靶向果蝇Kr-h1基因的mi RNA预测及其生物信息学分析
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摘要
目的预测靶向果蝇Kr-h1(Krǜppel homolog1)基因的miRNA,并对其生物学功能及相关生物信息学进行分析,为进一步研究miRNA通过调控Kr-h1的表达而参与保幼激素(juvenile hormone,JH)对果蝇变态发育的调控奠定基础。方法通过microT-CDS、Targetscan和miRanda在线预测网站,对靶向Kr-h1基因的miRNA进行预测,对预测得到的多个miRNA按靶向结合可能性的大小进行汇总,3个网站均能预测到的miRNA为交集miRNA,对交集miRNA的靶基因及Kr-h1基因进行生物信息学功能分析。结果 microT-CDS、Targetscan和miRanda分别预测到30、7和11个靶向Kr-h1的miRNA,其中交集miRNA有4个,为miR-8、miR-277、miR-927和miR-964。功能分析发现,交集miRNA的靶基因主要参与细胞过程、生物过程和代谢过程,Kr-h1基因主要与昆虫生长发育及生殖相关。结论潜在靶向Kr-h1的miRNA涉及多个生物学过程,与昆虫的生长发育密切相关。
Objective To predict the miRNA targeting the Kr-h1(Krǜppel homolog1) gene of Drosophila,analyze the biological function and the relevant bioinformatics of the gene and provide a theoretical basis for study on the role of miRNA in metamorphosis of Drosophila melanogaster. Methods The miRNA targeting Kr-h1 gene was predicted by using microT-CDS,Targetscan and miRanda online prediction websites,and the possibilities of target binding of the obtained miRNAs were analyzed. The bioinformatics of target and Kr-h1 genes of intersecting miRNAs,i.e. the miRNAs predicted by all the three websites,were analyzed. Results A total of 30,7 and 11 miRNAs targeting Kr-h1 genes were obtained by prediction using microT-CDS,Targetscan and miRanda websites respectively,of which miR-8,miR-277,miR-927 and miR-964 were intersecting miRNAs. Bioinformatics analysis showed that the target genes of intersecting miRNAs mainly involved in the cellular,biological and metabolic processes,while Kr-h1 gene was mainly associated with the growth,development and reproduction of insects. Conclusion The miRNAs potentially targeting Kr-hl involved in various biological processes and were closely associated with the growth and development of insects.
Objective To predict the miRNA targeting the Kr-h1(Krǜppel homolog1) gene of Drosophila,analyze the biological function and the relevant bioinformatics of the gene and provide a theoretical basis for study on the role of miRNA in metamorphosis of Drosophila melanogaster. Methods The miRNA targeting Kr-h1 gene was predicted by using microT-CDS,Targetscan and miRanda online prediction websites,and the possibilities of target binding of the obtained miRNAs were analyzed. The bioinformatics of target and Kr-h1 genes of intersecting miRNAs,i.e. the miRNAs predicted by all the three websites,were analyzed. Results A total of 30,7 and 11 miRNAs targeting Kr-h1 genes were obtained by prediction using microT-CDS,Targetscan and miRanda websites respectively,of which miR-8,miR-277,miR-927 and miR-964 were intersecting miRNAs. Bioinformatics analysis showed that the target genes of intersecting miRNAs mainly involved in the cellular,biological and metabolic processes,while Kr-h1 gene was mainly associated with the growth,development and reproduction of insects. Conclusion The miRNAs potentially targeting Kr-hl involved in various biological processes and were closely associated with the growth and development of insects.
引文
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[12] WEN D, RIVERA. PEREZ C, ABDOU M, et al. Methyl farnesoate plays a dual role in regulating Drosophila metamorphosis[J]. PLoS Genet, 2015, 11(3):e1005038. doi:10.1371/j ournal.pgen. 100503 8.
[13] LIU S,LI K,GAO Y,et al. Antagonistic actions of juvenile hormone and 20-hydroxyecdysone within the ring gland determine developmental transitions in Drosophila[J]. Proc Natl Acad Sci USA, 2018, 115(1):139-144.
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[15] WANG H B, ALI S M, MORIYAMA M, et al. 20-hydroxyecdysone and juvenile hormone analog prevent precocious metamorphosis in recessive trimolter mutants of Bombyx mori[J].Insect Biochem Mol Biol,2012,42(2):102-108.
[16] KAYUKAWA T, MURATA M, KOBAYASHI I, et al. Hormonal regulation and developmental role of Kruppel homolog 1, a repressor of metamorphosis, in the silkworm Bombyx mori[J].Dev Biol, 2014, 388(1):48-56.
[17] MINAKUCHI C, NAMIKI T, SHINODA T. Kruppel homolog I,an early juvenile hormone. response gene downstream of Methoprene. tolerant,mediates its anti. metamorphic action in the red flour beetle Tribolium castaneum[J]. Dev Biol, 2009, 325(2):341-350.
