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Serafini PP, Righetti BPH, Vanstreels RET, Bugoni L, Piazza CE, Lima D, Mattos JJ, Kolesnikovas CKM, Pereira A, Maraschin M, Piccinin I, Guilford T, Gallo L, Uhart MM, Lourenço RA, Bainy ACD, Lüchmann KH. Biochemical and molecular biomarkers and their association with anthropogenic chemicals in wintering Manx shearwaters (Puffinus puffinus). MARINE POLLUTION BULLETIN 2024; 203:116398. [PMID: 38723548 DOI: 10.1016/j.marpolbul.2024.116398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 06/06/2024]
Abstract
Anthropogenic pollution poses a threat to marine conservation by causing chronic toxic effects. Seabirds have contact throughout their lives with pollutants like plastic, metals, polychlorinated biphenyls (PCBs), and organochlorine pesticides such as hexachlorocyclohexanes (HCHs). We assessed 155 Manx shearwaters (Puffinus puffinus) stranded along the Brazilian coast, analyzing associations between organic pollutants, plastic ingestion, biomarkers (transcript levels of aryl hydrocarbon receptor, cytochrome P450-1A-5 [CYP1A5], UDP-glucuronosyl-transferase [UGT1], estrogen receptor alpha-1 [ESR1], and heat shock protein-70 genes) and enzymes activity (ethoxy-resorufin O-deethylase and glutathione S-transferase [GST]). Plastic debris was found in 29 % of the birds. The transcription of UGT1 and CYP1A5 was significantly associated with hexachlorobenzene (HCB) and PCBs levels. ESR1 was associated with HCB and Mirex, and GST was associated with Drins and Mirex. While organic pollutants affected shearwaters more than plastic ingestion, reducing plastic availability remains relevant as xenobiotics are also potentially adsorbed onto plastics.
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Affiliation(s)
- Patricia P Serafini
- Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina - UFSC, Florianópolis, SC, Brazil; Centro Nacional de Pesquisa e Conservação de Aves Silvestres, Instituto Chico Mendes de Conservação da Biodiversidade - ICMBio, Florianópolis, SC, Brazil
| | - Bárbara P H Righetti
- Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina - UFSC, Florianópolis, SC, Brazil
| | - Ralph E T Vanstreels
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, USA
| | - Leandro Bugoni
- Laboratório de Aves Aquáticas e Tartarugas Marinhas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Clei E Piazza
- Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina - UFSC, Florianópolis, SC, Brazil
| | - Daína Lima
- Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina - UFSC, Florianópolis, SC, Brazil
| | - Jacó J Mattos
- Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina - UFSC, Florianópolis, SC, Brazil
| | | | | | - Marcelo Maraschin
- Plant Morphogenesis and Biochemistry Laboratory, UFSC, Florianópolis, SC, Brazil
| | - Isadora Piccinin
- Plant Morphogenesis and Biochemistry Laboratory, UFSC, Florianópolis, SC, Brazil
| | - Tim Guilford
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Luciana Gallo
- Instituto de Biología de Organismos Marinos, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Chubut, Argentina; Coordinación Regional de Inocuidad y Calidad Agroalimentaria, Regional Patagonia Sur, Servicio Nacional de Sanidad y Calidad Agroalimentaria, Puerto Madryn, Chubut, Argentina
| | - Marcela M Uhart
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, USA
| | - Rafael A Lourenço
- Instituto Oceanográfico, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Afonso C D Bainy
- Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina - UFSC, Florianópolis, SC, Brazil
| | - Karim H Lüchmann
- Departamento de Educação Científica e Tecnológica, Universidade do Estado de Santa Catarina - UDESC, Florianópolis, SC, Brazil.
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Kreitsberg R, Nääb L, Meitern R, Carbillet J, Fort J, Giraudeau M, Sepp T. The effect of environmental pollution on gene expression of seabirds: A review. MARINE ENVIRONMENTAL RESEARCH 2023; 189:106067. [PMID: 37393763 DOI: 10.1016/j.marenvres.2023.106067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
One of the biggest challenges for ecotoxicologists is to detect harmful effects of contaminants on individual organisms before they have caused significant harm to natural populations. One possible approach for discovering sub-lethal, negative health effects of pollutants is to study gene expression, to identify metabolic pathways and physiological processes affected by contaminants. Seabirds are essential components of ecosystems but highly threatened by environmental changes. Being at the top of the food chain and exhibiting a slow pace of life, they are highly exposed to contaminants and to their ultimate impacts on populations. Here we provide an overview of the currently available seabird-related gene expression studies in the context of environmental pollution. We show that studies conducted, so far, mainly focus on a small selection of xenobiotic metabolism genes, often using lethal sampling protocols, while the greater promise of gene expression studies for wild species may lie in non-invasive procedures focusing on a wider range of physiological processes. However, as whole genome approaches might still be too expensive for large-scale assessments, we also bring out the most promising candidate biomarker genes for future studies. Based on the biased geographical representativeness of the current literature, we suggest expanding studies to temperate and tropical latitudes and urban environments. Also, as links with fitness traits are very rare in the current literature, but would be highly relevant for regulatory purposes, we point to an urgent need for establishing long-term monitoring programs in seabirds that would link pollutant exposure and gene expression to fitness traits.
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Affiliation(s)
- Randel Kreitsberg
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia.
| | - Lisanne Nääb
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Richard Meitern
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Jeffrey Carbillet
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Mathieu Giraudeau
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Tuul Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
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Yan J, Zhang C, Zhang M, Zhou H, Zuo Z, Ding X, Zhang R, Li F, Gao Y. Chromosome-level genome assembly of the Colorado potato beetle, Leptinotarsa decemlineata. Sci Data 2023; 10:36. [PMID: 36653371 PMCID: PMC9849343 DOI: 10.1038/s41597-023-01950-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
The Colorado potato beetle (Leptinotarsa decemlineata) is one of the most notorious insect pests of potatoes globally. Here, we generated a high-quality chromosome-level genome assembly of L. decemlineata using a combination of the PacBio HiFi sequencing and Hi-C scaffolding technologies. The genome assembly (-1,008 Mb) is anchored to 18 chromosomes (17 + XO), with a scaffold N50 of 58.32 Mb. It contains 676 Mb repeat sequences and 29,606 protein-coding genes. The chromosome-level genome assembly of L. decemlineata provides in-depth knowledge and will be a helpful resource for the beetle and invasive biology research communities.
