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Silva IMD, Vacario BGL, Okuyama NCM, Barcelos GRM, Fuganti PE, Guembarovski RL, Cólus IMDS, Serpeloni JM. Polymorphisms in drug-metabolizing genes and urinary bladder cancer susceptibility and prognosis: Possible impacts and future management. Gene 2024; 907:148252. [PMID: 38350514 DOI: 10.1016/j.gene.2024.148252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/22/2024] [Accepted: 02/05/2024] [Indexed: 02/15/2024]
Abstract
Epidemiological studies have shown the association of genetic variants with risks of occupational and environmentally induced cancers, including bladder (BC). The current review summarizes the effects of variants in genes encoding phase I and II enzymes in well-designed studies to highlight their contribution to BC susceptibility and prognosis. Polymorphisms in genes codifying drug-metabolizing proteins are of particular interest because of their involvement in the metabolism of exogenous genotoxic compounds, such as tobacco and agrochemicals. The prognosis between muscle-invasive and non-muscle-invasive diseases is very different, and it is difficult to predict which will progress worse. Web of Science, PubMed, and Medline were searched to identify studies published between January 1, 2010, and February 2023. We included 73 eligible studies, more than 300 polymorphisms, and 46 genes/loci. The most studied candidate genes/loci of phase I metabolism were CYP1B1, CYP1A1, CYP1A2, CYP3A4, CYP2D6, CYP2A6, CYP3E1, and ALDH2, and those in phase II were GSTM1, GSTT1, NAT2, GSTP1, GSTA1, GSTO1, and UGT1A1. We used the 46 genes to construct a network of proteins and to evaluate their biological functions based on the Reactome and KEGG databases. Lastly, we assessed their expression in different tissues, including normal bladder and BC samples. The drug-metabolizing pathway plays a relevant role in BC, and our review discusses a list of genes that could provide clues for further exploration of susceptibility and prognostic biomarkers.
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Affiliation(s)
- Isabely Mayara da Silva
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Beatriz Geovana Leite Vacario
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil; Center of Health Sciences, State University of West Paraná (UNIOESTE), Francisco Beltrão-Paraná, 85605-010, Brazil.
| | - Nádia Calvo Martins Okuyama
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Gustavo Rafael Mazzaron Barcelos
- Department of Biosciences, Institute for Health and Society, Federal University of São Paulo (UNIFESP), Santos 11.060-001, Brazil.
| | | | - Roberta Losi Guembarovski
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Ilce Mara de Syllos Cólus
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Juliana Mara Serpeloni
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
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2
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Choudhury C, Gill MK, McAleese CE, Butcher NJ, Ngo ST, Steyn FJ, Minchin RF. The Arylamine N-Acetyltransferases as Therapeutic Targets in Metabolic Diseases Associated with Mitochondrial Dysfunction. Pharmacol Rev 2024; 76:300-320. [PMID: 38351074 DOI: 10.1124/pharmrev.123.000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024] Open
Abstract
In humans, there are two arylamine N-acetyltransferase genes that encode functional enzymes (NAT1 and NAT2) as well as one pseudogene, all of which are located together on chromosome 8. Although they were first identified by their role in the acetylation of drugs and other xenobiotics, recent studies have shown strong associations for both enzymes in a variety of diseases, including cancer, cardiovascular disease, and diabetes. There is growing evidence that this association may be causal. Consistently, NAT1 and NAT2 are shown to be required for healthy mitochondria. This review discusses the current literature on the role of both NAT1 and NAT2 in mitochondrial bioenergetics. It will attempt to relate our understanding of the evolution of the two genes with biologic function and then present evidence that several major metabolic diseases are influenced by NAT1 and NAT2. Finally, it will discuss current and future approaches to inhibit or enhance NAT1 and NAT2 activity/expression using small-molecule drugs. SIGNIFICANCE STATEMENT: The arylamine N-acetyltransferases (NATs) NAT1 and NAT2 share common features in their associations with mitochondrial bioenergetics. This review discusses mitochondrial function as it relates to health and disease, and the importance of NAT in mitochondrial function and dysfunction. It also compares NAT1 and NAT2 to highlight their functional similarities and differences. Both NAT1 and NAT2 are potential drug targets for diseases where mitochondrial dysfunction is a hallmark of onset and progression.
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Affiliation(s)
- Chandra Choudhury
- School of Biomedical Sciences (C.C., M.K.G., C.E.M., N.J.B., F.J.S., R.F.M.) and Australian Institute for Bioengineering and Nanotechnology (S.T.N.), University of Queensland, Brisbane, Australia
| | - Melinder K Gill
- School of Biomedical Sciences (C.C., M.K.G., C.E.M., N.J.B., F.J.S., R.F.M.) and Australian Institute for Bioengineering and Nanotechnology (S.T.N.), University of Queensland, Brisbane, Australia
| | - Courtney E McAleese
- School of Biomedical Sciences (C.C., M.K.G., C.E.M., N.J.B., F.J.S., R.F.M.) and Australian Institute for Bioengineering and Nanotechnology (S.T.N.), University of Queensland, Brisbane, Australia
| | - Neville J Butcher
- School of Biomedical Sciences (C.C., M.K.G., C.E.M., N.J.B., F.J.S., R.F.M.) and Australian Institute for Bioengineering and Nanotechnology (S.T.N.), University of Queensland, Brisbane, Australia
| | - Shyuan T Ngo
- School of Biomedical Sciences (C.C., M.K.G., C.E.M., N.J.B., F.J.S., R.F.M.) and Australian Institute for Bioengineering and Nanotechnology (S.T.N.), University of Queensland, Brisbane, Australia
| | - Frederik J Steyn
- School of Biomedical Sciences (C.C., M.K.G., C.E.M., N.J.B., F.J.S., R.F.M.) and Australian Institute for Bioengineering and Nanotechnology (S.T.N.), University of Queensland, Brisbane, Australia
| | - Rodney F Minchin
- School of Biomedical Sciences (C.C., M.K.G., C.E.M., N.J.B., F.J.S., R.F.M.) and Australian Institute for Bioengineering and Nanotechnology (S.T.N.), University of Queensland, Brisbane, Australia
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3
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Specific Gene Duplication and Loss of Cytochrome P450 in Families 1-3 in Carnivora (Mammalia, Laurasiatheria). Animals (Basel) 2022; 12:ani12202821. [PMID: 36290207 PMCID: PMC9597770 DOI: 10.3390/ani12202821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary In this study we investigated the specific duplication and loss events of cytochrome P450 (CYP) genes in families 1-3 in Carnivora. These genes have been recognized as essential detoxification enzymes, and, using genomic data, we demonstrated a synteny analysis of the CYP coding cluster and a phylogenetic analysis of these genes. We discovered the CYP2Cs and CYP3As expansion in omnivorous species such as the badger, the brown bear, the black bear, and the dog. Furthermore, phylogenetic analysis revealed the evolution of CYP2Cs and 3As in Carnivora. These findings are essential for the appropriate estimation of pharmacokinetics or toxicokinetic in wild carnivorans. Abstract Cytochrome P450s are among the most important xenobiotic metabolism enzymes that catalyze the metabolism of a wide range of chemicals. Through duplication and loss events, CYPs have created their original feature of detoxification in each mammal. We performed a comprehensive genomic analysis to reveal the evolutionary features of the main xenobiotic metabolizing family: the CYP1-3 families in Carnivora. We found specific gene expansion of CYP2Cs and CYP3As in omnivorous animals, such as the brown bear, the black bear, the dog, and the badger, revealing their daily phytochemical intake as providing the causes of their evolutionary adaptation. Further phylogenetic analysis of CYP2Cs revealed Carnivora CYP2Cs were divided into CYP2C21, 2C41, and 2C23 orthologs. Additionally, CYP3As phylogeny also revealed the 3As’ evolution was completely different to that of the Caniformia and Feliformia taxa. These studies provide us with fundamental genetic and evolutionary information on CYPs in Carnivora, which is essential for the appropriate interpretation and extrapolation of pharmacokinetics or toxicokinetic data from experimental mammals to wild Carnivora.
