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Zhao Y, Su C, He B, Nie R, Wang Y, Ma J, Song J, Yang Q, Hao J. Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome. Nat Commun 2023; 14:8190. [PMID: 38081828 PMCID: PMC10713551 DOI: 10.1038/s41467-023-44023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.
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Affiliation(s)
- Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Ruie Nie
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Junye Ma
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jingyu Song
- College of Animal Science, Shandong Agricultural University, Taian, 271000, China
| | - Qun Yang
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China.
- Nanjing College, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
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2
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Peláez JN, Gloss AD, Goldman-Huertas B, Kim B, Lapoint RT, Pimentel-Solorio G, Verster KI, Aguilar JM, Nelson Dittrich AC, Singhal M, Suzuki HC, Matsunaga T, Armstrong EE, Charboneau JLM, Groen SC, Hembry DH, Ochoa CJ, O’Connor TK, Prost S, Zaaijer S, Nabity PD, Wang J, Rodas E, Liang I, Whiteman NK. Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. G3 (BETHESDA, MD.) 2023; 13:jkad133. [PMID: 37317982 PMCID: PMC10411586 DOI: 10.1093/g3journal/jkad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/19/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.
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Affiliation(s)
- Julianne N Peláez
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Benjamin Goldman-Huertas
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Richard T Lapoint
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Kirsten I Verster
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Anna C Nelson Dittrich
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Malvika Singhal
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Hiromu C Suzuki
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Simon C Groen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Department of Nematology, University of California Riverside, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - David H Hembry
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology, University of Texas Permian Basin, Odessa, TX 79762, USA
| | - Christopher J Ochoa
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy K O’Connor
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Sophie Zaaijer
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Jacobs Institute, Cornell Tech, New York, NY 10044, USA
- FIND Genomics, New York, NY 10044, USA
| | - Paul D Nabity
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Jiarui Wang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - Esteban Rodas
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Irene Liang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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3
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Aioub AAA, Hashem AS, El-Sappah AH, El-Harairy A, Abdel-Hady AAA, Al-Shuraym LA, Sayed S, Huang Q, Abdel-Wahab SIZ. Identification and Characterization of Glutathione S-transferase Genes in Spodoptera frugiperda (Lepidoptera: Noctuidae) under Insecticides Stress. TOXICS 2023; 11:542. [PMID: 37368642 DOI: 10.3390/toxics11060542] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Insect glutathione S-transferases (GSTs) serve critical roles in insecticides and other forms of xenobiotic chemical detoxification. The fall armyworm, Spodoptera frugiperda (J. E. Smith), is a major agricultural pest in several countries, especially Egypt. This is the first study to identify and characterize GST genes in S. frugiperda under insecticidal stress. The present work evaluated the toxicity of emamectin benzoate (EBZ) and chlorantraniliprole (CHP) against the third-instar larvae of S. frugiperda using the leaf disk method. The LC50 values of EBZ and CHP were 0.029 and 1.250 mg/L after 24 h of exposure. Moreover, we identified 31 GST genes, including 28 cytosolic and 3 microsomal SfGSTs from a transcriptome analysis and the genome data of S. frugiperda. Depending on the phylogenetic analysis, sfGSTs were divided into six classes (delta, epsilon, omega, sigma, theta, and microsomal). Furthermore, we investigated the mRNA levels of 28 GST genes using qRT-PCR under EBZ and CHP stress in the third-instar larvae of S. frugiperda. Interestingly, SfGSTe10 and SfGSTe13 stood out with the highest expression after the EBZ and CHP treatments. Finally, a molecular docking model was constructed between EBZ and CHP using the most upregulated genes (SfGSTe10 and SfGSTe13) and the least upregulated genes (SfGSTs1 and SfGSTe2) of S. frugiperda larvae. The molecular docking study showed EBZ and CHP have a high binding affinity with SfGSTe10, with docking energy values of -24.41 and -26.72 kcal/mol, respectively, and sfGSTe13, with docking energy values of -26.85 and -26.78 kcal/mol, respectively. Our findings are important for understanding the role of GSTs in S. frugiperda regarding detoxification processes for EBZ and CHP.
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Affiliation(s)
- Ahmed A A Aioub
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Ahmed S Hashem
- Stored Product Pests Research Department, Plant Protection Research Institute, Agricultural Research Center, Sakha, Kafr El-Sheikh 33717, Egypt
| | - Ahmed H El-Sappah
- Department of Genetics, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, China
| | - Amged El-Harairy
- Unit of Entomology, Plant Protection Department, Desert Research Center, Mathaf El-Matariya St. 1, El-Matariya, Cairo 11753, Egypt
- Department of Integrated Pest Management, Plant Protection Institute, Hungarian University of Agriculture and Life Sciences, Páter Károly utca 1, 2103 Gödöllő, Hungary
| | - Amira A A Abdel-Hady
- Economic Entomology Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
| | - Laila A Al-Shuraym
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Samy Sayed
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
- Department of Science and Technology, University College-Ranyah, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Qiulan Huang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, China
| | - Sarah I Z Abdel-Wahab
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
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4
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Hartline DK, Cieslak MC, Castelfranco AM, Lieberman B, Roncalli V, Lenz PH. De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Sci Data 2023; 10:242. [PMID: 37105953 PMCID: PMC10140051 DOI: 10.1038/s41597-023-02130-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. 'Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study's primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive.
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Affiliation(s)
- Daniel K Hartline
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Matthew C Cieslak
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Ann M Castelfranco
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Brandon Lieberman
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Vittoria Roncalli
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Naples, Italy.
| | - Petra H Lenz
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
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5
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Sun X, Liu W, Peng Y, Meng L, Zhang J, Pan Y, Wang D, Zhu J, Wang C, Yan C. Genome-wide analyses of Glutathione S-transferase gene family and expression profiling under deltamethrin exposure in non-biting midge Propsilocerus akamusi. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101081. [PMID: 37150092 DOI: 10.1016/j.cbd.2023.101081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023]
Abstract
Glutathione S-transferases (GSTs) are major enzymes in detoxification phase II, and have been functioned in resistance to various insecticides or oxidative stress. Herein, we selected the non-biting midge, Propsilocerus akamusi, widespread in Asian aquatic ecosystems, to uncover the gene location, structure, and phylogenetics relationship of GSTs at genome scale first time. Thirty-three cytosolic and four microsomal GST genes were identified and located on the four chromosomes. The cytosolic GSTs involved in the eight subclasses and five GST genes were unclassified. The expansion of GST genes in P. akamusi experienced duplication events on the delta, theta, xi, iota, and unclassified subclasses. The RNA-Seq analyses and RT-qPCR validation showed that the expression of PaGSTt2 gene is significantly elevated, with deltamethrin concentration increasing. The tertiary structure of PaGSTt2 enzyme was reconstructed, which was different from the other theta gene in the active site. In addition, the GST genes of six chironomids were first described based on the assembled genomes to explore the difference of those in the adaptation to kinds of environments. The GST frame for P. akmusi and its expression profiles provide valuable resources to understand their role in insecticide resistance of this species, as well as those of other biting midges.
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Affiliation(s)
- Xiaoya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Wenbin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Yuanyuan Peng
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Lingfei Meng
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Junyu Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Yahan Pan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Deyu Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Junhao Zhu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Chengyan Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Chuncai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China.
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Zhang Y, Cao KX, Niu QJ, Deng J, Zhao L, Khalil MM, Karrow NA, Kuča K, Sun LH. Alpha-class glutathione S-transferases involved in the detoxification of aflatoxin B 1 in ducklings. Food Chem Toxicol 2023; 174:113682. [PMID: 36813151 DOI: 10.1016/j.fct.2023.113682] [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: 01/12/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
The objective of this study was to identify the key glutathione S-transferase (GST) isozymes involved in the detoxification of Aflatoxin B1 (AFB1) in ducks' primary hepatocytes. The full-length cDNA encoding the 10 GST isozymes (GST, GST3, GSTM3, MGST1, MGST2, MGST3, GSTK1, GSTT1, GSTO1 and GSTZ1) were isolated/synthesized from ducks' liver and cloned into the pcDNA3.1(+) vector. The results showed that pcDNA3.1(+)-GSTs plasmids were successfully transferred into the ducks' primary hepatocytes and the mRNA of the 10 GST isozymes were overexpressed by 1.9-3274.7 times. Compared to the control, 75 μg/L (IC30) or 150 μg/L (IC50) AFB1 treatment reduced the cell viability by 30.0-50.0% and increased the LDH activity by 19.8-58.2% in the ducks' primary hepatocytes. Notably, the AFB1-induced changes in cell viability and LDH activity were mitigated by overexpression of GST and GST3. Compared to the cells treated with AFB1, exo-AFB1-8,9-epoxide (AFBO)-GSH, as the major detoxified product of AFB1, was increased in the cells overexpression of GST and GST3. Moreover, the sequences, phylogenetic and domain analysis revealed that the GST and GST3 were orthologous to Meleagris gallopavo GSTA3 and GSTA4. In conclusion, this study found that the ducks' GST and GST3 were orthologous to Meleagris gallopavo GSTA3 and GSTA4, which were involved in the detoxification of AFB1 in ducks' primary hepatocytes.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Newhope Liuhe Co. Ltd., Beijing, 100102, China
| | - Ke-Xin Cao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qin-Jian Niu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiang Deng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mahmoud Mohamed Khalil
- Monogastric Research Center, School of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | | | - Kamil Kuča
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic
| | - Lv-Hui Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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7
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Pelaez JN, Gloss AD, Goldman-Huertas B, Kim B, Lapoint RT, Pimentel-Solorio G, Verster KI, Aguilar JM, Dittrich ACN, Singhal M, Suzuki HC, Matsunaga T, Armstrong EE, Charboneau JL, Groen SC, Hembry DH, Ochoa CJ, O’Connor TK, Prost S, Zaaijer S, Nabity PD, Wang J, Rodas E, Liang I, Whiteman NK. Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532987. [PMID: 36993186 PMCID: PMC10055167 DOI: 10.1101/2023.03.16.532987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genetic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families - genes directly mediating interactions with plant chemical defenses - underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many lineages are ancient (>150 million years ago [mya]), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several non-herbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza have among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on plants (bitter or electrophilic phytotoxins) or their ancestral diet (yeast and fruit volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight strong gene candidates that have also been linked to other dietary transitions in Drosophila .