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Affiliation(s)
- Junjie Yan
- grid.410727.70000 0001 0526 1937State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Chaowei Zhang
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Mengdi Zhang
- grid.410727.70000 0001 0526 1937State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hang Zhou
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Zhangqi Zuo
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Xinhua Ding
- grid.433811.c0000 0004 1798 1482Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Runzhi Zhang
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fei Li
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Yulin Gao
- grid.410727.70000 0001 0526 1937State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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Fontaine SS, Kohl KD. The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming. J Exp Biol 2023; 226:286161. [PMID: 36546449 PMCID: PMC10086385 DOI: 10.1242/jeb.245191] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Phenotypic plasticity is an important strategy that animals employ to respond and adjust to changes in their environment. Plasticity may occur via changes in host gene expression or through functional changes in their microbiomes, which contribute substantially to host physiology. Specifically, the presence and function of host-associated microbes can impact how animals respond to heat stress. We previously demonstrated that 'depleted' tadpoles, with artificially disrupted microbiomes, are less tolerant to heat than 'colonized' tadpoles, with more natural microbiomes. However, the mechanisms behind these effects are unclear. Here, we compared gene expression profiles of the tadpole gut transcriptome, and tadpole gut microbial metagenome, between colonized and depleted tadpoles under cool or warm conditions. Our goal was to identify differences in host and microbial responses to heat between colonized and depleted tadpoles that might explain their observed differences in heat tolerance. We found that depleted tadpoles exhibited a much stronger degree of host gene expression plasticity in response to heat, while the microbiome of colonized tadpoles was significantly more heat sensitive. These patterns indicate that functional changes in the microbiome in response to heat may allow for a dampened host response, ultimately buffering hosts from the deleterious effects of heat stress. We also identified several specific host and microbial pathways that could be contributing to increased thermal tolerance in colonized tadpoles including amino acid metabolism, vitamin biosynthesis and ROS scavenging pathways. Our results demonstrate that the microbiome influences host plasticity and the response of hosts to environmental stressors.
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Affiliation(s)
- Samantha S Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Nandar YM, Duangmano S, Lucksiri A, Sirikul C, Palacajornsuk P, Anukul N. Introduction of new alternative pipeline using multiplexed fast COLD‑PCR together with sequencing approach highlighting pharmacoeconomics by detection of CYP variants. Biomed Rep 2022; 17:99. [PMID: 36606140 PMCID: PMC9808490 DOI: 10.3892/br.2022.1582] [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: 09/02/2022] [Accepted: 10/11/2022] [Indexed: 01/07/2023] Open
Abstract
In precision medicine, multiple factors are involved in clinical decision-making because of ethnic and racial genetic diversity, family history and other health factors. Although advanced techniques have evolved, there is still an economic obstacle to pharmacogenetic (PGx) implementation in developing countries. The aim of the present study was to provide an alternative pipeline that roughly estimate patient carrier type and prescreen out wild-type samples before sequencing or genotyping to determine genetic status. Fast co-amplification at lower denaturation temperature (COLD)-PCR was used to differentiate genetic variant non-carriers from carriers. The majority of drugs are hepatically cleared by cytochrome P450 (CYP) enzymes and genes encoding CYP enzymes are highly variable. Of all the CYPs, CYP2 family of CYP2C9, CYP2C19, and CYP2D6 isoforms have clinically significant impact on drugs of PGx testing. Therefore, five variants associated with these CYPs were selected for preliminary testing with this novel pipeline. For fast COLD-PCR, the optimal annealing temperature and critical denaturation temperature were determined and evaluated via Sanger sequencing of 27 randomly collected samples. According to precise Tc, to perform in a single-reaction is difficult. However, in this study, this issue was resolved by combination of precise Tc using 10+10+20 cycles. The results showed 100% sensitivity and specificity, with perfect agreement (κ=1.0) compared with Sanger sequencing. The present study provides a prescreening platform by introducing multiplex fast COLD-PCR as a pharmacoeconomic implementation. Our study just present in five variants which are not enough to describe patient metabolic status. Therefore, other actional genetic variants are still needed to cover the actual patient's genotypes. Nevertheless, the proposed method can well-present its efficiency and reliability for serving as a PGx budget platform in the future.
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Affiliation(s)
- Yu Myat Nandar
- Master's Degree Program in Medical Technology (International Program), Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, CMU Presidential Scholarship, Chiang Mai 50200, Thailand
| | - Suwit Duangmano
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Aroonrut Lucksiri
- Department of Pharmaceutical Care, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chonticha Sirikul
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Poonsub Palacajornsuk
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nampeung Anukul
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand,Correspondence to: Dr Nampeung Anukul, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, 110 Intawaroroj Road, Sripoom, Chiang Mai 50200, Thailand
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Adeola AC, Sola-Ojo FE, Opeyemi YA, Oguntunji AO, Nneji LM, Ewuola MK, Bello SF, Olaniyi WA, Adesoji AT, Karuno AP, Sanke OJ, Daniel EL. Genetic diversity and population structure of muscovy duck ( Cairina moschata) from Nigeria. PeerJ 2022; 10:e13236. [PMID: 35444865 PMCID: PMC9014852 DOI: 10.7717/peerj.13236] [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: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 01/15/2023] Open
Abstract
The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (F ST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.
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Affiliation(s)
- Adeniyi C. Adeola
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Foluke E. Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Yusuf A. Opeyemi
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Abel O. Oguntunji
- Department of Animal Science and Fisheries Management, Bowen University, Iwo, Osun, Nigeria
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States
| | - Muslim K. Ewuola
- Animal Breeding and Genetics Unit/Department of Animal Science, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Semiu F. Bello
- Department of Animal Genetics/Breeding and Reproduction/College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wasiu A. Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Adeosun T. Adesoji
- Department of Agricultural Education, Federal College of Education, Bichi, Kano, Nigeria
| | - Alex P. Karuno
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
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Yu C, Zhang B, Zhang Z, Wang S, Wei T, Li L, Zhao Y, Wei H, Li Y. Comparative transcriptome analysis reveals the impact of the daily rhythm on the hemolymph of the Chinese mitten crab ( Eriocheir sinensis). Chronobiol Int 2022; 39:805-817. [PMID: 35144513 DOI: 10.1080/07420528.2022.2035744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The daily rhythm affects a series of physiological functions in crustaceans. To study its effect on the physiological function in Eriocheir sinensis, a crustacean species of high economic value, we analyzed the hemolymph transcriptome during the daily rhythm by high-throughput sequencing. We sampled the hemolymph from crabs at four time points in a single day (06:00, 12:00, 18:00, and 24:00 h) and identified 3,01,661 and 1,03,998 transcripts and unigenes, respectively; some of the unigenes were annotated as core clock genes. Moreover, 15,564 differentially expressed genes (DEGs) were divided into nine different clusters. Functional enrichment analysis of DEGs indicated that the molting, metabolism, and immunity processes in E. sinensis were impacted by its daily rhythm. In addition, we mapped the DEGs involved in the daily entrainment pathway. To the best of our knowledge, this is the first comparative transcriptome analysis of crustacean hemolymph during the day-night cycle, and provides multi-level information for unraveling the finer regulatory effects of the daily cycle in crustaceans.