[18] LOZANO J, BELLES X. Conserved repressive function of Kriippel homolog 1 on insect metamorphosis in hemimetabolous and holometabolous species[J]. Sci Rep,2011,1:163. doi:10.1038/srep00163.
[19] JIN M N.Molecular cloning and functional study of Kruppel.homolog 1(Kr-hl)from Nilaparvata luge ns(Stal)[D]. Hangzhou:China Jiliang University,2013.(in Chinese)金敏娜.褐飞虱Kr-h1基因的克隆及功能研究[D].浙江杭州:中国计量学院,2013.
[20] SONG J, WU Z, WANG Z, et al. Kruppel. homolog 1 mediates juvenile hormone action to promote vitellogenesis and oocyte maturation in the migratory locust[J]. Insect Biochem Mol Biol,2014, 52(1):94-101.
[21] BOLIN K, RACHMANINOFF N, MONCADA K, et al. miR. 8modulates cytoskeletal regulators to influence cell survival and epithelial organization in Drosophila wings[J]. Dev Biol, 2016,412(1):83-98.
[22] TARIQ K, METZENDORF C, PENG W, et al. miR-8-3p regulates mitoferrin in the testes of Bactrocera dorsalis to ensure normal spermatogenesis[J]. Sci Rep,2016,6:22565. doi:10.1038/srep22565.
[23] LUCAS K J, ROY S, HA J, et al. MicroRNA-8 targets the Wingless signaling pathway in the female mosquito fat body to regulate reproductive processes[J]. Proc Natl Acad Sci USA,2015, 112(5):1440-1445.
[24] LING L, KOKOZA V A, ZHANG C, et al. MicroRNA-277 targets insulin-like peptides 7 and 8 to control lipid metabolism and reproduction in Aedes aegypti mosquitoes[J]. Proc Natl Acad Sci USA, 2017, 114(38):E8017-E8024.
[25] ESSLINGER S M, SCHWALB B, HELFER S, et al. Drosophila miR-277 controls branched-chain amino acid cata-bolism and affects lifespan[J]. RNA Biol, 2013, 10(6):1042-1056.
[26] MORIN M D, FRIG AULT J J, LYONS P J, et al. Amplification and quantification of cold. associated microRNAs in the Colorado potato beetle(Leptinotarsa decemlineata)agricultural pest[J]. Insect Mol Biol, 2017, 26(5):574-583.
[27] AVILA-BONILLA R G, YOCUPICIO-MONROY M, MARCHAT L A, et al. Analysis of the miRNA profile in C6/36 cells persistently infected with dengue virus type 2[J]. Virus Res,2017, 232:139-151.
[2] WEN D,RIVERA. PEREZ C,ABDOU M,et al. Correction:methyl farnesoate plays a dual role in regulating Drosophila metamorphosis[J].PLoS Genet,2017,13(1):e1006559. doi:10.1371/journal.pgen. 1006559.
[3] FEYEREISEN R, JINDRA M. The silkworm coming of age.early[J]. Plos Genet, 2012, 8(3):e1002591. doi:10.1371/journal.pgen. 1002591.
[4] LI Y L. Functional analysis of Juvenile hormone signaling pathway genes Met and Kr-hl IN Bactrocera dorsalis(Hendel)[D]. Chongqing:Southwest University,2016.(in Chinese)李亚丽.桔小实蝇保幼激素信号通路Met和Kr. h1基因功能初探[J].重庆:西南大学,2016.
[5] MINAKUCHI C,TANAKA M,MIURA K, et al. Developmental profile and hormonal regulation of the transcription factors broad,and Kruppel homolog 1,in hemimetabolous thrips[J]. Insect Biochem Mol Biol, 2011, 41(2):125-134.
[6] FUSSNECKER B, GROZINGER C. Dissecting the role of Krhl brin gene expression in foraging behavior in honey bees(Apis mellifera)[J]. Insect Mol Biol, 2008, 17(5):515-522.
[7] SANTA. MARIA I, ALANIZ M E, RENWICK N, et al. Dysregulation of microRNA-219 promotes neurodegeneration through post-transcriptional regulation of tau[J]. J Clin Invest,2015, 125(2):681-686.
[8] BOLIN K, RACHMANINOFF N, MONCADA K, et al. miR-8modulates cytoskeletal regulators to influence cell survival and epithelial organization in Drosophila wings[J]. Develop Biol,2016, 412(1):83-98.
[9] SONG J S, GUO W, JIANG F, et al. Argonaute 1 is indispensable for juvenile hormone mediated oogenesis in the migratory locust, Locuasta migratoria[J]. Insect Biochem Mol Biol, 2013,43(9):879-887.