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Affiliation(s)
- Julianne N. Pelaez
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Andrew D. Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Benjamin Goldman-Huertas
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Richard T. Lapoint
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- National Center for Biotechnology Information, Bethesda, MD 20894, USA
| | | | - Kirsten I. Verster
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Jessica M. Aguilar
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Anna C. Nelson Dittrich
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Boyce Thompson Institute, Ithaca NY 14853 USA
| | - Malvika Singhal
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry & Biochemistry, University of Oregon, OR, CA 97403, USA
| | - Hiromu C. Suzuki
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | | | - Joseph L.M. Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Simon C. Groen
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Department of Nematology, University of California-Riverside, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - David H. Hembry
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology, University of Texas Permian Basin, Odessa, TX 79762, USA
| | - Christopher J. Ochoa
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy K. O’Connor
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Sophie Zaaijer
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Jacobs Institute, Cornell Tech, New York, NY 10044, USA
- FIND Genomics, New York, NY 10044, USA
| | - Paul D. Nabity
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
| | - Jiarui Wang
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - Esteban Rodas
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Irene Liang
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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8
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Yan S, Li N, Guo Y, Chen Y, Ji C, Yin M, Shen J, Zhang J. Chronic exposure to the star polycation (SPc) nanocarrier in the larval stage adversely impairs life history traits in Drosophila melanogaster. J Nanobiotechnology 2022; 20:515. [PMID: 36482441 PMCID: PMC9730587 DOI: 10.1186/s12951-022-01705-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Nanomaterials are widely used as pesticide adjuvants to increase pesticide efficiency and minimize environmental pollution. But it is increasingly recognized that nanocarrier is a double-edged sword, as nanoparticles are emerging as new environmental pollutants. This study aimed to determine the biotoxicity of a widely applied star polycation (SPc) nanocarrier using Drosophila melanogaster, the fruit fly, as an in vivo model. RESULTS The lethal concentration 50 (LC50) value of SPc was identified as 2.14 g/L toward third-instar larvae and 26.33 g/L for adults. Chronic exposure to a sub lethal concentration of SPc (1 g/L) in the larval stage showed long-lasting adverse effects on key life history traits. Exposure to SPc at larval stage adversely impacted the lifespan, fertility, climbing ability as well as stresses resistance of emerged adults. RNA-sequencing analysis found that SPc resulted in aberrant expression of genes involved in metabolism, innate immunity, stress response and hormone production in the larvae. Orally administrated SPc nanoparticles were mainly accumulated in intestine cells, while systemic responses were observed. CONCLUSIONS These findings indicate that SPc nanoparticles are hazardous to fruit flies at multiple levels, which could help us to develop guidelines for further large-scale application.
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Affiliation(s)
- Shuo Yan
- grid.22935.3f0000 0004 0530 8290Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193 China
| | - Na Li
- grid.22935.3f0000 0004 0530 8290Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193 China
| | - Yuankang Guo
- grid.22935.3f0000 0004 0530 8290Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193 China
| | - Yao Chen
- grid.22935.3f0000 0004 0530 8290Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193 China
| | - Chendong Ji
- grid.48166.3d0000 0000 9931 8406State Key Lab of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing, China
| | - Meizhen Yin
- grid.48166.3d0000 0000 9931 8406State Key Lab of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing, China
| | - Jie Shen
- grid.22935.3f0000 0004 0530 8290Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193 China
| | - Junzheng Zhang
- grid.22935.3f0000 0004 0530 8290Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193 China
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9
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Bailey E, Field L, Rawlings C, King R, Mohareb F, Pak KH, Hughes D, Williamson M, Ganko E, Buer B, Nauen R. A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution. BMC Genomics 2022; 23:198. [PMID: 35279098 PMCID: PMC8917705 DOI: 10.1186/s12864-022-08436-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs). METHODS AND FINDINGS In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species. CONCLUSION AND SIGNIFICANCE This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.
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Affiliation(s)
- Emma Bailey
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK.
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK.
| | - Linda Field
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Christopher Rawlings
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Rob King
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Fady Mohareb
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | - Keywan-Hassani Pak
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - David Hughes
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Martin Williamson
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Eric Ganko
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA
| | - Benjamin Buer
- Bayer AG, Crop Science Division, R&D, Monheim, Germany
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Monheim, Germany
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10
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Brown B, Mitra S, Roach FD, Vasudevan D, Ryoo HD. The transcription factor Xrp1 is required for PERK-mediated antioxidant gene induction in Drosophila. eLife 2021; 10:74047. [PMID: 34605405 PMCID: PMC8514241 DOI: 10.7554/elife.74047] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
PERK is an endoplasmic reticulum (ER) transmembrane sensor that phosphorylates eIF2α to initiate the Unfolded Protein Response (UPR). eIF2α phosphorylation promotes stress-responsive gene expression most notably through the transcription factor ATF4 that contains a regulatory 5’ leader. Possible PERK effectors other than ATF4 remain poorly understood. Here, we report that the bZIP transcription factor Xrp1 is required for ATF4-independent PERK signaling. Cell-type-specific gene expression profiling in Drosophila indicated that delta-family glutathione-S-transferases (gstD) are prominently induced by the UPR-activating transgene Rh1G69D. Perk was necessary and sufficient for such gstD induction, but ATF4 was not required. Instead, Perk and other regulators of eIF2α phosphorylation regulated Xrp1 protein levels to induce gstDs. The Xrp1 5’ leader has a conserved upstream Open Reading Frame (uORF) analogous to those that regulate ATF4 translation. The gstD-GFP reporter induction required putative Xrp1 binding sites. These results indicate that antioxidant genes are highly induced by a previously unrecognized UPR signaling axis consisting of PERK and Xrp1.
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Affiliation(s)
- Brian Brown
- NYU Grossman School of Medicine, New York, United States
| | - Sahana Mitra
- NYU Grossman School of Medicine, New York, United States
| | | | | | - Hyung Don Ryoo
- NYU Grossman School of Medicine, New York, United States
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11
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Ren Y, MacPhillamy C, To TH, Smith TPL, Williams JL, Low WY. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics 2021; 113:3599-3609. [PMID: 34455036 DOI: 10.1016/j.ygeno.2021.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
Abstract
River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding.
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Affiliation(s)
- Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Thu-Hien To
- Norwegian University of Life Sciences: NMBU, Universitetstunet 3, 1430 Ås, Norway
| | | | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia; Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
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12
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Wang YJ, Wang HL, Wang XW, Liu SS. Transcriptome analysis and comparison reveal divergence between the Mediterranean and the greenhouse whiteflies. PLoS One 2020; 15:e0237744. [PMID: 32841246 PMCID: PMC7447059 DOI: 10.1371/journal.pone.0237744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/31/2020] [Indexed: 12/24/2022] Open
Abstract
Both the Mediterranean (MED) species of the Bemisia tabaci whitefly complex and the greenhouse whitefly (Trialeurodes vaporariorum, TV) are important agricultural pests. The two species of whiteflies differ in many aspects such as morphology, geographical distribution, host plant range, plant virus transmission, and resistance to insecticides. However, the molecular basis underlying their differences remains largely unknown. In this study, we analyzed the genetic divergences between the transcriptomes of MED and TV. In total, 2,944 pairs of orthologous genes were identified. The average identity of amino acid sequences between the two species is 93.6%. The average nonsynonymous (Ka) and synonymous (Ks) substitution rates and the ratio of Ka/Ks of the orthologous genes are 0.0389, 2.23 and 0.0204, respectively. The low average Ka/Ks ratio indicates that orthologous genes tend to be under strong purified selection. The most divergent gene classes are related to the metabolisms of xenobiotics, cofactors, vitamins and amino acids, and this divergence may underlie the different biological characteristics between the two species of whiteflies. Genes of differential expression between the two species are enriched in carbohydrate metabolism and regulation of autophagy. These findings provide molecular clues to uncover the biological and molecular differences between the two species of whiteflies.
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Affiliation(s)
- Yu-Jun Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hua-Ling Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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13
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Scanlan JL, Gledhill-Smith RS, Battlay P, Robin C. Genomic and transcriptomic analyses in Drosophila suggest that the ecdysteroid kinase-like (EcKL) gene family encodes the 'detoxification-by-phosphorylation' enzymes of insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:103429. [PMID: 32540344 DOI: 10.1016/j.ibmb.2020.103429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/25/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a phase II detoxification reaction that, among animals, occurs near exclusively in insects, but the enzymes responsible have never been cloned or otherwise identified. We propose the hypothesis that members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene family in 12 species of Drosophila and explored their evolution within the genus. Many ancestral EcKL clades are evolutionarily unstable and have experienced repeated gene gain and loss events, while others are conserved as single-copy orthologs. Leveraging multiple published gene expression datasets from D. melanogaster, and using the cytochrome P450s-a classical detoxification family-as a test case, we demonstrate relationships between xenobiotic induction, detoxification tissue-enriched expression and evolutionary instability in the EcKLs and the P450s. We devised a systematic method for identifying candidate detoxification genes in large gene families that is concordant with experimentally determined functions of P450 genes in D. melanogaster. Applying this method to the EcKLs suggested a significant proportion of these genes play roles in detoxification, and that the EcKLs may constitute a detoxification gene family in insects. Additionally, we estimate that between 11 and 16 uncharacterised D. melanogaster P450s are strong detoxification candidates. Lastly, we also found previously unreported genomic and transcriptomic variation in a number of EcKLs and P450s associated with toxic stress phenotypes using a targeted phenome-wide association study (PheWAS) approach in D. melanogaster, presenting multiple future avenues of research for detoxification genetics in this species.
