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Alibrandi S, Nicita F, Donato L, Scimone C, Rinaldi C, D’Angelo R, Sidoti A. Adaptive Modelling of Mutated FMO3 Enzyme Could Unveil Unexplored Scenarios Linking Variant Haplotypes to TMAU Phenotypes. Molecules 2021; 26:molecules26227045. [PMID: 34834137 PMCID: PMC8618768 DOI: 10.3390/molecules26227045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/10/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Trimethylaminuria (TMAU) is a rare genetic disease characterized by the accumulation of trimethylamine (TMA) and its subsequent excretion trough main body fluids, determining the characteristic fish odour in affected patients. We realized an experimental study to investigate the role of several coding variants in the causative gene FMO3, that were only considered as polymorphic or benign, even if the available literature on them did not functionally explain their ineffectiveness on the encoded enzyme. Methods: Mutational analysis of 26 TMAU patients was realized by Sanger sequencing. Detected variants were, subsequently, deeply statistically and in silico characterized to determine their possible effects on the enzyme activity. To achieve this goal, a docking prediction for TMA/FMO3 and an unbinding pathway study were performed. Finally, a TMAO/TMA urine quantification by 1H-NMR spectroscopy was performed to support modelling results. Results: The FMO3 screening of all patients highlighted the presence of 17 variants distributed in 26 different haplotypes. Both non-sense and missense considered variants might impair the enzymatic kinetics of FMO3, probably reducing the interaction time between the protein catalytic site and TMA, or losing the wild-type binding site. Conclusions: Even if further functional assays will confirm our predictive results, considering the possible role of FMO3 variants with still uncertain effects, might be a relevant step towards the detection of novel scenarios in TMAU etiopathogenesis.
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Affiliation(s)
- Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (S.A.); (F.N.); (C.S.); (C.R.); (R.D.); (A.S.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98125 Messina, Italy
| | - Fabiana Nicita
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (S.A.); (F.N.); (C.S.); (C.R.); (R.D.); (A.S.)
| | - Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (S.A.); (F.N.); (C.S.); (C.R.); (R.D.); (A.S.)
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, I.E.ME.S.T., 90139 Palermo, Italy
- Correspondence: ; Tel.: +39-090-221-3136
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (S.A.); (F.N.); (C.S.); (C.R.); (R.D.); (A.S.)
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, I.E.ME.S.T., 90139 Palermo, Italy
| | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (S.A.); (F.N.); (C.S.); (C.R.); (R.D.); (A.S.)
| | - Rosalia D’Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (S.A.); (F.N.); (C.S.); (C.R.); (R.D.); (A.S.)
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (S.A.); (F.N.); (C.S.); (C.R.); (R.D.); (A.S.)
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Crocker L, Fruk L. Flavin Conjugated Polydopamine Nanoparticles Displaying Light-Driven Monooxygenase Activity. Front Chem 2019; 7:278. [PMID: 31080793 PMCID: PMC6497766 DOI: 10.3389/fchem.2019.00278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
A hybrid of flavin and polydopamine (PDA) has been explored as a photocatalyst, drawing inspiration from natural flavoenzymes. Light-driven monoxygenase activity has been demonstrated through the oxidation of indole under blue light irradiation in ambient conditions, to afford indigo and indirubin dyes. Compared to riboflavin, a flavin-polydopamine hybrid is shown to be more resistant to photobleaching and more selective toward dye production. In addition, it has been demonstrated that it can be recycled from the solution and used for up to four cycles without a marked loss of activity, which is a significant improvement compared to other heterogenous flavin catalysts. The mechanism of action has been explored, indicating that the PDA shell plays an important role in the stabilization of the intermediate flavin-peroxy species, an active component of the catalytic system rather than acting only as a passive nanocarrier of active centers.
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Affiliation(s)
- Leander Crocker
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Ljiljana Fruk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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Li X, Yuan G, Chen X, Guo Y, Yang N, Pi J, Zhang H, Zheng J. Fishy Odor and TMA Content Levels in Duck Egg Yolks. J Food Sci 2017; 83:39-45. [PMID: 29210463 DOI: 10.1111/1750-3841.13977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 10/05/2017] [Accepted: 10/10/2017] [Indexed: 11/30/2022]
Abstract
The differences between the trimethylamine (TMA) content levels in duck and chicken egg yolks under normal dietary conditions were compared. Moreover, the association between the polymorphisms of the duck FMO3 gene and TMA content levels in duck egg yolks was analyzed. Then, to detect the mutations associated with the fish-flavor trait, duck populations were selected for a high-choline diet experiment, which was followed by full-length sequencing of the FMO3 exons. The results showed that the TMA content levels in duck eggs (3.60 μg/g) were significantly higher than those in chicken eggs (2.35 μg/g) under normal dietary conditions (P < 0.01). With regard to the high-choline diet, the average TMA content levels in duck egg yolks (9.21 μg/g; P < 0.01) increased significantly. Furthermore, 5 SNPs reported in Ensembl database were detected in duck FMO3 exons. However, no mutation loci were found to be significantly associated with the TMA content levels in duck egg yolks. Besides, duck liver FMO3 mRNA expression levels were not associated with the TMA content levels. The results indicated that excessive TMA deposition in duck eggs is one of main factors causing the fishy odor in duck eggs, and the addition of choline in the ducks' diets was responsible for inducing an increase in the TMA content levels in duck eggs. PRACTICAL APPLICATION Our study can help to diminish the fishy taste in duck eggs by reducing the amount of supplemented choline. Furthermore, this study laid a solid foundation for revealing the genetic factors involved in the fishy odor in duck eggs.