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Affiliation(s)
- Changyue Yu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Baoli Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhiyuan Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Simiao Wang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Tingyu Wei
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Lisong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yingying Zhao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hua Wei
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yingdong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Yin SJ, Qian GY, Yang JM, Lee J, Park YD. Detection of melanogenesis- and anti-apoptosis-associated melanoma factors: Array CGH and PPI mapping integrating study. Protein Pept Lett 2021; 28:1408-1424. [PMID: 34749602 DOI: 10.2174/0929866528666211105112927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/02/2021] [Accepted: 08/26/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND We investigated melanogenesis- and anti-apoptosis-related melanoma factors in melanoma cells (TXM1, TXM18, A375P, and A375SM). OBJECTIVE To find melanoma associated hub factor, high-throughput screening-based techniques integrating with bioinformatics were investigated. METHODS Array CGH analysis was conducted with a commercial system. Total genomic DNAs prepared individually from each cell line with control DNA were properly labeled with Cy3-dCTP and Cy5-dCTP and hybridizations and subsequently performed data treatment by the log2 green (G; test) to red (R; reference) fluorescence ratios (G/R). Gain or loss of copy number was judged by spots with log2-transformed ratios. PPI mapping analysis of detected candidate genes based on the array CGH results was conducted using the human interactome in the STRING database. Energy minimization and a short molecular dynamics (MD) simulation using the implicit solvation model in CHARMM were performed to analyze the interacting residues between YWHAZ and YWHAB. RESULTS Three genes (BMP-4, BFGF, LEF-1) known to be involved in melanogenesis were found to lose chromosomal copy numbers, and Chr. 6q23.3 was lost in all tested cell lines. Ten hub genes (CTNNB1, PEX13, PEX14, PEX5, IFNG, EXOSC3, EXOSC1, EXOSC8, UBC, and PEX10) were predicted to be functional interaction factors in the network of the 6q23.3 locus. The apoptosis-associated genes E2F1, p50, BCL2L1, and BIRC7 gained, and FGF2 lost chromosomal copy numbers in the tested melanoma cell lines. YWHAB, which gained chromosomal copy numbers, was predicted to be the most important hub protein in melanoma cells. Molecular dynamics simulations for binding YWHAB and YWHAZ were conducted, and the complex was predicted to be energetically and structurally stable through its 3 hydrogen-bond patterns. The number of interacting residues is 27. CONCLUSION Our study compares genome-wide screening interactomics predictions for melanoma factors and offers new information for understanding melanogenesis- and anti-apoptosis-associated mechanisms in melanoma. Especially, YWHAB was newly detected as a core factor in melanoma cells.
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Affiliation(s)
- Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100. China
| | - Guo-Ying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100. China
| | - Jun-Mo Yang
- Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul 135-710. Korea
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro, Yuseong-gu, Daejeon, 34141. Korea
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100. China
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Xing X, Yan M, Pang H, Wu F, Wang J, Sheng S. Cytochrome P450s Are Essential for Insecticide Tolerance in the Endoparasitoid Wasp Meteorus pulchricornis (Hymenoptera: Braconidae). INSECTS 2021; 12:insects12070651. [PMID: 34357311 PMCID: PMC8306486 DOI: 10.3390/insects12070651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022]
Abstract
With the widespread application of insecticides, parasitoid wasps may also be under risk when exposed to insecticides directly at their free-living stages. The endoparasitoid wasp Meteorus pulchricornis is the predominant natural enemy of many lepidopteran pests, such as Spodoptera litura and Helicoverpa armigera. The cytochrome P450 monooxygenases constitute a ubiquitous and complex superfamily of hydrophobic, haem-containing enzymes. P450s are involved in the detoxification of many xenobiotics. However, their exact roles in the tolerance mechanism in parasitoids toward insecticides has received less attention. Here, 28 P450 genes in M. pulchricornis were identified from a previously constructed transcriptome dataset. These P450 genes belonged to CYP2, -3, and -4, and mitochondrial clans. Subsequently, eight candidate MpulCYPs were selected from four CYP clans to validate their expression patterns under phoxim, cypermethrin, and chlorfenapyr exposure by qRT-PCR. The results showed that all three insecticides had significant effects on the expression of MpulCYPs. To further study the function of P450s, CYP369B3 was silenced, and its expression levels of CYP369B3 were significantly decreased. Survival analysis indicated that after dsRNA injection, the mortality rate of wasps was significantly increased when M. pulchricornis females were exposed to insecticides compared to control groups. Our findings provide a theoretical base for elucidating the mechanism of insecticide tolerance and promote functional research on P450 genes in parasitoid wasps.
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Affiliation(s)
- Xiaorong Xing
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China; (X.X.); (M.Y.); (H.P.); (F.W.); (J.W.)
| | - Mengwen Yan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China; (X.X.); (M.Y.); (H.P.); (F.W.); (J.W.)
| | - Huilin Pang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China; (X.X.); (M.Y.); (H.P.); (F.W.); (J.W.)
| | - Fu’an Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China; (X.X.); (M.Y.); (H.P.); (F.W.); (J.W.)
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212018, China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China; (X.X.); (M.Y.); (H.P.); (F.W.); (J.W.)
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212018, China
| | - Sheng Sheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China; (X.X.); (M.Y.); (H.P.); (F.W.); (J.W.)
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212018, China
- Correspondence:
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10
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Kawai YK, Itou K, Yoshino T, Iima H, Matsumoto F, Kubota A. Hepatic transcriptional profile and tissue distribution of cytochrome P450 1-3 genes in the red-crowned crane Grus japonensis. Comp Biochem Physiol C Toxicol Pharmacol 2020; 228:108643. [PMID: 31669699 DOI: 10.1016/j.cbpc.2019.108643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022]
Abstract
The endangered red-crowned crane (Grus japonensis) is a protected species in eastern Hokkaido and injured specimens are treated with medication. The present study aimed at understanding the expression profiles of cytochrome P450 (CYP) 1-3 genes in red-crowned crane tissues. We used 14 individuals found dead in the wild in eastern Hokkaido or in Kushiro City Zoo. Nine CYP1-3 genes expressed in the liver of the red-crowned crane were identified by high-throughput sequencing, and phylogenetically classified as CYP1A5, CYP2C23, CYP2C45, CYP2D49, CYP2G19, CYP2U1, CYP2AC1, CYP3A37, and CYP3A80. Based on the quantitative real-time PCR of 13 samples, the rank order of their median expression levels was as follows: CYP3A37 > CYP2AC1 > CYP2C45 > CYP2D49 > CYP2G19 > CYP1A5 > CYP3A80 > CYP2C23. The tissue distribution of the CYP transcripts indicated that many of the CYP1-3 genes examined were mainly expressed in the tissues where drug metabolism occurs, such as the liver, kidneys, and lungs. We found that CYP3A37 was dominant at the transcript level in the liver, indicating it might play a crucial role in liver physiology and xenobiotic metabolism. Similarly, an "orphan" CYP2AC1 was expressed at relatively high levels in the kidneys and liver, suggesting a possible role in renal and liver physiology and xenobiotic metabolism. Our results establish a foundation for future studies on red-crowned cranes aiming to further understand drug sensitivity and develop medication protocols, but also contribute to national and local projects for the conservation of red-crowned crane.