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Affiliation(s)
- Jack L Scanlan
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Rebecca S Gledhill-Smith
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Paul Battlay
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
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14
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Behavioral and Transcriptional Response to Selection for Olfactory Behavior in Drosophila. G3-GENES GENOMES GENETICS 2020; 10:1283-1296. [PMID: 32024668 PMCID: PMC7144070 DOI: 10.1534/g3.120.401117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The detection, discrimination, and behavioral responses to chemical cues in the environment can have marked effects on organismal survival and reproduction, eliciting attractive or aversive behavior. To gain insight into mechanisms mediating this hedonic valence, we applied thirty generations of divergent artificial selection for Drosophila melanogaster olfactory behavior. We independently selected for positive and negative behavioral responses to two ecologically relevant chemical compounds: 2,3-butanedione and cyclohexanone. We also tested the correlated responses to selection by testing behavioral responses to other odorants and life history traits. Measurements of behavioral responses of the selected lines and unselected controls to additional odorants showed that the mechanisms underlying responses to these odorants are, in some cases, differentially affected by selection regime and generalization of the response to other odorants was only detected in the 2,3-butanedione selection lines. Food consumption and lifespan varied with selection regime and, at times, sex. An analysis of gene expression of both selection regimes identified multiple differentially expressed genes. New genes and genes previously identified in mediating olfactory behavior were identified. In particular, we found functional enrichment of several gene ontology terms, including cell-cell adhesion and sulfur compound metabolic process, the latter including genes belonging to the glutathione S-transferase family. These findings highlight a potential role for glutathione S-transferases in the evolution of hedonic valence to ecologically relevant volatile compounds and set the stage for a detailed investigation into mechanisms by which these genes mediate attraction and aversion.
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15
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Aidlin Harari O, Santos-Garcia D, Musseri M, Moshitzky P, Patel M, Visendi P, Seal S, Sertchook R, Malka O, Morin S. Molecular Evolution of the Glutathione S-Transferase Family in the Bemisia tabaci Species Complex. Genome Biol Evol 2020; 12:3857-3872. [PMID: 31971586 PMCID: PMC7058157 DOI: 10.1093/gbe/evaa002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2019] [Indexed: 01/23/2023] Open
Abstract
The glutathione S-transferase (GST) family plays an important role in the adaptation of herbivorous insects to new host plants and other environmental constrains. The family codes for enzymes that neutralize reactive oxygen species and phytotoxins through the conjugation of reduced glutathione. Here, we studied the molecular evolution of the GST family in Bemisia tabaci, a complex of >35 sibling species, differing in their geographic and host ranges. We tested if some enzymes evolved different functionality, by comparing their sequences in six species, representing five of the six major genetic clades in the complex. Comparisons of the nonsynonymous to synonymous substitution ratios detected positive selection events in 11 codons of 5 cytosolic GSTs. Ten of them are located in the periphery of the GST dimer, suggesting a putative involvement in interactions with other proteins. Modeling the tertiary structure of orthologous enzymes, identified additional 19 mutations in 9 GSTs, likely affecting the enzymes' functionality. Most of the mutation events were found in the environmentally responsive classes Delta and Sigma, indicating a slightly different delta/sigma tool box in each species. At a broader genomic perspective, our analyses indicated a significant expansion of the Delta GST class in B. tabaci and a general association between the diet breadth of hemipteran species and their total number of GST genes. We raise the possibility that at least some of the identified changes improve the fitness of the B. tabaci species carrying them, leading to their better adaptation to specific environments.
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Affiliation(s)
- Ofer Aidlin Harari
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Diego Santos-Garcia
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mirit Musseri
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Pnina Moshitzky
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mitulkumar Patel
- Natural Resources Institute, University of Greenwich, Kent, United Kingdom
| | - Paul Visendi
- Natural Resources Institute, University of Greenwich, Kent, United Kingdom
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Kent, United Kingdom
| | | | - Osnat Malka
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
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16
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Contraction of the ROS Scavenging Enzyme Glutathione S-Transferase Gene Family in Cetaceans. G3-GENES GENOMES GENETICS 2019; 9:2303-2315. [PMID: 31092607 PMCID: PMC6643896 DOI: 10.1534/g3.119.400224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genes GSTA1, GSTA4, and GSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans.
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17
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Markow TA. Host use and host shifts in Drosophila. CURRENT OPINION IN INSECT SCIENCE 2019; 31:139-145. [PMID: 31109667 DOI: 10.1016/j.cois.2019.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 05/28/2023]
Abstract
Over a thousand Drosophila species have radiated onto a wide range of feeding and breeding sites. These radiations involve adaptations for locating, accepting, and growing in hosts with highly differing characteristics. In a number of species, owing to the availability of sequenced genomes, particular steps in host specialization and genes that control them, are being identified. Many cases of specialization involve the ability to detoxify some component of the host. Examples include Drosophila sechellia and the octanoic acid in Morinda citrifolia, alpha-amanitin in mycophagous drosophilids, and the alkaloids in cactophilic species. Owing to the known ecologies of many species for which genomes exist, the Drosophila model system provides an unprecedented opportunity to simultaneously examine the genes underlying HOST LOCATION, HOST ACCEPTANCE and HOST USE, the types of selection acting upon them and any coevolutionary interactions among the genes underlying these steps.
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Affiliation(s)
- Therese Ann Markow
- National Laboratory for the Genomics of Biodiversity, CINVESTAV, Irapuato, Mexico; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA.
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18
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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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Mateus RP, Nazario-Yepiz NO, Ibarra-Laclette E, Ramirez Loustalot-Laclette M, Markow TA. Developmental and Transcriptomal Responses to Seasonal Dietary Shifts in the CactophilicDrosophila mojavensisof North America. J Hered 2018; 110:58-67. [DOI: 10.1093/jhered/esy056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Rogerio Pincela Mateus
- Laboratório de Genética e Evolução, Universidade Estadual do Centro-Oeste – UNICENTRO, Guarapuava, Paraná, Brazil
- The Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, México
| | - Nestor O Nazario-Yepiz
- The Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, México
| | | | | | - Therese Ann Markow
- The Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, México
- The Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA
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20
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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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21
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Dual Roles of Glutathione in Ecdysone Biosynthesis and Antioxidant Function During Larval Development in Drosophila. Genetics 2017; 207:1519-1532. [PMID: 29021278 PMCID: PMC5714463 DOI: 10.1534/genetics.117.300391] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/08/2017] [Indexed: 01/08/2023] Open
Abstract
Ecdysteroids, including the biologically active hormone 20-hydroxyecdysone (20E), play essential roles in controlling many developmental and physiological events in insects. Ecdysteroid biosynthesis is achieved by a series of specialized enzymes encoded by the Halloween genes. Recently, a new class of Halloween gene, noppera-bo (nobo), encoding a glutathione S-transferase (GST) in dipteran and lepidopteran species, has been identified and characterized. GSTs are well known to conjugate substrates with the reduced form of glutathione (GSH), a bioactive tripeptide composed of glutamate, cysteine, and glycine. We hypothesized that GSH itself is required for ecdysteroid biosynthesis. However, the role of GSH in steroid hormone biosynthesis has not been examined in any organisms. Here, we report phenotypic analysis of a complete loss-of-function mutant in the γ-glutamylcysteine synthetase catalytic subunit (Gclc) gene in the fruit fly Drosophila melanogaster. Gclc encodes the evolutionarily conserved catalytic component of the enzyme that conjugates glutamate and cysteine in the GSH biosynthesis pathway. Complete Gclc loss-of-function leads to drastic GSH deficiency in the larval body fluid. Gclc mutant animals show a larval-arrest phenotype. Ecdysteroid titer in Gclc mutant larvae decreases, and the larval-arrest phenotype is rescued by oral administration of 20E or cholesterol. Moreover, Gclc mutant animals exhibit abnormal lipid deposition in the prothoracic gland, a steroidogenic organ during larval development. All of these phenotypes are reminiscent to nobo loss-of-function animals. On the other hand, Gclc mutant larvae also exhibit a significant reduction in antioxidant capacity. Consistent with this phenotype, Gclc mutant larvae are more sensitive to oxidative stress response as compared to wild-type. Nevertheless, the ecdysteroid biosynthesis defect in Gclc mutant animals is not associated with loss of antioxidant function. Our data raise the unexpected hypothesis that a primary role of GSH in early D. melanogaster larval development is ecdysteroid biosynthesis, independent from the antioxidant role of GSH.
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22
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Macedo GE, Gomes KK, Rodrigues NR, Martins IK, Wallau GDL, Carvalho NRD, Cruz LCD, Costa Silva DGD, Boligon AA, Franco JL, Posser T. Senecio brasiliensis impairs eclosion rate and induces apoptotic cell death in larvae of Drosophila melanogaster. Comp Biochem Physiol C Toxicol Pharmacol 2017; 198:45-57. [PMID: 28529177 DOI: 10.1016/j.cbpc.2017.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/05/2017] [Accepted: 05/14/2017] [Indexed: 12/31/2022]
Abstract
Senecio brasilienis (Spreng) Less., is a species native from Brazil, popularly known as "Maria mole", and known to induce hepatotoxicity due to its high content of Pyrrolizidine alkaloids. Despite its toxicity, this plant is widely used in Brazilian folk medicine. Considering the antagonizing effects described for S. brasiliensis, we describe here molecular markers involved in the toxicity of hydroalcoholic extract from leaves of S. brasiliensis (HESB) in Drosophila melanogaster. Phytochemical analysis of HESB revealed the presence of phenolic acids and flavonoids. A significant antioxidant potential against ABTS+ and DPPH radical was found in parallel. Ingestion of extract did not alter the survival and locomotor activity of adult flies. However when ingested along the larval developmental phase, the eclosion rate of flies was interrupted at higher concentration of extract. To comprehend this phenomenon several analysis were conducted in larvae. HESB stimulated activity of antioxidant enzymes SOD and GST, and increased GSH/GSSG ratio and ROS production. Additionally, HESB caused a significant decrease of cell viability. The mRNA expression of Nrf2, TrxR, CAT, Drice and Dilp6 were also significantly up-regulated. HESB caused significant decrease on the phosphorylation of MAPKs and AKT. In parallel, PARP cleavage and caspases 3/7 activity were stimulated. In addition, glucose, glycogen and triglycerides levels were decreased. Taken together our study depicts a disruption in the eclosion of D. melanogaster possibly attributed to the inhibition of kinases implied in developmental process, energetic demand and induction of apoptotic cell death process.