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Affiliation(s)
- Xingzheng Li
- the National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural Univ., Beijing 100193, China
| | - Gongjiao Yuan
- the National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural Univ., Beijing 100193, China
| | - Xia Chen
- the National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural Univ., Beijing 100193, China
| | - Yuying Guo
- the National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural Univ., Beijing 100193, China
| | - Ning Yang
- the National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural Univ., Beijing 100193, China
| | - Jinsong Pi
- The Instit. of Animal Science, Hubei Acad. of Agricultural Science, Wuhan 430072, Hubei Province, China
| | - Hao Zhang
- The Instit. of Animal Science, Hubei Acad. of Agricultural Science, Wuhan 430072, Hubei Province, China
| | - Jiangxia Zheng
- the National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural Univ., Beijing 100193, China
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Inactivation mechanism of N61S mutant of human FMO3 towards trimethylamine. Sci Rep 2017; 7:14668. [PMID: 29116146 PMCID: PMC5676948 DOI: 10.1038/s41598-017-15224-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
Human flavin-containing monooxygenase 3 (hFMO3) catalyses the oxygenation of a wide variety of compounds including drugs as well as dietary compounds. It is the major hepatic enzyme involved in the production of the N-oxide of trimethylamine (TMAO) and clinical studies have uncovered a striking correlation between plasma TMAO concentration and cardiovascular disease. Certain mutations within the hFMO3 gene cause defective trimethylamine (TMA) N-oxygenation leading to trimethylaminuria (TMAU) also known as fish-odour syndrome. In this paper, the inactivation mechanism of a TMAU-causing polymorphic variant, N61S, is investigated. Transient kinetic experiments show that this variant has a > 170-fold lower NADPH binding affinity than the wild type. Thermodynamic and spectroscopic experiments reveal that the poor NADP+ binding affinity accelerates the C4a-hydroperoxyFAD intermediate decay, responsible for an unfavourable oxygen transfer to the substrate. Steady-state kinetic experiments show significantly decreased N61S catalytic activity towards other substrates; methimazole, benzydamine and tamoxifen. The in vitro data are corroborated by in silico data where compared to the wild type enzyme, a hydrogen bond required for the stabilisation of the flavin intermediate is lacking. Taken together, the data presented reveal the molecular basis for the loss of function observed in N61S mutant.
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Xu M, Bhatt DK, Yeung CK, Claw KG, Chaudhry AS, Gaedigk A, Pearce RE, Broeckel U, Gaedigk R, Nickerson DA, Schuetz E, Rettie AE, Leeder JS, Thummel KE, Prasad B. Genetic and Nongenetic Factors Associated with Protein Abundance of Flavin-Containing Monooxygenase 3 in Human Liver. J Pharmacol Exp Ther 2017; 363:265-274. [PMID: 28819071 PMCID: PMC5697103 DOI: 10.1124/jpet.117.243113] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/14/2017] [Indexed: 01/20/2023] Open
Abstract
Hepatic flavin-containing mono-oxygenase 3 (FMO3) metabolizes a broad array of nucleophilic heteroatom (e.g., N or S)-containing xenobiotics (e.g., amphetamine, sulindac, benzydamine, ranitidine, tamoxifen, nicotine, and ethionamide), as well as endogenous compounds (e.g., catecholamine and trimethylamine). To predict the effect of genetic and nongenetic factors on the hepatic metabolism of FMO3 substrates, we quantified FMO3 protein abundance in human liver microsomes (HLMs; n = 445) by liquid chromatography-tandem mass chromatography proteomics. Genotyping/gene resequencing, mRNA expression, and functional activity (with benzydamine as probe substrate) of FMO3 were also evaluated. FMO3 abundance increased 2.2-fold (13.0 ± 11.4 pmol/mg protein vs. 28.0 ± 11.8 pmol/mg protein) from neonates to adults. After 6 years of age, no significant difference in FMO3 abundance was found between children and adults. Female donors exhibited modestly higher mRNA fragments per kilobase per million reads values (139.9 ± 76.9 vs. 105.1 ± 73.1; P < 0.001) and protein FMO3 abundance (26.7 ± 12.0 pmol/mg protein vs. 24.1 ± 12.1 pmol/mg protein; P < 0.05) compared with males. Six single nucleotide polymorphisms (SNPs), including rs2064074, rs28363536, rs2266782 (E158K), rs909530 (N285N), rs2266780 (E308G), and rs909531, were associated with significantly decreased protein abundance. FMO3 abundance in individuals homozygous and heterozygous for haplotype 3 (H3), representing variant alleles for all these SNPs (except rs2066534), were 50.8% (P < 0.001) and 79.5% (P < 0.01), respectively, of those with the reference homozygous haplotype (H1, representing wild-type). In summary, FMO3 protein abundance is significantly associated with age, gender, and genotype. These data are important in predicting FMO3-mediated heteroatom-oxidation of xenobiotics and endogenous biomolecules in the human liver.
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Affiliation(s)
- Meijuan Xu
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Deepak Kumar Bhatt
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Catherine K Yeung
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Katrina G Claw
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Amarjit S Chaudhry
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Andrea Gaedigk
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Robin E Pearce
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Ulrich Broeckel
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Roger Gaedigk
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Deborah A Nickerson
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Erin Schuetz
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Allan E Rettie
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - J Steven Leeder
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Kenneth E Thummel
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
| | - Bhagwat Prasad
- Departments of Pharmaceutics (M.X., D.K.B., K.G.C., K.E.T., B.P.), Medicinal Chemistry (C.K.Y., A.E.R.), and Genome Sciences (D.N.), University of Washington, Seattle, Washington; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China (M.X.); Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.S.); Division of Pediatric Pharmacology and Medical Toxicology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (A.G., R.E.P., R.G., J.S.L.); and Section of Genomic Pediatrics, Department of Pediatrics, and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin (U.B.)
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Guo Y, Hwang LD, Li J, Eades J, Yu CW, Mansfield C, Burdick-Will A, Chang X, Chen Y, Duke FF, Zhang J, Fakharzadeh S, Fennessey P, Keating BJ, Jiang H, Hakonarson H, Reed DR, Preti G. Genetic analysis of impaired trimethylamine metabolism using whole exome sequencing. BMC MEDICAL GENETICS 2017; 18:11. [PMID: 28196478 PMCID: PMC5310055 DOI: 10.1186/s12881-017-0369-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/17/2017] [Indexed: 12/27/2022]
Abstract
Background Trimethylaminuria (TMAU) is a genetic disorder whereby people cannot convert trimethylamine (TMA) to its oxidized form (TMAO), a process that requires the liver enzyme FMO3. Loss-of-function variants in the FMO3 gene are a known cause of TMAU. In addition to the inability to metabolize TMA precursors like choline, patients often emit a characteristic odor because while TMAO is odorless, TMA has a fishy smell. The Monell Chemical Senses Center is a research institute with a program to evaluate people with odor complaints for TMAU. Methods Here we evaluated ten subjects by (1) odor evaluation by a trained sensory panel, (2) analysis of their urine concentration of TMA relative to TMAO before and after choline ingestion, and (3) whole exome sequencing as well as subsequent variant analysis of all ten samples to investigate the genetics of TMAU. Results While all subjects reported they often emitted a fish-like odor, none had this malodor during sensory evaluation. However, all were impaired in their ability to produce >90% TMAO/TMA in their urine and thus met the criteria for TMAU. To probe for genetic causes, the exome of each subject was sequenced, and variants were filtered by genes with a known (FMO3) or expected effect on TMA metabolism function (other oxidoreductases). We filtered the remaining variants by allele frequency and predicated functional effects. We identified one subject that had a rare loss-of-function FMO3 variant and six with more common decreased-function variants. In other oxidoreductases genes, five subjects had four novel rare single-nucleotide polymorphisms as well as one rare insertion/deletion. Novel in this context means no investigators have previously linked these variants to TMAU although they are in dbSNP. Conclusions Thus, variants in genes other than FMO3 may cause TMAU and the genetic variants identified here serve as a starting point for future studies of impaired TMA metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0369-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiran Guo
- Center for Applied Genomics, the Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Res Cntr, Ste 1016H, Philadelphia, PA, 19104, USA.