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Affiliation(s)
- Yusuke K Kawai
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Kiwamu Itou
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Tomoo Yoshino
- Kushiro City Zoo, 11 Shimoninishibetsu, Akan, Kushiro, Hokkaido 085-0204, Japan
| | - Hiroko Iima
- Kushiro City Zoo, 11 Shimoninishibetsu, Akan, Kushiro, Hokkaido 085-0204, Japan
| | - Fumio Matsumoto
- Kushiro City Zoo, 11 Shimoninishibetsu, Akan, Kushiro, Hokkaido 085-0204, Japan
| | - Akira Kubota
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
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11
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Zhao MM, Liu TJ, Wang Q, Zhang R, Liu L, Gong DQ, Geng TY. Fatty acids modulate the expression of pyruvate kinase and arachidonate-lipoxygenase through PPARγ/CYP2C45 pathway: a link to goose fatty liver. Poult Sci 2019; 98:4346-4358. [PMID: 31287882 DOI: 10.3382/ps/pez395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/24/2019] [Indexed: 12/30/2022] Open
Abstract
Cytochrome P-450 2C45 (CYP2C45) is the most highly expressed cytochrome P-450 isoform in chicken liver, and may play an important role in avian liver biology. However, information regarding the function of CYP2C45 in fatty liver is generally limited. The aim of this study was to investigate the role of CYP2C45 during the development of goose fatty liver. Our result indicated that the transcription of CYP2C45, together with PK and ALOX5, was increased in goose liver upon overfeeding for 19 D (P < 0.05). In goose primary hepatocytes, CYP2C45 RNA expression was also upgraded by the treatment with various chemicals like insulin, the fatty acids, and PPAR agonists (P < 0.05). We also found that both CYP2C45 overexpression and troglitazone treatment could increase the expression of pyruvate kinase (PK) and arachidonate 5-lipoxygenase (ALOX5), and furthermore, showed that the up-regulation of PK and ALOX5 induced by troglitazone could be suppressed by small interfering RNAs targeting CYP2C45 (P < 0.05). These findings suggest that fatty acids treatment and the overfeeding can induce the up-regulation of CYP2C45 expression possibly via PPARγ and that the induction of PK and ALOX5 in goose fatty liver is at least partially attributed to fatty acid-induced expression of CYP2C45. Thus, our data provides an insight into the mechanism by which glycolysis and arachidonic acid metabolism are modulated in goose fatty liver.
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Affiliation(s)
- M M Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - T J Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Q Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - R Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - L Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - D Q Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - T Y Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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12
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Zimmerman SJ, Aldridge CL, Oh KP, Cornman RS, Oyler‐McCance SJ. Signatures of adaptive divergence among populations of an avian species of conservation concern. Evol Appl 2019; 12:1661-1677. [PMID: 31462921 PMCID: PMC6708427 DOI: 10.1111/eva.12825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the genetic underpinning of adaptive divergence among populations is a key goal of evolutionary biology and conservation. Gunnison sage-grouse (Centrocercus minimus) is a sagebrush obligate species with a constricted range consisting of seven discrete populations, each with distinctly different habitat and climatic conditions. Though geographically close, populations have low levels of natural gene flow resulting in relatively high levels of differentiation. Here, we use 15,033 SNP loci in genomic outlier analyses, genotype-environment association analyses, and gene ontology enrichment tests to examine patterns of putatively adaptive genetic differentiation in an avian species of conservation concern. We found 411 loci within 5 kbp of 289 putative genes associated with biological functions or pathways that were overrepresented in the assemblage of outlier SNPs. The identified gene set was enriched for cytochrome P450 gene family members (CYP4V2, CYP2R1, CYP2C23B, CYP4B1) and could impact metabolism of plant secondary metabolites, a critical challenge for sagebrush obligates. Additionally, the gene set was also enriched with members potentially involved in antiviral response (DEAD box helicase gene family and SETX). Our results provide a first look at local adaption for isolated populations of a single species and suggest adaptive divergence in multiple metabolic and biochemical pathways may be occurring. This information can be useful in managing this species of conservation concern, for example, to identify unique populations to conserve, avoid translocation or release of individuals that may swamp locally adapted genetic diversity, or guide habitat restoration efforts.
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Affiliation(s)
- Shawna J. Zimmerman
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Cameron L. Aldridge
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Kevin P. Oh
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Robert S. Cornman
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
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13
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Global Investigation of Cytochrome P450 Genes in the Chicken Genome. Genes (Basel) 2019; 10:genes10080617. [PMID: 31416226 PMCID: PMC6723978 DOI: 10.3390/genes10080617] [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: 06/21/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Cytochrome P450 (CYP) superfamily enzymes are broadly involved in a variety of physiological and toxicological processes. However, genome-wide analysis of this superfamily has never been investigated in the chicken genome. In this study, genome-wide analyses identified 45 chicken CYPs (cCYPs) from the chicken genome, and their classification and evolutionary relationships were investigated by phylogenetic, conserved protein motif, and gene structure analyses. The comprehensive evolutionary data revealed several remarkable characteristics of cCYPs, including the highly divergent and rapid evolution of the cCYPs, and the loss of cCYP2AF in the chicken genome. Furthermore, the cCYP expression profile was investigated by RNA-sequencing. The differential expression of cCYPs in developing embryos revealed the involvement of cCYPs in embryonic development. The significantly regulated cCYPs suggested its potential role in hepatic metabolism. Additionally, 11 cCYPs, including cCYP2AC1, cCYP2C23a, and cCYP2C23b, were identified as estrogen-responsive genes, which indicates that these cCYPs are involved in the estrogen-signaling pathway. Meanwhile, an expression profile analysis highlights the divergent role of different cCYPs. These data expand our view of the phylogeny and evolution of cCYPs, provide evolutionary insight, and can help elucidate the roles of cCYPs in physiological and toxicological processes in chicken.
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14
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Zacchi FL, Flores-Nunes F, Mattos JJ, Lima D, Lüchmann KH, Sasaki ST, Bícego MC, Taniguchi S, Montone RC, de Almeida EA, Bainy ACD. Biochemical and molecular responses in oysters Crassostrea brasiliana collected from estuarine aquaculture areas in Southern Brazil. MARINE POLLUTION BULLETIN 2018; 135:110-118. [PMID: 30301007 DOI: 10.1016/j.marpolbul.2018.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/01/2018] [Accepted: 07/04/2018] [Indexed: 06/08/2023]
Abstract
Biochemical and molecular responses were evaluated in oysters Crassostrea brasiliana collected from three oyster farms, at Guaratuba Bay, southern Brazil, forming a pollutant gradient: Farm 1 (reference site - farther from the urban area), Farm 2 (intermediate site) and Farm 3 (nearest to the urban area). Oxidative stress markers, DNA damage and transcript levels of CYP2AU1, CYP2-like1, CYP2-like2, SULT-like, GPx-like, SOD-like, CAT-like, GSTmicrosomal-like, GSTomega-like, FABP-like and ALAd-like genes were analyzed in the gills. The levels of polycyclic aromatic hydrocarbons, linear alkylbenzenes and polychlorinated biphenyls were also evaluated in the soft tissues of the oysters and in the sediment of the Farms. Higher GSTomega-like, CYP2AU1 and FABP-like transcript levels, GR and G6PDH activities and lipid peroxidation levels were observed in oysters from Farms 2 and 3, suggesting pollutant effects on oysters. Alterations in oxidative stress markers also suggest a response against a prooxidant condition in C. brasiliana due to pollutant effects.