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Functional variability of rhesus macaque (Macaca mulatta) NAT2 gene for drug-metabolising arylamine N-acetyltransferase 2. Biochem Pharmacol 2021; 188:114545. [PMID: 33831395 DOI: 10.1016/j.bcp.2021.114545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/21/2022]
Abstract
Human NAT2 is a polymorphic pharmacogene encoding for N-acetyltransferase 2, a hepatic enzyme active towards arylamine and arylhydrazine drugs, including the anti-tubercular antibiotic isoniazid. The isoenzyme also modulates susceptibility to chemical carcinogenesis, particularly of the bladder. Human NAT2 represents an ideal model for anthropological investigations into the demographic adaptation of worldwide populations to their xenobiotic environment. Its sequence appears to be subject to positive selection pressures that are population-specific and may be attributed to gene-environment interactions directly associated with exogenous chemical challenges. However, recent evidence suggests that the same evolutionary pattern may not be observed in other primates. Here, we report NAT2 polymorphism in 25 rhesus macaques (Macaca mulatta) and compare the frequencies and functional characteristics of 12 variants. Seven non-synonymous single nucleotide variations (SNVs) were identified, including one nonsense mutation. The missense SNVs were demonstrated to affect enzymatic function in a substrate-dependent manner, albeit more moderately than certain NAT1 SNVs recently characterised in the same cohort. Haplotypic and functional variability of NAT2 was comparable to that previously observed for NAT1 in the same population sample, suggesting that the two paralogues may have evolved under similar selective pressures in the rhesus macaque. This is different to the population variability distribution pattern reported for humans and chimpanzees. Recorded SNVs were also different from those found in other primates. The study contributes to further understanding of NAT2 functional polymorphism in the rhesus macaque, a non-human primate model used in biomedicine and pharmacology, indicating variability in xenobiotic acetylation that could affect drug metabolism.
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5
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Genetic Adaptations in Mudskipper and Tetrapod Give Insights into Their Convergent Water-to-Land Transition. Animals (Basel) 2021; 11:ani11020584. [PMID: 33672418 PMCID: PMC7926366 DOI: 10.3390/ani11020584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/20/2021] [Indexed: 11/17/2022] Open
Abstract
Water-to-land transition has been independently evolved in multiple vertebrate lineages including the most recent common ancestor of tetrapod and multiple fish clades, and among them, mudskippers uniquely adapted to the mudflat. Even though physiological and morphological adaptation of mudskippers is thought to resemble that of the ancestral tetrapod, it is unclear if they share genome-wide evolutionary signatures. To detect potential signatures of positive selection in mudskipper and tetrapods, we analyzed 4118 singleton orthologues of terrestrial tetrapods, coelacanth, mudskipper, and fully aquatic fishes. Among positively selected genes identified in mudskipper and tetrapod lineages, genes involved in immune responses, mitochondrial oxidative phosphorylation, and kidney development were detected. On the other hand, tetrapod-specific and mudskipper-specific positively selected genes were functionally enriched for DNA repair processes, which could be associated with higher exposure to UV light. We also performed gene family analysis and discovered convergent contraction of eight gene families, including βγ-crystallin coding genes in both tetrapod and mudskipper lineages. Findings of this study suggest the similar genetic adaptation against environmental constraints between the ancient tetrapod and mudskippers for their land adaptation.
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Abstract
Drug metabolizing enzymes catalyze the biotransformation of many of drugs and chemicals. The drug metabolizing enzymes are distributed among several evolutionary families and catalyze a range of detoxication reactions, including oxidation/reduction, conjugative, and hydrolytic reactions that serve to detoxify potentially toxic compounds. This detoxication function requires that drug metabolizing enzymes exhibit substrate promiscuity. In addition to their catalytic functions, many drug metabolizing enzymes possess functions unrelated to or in addition to catalysis. Such proteins are termed 'moonlighting proteins' and are defined as proteins with multiple biochemical or biophysical functions that reside in a single protein. This review discusses the diverse moonlighting functions of drug metabolizing enzymes and the roles they play in physiological functions relating to reproduction, vision, cell signaling, cancer, and transport. Further research will likely reveal new examples of moonlighting functions of drug metabolizing enzymes.
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Affiliation(s)
- Philip G Board
- John Curtin School of Medical Research, ANU College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, NY, USA
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7
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El Kawak M, Dhaini HR, Jabbour ME, Moussa MA, El Asmar K, Aoun M. Slow N-acetylation as a possible contributor to bladder carcinogenesis. Mol Carcinog 2020; 59:1017-1027. [PMID: 32529781 DOI: 10.1002/mc.23232] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/08/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022]
Abstract
Bladder cancer (BCa) is an exophytic tumor that presents as either noninvasive confined to the mucosa (NMIBC) or invading the detrusor muscle (MIBC), and was recently further subgrouped into molecular subtypes. Arylamines, major BCa environmental and occupational risk factors, are mainly metabolized by the genetically polymorphic N-acetyltransferases 1, NAT1 and NAT2. In this study, we investigated the association between N-acetyltransferases genetic polymorphism and key MIBC and NMIBC tumor biomarkers and subtypes. A cohort of 250 males with histologically confirmed urothelial BCa was identified. Tumors were genotyped for NAT1 and NAT2 using real-time polymerase chain reaction (PCR), and characterized for mutations in TP53, RB1, and FGFR3 by PCR-restriction fragment length polymorphism. Pathology data and patients' smoking status were obtained from medical records. Pearson χ2 and Fisher exact tests were used to check for associations and interactions. Results show that NAT1 G560 A polymorphism is significantly associated with higher muscle-invasiveness (MIBC vs NMIBC; P = .001), higher tumor grade (high grade vs low grade; P = .011), and higher FGFR3 mutation frequency within the MIBC subgroup (P = .042; .027). NAT2 G857 A polymorphism is also found to be significantly associated with higher muscle-invasiveness (MIBC vs NMIBC; P = .041). Our results indicate that slow N-acetylation is a contributor to bladder carcinogenesis and muscle-invasiveness. These findings highlight NAT1 as a biomarker candidate in BCa and a potential target for drug development.