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Affiliation(s)
- Giulianna Echeverria Macedo
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Karen Kich Gomes
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Nathane Rosa Rodrigues
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Illana Kemmerich Martins
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Gabriel da Luz Wallau
- Entomology Department, Aggeu Magalhães Research Center, Fundação Oswaldo Cruz, FIOCRUZ, 50.740-465 Recife, PE, Brazil
| | - Nélson Rodrigues de Carvalho
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Litiele Cezar da Cruz
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Dennis Guilherme da Costa Silva
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Aline Augusti Boligon
- Phytochemical Research Laboratory, Department of Industrial Pharmacy, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Jeferson Luis Franco
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil
| | - Thaís Posser
- Oxidative Stress and Cell Signaling Research Group, Universidade Federal do Pampa, Campus São Gabriel, 97300-000 São Gabriel, RS, Brazil.
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23
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Evolution of GSTD1 in Cactophilic Drosophila. J Mol Evol 2017; 84:285-294. [DOI: 10.1007/s00239-017-9798-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/16/2017] [Indexed: 10/19/2022]
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24
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Schweizer F, Heidel-Fischer H, Vogel H, Reymond P. Arabidopsis glucosinolates trigger a contrasting transcriptomic response in a generalist and a specialist herbivore. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 85:21-31. [PMID: 28455184 DOI: 10.1016/j.ibmb.2017.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Phytophagous insects have to deal with toxic defense compounds from their host plants. Although it is known that insects have evolved genes and mechanisms to detoxify plant allochemicals, how specialist and generalist precisely respond to specific secondary metabolites at the molecular level is less understood. Here we studied the larval performance and transcriptome of the generalist moth Heliothis virescens and the specialist butterfly Pieris brassicae feeding on Arabidopsis thaliana genotypes with different glucosinolate (GS) levels. H. virescens larvae gained significantly more weight on the GS-deficient mutant quadGS compared to wild-type (Col-0) plants. On the contrary, P. brassicae was unaffected by the presence of GS and performed equally well on both genotypes. Strikingly, there was a considerable differential gene expression in H. virescens larvae feeding on Col-0 compared to quadGS. In contrast, compared to H. virescens, P. brassicae displayed a much-reduced transcriptional activation when fed on both plant genotypes. Transcripts coding for putative detoxification enzymes were significantly upregulated in H. virescens, along with digestive enzymes and transposable elements. These data provide an unprecedented view on transcriptional changes that are specifically activated by GS and illustrate differential molecular responses that are linked to adaptation to diet in lepidopteran herbivores.
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Affiliation(s)
- Fabian Schweizer
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hanna Heidel-Fischer
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland.
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25
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Yu QY, Fang SM, Zhang Z, Jiggins CD. The transcriptome response ofHeliconius melpomenelarvae to a novel host plant. Mol Ecol 2016; 25:4850-65. [PMID: 27572947 DOI: 10.1111/mec.13826] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Quan-You Yu
- School of Life Sciences; Chongqing University; Chongqing 401331 China
- Department of Zoology; University of Cambridge; Downing Street Cambridge CB2 3EJ UK
| | - Shou-Min Fang
- College of Life Science; China West Normal University; Nanchang 637002 China
| | - Ze Zhang
- School of Life Sciences; Chongqing University; Chongqing 401331 China
| | - Chris D. Jiggins
- Department of Zoology; University of Cambridge; Downing Street Cambridge CB2 3EJ UK
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26
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De Panis DN, Padró J, Furió-Tarí P, Tarazona S, Milla Carmona PS, Soto IM, Dopazo H, Conesa A, Hasson E. Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila. Mol Ecol 2016; 25:4534-50. [PMID: 27483442 DOI: 10.1111/mec.13785] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/14/2016] [Accepted: 07/21/2016] [Indexed: 12/20/2022]
Abstract
High-throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of host plant adaptation. Here, we investigate genome-wide expression in the fly Drosophila buzzatii raised in different conditions. This species uses decaying tissues of cactus of the genus Opuntia as primary rearing substrate and secondarily, the necrotic tissues of the columnar cactus Trichocereus terscheckii. The latter constitutes a harmful host, rich in mescaline and other related phenylethylamine alkaloids. We assessed the transcriptomic responses of larvae reared in Opuntia sulphurea and T. terscheckii, with and without the addition of alkaloids extracted from the latter. Whole-genome expression profiles were massively modulated by the rearing environment, mainly by the presence of T. terscheckii alkaloids. Differentially expressed genes were mainly related to detoxification, oxidation-reduction and stress response; however, we also found genes involved in development and neurobiological processes. In conclusion, our study contributes new data onto the role of transcriptional plasticity in response to alternative rearing environments.
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Affiliation(s)
- Diego N De Panis
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina.
| | - Julián Padró
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Pedro Furió-Tarí
- Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, Valencia, 46012, Spain
| | - Sonia Tarazona
- Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, Valencia, 46012, Spain.,Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Camí de Vera, Valencia, 46022, Spain
| | - Pablo S Milla Carmona
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina.,Laboratorio de Ecosistemas Marinos Fósiles, Instituto de Estudios Andinos Don Pablo Groeber (CONICET-UBA), Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Ignacio M Soto
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Hernán Dopazo
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Ana Conesa
- Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, Valencia, 46012, Spain. .,Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida at Gainesville, Gainesville, FL, 32603, USA.
| | - Esteban Hasson
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina.
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27
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Nguyen P, Kim AY, Jung JK, Donahue KM, Jung C, Choi MY, Koh YH. The Biochemical Adaptations of Spotted Wing Drosophila (Diptera: Drosophilidae) to Fresh Fruits Reduced Fructose Concentrations and Glutathione-S Transferase Activities. JOURNAL OF ECONOMIC ENTOMOLOGY 2016; 109:973-981. [PMID: 26921228 DOI: 10.1093/jee/tow019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Spotted wing drosophila, Drosophila suzukii Matsumura, is an invasive and economically damaging pest in Europe and North America. The females have a serrated ovipositor that enables them to infest almost all ripening small fruits. To understand the physiological and metabolic basis of spotted wing drosophila food preferences for healthy ripening fruits, we investigated the biological and biochemical characteristics of spotted wing drosophila and compared them with those of Drosophila melanogaster Meigen. We found that the susceptibility to oxidative stressors was significantly increased in spotted wing drosophila compared with those of D. melanogaster. In addition, we found that spotted wing drosophila had significantly reduced glutathione-S transferase (GST) activity and gene numbers. Furthermore, fructose concentrations found in spotted wing drosophila were significantly lower than those of D. melanogaster. Our data strongly suggest that the altered food preferences of spotted wing drosophila may stem from evolutionary adaptations to fresh foods accompanied by alterations in carbohydrate metabolism and GST activities.
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28
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Silva WM, Berger M, Bass C, Balbino VQ, Amaral MHP, Campos MR, Siqueira HAA. Status of pyrethroid resistance and mechanisms in Brazilian populations of Tuta absoluta. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 122:8-14. [PMID: 26071801 DOI: 10.1016/j.pestbp.2015.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/29/2014] [Accepted: 01/17/2015] [Indexed: 06/04/2023]
Abstract
The tomato leafminer, Tuta absoluta, is a major pest of tomato crops worldwide. This study surveyed the resistance of T. absoluta populations from four regions in Brazil to pyrethroid insecticides, the frequencies of L1014F, T929I and M918T Na channel mutations, and the role of detoxification metabolism in the resistance. Resistance ratios varied from 1- to 11-times among populations and insecticides, but control failure likelihood assays showed that all pyrethroids assessed exhibited no efficacy at all (and thus, 98-100% control failure likelihood) against all T. absoluta populations. The activity of glutathione S-transferase and cytochrome P450-mediated N-demethylation in biochemical assays was significantly correlated with the level of resistance to deltamethrin and permethrin suggesting that these enzymes may play a role in resistance. TaqMan assays were used to screen for the presence of knockdown resistance (kdr) mutations and revealed that the L1014F kdr mutation was fixed in all populations and associated with two super-kdr mutations, M918T and particularly T929I, at high frequency. Altogether, results suggest that control failures are because of mutations in the domain II of the sodium channel, as a prevailing mechanism of resistance to pyrethroids in populations of T. absoluta in Brazil. But, enhanced cytochrome P450-dependent monooxygenases and GST activities also play an important role in the resistance of some populations, which reinforce that pyrethroids must not be used overall to control T. absoluta.
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Affiliation(s)
- Wellington M Silva
- Departamento de Agronomia - (Entomologia), Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Madeleine Berger
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Chris Bass
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Valdir Q Balbino
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE 50732-970, Brazil
| | - Marcelo H P Amaral
- Departamento de Agronomia - (Entomologia), Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Mateus R Campos
- Departamento de Agronomia - (Entomologia), Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Herbert A A Siqueira
- Departamento de Agronomia - (Entomologia), Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil.