| | - Liang-Dar Hwang
- Monell Chemical Senses Center, 3500 Market St, Philadelphia, PA, 19104, USA
| | | | - Jason Eades
- Monell Chemical Senses Center, 3500 Market St, Philadelphia, PA, 19104, USA
| | - Chung Wen Yu
- Monell Chemical Senses Center, 3500 Market St, Philadelphia, PA, 19104, USA
| | - Corrine Mansfield
- Monell Chemical Senses Center, 3500 Market St, Philadelphia, PA, 19104, USA
| | | | - Xiao Chang
- Center for Applied Genomics, the Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Res Cntr, Ste 1016H, Philadelphia, PA, 19104, USA
| | | | - Fujiko F Duke
- Monell Chemical Senses Center, 3500 Market St, Philadelphia, PA, 19104, USA
| | | | - Steven Fakharzadeh
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul Fennessey
- University of Colorado Health Sciences Center, Denver, CO, USA
| | - Brendan J Keating
- Center for Applied Genomics, the Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Res Cntr, Ste 1016H, Philadelphia, PA, 19104, USA
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, 518083, China.,Shenzhen Key Laboratory of Genomics, Shenzhen, 518083, China.,The Guangdong Enterprise Key Laboratory of Human Disease Genomics, Shenzhen, 518083, China
| | - Hakon Hakonarson
- Center for Applied Genomics, the Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Res Cntr, Ste 1016H, Philadelphia, PA, 19104, USA
| | - Danielle R Reed
- Monell Chemical Senses Center, 3500 Market St, Philadelphia, PA, 19104, USA.
| | - George Preti
- Monell Chemical Senses Center, 3500 Market St, Philadelphia, PA, 19104, USA.,Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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7
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Ren L, Teng M, Zhang T, Zhang X, Sun B, Qin S, Zhong L, Peng Z, Fan J. Donors FMO3 polymorphisms affect tacrolimus elimination in Chinese liver transplant patients. Pharmacogenomics 2017; 18:265-275. [PMID: 28084894 DOI: 10.2217/pgs-2016-0098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AIM Flavin-containing monooxygenase (FMO) variants were potentially involved in tacrolimus metabolism in kidney transplantion. The influences of FMO3 genotypes on tacrolimus elimination in Chinese liver transplant patients remained unclear. PATIENTS & METHODS FMO3 SNPs and CYP3A5 rs776746 were analyzed in 110 Chinese patients. RESULTS Donor FMO3 rs1800822 allele T and rs909530 allele T were associated with fast tacrolimus elimination. Combination of polymorphisms of donor FMO3 rs1800822 and rs909530 genotype impacted on tacrolimus elimination (p = 0.0221). The number of donor rs1800822 allele T and rs909530 allele T was confirmed to be an independent predictor of the tacrolimus concentration-to-dose ratios for weeks 2, 3 and 4 in the multivariate analysis. CONCLUSION Donor's FMO3 polymorphisms might affect tacrolimus elimination.
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Affiliation(s)
- Lei Ren
- Department of Hepatobiliary Pancreatic Surgery, Shandong Qianfoshan Hospital, Shandong University, Jinan 250014, China
| | - Mujian Teng
- Department of Hepatobiliary Pancreatic Surgery, Shandong Qianfoshan Hospital, Shandong University, Jinan 250014, China
| | - Tao Zhang
- Department of Hepatobiliary Pancreatic Surgery, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Xiaoqing Zhang
- Department of Pharmacy, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Bo Sun
- Department of Pharmacy, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lin Zhong
- Department of Hepatobiliary Pancreatic Surgery, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Zhihai Peng
- Department of Hepatobiliary Pancreatic Surgery, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Junwei Fan
- Department of Hepatobiliary Pancreatic Surgery, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
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8
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Li CY, Chen XL, Zhang D, Wang P, Sheng Q, Peng M, Xie BB, Qin QL, Li PY, Zhang XY, Su HN, Song XY, Shi M, Zhou BC, Xun LY, Chen Y, Zhang YZ. Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide. Mol Microbiol 2017; 103:992-1003. [PMID: 27997715 DOI: 10.1111/mmi.13605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2016] [Indexed: 11/28/2022]
Abstract
Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are widespread in the ocean and are important nitrogen source for bacteria. TMA monooxygenase (Tmm), a bacterial flavin-containing monooxygenase (FMO), is found widespread in marine bacteria and is responsible for converting TMA to TMAO. However, the molecular mechanism of TMA oxygenation by Tmm has not been explained. Here, we determined the crystal structures of two reaction intermediates of a marine bacterial Tmm (RnTmm) and elucidated the catalytic mechanism of TMA oxidation by RnTmm. The catalytic process of Tmm consists of a reductive half-reaction and an oxidative half-reaction. In the reductive half-reaction, FAD is reduced and a C4a-hydroperoxyflavin intermediate forms. In the oxidative half-reaction, this intermediate attracts TMA through electronic interactions. After TMA binding, NADP+ bends and interacts with D317, shutting off the entrance to create a protected micro-environment for catalysis and exposing C4a-hydroperoxyflavin to TMA for oxidation. Sequence analysis suggests that the proposed catalytic mechanism is common for bacterial Tmms. These findings reveal the catalytic process of TMA oxidation by marine bacterial Tmm and first show that NADP+ undergoes a conformational change in the oxidative half-reaction of FMOs.