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Affiliation(s)
- Flávia Lucena Zacchi
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Fabrício Flores-Nunes
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Jacó Joaquim Mattos
- Aquaculture Pathology Research Center - NEPAQ, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Daína Lima
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Karim Hahn Lüchmann
- Fishery Engineering Department, Santa Catarina State University, Laguna 88790-000, Brazil
| | - Silvio Tarou Sasaki
- Laboratory of Marine Organic Chemistry - LABQOM, Oceanographic Institute, University of São Paulo, São Paulo 05508-120, Brazil
| | - Márcia Caruso Bícego
- Laboratory of Marine Organic Chemistry - LABQOM, Oceanographic Institute, University of São Paulo, São Paulo 05508-120, Brazil
| | - Satie Taniguchi
- Laboratory of Marine Organic Chemistry - LABQOM, Oceanographic Institute, University of São Paulo, São Paulo 05508-120, Brazil
| | - Rosalinda Carmela Montone
- Laboratory of Marine Organic Chemistry - LABQOM, Oceanographic Institute, University of São Paulo, São Paulo 05508-120, Brazil
| | | | - Afonso Celso Dias Bainy
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil.
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15
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Twyman H, Andersson S, Mundy NI. Evolution of CYP2J19, a gene involved in colour vision and red coloration in birds: positive selection in the face of conservation and pleiotropy. BMC Evol Biol 2018; 18:22. [PMID: 29439676 PMCID: PMC5812113 DOI: 10.1186/s12862-018-1136-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Exaggerated signals, such as brilliant colours, are usually assumed to evolve through antagonistic coevolution between senders and receivers, but the underlying genetic mechanisms are rarely known. Here we explore a recently identified "redness gene", CYP2J19, that is highly interesting in this context since it encodes a carotenoid-modifying enzyme (a C4 ketolase involved in both colour signalling and colour discrimination in the red (long wavelength) spectral region.) RESULTS: A single full-length CYP2J19 was retrieved from 43 species out of 70 avian genomes examined, representing all major avian clades. In addition, CYP2J19 sequences from 13 species of weaverbirds (Ploceidae), seven of which have red C4-ketocarotenoid coloration were analysed. Despite the conserved retinal function and pleiotropy of CYP2J19, analyses indicate that the gene has been positively selected throughout the radiation of birds, including sites within functional domains described in related CYP (cytochrome P450) loci. Analyses of eight further CYP loci across 25 species show that positive selection is common in this gene family in birds. There was no evidence for a change in selection pressure on CYP2J19 following co-option for red coloration in the weaverbirds. CONCLUSIONS The results presented here are consistent with an ancestral conserved function of CYP2J19 in the pigmentation of red retinal oil droplets used for colour vision, and its subsequent co-option for red integumentary coloration. The cause of positive selection on CYP2J19 is unclear, but may be partly related to compensatory mutations related to selection at the adjacent gene CYP2J40.
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Affiliation(s)
- Hanlu Twyman
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ UK
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Göteborg, Sweden
| | - Nicholas I. Mundy
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ UK
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16
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Membrane-bound human orphan cytochrome P450 2U1: Sequence singularities, construction of a full 3D model, and substrate docking. Biochimie 2017; 140:166-175. [DOI: 10.1016/j.biochi.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022]
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17
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Dhers L, Ducassou L, Boucher JL, Mansuy D. Cytochrome P450 2U1, a very peculiar member of the human P450s family. Cell Mol Life Sci 2017; 74:1859-1869. [PMID: 28083596 PMCID: PMC11107762 DOI: 10.1007/s00018-016-2443-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/14/2022]
Abstract
Cytochrome P450 2U1 (CYP2U1) exhibits several distinctive characteristics among the 57 human CYPs, such as its presence in almost all living organisms with a highly conserved sequence, its particular gene organization with only five exons, its major location in thymus and brain, and its protein sequence involving an unusually long N-terminal region containing 8 proline residues and an insert of about 20 amino acids containing 5 arginine residues after the transmembrane helix. Few substrates, including fatty acids, N-arachidonoylserotonin (AS), and some drugs, have been reported so far. However, its biological roles remain largely unknown, even though CYP2U1 mutations have been involved in some pathological situations, such as complicated forms of hereditary spastic paraplegia. These data together with its ability to hydroxylate some fatty acids and AS suggest its possible role in lipid metabolism.
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Affiliation(s)
- L Dhers
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France
| | - L Ducassou
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France
| | - J-L Boucher
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France.
| | - D Mansuy
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France
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18
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Dhers L, Pietrancosta N, Ducassou L, Ramassamy B, Dairou J, Jaouen M, André F, Mansuy D, Boucher JL. Spectral and 3D model studies of the interaction of orphan human cytochrome P450 2U1 with substrates and ligands. Biochim Biophys Acta Gen Subj 2017; 1861:3144-3153. [DOI: 10.1016/j.bbagen.2016.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/06/2016] [Accepted: 07/21/2016] [Indexed: 02/08/2023]
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19
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Pan ST, Xue D, Li ZL, Zhou ZW, He ZX, Yang Y, Yang T, Qiu JX, Zhou SF. Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery. Int J Mol Sci 2016; 17:E1020. [PMID: 27367670 PMCID: PMC4964396 DOI: 10.3390/ijms17071020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/02/2016] [Accepted: 06/07/2016] [Indexed: 12/31/2022] Open
Abstract
The human cytochrome P450 (CYP) superfamily consisting of 57 functional genes is the most important group of Phase I drug metabolizing enzymes that oxidize a large number of xenobiotics and endogenous compounds, including therapeutic drugs and environmental toxicants. The CYP superfamily has been shown to expand itself through gene duplication, and some of them become pseudogenes due to gene mutations. Orthologs and paralogs are homologous genes resulting from speciation or duplication, respectively. To explore the evolutionary and functional relationships of human CYPs, we conducted this bioinformatic study to identify their corresponding paralogs, homologs, and orthologs. The functional implications and implications in drug discovery and evolutionary biology were then discussed. GeneCards and Ensembl were used to identify the paralogs of human CYPs. We have used a panel of online databases to identify the orthologs of human CYP genes: NCBI, Ensembl Compara, GeneCards, OMA ("Orthologous MAtrix") Browser, PATHER, TreeFam, EggNOG, and Roundup. The results show that each human CYP has various numbers of paralogs and orthologs using GeneCards and Ensembl. For example, the paralogs of CYP2A6 include CYP2A7, 2A13, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 2F1, 2J2, 2R1, 2S1, 2U1, and 2W1; CYP11A1 has 6 paralogs including CYP11B1, 11B2, 24A1, 27A1, 27B1, and 27C1; CYP51A1 has only three paralogs: CYP26A1, 26B1, and 26C1; while CYP20A1 has no paralog. The majority of human CYPs are well conserved from plants, amphibians, fishes, or mammals to humans due to their important functions in physiology and xenobiotic disposition. The data from different approaches are also cross-validated and validated when experimental data are available. These findings facilitate our understanding of the evolutionary relationships and functional implications of the human CYP superfamily in drug discovery.