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Affiliation(s)
- Michelle El Kawak
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Hassan R Dhaini
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Michel E Jabbour
- Department of Urology, St George Hospital University Medical Center, Beirut, Lebanon
| | - Mohamad A Moussa
- Division of Urology, Al Zahraa University Hospital, Beirut, Lebanon
| | - Khalil El Asmar
- Department of Epidemiology and Population Health, American University of Beirut, Beirut, Lebanon
| | - Mona Aoun
- Department of Pathology, St George Hospital University Medical Center, Beirut, Lebanon
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8
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Fuselli S. Beyond drugs: the evolution of genes involved in human response to medications. Proc Biol Sci 2019; 286:20191716. [PMID: 31640517 DOI: 10.1098/rspb.2019.1716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genetic variation of our species reflects human demographic history and adaptation to diverse local environments. Part of this genetic variation affects individual responses to exogenous substances, such as food, pollutants and drugs, and plays an important role in drug efficacy and safety. This review provides a synthesis of the evolution of loci implicated in human pharmacological response and metabolism, interpreted within the theoretical framework of population genetics and molecular evolution. In particular, I review and discuss key evolutionary aspects of different pharmacogenes in humans and other species, such as the relationship between the type of substrates and rate of evolution; the selective pressure exerted by landscape variables or dietary habits; expected and observed patterns of rare genetic variation. Finally, I discuss how this knowledge can be translated directly or after the implementation of specific studies, into practical guidelines.
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Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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9
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Population variability of rhesus macaque (Macaca mulatta) NAT1 gene for arylamine N-acetyltransferase 1: Functional effects and comparison with human. Sci Rep 2019; 9:10937. [PMID: 31358821 PMCID: PMC6662693 DOI: 10.1038/s41598-019-47485-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/08/2019] [Indexed: 12/25/2022] Open
Abstract
Human NAT1 gene for N-acetyltransferase 1 modulates xenobiotic metabolism of arylamine drugs and mutagens. Beyond pharmacogenetics, NAT1 is also relevant to breast cancer. The population history of human NAT1 suggests evolution through purifying selection, but it is unclear whether this pattern is evident in other primate lineages where population studies are scarce. We report NAT1 polymorphism in 25 rhesus macaques (Macaca mulatta) and describe the haplotypic and functional characteristics of 12 variants. Seven non-synonymous single nucleotide variations (SNVs) were identified and experimentally demonstrated to compromise enzyme function, mainly through destabilization of NAT1 protein and consequent activity loss. One non-synonymous SNV (c.560G > A, p.Arg187Gln) has also been characterized for human NAT1 with similar effects. Population haplotypic and functional variability of rhesus NAT1 was considerably higher than previously reported for its human orthologue, suggesting different environmental pressures in the two lineages. Known functional elements downstream of human NAT1 were also differentiated in rhesus macaque and other primates. Xenobiotic metabolizing enzymes play roles beyond mere protection from exogenous chemicals. Therefore, any link to disease, particularly carcinogenesis, may be via modulation of xenobiotic mutagenicity or more subtle interference with cell physiology. Comparative analyses add the evolutionary dimension to such investigations, assessing functional conservation/diversification among primates.
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10
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Redmond AK, Zou J, Secombes CJ, Macqueen DJ, Dooley H. Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons. Front Immunol 2019; 10:1558. [PMID: 31354716 PMCID: PMC6640115 DOI: 10.3389/fimmu.2019.01558] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/21/2019] [Indexed: 12/31/2022] Open
Abstract
Interferons orchestrate host antiviral responses in jawed vertebrates. They are categorized into three classes; IFN1 and IFN3 are the primary antiviral cytokine lineages, while IFN2 responds to a broader variety of pathogens. The evolutionary relationships within and between these three classes have proven difficult to resolve. Here, we reassess interferon evolution, considering key phylogenetic pitfalls including taxon sampling, alignment quality, model adequacy, and outgroup choice. We reveal that cartilaginous fishes, and hence the jawed vertebrate ancestor, possess(ed) orthologs of all three interferon classes. We show that IFN3 groups sister to IFN1, resolve the origins of the human IFN3 lineages, and find that intronless IFN3s emerged at least three times. IFN2 genes are highly conserved, except for IFN-γ-rel, which we confirm resulted from a teleost-specific duplication. Our analyses show that IFN1 phylogeny is highly sensitive to phylogenetic error. By accounting for this, we describe a new backbone IFN1 phylogeny that implies several IFN1 genes existed in the jawed vertebrate ancestor. One of these is represented by the intronless IFN1s of tetrapods, including mammalian-like repertoires of reptile IFN1s and a subset of amphibian IFN1s, in addition to newly-identified intron-containing shark IFN1 genes. IFN-f, previously only found in teleosts, likely represents another ancestral jawed vertebrate IFN1 family member, suggesting the current classification of fish IFN1s into two groups based on the number of cysteines may need revision. The providence of the remaining fish IFN1s and the coelacanth IFN1s proved difficult to resolve, but they may also be ancestral jawed vertebrate IFN1 lineages. Finally, a large group of amphibian-specific IFN1s falls sister to all other IFN1s and was likely also present in the jawed vertebrate ancestor. Our results verify that intronless IFN1s have evolved multiple times in amphibians and indicate that no one-to-one orthology exists between mammal and reptile IFN1s. Our data also imply that diversification of the multiple IFN1s present in the jawed vertebrate ancestor has occurred through a rapid birth-death process, consistent with functional maintenance over a 450-million-year host-pathogen arms race. In summary, this study reveals a new model of interferon evolution important to our understanding of jawed vertebrate antiviral immunity.
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Affiliation(s)
- Anthony K Redmond
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom.,Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, United Kingdom.,Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Jun Zou
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom.,Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Christopher J Secombes
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom.,Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Helen Dooley
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States.,Institute of Marine and Environmental Technology, Baltimore, MD, United States
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11
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Humans and Chimpanzees Display Opposite Patterns of Diversity in Arylamine N-Acetyltransferase Genes. G3-GENES GENOMES GENETICS 2019; 9:2199-2224. [PMID: 31068377 PMCID: PMC6643899 DOI: 10.1534/g3.119.400223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among the many genes involved in the metabolism of therapeutic drugs, human arylamine N-acetyltransferases (NATs) genes have been extensively studied, due to their medical importance both in pharmacogenetics and disease epidemiology. One member of this small gene family, NAT2, is established as the locus of the classic human acetylation polymorphism in drug metabolism. Current hypotheses hold that selective processes favoring haplotypes conferring lower NAT2 activity have been operating in modern humans’ recent history as an adaptation to local chemical and dietary environments. To shed new light on such hypotheses, we investigated the genetic diversity of the three members of the NAT gene family in seven hominid species, including modern humans, Neanderthals and Denisovans. Little polymorphism sharing was found among hominids, yet all species displayed high NAT diversity, but distributed in an opposite fashion in chimpanzees and bonobos (Pan genus) compared to modern humans, with higher diversity in Pan species at NAT1 and lower at NAT2, while the reverse is observed in humans. This pattern was also reflected in the results returned by selective neutrality tests, which suggest, in agreement with the predicted functional impact of mutations detected in non-human primates, stronger directional selection, presumably purifying selection, at NAT1 in modern humans, and at NAT2 in chimpanzees. Overall, the results point to the evolution of divergent functions of these highly homologous genes in the different primate species, possibly related to their specific chemical/dietary environment (exposome) and we hypothesize that this is likely linked to the emergence of controlled fire use in the human lineage.