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29
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Abstract
Flies of the genus Drosophila, and particularly those of the species Drosophila melanogaster, are best known as laboratory organisms. As with all model organisms, they were domesticated for empirical studies, but they also continue to exist as wild populations. Decades of research on these flies in the laboratory have produced astounding and important insights into basic biological processes, but we have only scratched the surface of what they have to offer as research organisms. An outstanding challenge now is to build on this knowledge and explore how natural history has shaped D. melanogaster in order to advance our understanding of biology more generally. DOI:http://dx.doi.org/10.7554/eLife.06793.001
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Affiliation(s)
- Therese Ann Markow
- Division of Biological Sciences, Laboratorio Nacional para Genomica de la Biodiversidad, La Jolla, United States
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30
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You Y, Xie M, Ren N, Cheng X, Li J, Ma X, Zou M, Vasseur L, Gurr GM, You M. Characterization and expression profiling of glutathione S-transferases in the diamondback moth, Plutella xylostella (L.). BMC Genomics 2015; 16:152. [PMID: 25887517 PMCID: PMC4358871 DOI: 10.1186/s12864-015-1343-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/12/2015] [Indexed: 12/02/2022] Open
Abstract
Background Glutathione S-transferases (GSTs) are multifunctional detoxification enzymes that play important roles in insects. The completion of several insect genome projects has enabled the identification and characterization of GST genes over recent years. This study presents a genome-wide investigation of the diamondback moth (DBM), Plutella xylostella, a species in which the GSTs are of special importance because this pest is highly resistant to many insecticides. Results A total of 22 putative cytosolic GSTs were identified from a published P. xylostella genome and grouped into 6 subclasses (with two unclassified). Delta, Epsilon and Omega GSTs were numerically superior with 5 genes for each of the subclasses. The resulting phylogenetic tree showed that the P. xylostella GSTs were all clustered into Lepidoptera-specific branches. Intron sites and phases as well as GSH binding sites were strongly conserved within each of the subclasses in the GSTs of P. xylostella. Transcriptome-, RNA-seq- and qRT-PCR-based analyses showed that the GST genes were developmental stage- and strain-specifically expressed. Most of the highly expressed genes in insecticide resistant strains were also predominantly expressed in the Malpighian tubules, midgut or epidermis. Conclusions To date, this is the most comprehensive study on genome-wide identification, characterization and expression profiling of the GST family in P. xylostella. The diversified features and expression patterns of the GSTs are inferred to be associated with the capacity of this species to develop resistance to a wide range of pesticides and biological toxins. Our findings provide a base for functional research on specific GST genes, a better understanding of the evolution of insecticide resistance, and strategies for more sustainable management of the pest. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1343-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanchun You
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
| | - Miao Xie
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
| | - Nana Ren
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
| | - Xuemin Cheng
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
| | - Jianyu Li
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
| | - Xiaoli Ma
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
| | - Minming Zou
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
| | - Liette Vasseur
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada.
| | - Geoff M Gurr
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China. .,EH Graham Centre, Charles Sturt University, Orange, NSW, 2800, Australia.
| | - Minsheng You
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management of Fujian and Taiwan, China Ministry of Agriculture, Fuzhou, 350002, China.
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31
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Chan WC, Chien YC, Chien CI. Aniline exposure associated with up-regulated transcriptional responses of three glutathione S-transferase Delta genes in Drosophila melanogaster. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 39:622-627. [PMID: 25682008 DOI: 10.1016/j.etap.2014.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 06/04/2023]
Abstract
Complex transcriptional profile of glutathione S-transferase Delta cluster genes occurred in the developmental process of the fruit fly Drosophila melanogaster. The purpose of this project was to quantify the expression levels of Gst Delta class genes altered by aniline exposure and to understand the relationship between aniline dosages and the variation of Gst Delta genes expressed in D. melanogaster. Using RT-PCR expression assays, the expression patterns of the transcript mRNAs of the glutathione S-transferase Delta genes were revealed and their expression levels were measured at eggs, larvae, pupae and adults. The adult stage was selected for further dose-response assays. After analysis, the results indicated that three Gst Delta genes (Gst D2, Gst D5 and Gst D6) were found to show a peak of up-regulated transcriptional response at 6-8h of exposure of aniline. Furthermore, the dose-response relationship of their induction levels within the dose regiments (from 1.2 to 2.0 μl/tube) had been measured. The expression patterns and annotations of these genes were discussed in the context.
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Affiliation(s)
- Wen-Chiao Chan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Yi-Chih Chien
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Cheng-I Chien
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan.
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Abstract
The prodrug azathioprine is primarily used for maintaining remission in inflammatory bowel disease, but approximately 30% of the patients suffer adverse side effects. The prodrug is activated by glutathione conjugation and release of 6-mercaptopurine, a reaction most efficiently catalyzed by glutathione transferase (GST) A2-2. Among five genotypes of GST A2-2, the variant A2*E has threefold-fourfold higher catalytic efficiency with azathioprine, suggesting that the expression of A2*E could boost 6-mercaptopurine release and adverse side effects in treated patients. Structure-activity studies of the GST A2-2 variants and homologous alpha class GSTs were made to delineate the determinants of high catalytic efficiency compared to other alpha class GSTs. Engineered chimeras identified GST peptide segments of importance, and replacing the corresponding regions in low-activity GSTs by these short segments produced chimeras with higher azathioprine activity. By contrast, H-site mutagenesis led to decreased azathioprine activity when active-site positions 208 and 213 in these favored segments were mutagenized. Alternative substitutions indicated that hydrophobic residues were favored. A pertinent question is whether variant A2*E represents the highest azathioprine activity achievable within the GST structural framework. This issue was addressed by mutagenesis of H-site residues assumed to interact with the substrate based on molecular modeling. The mutants with notably enhanced activities had small or polar residues in the mutated positions. The most active mutant L107G/L108D/F222H displayed a 70-fold enhanced catalytic efficiency with azathioprine. The determination of its structure by X-ray crystallography showed an expanded H-site, suggesting improved accommodation of the transition state for catalysis.
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Affiliation(s)
- Olof Modén
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Bengt Mannervik
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden; Department of Neurochemistry, Stockholm University, Stockholm, Sweden.
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Markov GV, Baskaran P, Sommer RJ. The Same or Not the Same: Lineage-Specific Gene Expansions and Homology Relationships in Multigene Families in Nematodes. J Mol Evol 2014; 80:18-36. [DOI: 10.1007/s00239-014-9651-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/06/2014] [Indexed: 11/30/2022]
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Micro-plasticity of genomes as illustrated by the evolution of glutathione transferases in 12 Drosophila species. PLoS One 2014; 9:e109518. [PMID: 25310450 PMCID: PMC4195677 DOI: 10.1371/journal.pone.0109518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/03/2014] [Indexed: 12/05/2022] Open
Abstract
Glutathione transferases (GST) are an ancient superfamily comprising a large number of paralogous proteins in a single organism. This multiplicity of GSTs has allowed the copies to diverge for neofunctionalization with proposed roles ranging from detoxication and oxidative stress response to involvement in signal transduction cascades. We performed a comparative genomic analysis using FlyBase annotations and Drosophila melanogaster GST sequences as templates to further annotate the GST orthologs in the 12 Drosophila sequenced genomes. We found that GST genes in the Drosophila subgenera have undergone repeated local duplications followed by transposition, inversion, and micro-rearrangements of these copies. The colinearity and orientations of the orthologous GST genes appear to be unique in many of the species which suggests that genomic rearrangement events have occurred multiple times during speciation. The high micro-plasticity of the genomes appears to have a functional contribution utilized for evolution of this gene family.
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Younus F, Chertemps T, Pearce SL, Pandey G, Bozzolan F, Coppin CW, Russell RJ, Maïbèche-Coisne M, Oakeshott JG. Identification of candidate odorant degrading gene/enzyme systems in the antennal transcriptome of Drosophila melanogaster. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 53:30-43. [PMID: 25038463 DOI: 10.1016/j.ibmb.2014.07.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 06/03/2023]
Abstract
The metabolism of volatile signal molecules by odorant degrading enzymes (ODEs) is crucial to the ongoing sensitivity and specificity of chemoreception in various insects, and a few specific esterases, cytochrome P450s, glutathione S-transferases (GSTs) and UDP-glycosyltransferases (UGTs) have previously been implicated in this process. Significant progress has been made in characterizing ODEs in Lepidoptera but very little is known about them in Diptera, including in Drosophila melanogaster, a major insect model. We have therefore carried out a transcriptomic analysis of the antennae of D. melanogaster in order to identify candidate ODEs. Virgin male and female and mated female antennal transcriptomes were determined by RNAseq. As with the Lepidoptera, we found that many esterases, cytochrome P450 enzymes, GSTs and UGTs are expressed in D. melanogaster antennae. As olfactory genes generally show selective expression in the antennae, a comparison to previously published transcriptomes for other tissues has been performed, showing preferential expression in the antennae for one esterase, JHEdup, one cytochrome P450, CYP308a1, and one GST, GSTE4. These largely uncharacterized enzymes are now prime candidates for ODE functions. JHEdup was expressed heterologously and found to have high catalytic activity against a chemically diverse group of known ester odorants for this species. This is a finding consistent with an ODE although it might suggest a general role in clearing several odorants rather than a specific role in clearing a particular odorant. Our findings do not preclude the possibility of odorant degrading functions for other antennally expressed esterases, P450s, GSTs and UGTs but, if so, they suggest that these enzymes also have additional functions in other tissues.