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Affiliation(s)
- Shu-Ting Pan
- Department of Oral and Maxillofacial Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330003, China.
| | - Danfeng Xue
- Department of Oral and Maxillofacial Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330003, China.
| | - Zhi-Ling Li
- Department of Pharmacy, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China.
| | - Zhi-Wei Zhou
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA.
| | - Zhi-Xu He
- Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center & Sino-US Joint Laboratory for Medical Sciences, Guizhou Medical University, Guiyang 550004, China.
| | - Yinxue Yang
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan 750004, China.
| | - Tianxin Yang
- Department of Internal Medicine, University of Utah and Salt Lake Veterans Affairs Medical Center, Salt Lake City, UT 84132, USA.
| | - Jia-Xuan Qiu
- Department of Oral and Maxillofacial Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330003, China.
| | - Shu-Feng Zhou
- Department of Chemical and Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian, China.
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Mundy N, Stapley J, Bennison C, Tucker R, Twyman H, Kim KW, Burke T, Birkhead T, Andersson S, Slate J. Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster. Curr Biol 2016; 26:1435-40. [DOI: 10.1016/j.cub.2016.04.047] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/18/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
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21
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Cyp2aa9 regulates haematopoietic stem cell development in zebrafish. Sci Rep 2016; 6:26608. [PMID: 27197559 PMCID: PMC4873737 DOI: 10.1038/srep26608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/05/2016] [Indexed: 01/08/2023] Open
Abstract
Definitive haematopoiesis occurs during the lifetime of an individual, which continuously replenishes all blood and immune cells. During embryonic development, haematopoietic stem cell (HSC) formation is tightly controlled by growth factors, signalling molecules and transcription factors. But little is known about roles of the cytochrome P450 (CYP) 2 family member in the haematopoiesis. Here we report characterization and functional studies of Cyp2aa9, a novel zebrafish Cyp2 family member. And demonstrate that the cyp2aa9 is required for the HSC formation and homeostasis. Knockdown of cyp2aa9 by antisense morpholino oligos resulted the definitive HSC development is defective and the Wnt/β-catenin activity becomes reduced. The impaired HSC formation caused by cyp2aa9 morpholino can be rescued by administration of PGE2 through the cAMP/PKA pathway. Furthermore, the in vivo PGE2 level decreases in the cyp2aa9 morphants, and none of the PGE2 precursors is able to rescue phenotypes in the Cyp2aa9-deficient embryos. Taken together, these data indicate that Cyp2aa9 is functional in the step of PGE2 synthesis from PGH2, thus promoting Wnt activation and definitive HSC development.
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22
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Lüchmann KH, Clark MS, Bainy ACD, Gilbert JA, Craft JA, Chipman JK, Thorne MAS, Mattos JJ, Siebert MN, Schroeder DC. Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 166:10-20. [PMID: 26186662 DOI: 10.1016/j.aquatox.2015.06.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
The Brazilian oyster Crassostrea brasiliana was challenged to three common environmental contaminants: phenanthrene, diesel fuel water-accommodated fraction (WAF) and domestic sewage. Total RNA was extracted from the gill and digestive gland, and cDNA libraries were sequenced using the 454 FLX platform. The assembled transcriptome resulted in ̃20,000 contigs, which were annotated to produce the first de novo transcriptome for C. brasiliana. Sequences were screened to identify genes potentially involved in the biotransformation of xenobiotics and associated antioxidant defence mechanisms. These gene families included those of the cytochrome P450 (CYP450), 70kDa heat shock, antioxidants, such as glutathione S-transferase, superoxide dismutase, catalase and also multi-drug resistance proteins. Analysis showed that the massive expansion of the CYP450 and HSP70 family due to gene duplication identified in the Crassostrea gigas genome also occurred in C. brasiliana, suggesting these processes form the base of the Crassostrea lineage. Preliminary expression analyses revealed several candidates biomarker genes that were up-regulated during each of the three treatments, suggesting the potential for environmental monitoring.
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Affiliation(s)
- Karim H Lüchmann
- Fishery Engineering Department, Santa Catarina State University, Laguna, Brazil.
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK.
| | - Afonso C D Bainy
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis, Brazil.
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, Argonne, USA; Department of Ecology and Evolution, University of Chicago, Chicago, USA; Marine Biological Laboratory, Woods Hole, USA; College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
| | - John A Craft
- Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, UK.
| | - J Kevin Chipman
- School of Biological Sciences, The University of Birmingham, Birmingham, UK.
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK.
| | - Jacó J Mattos
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis, Brazil.
| | - Marília N Siebert
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis, Brazil.
| | - Declan C Schroeder
- Marine Biological Association of the United Kingdom (MBA), Plymouth, UK.
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23
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Luoga W, Mansur F, Lowe A, Duce IR, Buttle DJ, Behnke JM. Factors affecting the anthelmintic efficacy of papaya latex in vivo: host sex and intensity of infection. Parasitol Res 2015; 114:2535-41. [PMID: 25855350 DOI: 10.1007/s00436-015-4456-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/24/2015] [Indexed: 01/09/2023]
Abstract
The development of plant-derived cysteine proteinases, such as those in papaya latex, as novel anthelmintics requires that the variables affecting efficacy be fully evaluated. Here, we conducted two experiments, the first to test for any effect of host sex and the second to determine whether the intensity of the worm burden carried by mice would influence efficacy. In both experiments, we used the standard C3H mouse reference strain in which papaya latex supernatant (PLS) consistently shows >80 % reduction in Heligmosomoides bakeri worm burdens, but to broaden the perspective, we also included for comparison mice of other strains that are known to respond more poorly to treatment with papaya latex. Our results confirmed that there is a strong genetic influence affecting efficacy of PLS in removing adult worm burdens. However, there was no effect of host sex on efficacy (C3H and NIH) and no effect of infection intensity (C3H and BALB/c). These results offer optimism that plant-derived cysteine proteinases (CPs), such as these from papaya latex, can function as effective anthelmintics, with neither host sex nor infection intensity presenting further hurdles to impede their development for future medicinal and veterinary usage.