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12
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Wang L, Minchin RF, Essebier PJ, Butcher NJ. Loss of human arylamine N-acetyltransferase I regulates mitochondrial function by inhibition of the pyruvate dehydrogenase complex. Int J Biochem Cell Biol 2019; 110:84-90. [PMID: 30836144 DOI: 10.1016/j.biocel.2019.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 11/29/2022]
Abstract
Human arylamine N-acetyltransferase 1 (NAT1) has been widely reported to affect cancer cell growth and survival and recent studies suggest it may alter cell metabolism. In this study, the effects of NAT1 deletion on mitochondrial function was examined in 2 human cell lines, breast carcinoma MDA-MB-231 and colon carcinoma HT-29 cells. Using a Seahorse XFe96 Flux Analyzer, NAT1 deletion was shown to decrease oxidative phosphorylation with a significant loss in respiratory reserve capacity in both cell lines. There also was a decrease in glycolysis without a change in glucose uptake. The changes in mitochondrial function was due to a decrease in pyruvate dehydrogenase activity, which could be reversed with the pyruvate dehydrogenase kinase inhibitor dichloroacetate. In the MDA-MB-231 and HT-29 cells, pyruvate dehydrogenase activity was attenuated either by an increase in phosphorylation or a decrease in total protein expression. These results may help explain some of the cellular events that have been reported recently in cell and animal models of NAT1 deficiency.
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Affiliation(s)
- Lili Wang
- Molecular and Cellular Pharmacology Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, 4072 Australia
| | - Rodney F Minchin
- Molecular and Cellular Pharmacology Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, 4072 Australia.
| | - Patricia J Essebier
- Molecular and Cellular Pharmacology Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, 4072 Australia
| | - Neville J Butcher
- Molecular and Cellular Pharmacology Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, 4072 Australia
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13
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Tan HM, Low WY. Rapid birth-death evolution and positive selection in detoxification-type glutathione S-transferases in mammals. PLoS One 2018; 13:e0209336. [PMID: 30586459 PMCID: PMC6306238 DOI: 10.1371/journal.pone.0209336] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/04/2018] [Indexed: 01/04/2023] Open
Abstract
Glutathione S-Transferases (GSTs) are phase II detoxification enzymes that may have evolved in response to changes of environmental substrates. GST genes formed a multigene family and in mammals, there are six classes known as Alpha, Mu, Omega, Pi, Theta, and Zeta. Recent studies in phase I detoxification system specifically the cytochrome P450s provided a general explanation on why genes from a common origin such as those in a multigene family have both phylogenetically stable and unstable genes. Genes that participate in core functions of organisms such as development and physiology are stable whereas genes that play a role in detoxification are unstable and evolve in a process known as birth-death evolution, which is characterised by frequent gene gains and losses. The generality of the birth-death model at explaining the evolution of detoxification enzymes beyond the phase I enzyme has not been comprehensively explored. This work utilized 383 Gst genes and 300 pseudogenes across 22 mammalian species to study gene gains and losses. GSTs vary greatly in their phylogenetic stability despite their overall sequence similarity. Stable Gst genes from Omega and Zeta classes do not show fluctuation in gene numbers from human to opossum. These genes play a role in biosynthesis related functions. Unstable genes that include Alpha, Mu, Pi and Theta undergo frequent gene gain and loss in a process known as birth-death evolution. Gene members of these four classes are well known for their roles in detoxification. Our positive selection screen identified five positively selected sites in mouse GSTA3. Previous studies showed two of these sites (108H and 208E) were biochemically tested as important residues that conferred catalytic activity against the toxic aflatoxin B1-8,9-epoxide. The functional significance against aflatoxin of the remaining three positively selected sites warrant further investigation.
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Affiliation(s)
- Hui Ming Tan
- Center for Bioinformatics, Perdana University School of Data Science, Serdang, Selangor, Malaysia
| | - Wai Yee Low
- Center for Bioinformatics, Perdana University School of Data Science, Serdang, Selangor, Malaysia
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- * E-mail:
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Romero V, Nakaoka H, Hosomichi K, Inoue I. High Order Formation and Evolution of Hornerin in Primates. Genome Biol Evol 2018; 10:3167-3175. [PMID: 30256937 PMCID: PMC6280949 DOI: 10.1093/gbe/evy208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
Genomic duplication or loss can accelerate evolution because the number of repeats could affect molecular pathways and phenotypes. We have previously reported that the repeated region of filaggrin (FLG), a crucial component of the outer layers of mammalian skin, had high levels of nucleotide diversity with species-specific divergence and expansion and that it evolved under the birth-and-death model. We focused on hornerin (HRNR), a member of the same gene family that harbor similar tandem repeats as FLG, and examined the formation process of repeated regions and the evolutional model that best fit the HRNR repeated region in the crab-eating macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes) and compared them with the human (Homo sapiens) sequence. Paar et al. (2011) and Takaishi et al. (2005) have different theories as to the formation of the repeated region of HRNR; both groups share the longest repeat length of 1,404 bp (quartic or longest unit), but they differed in the process. We identified the formation described by Paar et al. {[(“39 bp (primary) × 9” × 2 (secondary)) × 2 (tertiary)] × 5 (quartic)} to be conserved in all species except the crab-eating macaque. We detected high nucleotide diversities between the longest repeats, which fits the birth-and-death model. We concluded that the high order repeat formation of HRNR was conserved in primates except the crab-eating macaque. As previously identified in FLG, the longest repeats have high levels of nucleotide diversity, which could contribute to phenotypic differences between closely related species.
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Affiliation(s)
- Vanessa Romero
- Department of Genetics School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Hirofumi Nakaoka
- Department of Genetics School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - Ituro Inoue
- Department of Genetics School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
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15
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Comparative analysis of xenobiotic metabolising N-acetyltransferases from ten non-human primates as in vitro models of human homologues. Sci Rep 2018; 8:9759. [PMID: 29950659 PMCID: PMC6021393 DOI: 10.1038/s41598-018-28094-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/14/2018] [Indexed: 12/13/2022] Open
Abstract
Xenobiotic metabolising N-acetyltransferases (NATs) perform biotransformation of drugs and carcinogens. Human NAT1 is associated with endogenous metabolic pathways of cells and is a candidate drug target for cancer. Human NAT2 is a well-characterised polymorphic xenobiotic metabolising enzyme, modulating susceptibility to drug-induced toxicity. Human NATs are difficult to express to high purification yields, complicating large-scale production for high-throughput screens or use in sophisticated enzymology assays and crystallography. We undertake comparative functional investigation of the NAT homologues of ten non-human primates, to characterise their properties and evaluate their suitability as models of human NATs. Considering the amount of generated recombinant protein, the enzymatic activity and thermal stability, the NAT homologues of non-human primates are demonstrated to be a much more effective resource for in vitro studies compared with human NATs. Certain NAT homologues are proposed as better models, such as the NAT1 of macaques Macaca mulatta and M. sylvanus, the NAT2 of Erythrocebus patas, and both NAT proteins of the gibbon Nomascus gabriellae which show highest homology to human NATs. This comparative investigation will facilitate in vitro screens towards discovery and optimisation of candidate pharmaceutical compounds for human NAT isoenzymes, while enabling better understanding of NAT function and evolution in primates.