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Affiliation(s)
- Faisal Younus
- CSIRO Ecosystems Sciences, Black Mountain, Clunies Ross Street, Canberra, ACT 0200, Australia; Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Thomas Chertemps
- Université Pierre et Marie Curie, Institut d'Ecologie et des Sciences de l'Environnement de Paris, F-75252 Paris, France
| | - Stephen L Pearce
- CSIRO Ecosystems Sciences, Black Mountain, Clunies Ross Street, Canberra, ACT 0200, Australia; Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Gunjan Pandey
- CSIRO Ecosystems Sciences, Black Mountain, Clunies Ross Street, Canberra, ACT 0200, Australia
| | - Françoise Bozzolan
- Université Pierre et Marie Curie, Institut d'Ecologie et des Sciences de l'Environnement de Paris, F-75252 Paris, France
| | - Christopher W Coppin
- CSIRO Ecosystems Sciences, Black Mountain, Clunies Ross Street, Canberra, ACT 0200, Australia
| | - Robyn J Russell
- CSIRO Ecosystems Sciences, Black Mountain, Clunies Ross Street, Canberra, ACT 0200, Australia
| | - Martine Maïbèche-Coisne
- Université Pierre et Marie Curie, Institut d'Ecologie et des Sciences de l'Environnement de Paris, F-75252 Paris, France
| | - John G Oakeshott
- CSIRO Ecosystems Sciences, Black Mountain, Clunies Ross Street, Canberra, ACT 0200, Australia.
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Whole-genome expression analysis in the third instar larval midgut of Drosophila melanogaster. G3-GENES GENOMES GENETICS 2014; 4:2197-205. [PMID: 25193493 PMCID: PMC4232545 DOI: 10.1534/g3.114.013870] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Survival of insects on a substrate containing toxic substances such as plant secondary metabolites or insecticides is dependent on the metabolism or excretion of those xenobiotics. The primary sites of xenobiotic metabolism are the midgut, Malpighian tubules, and fat body. In general, gene expression in these organs is reported for the entire tissue by online databases, but several studies have shown that gene expression within the midgut is compartmentalized. Here, RNA sequencing is used to investigate whole-genome expression in subsections of third instar larval midguts of Drosophila melanogaster. The data support functional diversification in subsections of the midgut. Analysis of the expression of gene families that are implicated in the metabolism of xenobiotics suggests that metabolism may not be uniform along the midgut. These data provide a starting point for investigating gene expression and xenobiotic metabolism and other functions of the larval midgut.
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Srivastava H, Huong NT, Arunyawat U, Das A. Molecular population genetics of the NADPH cytochrome P450 reductase (CPR) gene in Anopheles minimus. Genetica 2014; 142:295-315. [PMID: 25038863 DOI: 10.1007/s10709-014-9775-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 06/23/2014] [Indexed: 12/01/2022]
Abstract
Development of insecticide resistance (IR) in mosquito vectors is a primary huddle to malaria control program. Since IR has genetic basis, and genes constantly evolve with response to environment for adaptation to organisms, it is important to know evolutionary pattern of genes conferring IR in malaria vectors. The mosquito Anopheles minimus is a major malaria vector of the Southeast (SE) Asia and India and is susceptible to all insecticides, and thus of interest to know if natural selection has shaped variations in the gene conferring IR. If not, the DNA fragment of such a gene could be used to infer population structure and demography of this species of malaria vector. We have therefore sequenced a ~569 bp DNA segment of the NADPH cytochrome P450 reductase (CPR) gene (widely known to confer IR) in 123 individuals of An. minimus collected in 10 different locations (eight Indian, one Thai and one Vietnamese). Two Indian population samples were completely mono-morphic in the CPR gene. In general, low genetic diversity was found with no evidence of natural selection in this gene. The data were therefore analyzed to infer population structure and demography of this species. The 10 populations could be genetically differentiated into four different groups; the samples from Thailand and Vietnam contained high nucleotide diversity. All the 10 populations conform to demographic equilibrium model with signature of past population expansion in four populations. The results in general indicate that the An. minimus mosquitoes sampled in the two SE Asian localities contain several genetic characteristics of being parts of the ancestral population.
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Affiliation(s)
- Hemlata Srivastava
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi, India
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Gloss AD, Vassão DG, Hailey AL, Nelson Dittrich AC, Schramm K, Reichelt M, Rast TJ, Weichsel A, Cravens MG, Gershenzon J, Montfort WR, Whiteman NK. Evolution in an ancient detoxification pathway is coupled with a transition to herbivory in the drosophilidae. Mol Biol Evol 2014; 31:2441-56. [PMID: 24974374 DOI: 10.1093/molbev/msu201] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chemically defended plant tissues present formidable barriers to herbivores. Although mechanisms to resist plant defenses have been identified in ancient herbivorous lineages, adaptations to overcome plant defenses during transitions to herbivory remain relatively unexplored. The fly genus Scaptomyza is nested within the genus Drosophila and includes species that feed on the living tissue of mustard plants (Brassicaceae), yet this lineage is derived from microbe-feeding ancestors. We found that mustard-feeding Scaptomyza species and microbe-feeding Drosophila melanogaster detoxify mustard oils, the primary chemical defenses in the Brassicaceae, using the widely conserved mercapturic acid pathway. This detoxification strategy differs from other specialist herbivores of mustard plants, which possess derived mechanisms to obviate mustard oil formation. To investigate whether mustard feeding is coupled with evolution in the mercapturic acid pathway, we profiled functional and molecular evolutionary changes in the enzyme glutathione S-transferase D1 (GSTD1), which catalyzes the first step of the mercapturic acid pathway and is induced by mustard defense products in Scaptomyza. GSTD1 acquired elevated activity against mustard oils in one mustard-feeding Scaptomyza species in which GstD1 was duplicated. Structural analysis and mutagenesis revealed that substitutions at conserved residues within and near the substrate-binding cleft account for most of this increase in activity against mustard oils. Functional evolution of GSTD1 was coupled with signatures of episodic positive selection in GstD1 after the evolution of herbivory. Overall, we found that preexisting functions of generalized detoxification systems, and their refinement by natural selection, could play a central role in the evolution of herbivory.
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Affiliation(s)
- Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona
| | - Daniel G Vassão
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | | | - Katharina Schramm
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Timothy J Rast
- Department of Ecology and Evolutionary Biology, University of Arizona
| | | | - Matthew G Cravens
- Department of Ecology and Evolutionary Biology, University of Arizona
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Noah K Whiteman
- Department of Ecology and Evolutionary Biology, University of Arizona
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Xu Z, Zhu W, Liu Y, Liu X, Chen Q, Peng M, Wang X, Shen G, He L. Analysis of insecticide resistance-related genes of the Carmine spider mite Tetranychus cinnabarinus based on a de novo assembled transcriptome. PLoS One 2014; 9:e94779. [PMID: 24830288 PMCID: PMC4022505 DOI: 10.1371/journal.pone.0094779] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/19/2014] [Indexed: 12/04/2022] Open
Abstract
The carmine spider mite (CSM), Tetranychus cinnabarinus, is an important pest mite in agriculture, because it can develop insecticide resistance easily. To gain valuable gene information and molecular basis for the future insecticide resistance study of CSM, the first transcriptome analysis of CSM was conducted. A total of 45,016 contigs and 25,519 unigenes were generated from the de novo transcriptome assembly, and 15,167 unigenes were annotated via BLAST querying against current databases, including nr, SwissProt, the Clusters of Orthologous Groups (COGs), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). Aligning the transcript to Tetranychus urticae genome, the 19255 (75.45%) of the transcripts had significant (e-value <10-5) matches to T. urticae DNA genome, 19111 sequences matched to T. urticae proteome with an average protein length coverage of 42.55%. Core Eukaryotic Genes Mapping Approach (CEGMA) analysis identified 435 core eukaryotic genes (CEGs) in the CSM dataset corresponding to 95% coverage. Ten gene categories that relate to insecticide resistance in arthropod were generated from CSM transcriptome, including 53 P450-, 22 GSTs-, 23 CarEs-, 1 AChE-, 7 GluCls-, 9 nAChRs-, 8 GABA receptor-, 1 sodium channel-, 6 ATPase- and 12 Cyt b genes. We developed significant molecular resources for T. cinnabarinus putatively involved in insecticide resistance. The transcriptome assembly analysis will significantly facilitate our study on the mechanism of adapting environmental stress (including insecticide) in CSM at the molecular level, and will be very important for developing new control strategies against this pest mite.
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Affiliation(s)
- Zhifeng Xu
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Wenyi Zhu
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Yanchao Liu
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Xing Liu
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Qiushuang Chen
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Miao Peng
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Xiangzun Wang
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Guangmao Shen
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
| | - Lin He
- Key Laboratory of Entomology and Pest Control Engineering of Chongqing, College of Plant Protection, Southwest University, Chongqing, China
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Good RT, Gramzow L, Battlay P, Sztal T, Batterham P, Robin C. The molecular evolution of cytochrome P450 genes within and between drosophila species. Genome Biol Evol 2014; 6:1118-34. [PMID: 24751979 PMCID: PMC4040991 DOI: 10.1093/gbe/evu083] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We map 114 gene gains and 74 gene losses in the P450 gene family across the phylogeny of 12 Drosophila species by examining the congruence of gene trees and species trees. Although the number of P450 genes varies from 74 to 94 in the species examined, we infer that there were at least 77 P450 genes in the ancestral Drosophila genome. One of the most striking observations in the data set is the elevated loss of P450 genes in the Drosophila sechellia lineage. The gain and loss events are not evenly distributed among the P450 genes-with 30 genes showing no gene gains or losses whereas others show as many as 20 copy number changes among the species examined. The P450 gene clades showing the fewest number of gene gain and loss events tend to be those evolving with the most purifying selection acting on the protein sequences, although there are exceptions, such as the rapid rate of amino acid replacement observed in the single copy phantom (Cyp306a1) gene. Within D. melanogaster, we observe gene copy number polymorphism in ten P450 genes including multiple cases of interparalog chimeras. Nonallelic homologous recombination (NAHR) has been associated with deleterious mutations in humans, but here we provide a second possible example of an NAHR event in insect P450s being adaptive. Specifically, we find that a polymorphic Cyp12a4/Cyp12a5 chimera correlates with resistance to an insecticide. Although we observe such interparalog exchange in our within-species data sets, we have little evidence of it between species, raising the possibility that such events may occur more frequently than appreciated but are masked by subsequent sequence change.