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Affiliation(s)
- Wenceslaus Luoga
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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24
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Lüchmann KH, Dafre AL, Trevisan R, Craft JA, Meng X, Mattos JJ, Zacchi FL, Dorrington TS, Schroeder DC, Bainy ACD. A light in the darkness: new biotransformation genes, antioxidant parameters and tissue-specific responses in oysters exposed to phenanthrene. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 152:324-334. [PMID: 24813265 DOI: 10.1016/j.aquatox.2014.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/15/2014] [Accepted: 04/16/2014] [Indexed: 06/03/2023]
Abstract
Phenanthrene (PHE), a major component of crude oil, is one of the most abundant polycyclic aromatic hydrocarbons (PAHs) in aquatic ecosystems, and is readily bioavailable to marine organisms. Understanding the toxicity of PAHs in animals requires knowledge of the systems for xenobiotic biotransformation and antioxidant defence and these are poorly understood in bivalves. We report, for the first time, new transcripts and tissue-specific transcription in gill and digestive gland from the oyster Crassostrea brasiliana following 24h exposure to 100 and 1000μgL(-1) PHE, a model PAH. Six new cytochrome P450 (CYP) and four new glutathione S-transferase (GST) genes were analysed by means of quantitative reverse transcription PCR (qRT-PCR). Different antioxidant endpoints, including both enzymatic and non-enzymatic parameters, were assessed as potential biomarkers of oxidative stress. GST activity was measured as an indicator of phase II biotransformation. Rapid clearance of PHE was associated with upregulation of both phase I and II genes, with more pronounced effects in the gill at 1000μgL(-1) PHE. After 24h of exposure, PHE also caused impairment of the antioxidant system, decreasing non-protein thiols and glutathione levels. On the other hand, no change in antioxidant enzymes was observed. PHE treatment (100μgL(-1)) significantly decreased GST activity in the gill of exposed oysters. Both CYP and GST were transcribed in a tissue-specific manner, reflecting the importance of the gill in the detoxification of PAHs. Likewise, the antioxidant parameters followed a similar pattern. The data provide strong evidence that these genes play key roles in C. brasiliana biotransformation of PHE and highlight the importance of gill in xenobiotic metabolism.
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Affiliation(s)
- Karim H Lüchmann
- Fishery Engineering Department, Santa Catarina State University, Laguna 88790-000, Brazil.
| | - Alcir L Dafre
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Rafael Trevisan
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - John A Craft
- Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
| | - Xiang Meng
- Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
| | - Jacó J Mattos
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Flávia L Zacchi
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Tarquin S Dorrington
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Declan C Schroeder
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth PL1 2PB, United Kingdom
| | - Afonso C D Bainy
- Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
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25
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Avian cytochrome P450 (CYP) 1-3 family genes: isoforms, evolutionary relationships, and mRNA expression in chicken liver. PLoS One 2013; 8:e75689. [PMID: 24098714 PMCID: PMC3786927 DOI: 10.1371/journal.pone.0075689] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 08/18/2013] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450 (CYP) of chicken and other avian species have been studied primarily with microsomes or characterized by cloning and protein expression. However, the overall existing isoforms in avian CYP1-3 families or dominant isoforms in avian xenobiotic metabolism have not yet been elucidated. In this study, we aimed to clarify and classify all of the existing isoforms of CYP1-3 in avian species using available genome assemblies for chicken, zebra finch, and turkey. Furthermore, we performed qRT-PCR assay to identify dominant CYP genes in chicken liver. Our results suggested that avian xenobiotic-metabolizing CYP genes have undergone unique evolution such as CYP2C and CYP3A genes, which have undergone avian-specific gene duplications. qRT-PCR experiments showed that CYP2C45 was the most highly expressed isoform in chicken liver, while CYP2C23b was the most highly induced gene by phenobarbital. Considering together with the result of further enzymatic characterization, CYP2C45 may have a dominant role in chicken xenobiotic metabolism due to the constitutive high expression levels, while CYP2C23a and CYP2C23b can be greatly induced by chicken xenobiotic receptor (CXR) activators. These findings will provide not only novel insights into avian xenobiotic metabolism, but also a basis for the further characterization of each CYP gene.
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26
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Kubota A, Bainy ACD, Woodin BR, Goldstone JV, Stegeman JJ. The cytochrome P450 2AA gene cluster in zebrafish (Danio rerio): expression of CYP2AA1 and CYP2AA2 and response to phenobarbital-type inducers. Toxicol Appl Pharmacol 2013; 272:172-9. [PMID: 23726801 DOI: 10.1016/j.taap.2013.05.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/15/2013] [Accepted: 05/18/2013] [Indexed: 11/17/2022]
Abstract
The cytochrome P450 (CYP) 2 gene family is the largest and most diverse CYP gene family in vertebrates. In zebrafish, we have identified 10 genes in a new subfamily, CYP2AA, which does not show orthology to any human or other mammalian CYP genes. Here we report evolutionary and structural relationships of the 10 CYP2AA genes and expression of the first two genes, CYP2AA1 and CYP2AA2. Parsimony reconstruction of the tandem duplication pattern for the CYP2AA cluster suggests that CYP2AA1, CYP2AA2 and CYP2AA3 likely arose in the earlier duplication events and thus are most diverged in function from the other CYP2AAs. On the other hand, CYP2AA8 and CYP2AA9 are genes that arose in the latest duplication event, implying functional similarity between these two CYPs. A molecular model of CYP2AA1 showing the sequence conservation across the CYP2AA cluster reveals that the regions with the highest variability within the cluster map onto CYP2AA1 near the substrate access channels, suggesting differing substrate specificities. Zebrafish CYP2AA1 transcript was expressed predominantly in the intestine, while CYP2AA2 was most highly expressed in the kidney, suggesting differing roles in physiology. In the liver CYP2AA2 expression but not that of CYP2AA1, was increased by 1,4-bis [2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP) and, to a lesser extent, by phenobarbital (PB). In contrast, pregnenolone 16α-carbonitrile (PCN) increased CYP2AA1 expression, but not CYP2AA2 in the liver. The results identify a CYP2 subfamily in zebrafish that includes genes apparently induced by PB-type chemicals and PXR agonists, the first concrete in vivo evidence for a PB-type response in fish.
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Affiliation(s)
- Akira Kubota
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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27
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Kawai YK, Watanabe KP, Ishii A, Ohnuma A, Sawa H, Ikenaka Y, Ishizuka M. De novo sequence analysis of cytochrome P450 1-3 genes expressed in ostrich liver with highest expression of CYP2G19. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2013; 8:201-8. [PMID: 23732888 DOI: 10.1016/j.cbd.2013.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/05/2013] [Accepted: 05/07/2013] [Indexed: 01/06/2023]
Abstract
The cytochrome P450 (CYP) 1-3 families are involved in xenobiotic metabolism, and are expressed primarily in the liver. Ostriches (Struthio camelus) are members of Palaeognathae with the earliest divergence from other bird lineages. An understanding of genes coding for ostrich xenobiotic metabolizing enzyme contributes to knowledge regarding the xenobiotic metabolisms of other Palaeognathae birds. We investigated CYP1-3 genes expressed in female ostrich liver using a next-generation sequencer. We detected 10 CYP genes: CYP1A5, CYP2C23, CYP2C45, CYP2D49, CYP2G19, CYP2W2, CYP2AC1, CYP2AC2, CYP2AF1, and CYP3A37. We compared the gene expression levels of CYP1A5, CYP2C23, CYP2C45, CYP2D49, CYP2G19, CYP2AF1, and CYP3A37 in ostrich liver and determined that CYP2G19 exhibited the highest expression level. The mRNA expression level of CYP2G19 was approximately 2-10 times higher than those of other CYP genes. The other CYP genes displayed similar expression levels. Our results suggest that CYP2G19, which has not been a focus of previous bird studies, has an important role in ostrich xenobiotic metabolism.