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Affiliation(s)
- Chun-Yang Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Dian Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Bai-Cheng Zhou
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Lu-Ying Xun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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9
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Human flavin-containing monooxygenase 3: Structural mapping of gene polymorphisms and insights into molecular basis of drug binding. Gene 2016; 593:91-99. [DOI: 10.1016/j.gene.2016.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/07/2016] [Accepted: 08/10/2016] [Indexed: 11/21/2022]
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10
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Lee YS, Kim BH, Kim BC, Shin A, Kim JS, Hong SH, Hwang JA, Lee JA, Nam S, Lee SH, Bhak J, Park JW. SLC15A2 genomic variation is associated with the extraordinary response of sorafenib treatment: whole-genome analysis in patients with hepatocellular carcinoma. Oncotarget 2016; 6:16449-60. [PMID: 25965825 PMCID: PMC4599281 DOI: 10.18632/oncotarget.3758] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/10/2015] [Indexed: 12/13/2022] Open
Abstract
Reliable biomarkers are required to predict the response to sorafenib. We investigated genomic variations associated with responsiveness to sorafenib for patients with unresectable hepatocellular carcinoma (HCC). Blood samples from 2 extreme, 2 strong and 3 poor responders to sorafenib were subjected to whole-genome analysis. Then, we validated candidate genomic variations with another 174 HCC patients, and performed in vitro functional analysis and in silico analyses. Genomic data of >96 gigabases/sample was generated at average of ~34X sequencing depth. In total, 1813 genomic variations were matched to sorafenib responses in clinical data; 708 were located within regions for sorafenib-target genes or drug absorption, distribution, metabolism, and excretion (ADME)-related genes. From them, 36 variants were within the coding regions and 6 identified as non-synonymous single-nucleotide variants from 4 ADME-related genes (ABCB1, FMO3, MUSK, and SLC15A2). Validation genotyping confirmed sequencing results and revealed patients genotype for rs2257212 in SLC15A2 showed longer progression-free survival (HR = 2.18). In vitro study displayed different response to sorafenib depending on the genotype of SLC15A2. Structural prediction analysis revealed changes of the phosphorylation levels in protein, potentially affecting sorafenib-associated enzymatic activity. Our finding using extreme responder seems to generate robust biomarker to predict the response of sorafenib treatment for HCC.
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Affiliation(s)
- Yeon-Su Lee
- Cancer Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Bo Hyun Kim
- Center for Liver Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Byung Chul Kim
- The Genomics Institute, Biomedical Engineering, UNIST, Ulsan, Republic of Korea
| | - Aesun Shin
- Molecular Epidemiology Branch, National Cancer Center, Goyang, Republic of Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin Sook Kim
- Liver and Pancreatobiliary Cancer Branch, National Cancer Center, Goyang, Republic of Korea
| | - Seung-Hyun Hong
- Cancer Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Jung-Ah Hwang
- Cancer Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Jung Ahn Lee
- Liver and Pancreatobiliary Cancer Branch, National Cancer Center, Goyang, Republic of Korea
| | - Seungyoon Nam
- New Experimental Therapeutics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Sung Hoon Lee
- Personal Genomics Institute, Genome Research Foundation, TheragenEtex, Suwon, Republic of Korea.,Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea
| | - Jong Bhak
- The Genomics Institute, Biomedical Engineering, UNIST, Ulsan, Republic of Korea.,Personal Genomics Institute, Genome Research Foundation, TheragenEtex, Suwon, Republic of Korea
| | - Joong-Won Park
- Center for Liver Cancer, National Cancer Center, Goyang, Republic of Korea.,Liver and Pancreatobiliary Cancer Branch, National Cancer Center, Goyang, Republic of Korea
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11
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Moffat I, Chepelev N, Labib S, Bourdon-Lacombe J, Kuo B, Buick JK, Lemieux F, Williams A, Halappanavar S, Malik A, Luijten M, Aubrecht J, Hyduke DR, Fornace AJ, Swartz CD, Recio L, Yauk CL. Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. Crit Rev Toxicol 2015; 45:1-43. [PMID: 25605026 DOI: 10.3109/10408444.2014.973934] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Toxicogenomics is proposed to be a useful tool in human health risk assessment. However, a systematic comparison of traditional risk assessment approaches with those applying toxicogenomics has never been done. We conducted a case study to evaluate the utility of toxicogenomics in the risk assessment of benzo[a]pyrene (BaP), a well-studied carcinogen, for drinking water exposures. Our study was intended to compare methodologies, not to evaluate drinking water safety. We compared traditional (RA1), genomics-informed (RA2) and genomics-only (RA3) approaches. RA2 and RA3 applied toxicogenomics data from human cell cultures and mice exposed to BaP to determine if these data could provide insight into BaP's mode of action (MOA) and derive tissue-specific points of departure (POD). Our global gene expression analysis supported that BaP is genotoxic in mice and allowed the development of a detailed MOA. Toxicogenomics analysis in human lymphoblastoid TK6 cells demonstrated a high degree of consistency in perturbed pathways with animal tissues. Quantitatively, the PODs for traditional and transcriptional approaches were similar (liver 1.2 vs. 1.0 mg/kg-bw/day; lungs 0.8 vs. 3.7 mg/kg-bw/day; forestomach 0.5 vs. 7.4 mg/kg-bw/day). RA3, which applied toxicogenomics in the absence of apical toxicology data, demonstrates that this approach provides useful information in data-poor situations. Overall, our study supports the use of toxicogenomics as a relatively fast and cost-effective tool for hazard identification, preliminary evaluation of potential carcinogens, and carcinogenic potency, in addition to identifying current limitations and practical questions for future work.