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Affiliation(s)
- Robert T Good
- Department of Genetics, University of Melbourne, AustraliaPresent address: Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, GermanyPresent address: School of Biological Sciences, Monash University, Australia
| | - Lydia Gramzow
- Present address: Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, Germany
| | - Paul Battlay
- Department of Genetics, University of Melbourne, AustraliaPresent address: Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, GermanyPresent address: School of Biological Sciences, Monash University, Australia
| | - Tamar Sztal
- Present address: School of Biological Sciences, Monash University, Australia
| | - Philip Batterham
- Department of Genetics, University of Melbourne, AustraliaPresent address: Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, GermanyPresent address: School of Biological Sciences, Monash University, Australia
| | - Charles Robin
- Department of Genetics, University of Melbourne, AustraliaPresent address: Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, GermanyPresent address: School of Biological Sciences, Monash University, Australia
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Harrop TWR, Sztal T, Lumb C, Good RT, Daborn PJ, Batterham P, Chung H. Evolutionary changes in gene expression, coding sequence and copy-number at the Cyp6g1 locus contribute to resistance to multiple insecticides in Drosophila. PLoS One 2014; 9:e84879. [PMID: 24416303 PMCID: PMC3885650 DOI: 10.1371/journal.pone.0084879] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/28/2013] [Indexed: 01/25/2023] Open
Abstract
Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However, it is not known whether the ability of the CYP6G1 enzyme to provide resistance to multiple insecticides evolved recently in D. melanogaster or if this function is present in all Drosophila species. Here we show that duplication of the Cyp6g1 gene occurred at least four times during the evolution of different Drosophila species, and the ability of CYP6G1 to confer resistance to multiple insecticides exists in D. melanogaster and D. simulans but not in Drosophila willistoni or Drosophila virilis. In D. virilis, which has multiple copies of Cyp6g1, one copy confers resistance to DDT and another to nitenpyram, suggesting that the divergence of protein sequence between copies subsequent to the duplication affected the activity of the enzyme. All orthologs tested conferred resistance to one or more insecticides, suggesting that CYP6G1 had the capacity to provide resistance to anthropogenic chemicals before they existed. Finally, we show that expression of Cyp6g1 in the Malpighian tubules, which contributes to DDT resistance in D. melanogaster, is specific to the D. melanogaster–D. simulans lineage. Our results suggest that a combination of gene duplication, regulatory changes and protein coding changes has taken place at the Cyp6g1 locus during evolution and this locus may play a role in providing resistance to different environmental toxins in different Drosophila species.
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Affiliation(s)
- Thomas W. R. Harrop
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tamar Sztal
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Christopher Lumb
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robert T. Good
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Phillip J. Daborn
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Philip Batterham
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (PB); (HC)
| | - Henry Chung
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail: (PB); (HC)
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Salvador R, Príncipi D, Berretta M, Fernández P, Paniego N, Sciocco-Cap A, Hopp E. Transcriptomic survey of the midgut of Anthonomus grandis (Coleoptera: Curculionidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:219. [PMID: 25473064 PMCID: PMC5634044 DOI: 10.1093/jisesa/ieu081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 10/15/2013] [Indexed: 06/04/2023]
Abstract
Anthonomus grandis Boheman is a key pest in cotton crops in the New World. Its larval stage develops within the flower bud using it as food and as protection against its predators. This behavior limits the effectiveness of its control using conventional insecticide applications and biocontrol techniques. In spite of its importance, little is known about its genome sequence and, more important, its specific expression in key organs like the midgut. Total mRNA isolated from larval midguts was used for pyrosequencing. Sequence reads were assembled and annotated to generate a unigene data set. In total, 400,000 reads from A. grandis midgut with an average length of 237 bp were assembled and combined into 20,915 contigs. The assembled reads fell into 6,621 genes models. BlastX search using the NCBI-NR database showed that 3,006 unigenes had significant matches to known sequences. Gene Ontology (GO) mapping analysis evidenced that A. grandis is able to transcripts coding for proteins involved in catalytic processing of macromolecules that allows its adaptation to very different feeding source scenarios. Furthermore, transcripts encoding for proteins involved in detoxification mechanisms such as p450 genes, glutathione-S-transferase, and carboxylesterases are also expressed. This is the first report of a transcriptomic study in A. grandis and the largest set of sequence data reported for this species. These data are valuable resources to expand the knowledge of this insect group and could be used in the design of new control strategies based in molecular information.
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Affiliation(s)
- Ricardo Salvador
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (INTA, Castelar), N. Repetto y Los Reseros, 1686 Hurlingham, Argentina
| | - Darío Príncipi
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA, Castelar), N. Repetto y Los Reseros, 1686. Hurlingham, Argentina
| | - Marcelo Berretta
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (INTA, Castelar), N. Repetto y Los Reseros, 1686 Hurlingham, Argentina
| | - Paula Fernández
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA, Castelar), N. Repetto y Los Reseros, 1686. Hurlingham, Argentina
| | - Norma Paniego
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA, Castelar), N. Repetto y Los Reseros, 1686. Hurlingham, Argentina
| | - Alicia Sciocco-Cap
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (INTA, Castelar), N. Repetto y Los Reseros, 1686 Hurlingham, Argentina
| | - Esteban Hopp
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA, Castelar), N. Repetto y Los Reseros, 1686. Hurlingham, Argentina
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Dou W, Shen GM, Niu JZ, Ding TB, Wei DD, Wang JJ. Mining genes involved in insecticide resistance of Liposcelis bostrychophila Badonnel by transcriptome and expression profile analysis. PLoS One 2013; 8:e79878. [PMID: 24278202 PMCID: PMC3835895 DOI: 10.1371/journal.pone.0079878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/26/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Recent studies indicate that infestations of psocids pose a new risk for global food security. Among the psocids species, Liposcelis bostrychophila Badonnel has gained recognition in importance because of its parthenogenic reproduction, rapid adaptation, and increased worldwide distribution. To date, the molecular data available for L. bostrychophila is largely limited to genes identified through homology. Also, no transcriptome data relevant to psocids infection is available. METHODOLOGY AND PRINCIPAL FINDINGS In this study, we generated de novo assembly of L. bostrychophila transcriptome performed through the short read sequencing technology (Illumina). In a single run, we obtained more than 51 million sequencing reads that were assembled into 60,012 unigenes (mean size = 711 bp) by Trinity. The transcriptome sequences from different developmental stages of L. bostrychophila including egg, nymph and adult were annotated with non-redundant (Nr) protein database, gene ontology (GO), cluster of orthologous groups of proteins (COG), and KEGG orthology (KO). The analysis revealed three major enzyme families involved in insecticide metabolism as differentially expressed in the L. bostrychophila transcriptome. A total of 49 P450-, 31 GST- and 21 CES-specific genes representing the three enzyme families were identified. Besides, 16 transcripts were identified to contain target site sequences of resistance genes. Furthermore, we profiled gene expression patterns upon insecticide (malathion and deltamethrin) exposure using the tag-based digital gene expression (DGE) method. CONCLUSION The L. bostrychophila transcriptome and DGE data provide gene expression data that would further our understanding of molecular mechanisms in psocids. In particular, the findings of this investigation will facilitate identification of genes involved in insecticide resistance and designing of new compounds for control of psocids.
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Affiliation(s)
- Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Guang-Mao Shen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Jin-Zhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Tian-Bo Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Dan-Dan Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
- * E-mail:
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Wurmser F, Mary-Huard T, Daudin JJ, Joly D, Montchamp-Moreau C. Variation of gene expression associated with colonisation of an anthropized environment: comparison between African and European populations of Drosophila simulans. PLoS One 2013; 8:e79750. [PMID: 24260296 PMCID: PMC3832527 DOI: 10.1371/journal.pone.0079750] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/01/2013] [Indexed: 11/18/2022] Open
Abstract
The comparison of transcriptome profiles among populations is a powerful tool for investigating the role of gene expression change in adaptation to new environments. In this study, we use massively parallel sequencing of 3' cDNAs obtained from large samples of adult males, to compare a population of Drosophila simulans from a natural reserve within its ancestral range (eastern Africa) with a derived population collected in the strongly anthropized Rhône valley (France). The goal was to scan for adaptation linked to the invasion of new environments by the species. Among 15,090 genes retained for the analysis, 794 were found to be differentially expressed between the two populations. We observed an increase in expression of reproduction-related genes in eastern Africa, and an even stronger increase in expression of Cytochrome P450, Glutathione transferase and Glucuronosyl transferase genes in the derived population. These three gene families are involved in detoxification processes, which suggests that pesticides are a major environmental pressure for the species in this area. The survey of the Cyp6g1 upstream region revealed the insertion of a transposable element, Juan, in the regulatory sequence that is almost fixed in the Rhône Valley, but barely present in Mayotte. This shows that Cyp6g1 has undergone parallel evolution in derived populations of D. simulans as previously shown for D. melanogaster. The increasing amount of data produced by comparative population genomics and transcriptomics should permit the identification of additional genes associated with functional divergence among those differentially expressed.