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Affiliation(s)
- Yusuke K Kawai
- Laboratory of Toxicology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
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28
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Miksys S, Cappendijk SLT, Perry WM, Zhao B, Tyndale RF. Nicotine kinetics in zebra finches in vivo and in vitro. Drug Metab Dispos 2013; 41:1240-6. [PMID: 23530019 DOI: 10.1124/dmd.112.050765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nicotine enhances cognitive performance, and in the zebra finch (Taeniopygia guttata), which is a well-established model of cognition, the effects of nicotine on song production have been reported. Nicotine and cotinine plasma levels were assessed in vivo after subcutaneous injection of 0.18 mg/kg nicotine, a dose that elicits changes in song production. The half-life of nicotine elimination was 33 minutes, and levels were undetectable by 4 hours. Average plasma nicotine over 2 hours was 32 ng/ml, similar to levels seen in human smokers and rat models of nicotine behavior. Nicotine brain levels were 30 and 14 ng/g 1 and 2 hours after treatment. To understand the potential for drug interactions and the regulation of nicotine metabolism in zebra finches, we characterized in vitro nicotine metabolism and the hepatic enzyme involved. In humans, cytochrome P450 2A6 metabolizes nicotine to cotinine, and CYP2A-like activity and protein have been reported in some birds. Zebra finch liver microsomes metabolized nicotine and bupropion (a CYP2B substrate) but not coumarin (a CYP2A substrate). Nicotine was metabolized to cotinine with a Michaelis-Menten constant (K(m)) of 96 µM and a V(max) of 56 pmol/min per milligram. Nicotine and bupropion metabolism was inhibited by C-8-xanthate (a specific CYP2B inhibitor) but not by CYP2A-specific inhibitors, and hepatic levels of CYP2B-like but not CYP2A-like proteins correlated with nicotine (r = 0.52; P = 0.04) and bupropion metabolism (r = 0.81; P < 0.001), suggesting CYP2B-mediation of nicotine metabolism as seen in rats. These results will facilitate further investigation of nicotine's effects in zebra finches.
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Affiliation(s)
- Sharon Miksys
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Departments of Pharmacology and Toxicology and Psychiatry, University of Toronto, Toronto, Canada
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29
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Nelson DR, Goldstone JV, Stegeman JJ. The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120474. [PMID: 23297357 DOI: 10.1098/rstb.2012.0474] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The neighbourhoods of cytochrome P450 (CYP) genes in deuterostome genomes, as well as those of the cnidarians Nematostella vectensis and Acropora digitifera and the placozoan Trichoplax adhaerens were examined to find clues concerning the evolution of CYP genes in animals. CYP genes created by the 2R whole genome duplications in chordates have been identified. Both microsynteny and macrosynteny were used to identify genes that coexisted near CYP genes in the animal ancestor. We show that all 11 CYP clans began in a common gene environment. The evidence implies the existence of a single locus, which we term the 'cytochrome P450 genesis locus', where one progenitor CYP gene duplicated to create a tandem set of genes that were precursors of the 11 animal CYP clans: CYP Clans 2, 3, 4, 7, 19, 20, 26, 46, 51, 74 and mitochondrial. These early CYP genes existed side by side before the origin of cnidarians, possibly with a few additional genes interspersed. The Hox gene cluster, WNT genes, an NK gene cluster and at least one ARF gene were close neighbours to this original CYP locus. According to this evolutionary scenario, the CYP74 clan originated from animals and not from land plants nor from a common ancestor of plants and animals. The CYP7 and CYP19 families that are chordate-specific belong to CYP clans that seem to have originated in the CYP genesis locus as well, even though this requires many gene losses to explain their current distribution. The approach to uncovering the CYP genesis locus overcomes confounding effects because of gene conversion, sequence divergence, gene birth and death, and opens the way to understanding the biodiversity of CYP genes, families and subfamilies, which in animals has been obscured by more than 600 Myr of evolution.
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Affiliation(s)
- David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue Suite G01, Memphis, TN 38163, USA.
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30
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Moriya N, Kataoka H, Fujino H, Nishikawa JI, Kugawa F. Effect of Lipopolysaccharide on the Xenobiotic-Induced Expression and Activity of Hepatic Cytochrome P450 in Mice. Biol Pharm Bull 2012; 35:473-80. [DOI: 10.1248/bpb.35.473] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Nozomu Moriya
- Department of Biopharmaceutics, Hyogo University of Health Sciences
| | - Hiromi Kataoka
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women’s University
| | - Hideki Fujino
- Department of Biopharmaceutics, Hyogo University of Health Sciences
| | - Jun-ichi Nishikawa
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women’s University
| | - Fumihiko Kugawa
- Department of Biopharmaceutics, Hyogo University of Health Sciences
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31
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Yasukochi Y, Satta Y. Evolution of the CYP2D gene cluster in humans and four non-human primates. Genes Genet Syst 2011; 86:109-16. [PMID: 21670550 DOI: 10.1266/ggs.86.109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The human cytochrome P450 2D6 (CYP2D6) is a primary enzyme involved in the metabolism of about 25% of commonly used therapeutic drugs. CYP2D6 belongs to the CYP2D subfamily, a gene cluster located on chromosome 22, which comprises the CYP2D6 gene and pseudogenes CYP2D7P and CYP2D8P. Although the chemical and physiological properties of CYP2D6 have been extensively studied, there has been no study to date on molecular evolution of the CYP2D subfamily in the human genome. Such knowledge could greatly contribute to the understanding of drug metabolism in humans because it makes us to know when and how the current metabolic system has been constructed. The knowledge moreover can be useful to find differences in exogenous substrates in a particular metabolism between human and other animals such as experimental animals. Here, we conducted a preliminary study to investigate the evolution and gene organization of the CYP2D subfamily, focused on humans and four non-human primates (chimpanzees, orangutans, rhesus monkeys, and common marmosets). Our results indicate that CYP2D7P has been duplicated from CYP2D6 before the divergence between humans and great apes, whereas CYP2D6 and CYP2D8P have been already present in the stem lineages of New World monkeys and Catarrhini. Furthermore, the origin of the CYP2D subfamily in the human genome can be traced back to before the divergence between amniotes and amphibians. Our analyses also show that reported chimeric sequences of the CYP2D6 and CYP2D7 genes in the chimpanzee genome appear to be exchanged in its genome database.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Evolutionary Studies of Biosystems, the Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa 240-0193, Japan.
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