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Affiliation(s)
- Ivy Moffat
- Water and Air Quality Bureau, Health Canada, Ottawa, ON, Canada.,Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Nikolai Chepelev
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Sarah Labib
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Julie Bourdon-Lacombe
- Water and Air Quality Bureau, Health Canada, Ottawa, ON, Canada.,Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Julie K Buick
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - France Lemieux
- Water and Air Quality Bureau, Health Canada, Ottawa, ON, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Amal Malik
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Mirjam Luijten
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Daniel R Hyduke
- Biological Engineering Department, Utah State University, Logan, UT, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Carol D Swartz
- Integrated Laboratory Systems Inc., Research Triangle Park, NC, USA
| | - Leslie Recio
- Integrated Laboratory Systems Inc., Research Triangle Park, NC, USA
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
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12
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Shih DM, Wang Z, Lee R, Meng Y, Che N, Charugundla S, Qi H, Wu J, Pan C, Brown JM, Vallim T, Bennett BJ, Graham M, Hazen SL, Lusis AJ. Flavin containing monooxygenase 3 exerts broad effects on glucose and lipid metabolism and atherosclerosis. J Lipid Res 2014; 56:22-37. [PMID: 25378658 DOI: 10.1194/jlr.m051680] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We performed silencing and overexpression studies of flavin containing monooxygenase (FMO) 3 in hyperlipidemic mouse models to examine its effects on trimethylamine N-oxide (TMAO) levels and atherosclerosis. Knockdown of hepatic FMO3 in LDL receptor knockout mice using an antisense oligonucleotide resulted in decreased circulating TMAO levels and atherosclerosis. Surprisingly, we also observed significant decreases in hepatic lipids and in levels of plasma lipids, ketone bodies, glucose, and insulin. FMO3 overexpression in transgenic mice, on the other hand, increased hepatic and plasma lipids. Global gene expression analyses suggested that these effects of FMO3 on lipogenesis and gluconeogenesis may be mediated through the PPARα and Kruppel-like factor 15 pathways. In vivo and in vitro results were consistent with the concept that the effects were mediated directly by FMO3 rather than trimethylamine/TMAO; in particular, overexpression of FMO3 in the human hepatoma cell line, Hep3B, resulted in significantly increased glucose secretion and lipogenesis. Our results indicate a major role for FMO3 in modulating glucose and lipid homeostasis in vivo, and they suggest that pharmacologic inhibition of FMO3 to reduce TMAO levels would be confounded by metabolic interactions.
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Affiliation(s)
- Diana M Shih
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Zeneng Wang
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | | | - Yonghong Meng
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Nam Che
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Sarada Charugundla
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Hannah Qi
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Judy Wu
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Calvin Pan
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - J Mark Brown
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Thomas Vallim
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Brian J Bennett
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | | | - Stanley L Hazen
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Aldons J Lusis
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA Departments of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
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13
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Potential for drug interactions mediated by polymorphic flavin-containing monooxygenase 3 in human livers. Drug Metab Pharmacokinet 2014; 30:70-4. [PMID: 25760532 DOI: 10.1016/j.dmpk.2014.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 09/17/2014] [Accepted: 09/21/2014] [Indexed: 11/24/2022]
Abstract
Human flavin-containing monooxygenase 3 (FMO3) in the liver catalyzes a variety of oxygenations of nitrogen- and sulfur-containing medicines and xenobiotic substances. Because of growing interest in drug interactions mediated by polymorphic FMO3, benzydamine N-oxygenation by human FMO3 was investigated as a model reaction. Among the 41 compounds tested, trimethylamine, methimazole, itopride, and tozasertib (50 μM) suppressed benzydamine N-oxygenation at a substrate concentration of 50 μM by approximately 50% after co-incubation. Suppression of N-oxygenation of benzydamine, trimethylamine, itopride, and tozasertib and S-oxygenation of methimazole and sulindac sulfide after co-incubation with the other five of these six substrates was compared using FMO3 proteins recombinantly expressed in bacterial membranes. Apparent competitive inhibition by methimazole (0-50 μM) of sulindac sulfide S-oxygenation was observed with FMO3 proteins. Sulindac sulfide S-oxygenation activity of Arg205Cys variant FMO3 protein was likely to be suppressed more by methimazole than wild-type or Val257Met variant FMO3 protein was. These results suggest that genetic polymorphism in the human FMO3 gene may lead to changes of drug interactions for N- or S-oxygenations of xenobiotics and endogenous substances and that a probe battery system of benzydamine N-oxygenation and sulindac sulfide S-oxygenation activities is recommended to clarify the drug interactions mediated by FMO3.
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14
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Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq. Mol Biol Rep 2014; 41:6305-15. [PMID: 25008993 DOI: 10.1007/s11033-014-3513-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
Abstract
Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.
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15
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Hanouneh IA, Zein NN, Cikach F, Dababneh L, Grove D, Alkhouri N, Lopez R, Dweik RA. The breathprints in patients with liver disease identify novel breath biomarkers in alcoholic hepatitis. Clin Gastroenterol Hepatol 2014; 12:516-23. [PMID: 24036050 PMCID: PMC3971429 DOI: 10.1016/j.cgh.2013.08.048] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Selected-ion flow-tube mass spectrometry can precisely identify trace gases in the human breath, in the parts-per-billion range. We investigated whether concentrations of volatile compounds in breath samples correlate with the diagnosis of alcoholic hepatitis (AH) and the severity of liver disease in patients with AH. METHODS We recruited patients with liver disease from a single tertiary care center. The study population was divided between those with AH with cirrhosis (n = 40) and those with cirrhosis with acute decompensation from etiologies other than alcohol (n = 40); individuals without liver disease served as control subjects (n = 43). We used selected-ion flow-tube mass spectrometry to identify and measure 14 volatile compounds in breath samples from fasted subjects. We used various statistical analyses to compare clinical characteristics and breath levels of compounds among groups and to test the correlation between levels of compounds and severity of liver disease. Logistic regression analysis was performed to build a predictive model for AH. RESULTS We identified 6 compounds (2-propanol, acetaldehyde, acetone, ethanol, pentane, and trimethylamine [TMA]) whose levels were increased in patients with liver disease compared with control subjects. Mean concentrations of TMA and pentane (TAP) were particularly high in breath samples from patients with AH, compared with those with acute decompensation or control subjects (for both, P < .001). Using receiver operating characteristic curve analysis, we developed a model for the diagnosis of AH based on breath levels of TAP. TAP scores of 36 or higher identified the patients with AH (area under the receiver operating characteristic curves = 0.92) with 90% sensitivity and 80% specificity. The levels of exhaled TMA had a low level of correlation with the severity of AH based on model for end-stage liver disease score (r = 0.38; 95% confidence interval, 0.07-0.69; P = .018). CONCLUSIONS Based on levels of volatile compounds in breath samples, we can identify patients with AH vs patients with acute decompensation or individuals without liver disease. Levels of exhaled TMA moderately correlate with the severity of AH. These findings might be used in diagnosis of AH or in determining patient prognosis.
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Affiliation(s)
- Ibrahim A Hanouneh
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio
| | - Nizar N Zein
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio
| | - Frank Cikach
- Department of Pulmonary, Allergy, and Critical Care Medicine/Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Luma Dababneh
- Department of Pulmonary, Allergy, and Critical Care Medicine/Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - David Grove
- Department of Pulmonary, Allergy, and Critical Care Medicine/Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Naim Alkhouri
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio
| | - Rocio Lopez
- Department of Quantitative Health Science, Cleveland Clinic, Cleveland, Ohio
| | - Raed A Dweik
- Department of Pulmonary, Allergy, and Critical Care Medicine/Respiratory Institute, Cleveland Clinic, Cleveland, Ohio.