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Affiliation(s)
- François Wurmser
- Laboratoire Évolution Génomes et Spéciation, CNRS UPR9034, Gif-sur-Yvette, and Université Paris-Sud, Orsay, France
| | - Tristan Mary-Huard
- INRA UMR 518 MIA, Paris, France
- AgroParisTech, UMR 518 MIA, Paris, France
- UMR de Génétique Végétale, INRA, Université Paris-sud, CNRS, Gif-sur-Yvette, France
| | | | - Dominique Joly
- Laboratoire Évolution Génomes et Spéciation, CNRS UPR9034, Gif-sur-Yvette, and Université Paris-Sud, Orsay, France
| | - Catherine Montchamp-Moreau
- Laboratoire Évolution Génomes et Spéciation, CNRS UPR9034, Gif-sur-Yvette, and Université Paris-Sud, Orsay, France
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Chávez-Galarza J, Henriques D, Johnston JS, Azevedo JC, Patton JC, Muñoz I, De la Rúa P, Pinto MA. Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms. Mol Ecol 2013; 22:5890-907. [PMID: 24118235 DOI: 10.1111/mec.12537] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 09/12/2013] [Accepted: 09/19/2013] [Indexed: 12/30/2022]
Abstract
Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees collected across an environmental gradient in Iberia and used four FST -based outlier tests to identify genomic regions exhibiting signatures of selection. Additionally, we analysed associations between genetic and environmental data for the identification of factors that might be correlated or act as selective pressures. With these approaches, 4.4% (17 of 383) of outlier loci were cross-validated by four FST -based methods, and 8.9% (34 of 383) were cross-validated by at least three methods. Of the 34 outliers, 15 were found to be strongly associated with one or more environmental variables. Further support for selection, provided by functional genomic information, was particularly compelling for SNP outliers mapped to different genes putatively involved in the same function such as vision, xenobiotic detoxification and innate immune response. This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human-mediated environmental changes.
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Affiliation(s)
- Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal
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Yan H, Jia H, Gao H, Guo X, Xu B. Identification, genomic organization, and oxidative stress response of a sigma class glutathione S-transferase gene (AccGSTS1) in the honey bee, Apis cerana cerana. Cell Stress Chaperones 2013; 18:415-26. [PMID: 23250585 PMCID: PMC3682021 DOI: 10.1007/s12192-012-0394-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/01/2012] [Accepted: 12/03/2012] [Indexed: 01/10/2023] Open
Abstract
Glutathione S-transferases (GSTs) are members of a multifunctional antioxidant enzyme superfamily that play pivotal roles in both detoxification and protection against oxidative damage caused by reactive oxygen species. In this study, a complementary DNA (cDNA) encoding a sigma class GST was identified in the Chinese honey bee, Apis cerana cerana (AccGSTS1). AccGSTS1 was constitutively expressed in all tissues of adult worker bees, including the brain, fat body, epidermis, muscle, and midgut, with particularly robust transcription in the fat body. Relative messenger RNA expression levels of AccGSTS1 at different developmental stages varied, with the highest levels of expression observed in adults. The potential function of AccGSTS1 in cellular defenses against abiotic stresses (cold, heat, UV, H2O2, HgCl2, and insecticides) was investigated. AccGSTS1 was significantly upregulated in response to all of the treatment conditions examined, although the induction levels were varied. Recombinant AccGSTS1 protein showed characteristic glutathione-conjugating catalytic activity toward 1-chloro-2,4-dinitrobenzene. Functional assays revealed that AccGSTS1 could remove H2O2, thereby protecting DNA from oxidative damage. Escherichia coli overexpressing AccGSTS1 showed long-term resistance under conditions of oxidative stress. Together, these results suggest that AccGSTS1 is a crucial antioxidant enzyme involved in cellular antioxidant defenses and honey bee survival.
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Affiliation(s)
- Huiru Yan
- />College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Haihong Jia
- />College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Hongru Gao
- />College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Xingqi Guo
- />College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Baohua Xu
- />College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
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Yang N, Xie W, Yang X, Wang S, Wu Q, Li R, Pan H, Liu B, Shi X, Fang Y, Xu B, Zhou X, Zhang Y. Transcriptomic and proteomic responses of sweetpotato whitefly, Bemisia tabaci, to thiamethoxam. PLoS One 2013; 8:e61820. [PMID: 23671574 PMCID: PMC3650016 DOI: 10.1371/journal.pone.0061820] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/13/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), is one of the most widely distributed agricultural pests. Although it has developed resistance to many registered insecticides including the neonicotinoid insecticide thiamethoxam, the mechanisms that regulate the resistance are poorly understood. To understand the molecular basis of thiamethoxam resistance, "omics" analyses were carried out to examine differences between resistant and susceptible B. tabaci at both transcriptional and translational levels. RESULTS A total of 1,338 mRNAs and 52 proteins were differentially expressed between resistant and susceptible B. tabaci. Among them, 11 transcripts had concurrent transcription and translation profiles. KEGG analysis mapped 318 and 35 differentially expressed genes and proteins, respectively, to 160 and 59 pathways (p<0.05). Thiamethoxam treatment activated metabolic pathways (e.g., drug metabolism), in which 118 transcripts were putatively linked to insecticide resistance, including up-regulated glutathione-S-transferase, UDP glucuronosyltransferase, glucosyl/glucuronosyl transferase, and cytochrome P450. Gene Ontology analysis placed these genes and proteins into protein complex, metabolic process, cellular process, signaling, and response to stimulus categories. Quantitative real-time PCR analysis validated "omics" response, and suggested a highly overexpressed P450, CYP6CX1, as a candidate molecular basis for the mechanistic study of thiamethoxam resistance in whiteflies. Finally, enzymatic activity assays showed elevated detoxification activities in the resistant B. tabaci. CONCLUSIONS This study demonstrates the applicability of high-throughput omics tools for identifying molecular candidates related to thiamethoxam resistance in an agricultural important insect pest. In addition, transcriptomic and proteomic analyses provide a solid foundation for future functional investigations into the complex molecular mechanisms governing the neonicotinoid resistance in whiteflies.
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Affiliation(s)
- Nina Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xin Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Rumei Li
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huipeng Pan
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Baiming Liu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiaobin Shi
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yong Fang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Baoyun Xu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail: (XGZ); (YJZ)
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (XGZ); (YJZ)
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Alpha-class glutathione S-transferases in wild turkeys (Meleagris gallopavo): characterization and role in resistance to the carcinogenic mycotoxin aflatoxin B1. PLoS One 2013; 8:e60662. [PMID: 23613737 PMCID: PMC3628786 DOI: 10.1371/journal.pone.0060662] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/26/2013] [Indexed: 11/19/2022] Open
Abstract
Domestic turkeys (Meleagris gallopavo) are one of the most susceptible animals known to the toxic effects of the mycotoxin aflatoxin B1 (AFB1), a potent human hepatocarcinogen, and universal maize contaminant. We have demonstrated that such susceptibility is associated with the inability of hepatic glutathione S-transferases (GSTs) to detoxify the reactive electrophilic metabolite exo-AFB1-8,9-epoxide (AFBO). Unlike their domestic counterparts, wild turkeys, which are relatively AFB1-resistant, possess hepatic GST-mediated AFBO conjugating activity. Here, we characterized the molecular and functional properties of hepatic alpha-class GSTs (GSTAs) from wild and domestic turkeys to shed light on the differences in resistance between these closely related strains. Six alpha-class GST genes (GSTA) amplified from wild turkeys (Eastern and Rio Grande subspecies), heritage breed turkeys (Royal Palm) and modern domestic (Nicholas strain) turkeys were sequenced, and catalytic activities of heterologously-expressed recombinant enzymes determined. Alpha-class identity was affirmed by conserved GST domains and four signature motifs. All GSTAs contained single nucleotide polymorphisms (SNPs) in their coding regions: GSTA1.1 (5 SNPs), GSTA1.2 (7), GSTA1.3 (3), GSTA2 (3), GSTA3 (1) and GSTA4 (2). E. coli-expressed GSTAs possessed varying activities toward GST substrates 1-chloro-2,4-dinitrobenzene (CDNB), 1,2-dichloro-4-nitrobenzene (DCNB), ethacrynic acid (ECA), cumene hydroperoxide (CHP). As predicted by their relative resistance, livers from domestic turkeys lacked detectable GST-mediated AFBO detoxification activity, whereas those from wild and heritage birds possessed this critical activity, suggesting that intensive breeding and selection resulted in loss of AFB1-protective alleles during domestication. Our observation that recombinant tGSTAs detoxify AFBO, whereas their hepatic forms do not, implies that the hepatic forms of these enzymes are down-regulated, silenced, or otherwise modified by one or more mechanisms. These data may inform of possible molecular mechanisms of resistance to AFB1, and may also have the benefit of identifying genetic markers which could be used to enhance AFB1 resistance in modern domestic strains.
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Identification and characterization of an Apis cerana cerana Delta class glutathione S-transferase gene (AccGSTD) in response to thermal stress. Naturwissenschaften 2012; 100:153-63. [DOI: 10.1007/s00114-012-1006-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 11/18/2012] [Accepted: 12/06/2012] [Indexed: 01/21/2023]
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Daborn PJ, Lumb C, Harrop TWR, Blasetti A, Pasricha S, Morin S, Mitchell SN, Donnelly MJ, Müller P, Batterham P. Using Drosophila melanogaster to validate metabolism-based insecticide resistance from insect pests. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:918-924. [PMID: 23023059 DOI: 10.1016/j.ibmb.2012.09.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 06/01/2023]
Abstract
Identifying molecular mechanisms of insecticide resistance is important for preserving insecticide efficacy, developing new insecticides and implementing insect control. The metabolic detoxification of insecticides is a widespread resistance mechanism. Enzymes with the potential to detoxify insecticides are commonly encoded by members of the large cytochrome P450, glutathione S-transferase and carboxylesterase gene families, all rapidly evolving in insects. Here, we demonstrate that the model insect Drosophila melanogaster is useful for functionally validating the role of metabolic enzymes in conferring metabolism-based insecticide resistance. Alleles of three well-characterized genes from different pest insects were expressed in transgenic D. melanogaster : a carboxylesterase gene (αE7) from the Australian sheep blowfly Lucilia cuprina, a glutathione S-transferase gene (GstE2) from the mosquito Anopheles gambiae and a cytochrome P450 gene (Cyp6cm1) from the whitefly Bemisia tabaci. For all genes, expression in D. melanogaster resulted in insecticide resistance phenotypes mirroring those observed in resistant populations of the pest species. Using D. melanogaster to assess the potential for novel metabolic resistance mechanisms to evolve in pest species is discussed.
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Affiliation(s)
- Phillip J Daborn
- Department of Genetics and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
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