[10] LOZANO J, MONTANEZ R, BELLES X. MiR-2 family regulates insect metamorphosis by controlling the juvenile hormone signaling pathway[J]. Proc Natl Acad Sci USA, 2015, 112(12):3740-3745.
[11] MINAKUCHI C, ZHOU X, RIDDIFORD L M. Kruppel homolog 1(Kr-h1)mediates juvenile hormone action during metamorphosis of Drosophila melanogaster[J]. Mech Dev, 2008,125(1-2):91-105.
[12] WEN D, RIVERA. PEREZ C, ABDOU M, et al. Methyl farnesoate plays a dual role in regulating Drosophila metamorphosis[J]. PLoS Genet, 2015, 11(3):e1005038. doi:10.1371/j ournal.pgen. 100503 8.
[13] LIU S,LI K,GAO Y,et al. Antagonistic actions of juvenile hormone and 20-hydroxyecdysone within the ring gland determine developmental transitions in Drosophila[J]. Proc Natl Acad Sci USA, 2018, 115(1):139-144.
[14] REIFF T, JACOBSON J, COGNIGNI P, et al. Endocrine remodelling of the adult intestine sustains reproduction in Drosophila[J].Elife, 2015, 4:e06930. doi:10.7554/eLife.06930.
[15] WANG H B, ALI S M, MORIYAMA M, et al. 20-hydroxyecdysone and juvenile hormone analog prevent precocious metamorphosis in recessive trimolter mutants of Bombyx mori[J].Insect Biochem Mol Biol,2012,42(2):102-108.
[16] KAYUKAWA T, MURATA M, KOBAYASHI I, et al. Hormonal regulation and developmental role of Kruppel homolog 1, a repressor of metamorphosis, in the silkworm Bombyx mori[J].Dev Biol, 2014, 388(1):48-56.
[17] MINAKUCHI C, NAMIKI T, SHINODA T. Kruppel homolog I,an early juvenile hormone. response gene downstream of Methoprene. tolerant,mediates its anti. metamorphic action in the red flour beetle Tribolium castaneum[J]. Dev Biol, 2009, 325(2):341-350.
[18] LOZANO J, BELLES X. Conserved repressive function of Kriippel homolog 1 on insect metamorphosis in hemimetabolous and holometabolous species[J]. Sci Rep,2011,1:163. doi:10.1038/srep00163.
[19] JIN M N.Molecular cloning and functional study of Kruppel.homolog 1(Kr-hl)from Nilaparvata luge ns(Stal)[D]. Hangzhou:China Jiliang University,2013.(in Chinese)金敏娜.褐飞虱Kr-h1基因的克隆及功能研究[D].浙江杭州:中国计量学院,2013.
[20] SONG J, WU Z, WANG Z, et al. Kruppel. homolog 1 mediates juvenile hormone action to promote vitellogenesis and oocyte maturation in the migratory locust[J]. Insect Biochem Mol Biol,2014, 52(1):94-101.
[21] BOLIN K, RACHMANINOFF N, MONCADA K, et al. miR. 8modulates cytoskeletal regulators to influence cell survival and epithelial organization in Drosophila wings[J]. Dev Biol, 2016,412(1):83-98.
[22] TARIQ K, METZENDORF C, PENG W, et al. miR-8-3p regulates mitoferrin in the testes of Bactrocera dorsalis to ensure normal spermatogenesis[J]. Sci Rep,2016,6:22565. doi:10.1038/srep22565.
[23] LUCAS K J, ROY S, HA J, et al. MicroRNA-8 targets the Wingless signaling pathway in the female mosquito fat body to regulate reproductive processes[J]. Proc Natl Acad Sci USA,2015, 112(5):1440-1445.
[24] LING L, KOKOZA V A, ZHANG C, et al. MicroRNA-277 targets insulin-like peptides 7 and 8 to control lipid metabolism and reproduction in Aedes aegypti mosquitoes[J]. Proc Natl Acad Sci USA, 2017, 114(38):E8017-E8024.
[25] ESSLINGER S M, SCHWALB B, HELFER S, et al. Drosophila miR-277 controls branched-chain amino acid cata-bolism and affects lifespan[J]. RNA Biol, 2013, 10(6):1042-1056.
[26] MORIN M D, FRIG AULT J J, LYONS P J, et al. Amplification and quantification of cold. associated microRNAs in the Colorado potato beetle(Leptinotarsa decemlineata)agricultural pest[J]. Insect Mol Biol, 2017, 26(5):574-583.
[27] AVILA-BONILLA R G, YOCUPICIO-MONROY M, MARCHAT L A, et al. Analysis of the miRNA profile in C6/36 cells persistently infected with dengue virus type 2[J]. Virus Res,2017, 232:139-151.