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16
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Trimethylaminuria (fish odor syndrome): genotype characterization among Portuguese patients. Gene 2013; 527:366-70. [PMID: 23791655 DOI: 10.1016/j.gene.2013.05.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/21/2013] [Indexed: 11/23/2022]
Abstract
Trimethylaminuria (TMAu) or "fish odor syndrome" is a metabolic disorder characterized by the inability to convert malodorous dietarily-derived trimethylamine (TMA) to odorless TMA N-oxide by the flavin-containing monooxygenase 3 (FMO3). Affected individuals unable to complete this reaction exude a "fishy" body odor due to the secretion of TMA in their corporal fluids leading to a variety of psychosocial problems. Interindividual variability in the expression of FMO3 gene may affect drug and foreign chemical metabolism in the liver and other tissues. Therefore, it is important to screen for common TMAu mutations but also extend the search to other genetic variants in order to correlate genotype and disease-associated phenotypes. In this study, 25 Portuguese patients with phenotype suggestive of TMAu were evaluated for molecular screening of the FMO3 gene. Herein, we found 16 variants in the FMO3 coding region, some of which had not been previously documented (Gly38Trp, Asp232Val, Thr307Pro, Ser310Leu). Whenever common variants (Glu158Lys, Glu308Gly) were considered in combination a distinct pattern between the control population and patients was observed, mainly in what concerns the presence of Lys158 and Gly308 in homozygous state. Further studies are necessary to clarify the pathogenicity of novel variants identified in this study, as well as the effect of the common single nucleotide polymorphisms, which may play an important role in disease presentation and/or protective mechanism to xenobiotics drugs or environment.
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17
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Yamazaki H, Shimizu M. Survey of variants of human flavin-containing monooxygenase 3 (FMO3) and their drug oxidation activities. Biochem Pharmacol 2013; 85:1588-93. [DOI: 10.1016/j.bcp.2013.03.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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18
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Molecular cloning, sequence characterization, SNP detection, and tissue expression analysis of duck FMO3 gene. Mol Cell Biochem 2013; 379:141-51. [DOI: 10.1007/s11010-013-1636-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/27/2013] [Indexed: 10/26/2022]
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19
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Ozhan G, Topal P, Alpertunga B. Flavin-containing monooxygenase 3 gene polymorphisms in Turkish population. Toxicol Mech Methods 2012; 22:461-5. [PMID: 22409263 DOI: 10.3109/15376516.2012.672481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Flavin-containing monooxygenases (FMOs) represent the second most important human monooxygenase system, after cytochrome P450s (CYPs) and catalyze the oxygenation of many chemicals containing nitrogen-, sulphur-, phosphorous-, selenium- and other nucleophilic heteroatoms. FMO3 is the prominent FMO form in adult human liver. For FMO3, both interindividual variability within a single ethnic group and variability between ethnic groups have been reported. In our study, three prevalent functional FMO3 variants (E158K, V257M, and E308G) were genotyped in healthy Turkish people by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) methods. The frequencies of alleles and haplotypes were compared with those obtained from different populations. It was found that FMO3 158K, 257M and 308G alleles, demonstrate impaired metabolism toward many FMO3 substrates, were observed frequently in Turkish population similar to the other populations. Also, the frequencies of haplotypes were determined based on individual allelic frequencies and it was observed that the most common haplotypes were haplotip EVE and KVE (E158K/V257M/E308G), which together accounted for 80% of all haplotypes. The obtained data from the present study could be useful for further studies assessing sensitivity to therapeutic drugs, environmental toxicants and common disease.
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Affiliation(s)
- Gül Ozhan
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey
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20
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Han GH, Gim GH, Kim W, Seo SI, Kim SW. Enhanced indirubin production in recombinant Escherichia coli harboring a flavin-containing monooxygenase gene by cysteine supplementation. J Biotechnol 2012; 164:179-87. [PMID: 22954889 DOI: 10.1016/j.jbiotec.2012.08.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/10/2012] [Accepted: 08/15/2012] [Indexed: 10/28/2022]
Abstract
In our previous study, a batch fermentation of recombinant Escherichia coli DH5α cells harboring the fmo gene from Methylophaga aminisulfidivorans MP(T) produced indirubin (5.0mg/L) and indigo (920mg/L) in a 5L fermenter containing tryptophan medium (2g/L tryptophan, 5g/L yeast extract, 10g/L NaCl). In this study, it was found that indirubin production greatly increased when 0.36g/L cysteine was added to the tryptophan medium, although cysteine inhibited the growth of the recombinant E. coli harboring the fmo gene. However, the addition of cysteine did not inhibit the expression level and activity of FMO in the cell. Indigo was synthesized by the dimerization of two 3-hydroxyindole molecules under the non-enzymatic reaction. Cysteine influenced the regioselectivity of FMO and enhanced the synthesis of 2-hydroxyindole instead of 3-hydroxyindole, which might function to increase indirubin production. The optimal culture conditions for indirubin production in tryptophan medium were determined from the response surface methodology analysis: 2g/L tryptophan, 5g/L yeast extract, 10g/L NaCl, 0.36g/L (3mM) cysteine, pH 8.0 at 35°C. Under these conditions, the recombinant E. coli cells were capable of producing 223.6mg/L of indirubin from 2g/L of tryptophan. The intracellular accumulation of the indirubin crystals might stress the cell, which may be a main reason for the poor growth of the recombinant E. coli pBlue 1.7.