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16
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Saitou M, Satta Y, Gokcumen O, Ishida T. Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees. BMC Genomics 2018; 19:293. [PMID: 29695243 PMCID: PMC5918908 DOI: 10.1186/s12864-018-4676-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/15/2018] [Indexed: 02/06/2023] Open
Abstract
Background The common deletion of the glutathione S-transferase Mu 1 (GSTM1) gene in humans has been shown to be involved in xenobiotic metabolism and associated with bladder cancer. However, the evolution of this deletion has not been investigated. Results In this study, we conducted comparative analyses of primate genomes. We demonstrated that the GSTM gene family has evolved through multiple structural variations, involving gene duplications, losses, large inversions and gene conversions. We further showed experimentally that the GSTM1 was polymorphically deleted in both humans and also in chimpanzees, through independent deletion events. To generalize our results, we searched for genic deletions that are polymorphic in both humans and chimpanzees. Consequently, we found only two such deletions among the thousands that we have searched, one of them being the GSTM1 deletion and the other surprisingly being another metabolizing gene, the UGT2B17. Conclusions Overall, our results support the emerging notion that metabolizing gene families, such as the GSTM, NAT, UGT and CYP, have been evolving rapidly through gene duplication and deletion events in primates, leading to complex structural variation within and among species with unknown evolutionary consequences. Electronic supplementary material The online version of this article (10.1186/s12864-018-4676-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Saitou
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, State University of New York at Buffalo, Buffalo, USA
| | - Y Satta
- The Graduate University for Advanced Studies (SOKENDAI), Hayama, Japan
| | - O Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, USA.
| | - T Ishida
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.
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17
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Romero V, Hosomichi K, Nakaoka H, Shibata H, Inoue I. Structure and evolution of the filaggrin gene repeated region in primates. BMC Evol Biol 2017; 17:10. [PMID: 28077068 PMCID: PMC5225520 DOI: 10.1186/s12862-016-0851-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/12/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The evolutionary dynamics of repeat sequences is quite complex, with some duplicates never having differentiated from each other. Two models can explain the complex evolutionary process for repeated genes-concerted and birth-and-death, of which the latter is driven by duplications maintained by selection. Copy number variations caused by random duplications and losses in repeat regions may modulate molecular pathways and therefore affect phenotypic characteristics in a population, resulting in individuals that are able to adapt to new environments. In this study, we investigated the filaggrin gene (FLG), which codes for filaggrin-an important component of the outer layers of mammalian skin-and contains tandem repeats that exhibit copy number variation between and within species. To examine which model best fits the evolutionary pathway for the complete tandem repeats within a single exon of FLG, we determined the repeat sequences in crab-eating macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes) and compared these with the sequence in human (Homo sapiens). RESULTS In this study we compared concerted and birth-and-death evolution models, commonly used for gene copies. We found that there is high nucleotide diversity between filaggrin repeat regions, which fits the birth-and-death model. Phylogenetic analyses also suggested that independent duplication events created the repeat sequences in crab-eating macaques and orangutans, while different duplication and loss events created the repeats in gorillas, chimpanzees, and humans. Comparison of the repeat sequences detected purifying selection within species and lineage-specific duplications across species. We also found variation in the length of the repeated region within species such as chimpanzee and crab-eating macaque. CONCLUSIONS We conclude that the copy number variation in the repeat sequences of FLG between primates may be a consequence of species-specific divergence and expansion.
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Affiliation(s)
- Vanessa Romero
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan.,Present address: Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Hirofumi Nakaoka
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan. .,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan.
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18
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Association of oxidative stress gene polymorphisms with presbycusis. Gene 2016; 593:277-83. [PMID: 27562082 DOI: 10.1016/j.gene.2016.08.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/18/2016] [Accepted: 08/17/2016] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Presbycusis is characterised by etiopathological changes in the cochlea of the inner ear due to genetic and environmental factors and has a serious impact on quality of life. The present study was aimed to evaluate the role of oxidant stress gene polymorphisms in the development of presbycusis. SUBJECTS AND METHODS 220 subjects with confirmed presbycusis from ENT specialists of MAA ENT hospital, Hyderabad, India from 2012 to 2014 were considered for the study. 270 age and sex matched controls were included in the study. Analysis of gene polymorphisms of SNPs cytochrome P450 1A1 (CYP1A1) 3801 T>C, 2455 A>G and 2453 A>C; glutathione S transferase (GST) T1 and M1; N-acetyl transferase (NAT2) 282 C>T and 857 G>A; uncoupled proteins (UCP1) (-3826) A>G and (UCP2) (866)G>A was carried out. Variations in the allelic and genotypic frequencies obtained were computed and analysed using appropriate statistical methods. RESULTS The results of the study indicated that CYP1A1 gene polymorphism at 2453 C>A (adjusted OR: 1.59, 95% CI: 1.01-2.87) and 2455 A>G (adjusted OR: 1.87, 95% CI: 1.07-3.37), double null genotype of GSTM1 and GSTT1 (adjusted OR: 8.88, 95% CI: 4.10-19.19), NAT2 gene at C282T (adjusted OR: 1.77, 95% CI: 1.02-3.11) and G590 A (adjusted OR: 1.83, 95% CI 1.20-3.63) and UCP2 (-866) G>A (adjusted OR: 12.39; 95% CI: 6.51-23.56) showed increased risk for presbycusis while CYP1A1 at 3801 T>C and UCP1 (-3286) A>G exhibited no association. The haplotype combinations of T-G-A of CYP1A1 at 3801, 2455 and 2453 positions as well as T-A of NAT2*6 at 282 and 590 positions were found to contribute significant risk for the onset of presbycusis. CONCLUSIONS Gene polymorphisms of CYP1A1 (A2455G, C2453A), NAT2*6 (C282T, G590 A), GST T1/M1 (double null genotype) and UCP2 (G-866 A) were found to contribute significant risk to presbycusis.
