215E presented lower conformational stability and probably a perturbed elongation process. This is in accordance with the high association of V215E with AIP. Our results contribute to interpret the molecular mechanisms for dysfunction of HMBS mutants and to establish genotype–phenotype relations for AIP.
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44
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Azim N, Deery E, Warren MJ, Erskine P, Cooper JB, Wood SP, Akhtar M. Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Bacillus megaterium. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:906-8. [PMID: 23908040 PMCID: PMC3729171 DOI: 10.1107/s1744309113018526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/04/2013] [Indexed: 11/24/2022]
Abstract
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Expression in Escherichia coli of a His-tagged form of Bacillus megaterium PBGD permitted the crystallization and preliminary X-ray analysis of the enzyme from this species at high resolution.
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Affiliation(s)
- N. Azim
- School of Biological Sciences, University of Punjab, New Campus, Lahore 54590, Pakistan
| | - E. Deery
- School of Biosciences, University of Kent, Stacey Building, Canterbury, Kent CT2 7NJ, England
| | - M. J. Warren
- School of Biosciences, University of Kent, Stacey Building, Canterbury, Kent CT2 7NJ, England
| | - P. Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J. B. Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - S. P. Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - M. Akhtar
- School of Biological Sciences, University of Punjab, New Campus, Lahore 54590, Pakistan
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45
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Abstract
Heme, which is composed of iron and the small organic molecule protoporphyrin, is an essential component of hemoglobin as well as a variety of physiologically important hemoproteins. During erythropoiesis, heme synthesis is induced before, and is essential for, globin synthesis. Although all cells possess the ability to synthesize heme, there are distinct differences between regulation of the pathway in developing erythroid cells and all other types of cells. Disorders that compromise the ability of the developing red cell to synthesize heme can have profound medical implications. The biosynthetic pathway for heme and key regulatory features are reviewed herein, along with specific human genetic disorders that arise from defective heme synthesis such as X-linked sideroblastic anemia and erythropoietic protoporphyria.
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Affiliation(s)
- Harry A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA 30602, USA.
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46
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Roberts A, Gill R, Hussey RJ, Mikolajek H, Erskine PT, Cooper JB, Wood SP, Chrystal EJT, Shoolingin-Jordan PM. Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:471-85. [PMID: 23519422 DOI: 10.1107/s0907444912052134] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 12/31/2012] [Indexed: 11/10/2022]
Abstract
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem- and chlorophyll-biosynthesis pathways in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The active site possesses an unusual dipyrromethane cofactor which is extended during the reaction by the sequential addition of the four substrate molecules. The cofactor is linked covalently to the enzyme through a thioether bridge to the invariant Cys254. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. The expression of a codon-optimized gene for PBGD from Arabidopsis thaliana (thale cress) has permitted for the first time the X-ray analysis of the enzyme from a higher plant species at 1.45 Å resolution. The A. thaliana structure differs appreciably from the E. coli and human forms of the enzyme in that the active site is shielded by an extensive well defined loop region (residues 60-70) formed by highly conserved residues. This loop is completely disordered and uncharacterized in the E. coli and human PBGD structures. The new structure establishes that the dipyrromethane cofactor of the enzyme has become oxidized to the dipyrromethenone form, with both pyrrole groups approximately coplanar. Modelling of an intermediate of the elongation process into the active site suggests that the interactions observed between the two pyrrole rings of the cofactor and the active-site residues are highly specific and are most likely to represent the catalytically relevant binding mode. During the elongation cycle, it is thought that domain movements cause the bound cofactor and polypyrrole intermediates to move past the catalytic machinery in a stepwise manner, thus permitting the binding of additional substrate moieties and completion of the tetrapyrrole product. Such a model would allow the condensation reactions to be driven by the extensive interactions that are observed between the enzyme and the dipyrromethane cofactor, coupled with acid-base catalysis provided by the invariant aspartate residue Asp95.
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Affiliation(s)
- A Roberts
- School of Biological Sciences, University of Southampton, Southampton SO16 1BJ, England
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Roberts A, Gill R, Hussey RJ, Mikolajek H, Erskine PT, Cooper JB, Wood SP, Chrystal EJT, Shoolingin-Jordan PM. Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1491-3. [PMID: 23192030 PMCID: PMC3509971 DOI: 10.1107/s1744309112042212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/08/2012] [Indexed: 11/10/2022]
Abstract
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Since PBGD catalyses a reaction which is common to the biosynthesis of both haem and chlorophyll, structural studies of a plant PBGD enzyme offer great potential for the discovery of novel herbicides. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. Expression in E. coli of a codon-optimized gene for Arabidopsis thaliana PBGD has permitted for the first time the crystallization and preliminary X-ray analysis of the enzyme from a plant species at high resolution.
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Affiliation(s)
- A. Roberts
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - R. Gill
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - R. J. Hussey
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - H. Mikolajek
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - P. T. Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J. B. Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - S. P. Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - E. J. T. Chrystal
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, England
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Hamza I, Dailey HA. One ring to rule them all: trafficking of heme and heme synthesis intermediates in the metazoans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1617-32. [PMID: 22575458 DOI: 10.1016/j.bbamcr.2012.04.009] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/15/2012] [Accepted: 04/19/2012] [Indexed: 12/17/2022]
Abstract
The appearance of heme, an organic ring surrounding an iron atom, in evolution forever changed the efficiency with which organisms were able to generate energy, utilize gasses and catalyze numerous reactions. Because of this, heme has become a near ubiquitous compound among living organisms. In this review we have attempted to assess the current state of heme synthesis and trafficking with a goal of identifying crucial missing information, and propose hypotheses related to trafficking that may generate discussion and research. The possibilities of spatially organized supramolecular enzyme complexes and organelle structures that facilitate efficient heme synthesis and subsequent trafficking are discussed and evaluated. Recently identified players in heme transport and trafficking are reviewed and placed in an organismal context. Additionally, older, well established data are reexamined in light of more recent studies on cellular organization and data available from newer model organisms. This article is part of a Special Issue entitled: Cell Biology of Metals.