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Affiliation(s)
- Gui Hwan Han
- Department of Environmental Engineering, Chosun University, Gwangju, Republic of Korea
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21
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Individuals reporting idiopathic malodor production: demographics and incidence of trimethylaminuria. Am J Med 2011; 124:1058-63. [PMID: 21851918 DOI: 10.1016/j.amjmed.2011.05.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/31/2011] [Accepted: 05/22/2011] [Indexed: 11/24/2022]
Abstract
BACKGROUND Individuals with the metabolic disorder trimethylaminuria may sporadically produce malodors despite good hygiene. The psychosocial impact of trimethylaminuria can be considerable. However, trimethylaminuria is difficult to diagnose without specialized tests, in part because odor production is diet-dependent, and malodors may not be present during medical examinations. Thus, the prevalence and demographics of trimethylaminuria remain unclear. METHODS We tested 353 patients who had unexplained (idiopathic) malodor production for trimethylaminuria using a standard choline challenge. We also collected basic demographic information. RESULTS Approximately one third of patients (118) tested positive for trimethylaminuria. Consistent with previous reports, women, particularly African American women, were significantly overrepresented among trimethylaminuria-positive patients. Of note, the same pattern was seen among trimethylaminuria-negative patients. Also consistent with previous reports, trimethylaminuria-positive women who were still menstruating tended to produce higher levels of trimethylamine within ± 7 days of menses, although this trend was statistically marginal (P = .07). CONCLUSION If our patient sample is representative of patients with idiopathic malodor, demographic information (race and gender) may not be useful in a differential diagnosis of trimethylaminuria. However, undiagnosed cases of trimethylaminuria may be fairly common among patients with idiopathic malodor. If so, choline challenge testing should be indicated for all such patients because trimethylaminuria is responsive to dietary and other treatments. We speculate that testing also might reveal cases of trimethylaminuria among those diagnosed with certain psychologic disorders, including olfactory reference syndrome.
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22
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Cho HJ, Cho HY, Kim KJ, Kim MH, Kim SW, Kang BS. Structural and functional analysis of bacterial flavin-containing monooxygenase reveals its ping-pong-type reaction mechanism. J Struct Biol 2011; 175:39-48. [PMID: 21527346 DOI: 10.1016/j.jsb.2011.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 03/19/2011] [Accepted: 04/14/2011] [Indexed: 11/18/2022]
Abstract
A bacterial flavin-containing monooxygenase (bFMO) catalyses the oxygenation of indole to produce indigoid compounds. In the reductive half of the indole oxygenation reaction, NADPH acts as a reducing agent, and NADP(+) remains at the active site, protecting bFMO from reoxidation. Here, the crystal structures of bFMO and bFMO in complex with NADP(+), and a mutant bFMO(Y207S), which lacks indole oxygenation activity, with and without indole are reported. The crystal structures revealed overlapping binding sites for NADP(+) and indole, suggestive of a double-displacement reaction mechanism for bFMO. In biochemical assays, indole inhibited NADPH oxidase activity, and NADPH in turn inhibited the binding of indole and decreased indoxyl production. Comparison of the structures of bFMO with and without bound NADP(+) revealed that NADPH induces conformational changes in two active site motifs. One of the motifs contained Arg-229, which participates in interactions with the phosphate group of NADPH and appears be a determinant of the preferential binding of bFMO to NADPH rather than NADH. The second motif contained Tyr-207. The mutant bFMO(Y207S) exhibited very little indoxyl producing activity; however, the NADPH oxidase activity of the mutant was higher than the wild-type enzyme. It suggests a role for Y207, in the protection of hydroperoxyFAD. We describe an indole oxygenation reaction mechanism for bFMO that involves a ping-pong-like interaction of NADPH and indole.
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Affiliation(s)
- Hyo Je Cho
- School of Life Science and Biotechnology, Kyungpook National University, Buk-gu, Daegu 702-701, Republic of Korea
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23
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Capolongo F, Santi A, Anfossi P, Montesissa C. Benzydamine as a useful substrate of hepatic flavin-containing monooxygenase activity in veterinary species. J Vet Pharmacol Ther 2011; 33:341-6. [PMID: 20646194 DOI: 10.1111/j.1365-2885.2009.01145.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benzydamine (BZ), a weak base and an indazole derivative with analgesic and antipyretic properties used in human and veterinary medicine, is metabolized in human, rat, cattle and rabbit to a wide range of metabolites. One of the main metabolites, BZ N-oxide (BZ-NO), is produced in the liver and brain by flavin-containing monooxygenases (FMOs), by liver and brain enzymes. To evaluate the suitability of BZ as an FMO probe in veterinary species, BZ metabolism was studied in vitro using liver microsomes from bovine, rabbit and swine. Kinetic parameters, K(m) and V(max), of BZ-NO production, were evaluated to corroborate the pivotal role of FMOs. Inhibition studies were carried out by heat inactivation and by specific FMO chemical inhibitors: trimethylamine and methimazole. The results confirmed the presence of FMO activity in the liver and the role of BZ as a suitable marker of FMO enzyme activities for the veterinary species considered.
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Affiliation(s)
- F Capolongo
- Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padua, Legnaro, Padova, Italy.
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24
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Affiliation(s)
- Min Li
- Healthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, BC
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25
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Hou X, Liu S, Pierri F, Dai X, Qu LJ, Zhao Y. Allelic analyses of the Arabidopsis YUC1 locus reveal residues and domains essential for the functions of YUC family of flavin monooxygenases. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:54-62. [PMID: 21205174 PMCID: PMC3060657 DOI: 10.1111/j.1744-7909.2010.01007.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Flavin monooxygenases (FMOs) play critical roles in plant growth and development by synthesizing auxin and other signaling molecules. However, the structure and function relationship within plant FMOs is not understood. Here we defined the important residues and domains of the Arabidopsis YUC1 FMO, a key enzyme in auxin biosynthesis. We previously showed that simultaneous inactivation of YUC1 and its homologue YUC4 caused severe defects in vascular and floral development. We mutagenized the yuc4 mutant and screened for mutants with phenotypes similar to those of yuc1 yuc4 double mutants. Among the isolated mutants, five of them contained mutations in the YUC1 gene. Interestingly, the mutations identified in the new yuc1 alleles were concentrated in the two GXGXXG motifs that are highly conserved among the plant FMOs. One such motif presumably binds to flavin adenine dinucleotide (FAD) cofactor and the other binds to nicotinamide adenine dinucleotide phosphate (NADPH). We also identified the Ser(139) to Phe conversion in yuc1, a mutation that is located between the two nucleotide-binding sites. By analyzing a series of yuc1 mutants, we identified key residues and motifs essential for the functions of YUC1 FMO.