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Patillon B, Luisi P, Poloni ES, Boukouvala S, Darlu P, Genin E, Sabbagh A. A homogenizing process of selection has maintained an "ultra-slow" acetylation NAT2 variant in humans. Hum Biol 2015; 86:185-214. [PMID: 25836746 DOI: 10.13110/humanbiology.86.3.0185] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
N-Acetyltransferase 2 (NAT2) is an important enzyme involved in the metabolism of a wide spectrum of naturally occurring xenobiotics, including therapeutic drugs and common environmental carcinogens. Extensive polymorphism in NAT2 gives rise to a wide interindividual variation in acetylation capacity, which influences individual susceptibility to various drug-induced adverse reactions and cancers. Striking patterns of geographic differentiation have been described for the main slow acetylation variants of the NAT2 gene, suggesting the action of natural selection at this locus. In the present study, we took advantage of whole-genome sequence data available from the 1000 Genomes project to investigate the global patterns of population genetic differentiation at NAT2 and determine whether they are atypical compared with the remaining variation of the genome. The nonsynonymous substitution c.590G>A (rs1799930) defining the slow NAT2*6 haplotype cluster exhibited an unusually low FST value compared with the genome average (FST = 0.006, P = 0.016). It was indicated as the most likely target of a homogenizing process of selection promoting the same allelic variant in globally distributed populations. The rs1799930 A allele has been associated with the slowest acetylation capacity in vivo, and its substantial correlation with the subsistence strategy adopted by past human populations suggests that it may have conferred a selective advantage in populations shifting from foraging to agricultural and pastoral activities in the Neolithic period. Results of neutrality tests further supported an adaptive evolution of the NAT2 gene through either balancing selection or directional selection acting on multiple standing slow acetylation variants.
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Affiliation(s)
- B Patillon
- 1 IRD UMR216, Mère et enfant face aux infections tropicales, Paris, France
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20
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Kakehi M, Ikenaka Y, Nakayama SMM, Kawai YK, Watanabe KP, Mizukawa H, Nomiyama K, Tanabe S, Ishizuka M. Uridine Diphosphate-Glucuronosyltransferase (UGT) Xenobiotic Metabolizing Activity and Genetic Evolution in Pinniped Species. Toxicol Sci 2015; 147:360-9. [DOI: 10.1093/toxsci/kfv144] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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21
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Li F, Cao D, Liu Y, Yang T, Wang G. Transcriptome Sequencing of Lima Bean (Phaseolus lunatus) to Identify Putative Positive Selection in Phaseolus and Legumes. Int J Mol Sci 2015; 16:15172-87. [PMID: 26151849 PMCID: PMC4519893 DOI: 10.3390/ijms160715172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/05/2015] [Accepted: 06/11/2015] [Indexed: 01/15/2023] Open
Abstract
The identification of genes under positive selection is a central goal of evolutionary biology. Many legume species, including Phaseolus vulgaris (common bean) and Phaseolus lunatus (lima bean), have important ecological and economic value. In this study, we sequenced and assembled the transcriptome of one Phaseolus species, lima bean. A comparison with the genomes of six other legume species, including the common bean, Medicago, lotus, soybean, chickpea, and pigeonpea, revealed 15 and 4 orthologous groups with signatures of positive selection among the two Phaseolus species and among the seven legume species, respectively. Characterization of these positively selected genes using Non redundant (nr) annotation, gene ontology (GO) classification, GO term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these genes are mostly involved in thylakoids, photosynthesis and metabolism. This study identified genes that may be related to the divergence of the Phaseolus and legume species. These detected genes are particularly good candidates for subsequent functional studies.
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Affiliation(s)
- Fengqi Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, China.
| | - Depan Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, China.
| | - Yang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, China.
| | - Ting Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, China.
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, China.
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22
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Hiragaki S, Suzuki T, Mohamed AAM, Takeda M. Structures and functions of insect arylalkylamine N-acetyltransferase (iaaNAT); a key enzyme for physiological and behavioral switch in arthropods. Front Physiol 2015; 6:113. [PMID: 25918505 PMCID: PMC4394704 DOI: 10.3389/fphys.2015.00113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/25/2015] [Indexed: 11/26/2022] Open
Abstract
The evolution of N-acetyltransfeases (NATs) seems complex. Vertebrate arylalkylamine N-acetyltransferase (aaNAT) has been extensively studied since it leads to the synthesis of melatonin, a multifunctional neurohormone prevalent in photoreceptor cells, and is known as a chemical token of the night. Melatonin also serves as a scavenger for reactive oxygen species. This is also true with invertebrates. NAT therefore has distinct functional implications in circadian function, as timezymes (aaNAT), and also xenobiotic reactions (arylamine NAT or simply NAT). NATs belong to a broader enzyme group, the GCN5-related N-acetyltransferase superfamily. Due to low sequence homology and a seemingly fast rate of structural differentiation, the nomenclature for NATs can be confusing. The advent of bioinformatics, however, has helped to classify this group of enzymes; vertebrates have two distinct subgroups, the timezyme type and the xenobiotic type, which has a wider substrate range including imidazolamine, pharmacological drugs, environmental toxicants and even histone. Insect aaNAT (iaaNAT) form their own clade in the phylogeny, distinct from vertebrate aaNATs. Arthropods are unique, since the phylum has exoskeleton in which quinones derived from N-acetylated monoamines function in coupling chitin and arthropodins. Monoamine oxidase (MAO) activity is limited in insects, but NAT-mediated degradation prevails. However, unexpectedly iaaNAT occurs not only among arthropods but also among basal deuterostomia, and is therefore more apomorphic. Our analyses illustrate that iaaNATs has unique physiological roles but at the same time it plays a role in a timezyme function, at least in photoperiodism. Photoperiodism has been considered as a function of circadian system but the detailed molecular mechanism is not well understood. We propose a molecular hypothesis for photoperiodism in Antheraea pernyi based on the transcription regulation of NAT interlocked by the circadian system. Therefore, the enzyme plays both unique and universal roles in insects. The unique role of iaaNATs in physiological regulation urges the targeting of this system for integrated pest management (IPM). We indeed showed a successful example of chemical compound screening with reconstituted enzyme and further attempts seem promising.
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Affiliation(s)
- Susumu Hiragaki
- Graduate School of Agricultural Science, Kobe UniversityKobe, Japan
| | - Takeshi Suzuki
- Department of Biology, The University of Western OntarioLondon, ON, Canada
| | | | - Makio Takeda
- Graduate School of Agricultural Science, Kobe UniversityKobe, Japan
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Schlebusch CM, Gattepaille LM, Engström K, Vahter M, Jakobsson M, Broberg K. Human adaptation to arsenic-rich environments. Mol Biol Evol 2015; 32:1544-55. [PMID: 25739736 DOI: 10.1093/molbev/msv046] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adaptation drives genomic changes; however, evidence of specific adaptations in humans remains limited. We found that inhabitants of the northern Argentinean Andes, an arid region where elevated arsenic concentrations in available drinking water is common, have unique arsenic metabolism, with efficient methylation and excretion of the major metabolite dimethylated arsenic and a less excretion of the highly toxic monomethylated metabolite. We genotyped women from this population for 4,301,332 single nucleotide polymorphisms (SNPs) and found a strong association between the AS3MT (arsenic [+3 oxidation state] methyltransferase) gene and mono- and dimethylated arsenic in urine, suggesting that AS3MT functions as the major gene for arsenic metabolism in humans. We found strong genetic differentiation around AS3MT in the Argentinean Andes population, compared with a highly related Peruvian population (FST = 0.014) from a region with much less environmental arsenic. Also, 13 of the 100 SNPs with the highest genome-wide Locus-Specific Branch Length occurred near AS3MT. In addition, our examination of extended haplotype homozygosity indicated a selective sweep of the Argentinean Andes population, in contrast to Peruvian and Colombian populations. Our data show that adaptation to tolerate the environmental stressor arsenic has likely driven an increase in the frequencies of protective variants of AS3MT, providing the first evidence of human adaptation to a toxic chemical.