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Affiliation(s)
- Iqbal Hamza
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA.
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Unzu C, Sampedro A, Sardh E, Mauleón I, Enríquez de Salamanca R, Prieto J, Salido E, Harper P, Fontanellas A. Renal failure affects the enzymatic activities of the three first steps in hepatic heme biosynthesis in the acute intermittent porphyria mouse. PLoS One 2012; 7:e32978. [PMID: 22412963 PMCID: PMC3295788 DOI: 10.1371/journal.pone.0032978] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 02/02/2012] [Indexed: 12/15/2022] Open
Abstract
Chronic kidney disease is a long-term complication in acute intermittent porphyria (AIP). The pathophysiological significance of hepatic overproduction of the porphyrin precursors aminolevulinate acid (ALA) and porphobilinogen (PBG) in chronic kidney disease is unclear. We have investigated the effect of repetitive acute attacks on renal function and the effect of total or five-sixth nephrectomy causing renal insufficiency on hepatic heme synthesis in the porphobilinogen deaminase (PBGD)-deficient (AIP) mouse. Phenobarbital challenge in the AIP-mice increased urinary porphyrin precursor excretion. Successive attacks throughout 14 weeks led to minor renal lesions with no impact on renal function. In the liver of wild type and AIP mice, 5/6 nephrectomy enhanced transcription of the first and rate-limiting ALA synthase. As a consequence, urinary PBG excretion increased in AIP mice. The PBG/ALA ratio increased from 1 in sham operated AIP animals to over 5 (males) and over 13 (females) in the 5/6 nephrectomized mice. Total nephrectomy caused a rapid decrease in PBGD activity without changes in enzyme protein level in the AIP mice but not in the wild type animals. In conclusion, high concentration of porphyrin precursors had little impact on renal function. However, progressive renal insufficiency aggravates porphyria attacks and increases the PBG/ALA ratio, which should be considered a warning sign for potentially life-threatening impairment in AIP patients with signs of renal failure.
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Affiliation(s)
- Carmen Unzu
- Gene Therapy and Hepatology Area, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Ana Sampedro
- Gene Therapy and Hepatology Area, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Eliane Sardh
- Department of Internal Medicine, Karolinska Institutet, Stockholm Söder Hospital, Stockholm, Sweden
- Porphyria Centre Sweden, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Itsaso Mauleón
- Gene Therapy and Hepatology Area, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | | | - Jesús Prieto
- Gene Therapy and Hepatology Area, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), University Hospital of Canarias, University of La Laguna, La Laguna, Spain
| | - Pauline Harper
- Porphyria Centre Sweden, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Antonio Fontanellas
- Gene Therapy and Hepatology Area, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- * E-mail:
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50
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Paradisi I, Arias S. Marked geographic aggregation of acute intermittent porphyria families carrying mutation Q180X in Venezuelan populations, with description of further mutations. J Inherit Metab Dis 2010; 33 Suppl 3:S455-63. [PMID: 20978940 DOI: 10.1007/s10545-010-9228-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/28/2010] [Accepted: 09/30/2010] [Indexed: 10/18/2022]
Abstract
Acute intermittent porphyria (AIP) caused by mutations in the hydroxymethylbilane synthase gene (HMBS), has been reported in almost all human populations, with varying frequencies. A founder effect for a few specific mutations in geographic regions where prevalence is high (Sweden, The Netherlands, Switzerland) has been established through haplotype analyses, while some other mutations (R26H, R26C) have been repeatedly reported in many populations with different genetic backgrounds. Epidemiological, biochemical and molecular data on AIP in Venezuela were gathered during the last two decades; 24 independent families with AIP were ascertained, based on a deficient HMBS activity and increased porphobilinogen (PBG) urinary excretion. Molecular analyses of coding and splicing regions were performed in 23 families, to establish disease-causing changes, and haplotype analyses were used to assess ancestral kinships between them. Changes were detected in 16 out of 23 families, 9 of them being different: R26H, R26C, c.87+5G>A, c.267-54_61delgaaggggt, R116W, Q180X, c.825+1G>A, c.913-1delG, and 3' UTR *277G>A. Seven mutations were found, each one in a single family; one mutation was present in two unrelated families, whereas mutation Q180X was shared by 7 independent kindreds, all of which had the same haplotype (-);T;A;T;G;T;A;G (3167delG; 3530T>C; 3581A>G; 3982T>C; 6479G>T; 7052T>C; 7064A>C; 7779G>A). Six out of seven different Q180X carrier families came from the same geographic focus (Santa Lucía, Miranda State). Dense geographic aggregation with one identical haplotype strongly suggests a remote founder phenomenon for these Venezuelan AIP families, carrying an unreported but most frequent mutation.
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Affiliation(s)
- Irene Paradisi
- Laboratorio de Genética Humana, Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas, IVIC, Apartado 20632, Caracas, 1020-A Venezuela.
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