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Affiliation(s)
- Xianhui Hou
- National Laboratory for Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Sainan Liu
- National Laboratory for Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Florencia Pierri
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Xinhua Dai
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Li-Jia Qu
- National Laboratory for Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093-0116, USA
- Corresponding author Tel: +1 858 822 2670; Fax: 1 858 534 7108;
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Nagashima S, Shimizu M, Yano H, Murayama N, Kumai T, Kobayashi S, Guengerich FP, Yamazaki H. Inter-individual Variation in Flavin-containing Monooxygenase 3 in Livers from Japanese: Correlation with Hepatic Transcription Factors. Drug Metab Pharmacokinet 2009; 24:218-25. [DOI: 10.2133/dmpk.24.218] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase. Proc Natl Acad Sci U S A 2008; 105:6572-7. [PMID: 18443301 DOI: 10.1073/pnas.0800859105] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavin-containing monooxygenases (FMOs) are, after cytochromes P450, the most important monooxygenase system in humans and are involved in xenobiotics metabolism and variability in drug response. The x-ray structure of a soluble prokaryotic FMO from Methylophaga sp. strain SK1 has been solved at 2.6-A resolution and is now the protein of known structure with the highest sequence similarity to human FMOs. The structure possesses a two-domain architecture, with both FAD and NADP(+) well defined by the electron density maps. Biochemical analysis shows that the prokaryotic enzyme shares many functional properties with mammalian FMOs, including substrate specificity and the ability to stabilize the hydroperoxyflavin intermediate that is crucial in substrate oxygenation. On the basis of their location in the structure, the nicotinamide ring and the adjacent ribose of NADP(+) turn out to be an integral part of the catalytic site being actively engaged in the stabilization of the oxygenating intermediate. This feature suggests that NADP(H) has a moonlighting role, in that it adopts two binding modes that allow it to function in both flavin reduction and oxygen reactivity modulation, respectively. We hypothesize that a relative domain rotation is needed to bring NADP(H) to these distinct positions inside the active site. Localization of mutations in human FMO3 that are known to cause trimethylaminuria (fish-odor syndrome) in the elucidated FMO structure provides a structural explanation for their biological effects.
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28
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Motika MS, Zhang J, Cashman JR. Flavin-containing monooxygenase 3 and human disease. Expert Opin Drug Metab Toxicol 2008; 3:831-45. [PMID: 18028028 DOI: 10.1517/17425255.3.6.831] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review summarizes information concerning the association of the human flavin-containing monooxygenase 3 (FMO3) and human diseases. Human FMO3 oxygenates a wide variety of nucleophilic heteroatom-containing xenobiotics, including endogenous substrates and various clinically important drugs. In this article, the authors discuss the association of FMO3 with human disease, including: i) direct association of FMO3 genetic mutations to human genetic disease; ii) association of FMO3 genetic polymorphism to altered drug metabolism and, therefore, indirect association of FMO3 with drug therapeutic efficacy of human disease; and iii) the potential impact and/or effect of FMO3 transcriptional regulation during disease states. Even though many studies discussed for the latter two points are at a preliminary stage and require much more research to bring to a definite conclusion, the authors include these studies to stimulate general interest and invite further discussion.
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Affiliation(s)
- Meike S Motika
- Human Biomolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, USA
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29
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Swindell WR. Gene expression profiling of long-lived dwarf mice: longevity-associated genes and relationships with diet, gender and aging. BMC Genomics 2007; 8:353. [PMID: 17915019 PMCID: PMC2094713 DOI: 10.1186/1471-2164-8-353] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 10/03/2007] [Indexed: 12/27/2022] Open
Abstract
Background Long-lived strains of dwarf mice carry mutations that suppress growth hormone (GH) and insulin-like growth factor I (IGF-I) signaling. The downstream effects of these endocrine abnormalities, however, are not well understood and it is unclear how these processes interact with aging mechanisms. This study presents a comparative analysis of microarray experiments that have measured hepatic gene expression levels in long-lived strains carrying one of four mutations (Prop1df/df, Pit1dw/dw, Ghrhrlit/lit, GHR-KO) and describes how the effects of these mutations relate to one another at the transcriptional level. Points of overlap with the effects of calorie restriction (CR), CR mimetic compounds, low fat diets, gender dimorphism and aging were also examined. Results All dwarf mutations had larger and more consistent effects on IGF-I expression than dietary treatments. In comparison to dwarf mutations, however, the transcriptional effects of CR (and some CR mimetics) overlapped more strongly with those of aging. Surprisingly, the Ghrhrlit/lit mutation had much larger effects on gene expression than the GHR-KO mutation, even though both mutations affect the same endocrine pathway. Several genes potentially regulated or co-regulated with the IGF-I transcript in liver tissue were identified, including a DNA repair gene (Snm1) that is upregulated in proportion to IGF-I inhibition. A total of 13 genes exhibiting parallel differential expression patterns among all four strains of long-lived dwarf mice were identified, in addition to 30 genes with matching differential expression patterns in multiple long-lived dwarf strains and under CR. Conclusion Comparative analysis of microarray datasets can identify patterns and consistencies not discernable from any one dataset individually. This study implements new analytical approaches to provide a detailed comparison among the effects of life-extending mutations, dietary treatments, gender and aging. This comparison provides insight into a broad range of issues relevant to the study of mammalian aging. In this context, 43 longevity-associated genes are identified and individual genes with the highest level of support among all microarray experiments are highlighted. These results provide promising targets for future experimental investigation as well as potential clues for understanding the functional basis of lifespan extension in mammalian systems.
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Affiliation(s)
- William R Swindell
- Department of Pathology, University of Michigan, 3118 BSRB, Ann Arbor, MI, USA.
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30
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Abstract
Off flavours in pork sometimes produce tastes such as sourness, fishy, metallic or other non-typical flavours and are often caused by low pH. Loss of function mutations in flavin containing mono-oxygenase 3 (FMO3) are known to be associated with a fishy off flavour in both chicken eggs and cow's milk and a similar autosomal recessive disorder is present in humans resulting in a fishy odour. FMO3 is a member of a gene family that is clustered on human chromosome 1. Comparative mapping suggested that FMO3 and the remaining FMO genes (ex. FMO1 and FMO5) might map to the orthologous region on pig chromosome 9 (SSC9) where a quantitative trait locus (QTL) for off flavour was previously identified. Primers were designed to amplify FMO1, FMO3 and FMO5 gene fragments and several SNPs were discovered and genotyping tests developed. The genotypes from the Iowa State University Berkshire x Yorkshire resource population were used to linkage map FMO1 and FMO3 to SSC9 and FMO5 to pig chromosome 4 (SSC4). QTL and associations analyses were performed using the map containing FMO1 and FMO3. Results demonstrated that FMO3 and FMO1 mapped less than 1 cM away from the peak for the off flavour QTL previously detected on SSC9 and provide indications of an association between the FMO3 polymorphism and off flavour in pork.
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Affiliation(s)
- K L Glenn
- Department of Animal Science and the Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011-3150, USA
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