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Affiliation(s)
- Carina M Schlebusch
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Lucie M Gattepaille
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Karin Engström
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Marie Vahter
- Unit of Metals and Health, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Broberg
- Unit of Metals and Health, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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24
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PharmGKB summary: very important pharmacogene information for N-acetyltransferase 2. Pharmacogenet Genomics 2014; 24:409-25. [PMID: 24892773 DOI: 10.1097/fpc.0000000000000062] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Eny KM, Lutgers HL, Maynard J, Klein BEK, Lee KE, Atzmon G, Monnier VM, van Vliet-Ostaptchouk JV, Graaff R, van der Harst P, Snieder H, van der Klauw MM, Sell DR, Hosseini SM, Cleary PA, Braffett BH, Orchard TJ, Lyons TJ, Howard K, Klein R, Crandall JP, Barzilai N, Milman S, Ben-Avraham D, Wolffenbuttel BHR, Paterson AD. GWAS identifies an NAT2 acetylator status tag single nucleotide polymorphism to be a major locus for skin fluorescence. Diabetologia 2014; 57:1623-34. [PMID: 24934506 PMCID: PMC4079945 DOI: 10.1007/s00125-014-3286-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/28/2014] [Indexed: 11/24/2022]
Abstract
AIMS/HYPOTHESIS Skin fluorescence (SF) is a non-invasive marker of AGEs and is associated with the long-term complications of diabetes. SF increases with age and is also greater among individuals with diabetes. A familial correlation of SF suggests that genetics may play a role. We therefore performed parallel genome-wide association studies of SF in two cohorts. METHODS Cohort 1 included 1,082 participants, 35-67 years of age with type 1 diabetes. Cohort 2 included 8,721 participants without diabetes, aged 18-90 years. RESULTS rs1495741 was significantly associated with SF in Cohort 1 (p < 6 × 10(-10)), which is known to tag the NAT2 acetylator phenotype. The fast acetylator genotype was associated with lower SF, explaining up to 15% of the variance. In Cohort 2, the top signal associated with SF (p = 8.3 × 10(-42)) was rs4921914, also in NAT2, 440 bases upstream of rs1495741 (linkage disequilibrium r (2) = 1.0 for rs4921914 with rs1495741). We replicated these results in two additional cohorts, one with and one without type 1 diabetes. Finally, to understand which compounds are contributing to the NAT2-SF signal, we examined 11 compounds assayed from skin biopsies (n = 198): the fast acetylator genotype was associated with lower levels of the AGEs hydroimidazolones of glyoxal (p = 0.017). CONCLUSIONS/INTERPRETATION We identified a robust association between NAT2 and SF in people with and without diabetes. Our findings provide proof of principle that genetic variation contributes to interindividual SF and that NAT2 acetylation status plays a major role.
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Affiliation(s)
- Karen M. Eny
- Program in Genetics and Genomic Biology, Hospital for Sick Children, 686 Bay Street, Room 12.9830, Toronto, ON M5G 0A4 Canada
| | - Helen L. Lutgers
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, HPC AA31, PO Box 30001, 9700 RB Groningen, the Netherlands
| | | | - Barbara E. K. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Kristine E. Lee
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Gil Atzmon
- Department of Medicine, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Vincent M. Monnier
- Department of Pathology, Case Western Reserve University, Cleveland, OH USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH USA
| | - Jana V. van Vliet-Ostaptchouk
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, HPC AA31, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Reindert Graaff
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, HPC AA31, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Harold Snieder
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Melanie M. van der Klauw
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, HPC AA31, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - David R. Sell
- Department of Pathology, Case Western Reserve University, Cleveland, OH USA
| | - S. Mohsen Hosseini
- Program in Genetics and Genomic Biology, Hospital for Sick Children, 686 Bay Street, Room 12.9830, Toronto, ON M5G 0A4 Canada
| | | | | | - Trevor J. Orchard
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA USA
| | - Timothy J. Lyons
- Centre for Experimental Medicine, Institute of Clinical Science, Queen’s University of Belfast, Belfast, UK
| | - Kerri Howard
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Jill P. Crandall
- Department of Medicine, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY USA
| | - Nir Barzilai
- Department of Medicine, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Sofiya Milman
- Department of Medicine, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY USA
| | - Danny Ben-Avraham
- Department of Medicine, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | | | | | - Bruce H. R. Wolffenbuttel
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, HPC AA31, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Andrew D. Paterson
- Program in Genetics and Genomic Biology, Hospital for Sick Children, 686 Bay Street, Room 12.9830, Toronto, ON M5G 0A4 Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON Canada
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26
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Baum BR, Edwards T, Johnson DA. What does the nr5S DNA multigene family tell us about the genomic relationship between Dasypyrum breviaristatum and D. villosum (Triticeae: Poaceae)? Mol Genet Genomics 2014; 289:553-65. [PMID: 24609469 DOI: 10.1007/s00438-014-0825-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/06/2014] [Indexed: 01/08/2023]
Abstract
The genus Dasypyrum contains two species: the annual and widespread D. villosum (2x = 2n = 14) and the perennial and generally rare D. breviaristatum (2x = 2n = 14 and 4x = 2n = 28). The origin of the latter and its genome constitution have been subject of several studies. There is agreement that the genome of the diploid D. villosum (VV) is different from the diploid cytotype of D. breviaristatum (VbVb), but there is no agreement of the constitution of the tetraploid cytotype, specifically whether is it an autotetraploid or an allotetraploid. This is a long-standing disagreement that this study aims to resolve using the 5S nrDNA as a genomic marker. Our studies suggest that the 4x D. breviaristatum is an allotetraploid (VVVbVb).
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Affiliation(s)
- B R Baum
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A OC6, Canada,
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27
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Gorain B, Chakraborty S, Pal MM, Sarkar R, Samanta SK, Karmakar S, Sen T. Arylamine N-acetyl Transferase (NAT) in the blue secretion of Telescopium telescopium: xenobiotic metabolizing enzyme as a biomarker for detection of environmental pollution. SPRINGERPLUS 2014; 3:666. [PMID: 26034680 PMCID: PMC4447851 DOI: 10.1186/2193-1801-3-666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 10/24/2014] [Indexed: 11/25/2022]
Abstract
Telescopium telescopium, a marine mollusc collected from Sundarban mangrove, belongs to the largest mollusca phylum in the world and exudes a blue secretion when stimulated mechanically. The blue secretion was found to metabolize (preferentially) para-amino benzoic acid, a substrate for N-acetyl transferase (NAT), thereby indicating acetyl transferase like activity of the secretion. Attempts were also made to characterise bioactive fraction of the blue secretion and to further use this as a biomarker for monitoring of marine pollution. NAT like enzyme from marine mollusc is a potential candidate for detoxification of different harmful chemicals. A partially purified extract of blue secretion was obtained by fractional precipitation with (NH4)2SO4. From different fractions obtained by precipitation, the 0–30% fraction (30S) displayed NAT like activity (using para amino benzoic acid as a substrate with para nitrophenyl phosphate or acetyl coenzyme A as acetyl group donors). Maximum NAT like enzyme activity was attained at 25°C and at a pH of 6. The enzyme activity was found to be inhibited by 5 mM phenyl methyl sulfonyl fluoride. The divalent metal ions reduced NAT like activity of 30S. Moreover, Cu2+ and Zn2+ (at concentration of 1 mM) completely inhibited NAT activity. The thermal stability and bench-top stability studies were performed and it was found that the enzyme was stable at room temperature for more than 24 hours. Results from the present study further indicate that heavy metal content in blue secretion gradually decreased from pre-monsoon to post-monsoon season, which also corresponded to the change in NAT like activity. Therefore, this article stresses the importance of biomarker research for monitoring pollution.
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Affiliation(s)
- Bapi Gorain
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032 India
| | - Sumon Chakraborty
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032 India
| | - Murari Mohan Pal
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032 India
| | - Ratul Sarkar
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032 India ; School of Natural Product Studies, Jadavpur University, Kolkata, 700032 India
| | - Samir Kumar Samanta
- Calcutta Institute of Pharmaceutical Technology and AHS, Banitabla, Ulluberia, Howrah 711316 India
| | - Sanmoy Karmakar
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032 India
| | - Tuhinadri Sen
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032 India ; School of Natural Product Studies, Jadavpur University, Kolkata, 700032 India
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28
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Tsirka T, Boukouvala S, Agianian B, Fakis G. Polymorphism p.Val231Ile alters substrate selectivity of drug-metabolizing arylamine N-acetyltransferase 2 (NAT2) isoenzyme of rhesus macaque and human. Gene 2013; 536:65-73. [PMID: 24333853 DOI: 10.1016/j.gene.2013.11.085] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/10/2013] [Accepted: 11/30/2013] [Indexed: 10/25/2022]
Abstract
Arylamine N-acetyltransferases (NATs) are polymorphic enzymes mediating the biotransformation of arylamine/arylhydrazine xenobiotics, including pharmaceuticals and environmental carcinogens. The NAT1 and NAT2 genes, and their many polymorphic variants, have been thoroughly studied in humans by pharmacogeneticists and cancer epidemiologists. However, little is known about the function of NAT homologues in other primate species, including disease models. Here, we perform a comparative functional investigation of the NAT2 homologues of the rhesus macaque and human. We further dissect the functional impact of a previously described rhesus NAT2 gene polymorphism, causing substitution of valine by isoleucine at amino acid position 231. Gene constructs of rhesus and human NAT2, bearing or lacking non-synonymous polymorphism c.691G>A (p.Val231Ile), were expressed in Escherichia coli for comparative enzymatic analysis against various NAT1- and NAT2-selective substrates. The results suggest that the p.Val231Ile polymorphism does not compromise the stability or overall enzymatic activity of NAT2. However, substitution of Val231 by the bulkier isoleucine appears to alter enzyme substrate selectivity by decreasing the affinity towards NAT2 substrates and increasing the affinity towards NAT1 substrates. The experimental observations are supported by in silico modelling localizing polymorphic residue 231 close to amino acid loop 125-129, which forms part of the substrate binding pocket wall and determines the substrate binding preferences of the NAT isoenzymes. The p.Val231Ile polymorphism is the first natural polymorphism demonstrated to affect NAT substrate selectivity via this particular mechanism. The study is also the first to thoroughly characterize the properties of a polymorphic NAT isoenzyme in a non-human primate model.
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Affiliation(s)
- Theodora Tsirka
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Alexandroupolis, Greece
| | - Sotiria Boukouvala
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Alexandroupolis, Greece
| | - Bogos Agianian
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Alexandroupolis, Greece
| | - Giannoulis Fakis
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Alexandroupolis, Greece.
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29
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Pesch B, Gawrych K, Rabstein S, Weiss T, Casjens S, Rihs HP, Ding H, Angerer J, Illig T, Klopp N, Bueno-de-Mesquita B, Ros MM, Kaaks R, Chang-Claude J, Roswall N, Tjønneland A, Overvad K, Clavel-Chapelon F, Boutron-Ruault MC, Dossus L, Boeing H, Weikert S, Trichopoulos D, Palli D, Sieri S, Tumino R, Panico S, Quirós JR, González C, Sánchez MJ, Dorronsoro M, Navarro C, Barricarte A, Ljungberg B, Johansson M, Ulmert D, Ehrnström R, Khaw KT, Wareham N, Key TJ, Ferrari P, Romieu I, Riboli E, Brüning T, Vineis P. N-acetyltransferase 2 Phenotype, Occupation, and Bladder Cancer Risk: Results from the EPIC Cohort. Cancer Epidemiol Biomarkers Prev 2013; 22:2055-65. [DOI: 10.1158/1055-9965.epi-13-0119-t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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30
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Lan T, Wang XR, Zeng QY. Structural and functional evolution of positively selected sites in pine glutathione S-transferase enzyme family. J Biol Chem 2013; 288:24441-51. [PMID: 23846689 DOI: 10.1074/jbc.m113.456863] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phylogenetic analyses have identified positive selection as an important driver of protein evolution, both structural and functional. However, the lack of appropriate combined functional and structural assays has generally hindered attempts to elucidate patterns of positively selected sites and their effects on enzyme activity and substrate specificity. In this study we investigated the evolutionary divergence of the glutathione S-transferase (GST) family in Pinus tabuliformis, a pine that is widely distributed from northern to central China, including cold temperate and drought-stressed regions. GSTs play important roles in plant stress tolerance and detoxification. We cloned 44 GST genes from P. tabuliformis and found that 26 of the 44 belong to the largest (Tau) class of GSTs and are differentially expressed across tissues and developmental stages. Substitution models identified five positively selected sites in the Tau GSTs. To examine the functional significance of these positively selected sites, we applied protein structural modeling and site-directed mutagenesis. We found that four of the five positively selected sites significantly affect the enzyme activity and specificity; thus their variation broadens the GST family substrate spectrum. In addition, positive selection has mainly acted on secondary substrate binding sites or sites close to (but not directly at) the primary substrate binding site; thus their variation enables the acquisition of new catalytic functions without compromising the protein primary biochemical properties. Our study sheds light on selective aspects of the functional and structural divergence of the GST family in pine and other organisms.
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Affiliation(s)
- Ting Lan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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