灵芝精氨酸甲基转移酶基因鉴定及表达分析
|
摘要
目的:在灵芝转录组基础上,对灵芝蛋白质精氨酸甲基转移酶(PRMTs)GLPRMT1,GLPRMT2和GLPRMT3基因进行全面的生物信息学分析。方法:利用生物信息学方法对灵芝GLPRMT1,GLPRMT2和GLPRMT3基因编码氨基酸序列的理化特性、亲/疏水性、功能域、二级结构、三级结构和系统发育进化等进行分析和预测;利用转录组FPKM分析灵芝不同生长时期GLPRMT1,GLPRMT2和GLPRMT3基因的相对表达量。结果:GLPRMT1和GLPRMT2均具有完整的开放阅读框且为全长,而GLPRMT3不为全长互补脱氧核糖核酸;GLPRMT1,GLPRMT2和GLPRMT3都具有蛋白质精氨酸甲基转移酶最保守的Ado Met-MTases结构域;GLPRMT1,GLPRMT2,GLPRMT3分别与真菌的PRMT3家族,PRMT1家族和PRMT5家族聚为一支;GLPRMT2的表达量明显高于GLPRMT1和GLPRMT3,且3个蛋白质精氨酸甲基转移酶基因表达随着灵芝个体的发育均呈上升趋势。结论:本研究结果为揭示灵芝的表观调控机制提供理论基础。
Objective: This study was based on data of the transcriptome sequencing of Ganoderma,GLPRMT1,GLPRMT2 and GLPRMT3 were completed in detail by using bioinformatics method. Method:GLPRMT1,GLPRMT2 and GLPRMT3 were analyzed and predicted by the tools of bioinformatics in the following aspects: physical and chemical characteristics of amino acid sequences, function domain, hyophobicity or hydrophilicity,secondary structure and tertiary structure of protein,molecular phylogenetic evolution,and so on;expression levels of GLPRMT1,GLPRMT2 and GLPRMT3 were identified by FPKM from the transcriptome data.Result: Open reading frame finder indicated that GLPRMT1 and GLPRMT2 genes were full-length, while GLPRMT3 was partial; structural domain of GLPRMT1,GLPRMT2 and GLPRMT3 showed high homology with Ado Met-MTases domains; GLPRMT1,GLPRMT2 and GLPRMT3 had relative close relationship to PRMT3 family,PRMT1 family and PRMT5 family of fungus, respectively. From transcriptome data, transcripted level of GLPRMT2 was significantly higher than GLPRMT1 and GLPRMT3,and transcripted level of these three genes have increased significantly in growing periods of Ganoderma. Conclusion: These results provide basis for further understand the function of arginine methyltransferase and epigenetic regulation of Ganoderma.
Objective: This study was based on data of the transcriptome sequencing of Ganoderma,GLPRMT1,GLPRMT2 and GLPRMT3 were completed in detail by using bioinformatics method. Method:GLPRMT1,GLPRMT2 and GLPRMT3 were analyzed and predicted by the tools of bioinformatics in the following aspects: physical and chemical characteristics of amino acid sequences, function domain, hyophobicity or hydrophilicity,secondary structure and tertiary structure of protein,molecular phylogenetic evolution,and so on;expression levels of GLPRMT1,GLPRMT2 and GLPRMT3 were identified by FPKM from the transcriptome data.Result: Open reading frame finder indicated that GLPRMT1 and GLPRMT2 genes were full-length, while GLPRMT3 was partial; structural domain of GLPRMT1,GLPRMT2 and GLPRMT3 showed high homology with Ado Met-MTases domains; GLPRMT1,GLPRMT2 and GLPRMT3 had relative close relationship to PRMT3 family,PRMT1 family and PRMT5 family of fungus, respectively. From transcriptome data, transcripted level of GLPRMT2 was significantly higher than GLPRMT1 and GLPRMT3,and transcripted level of these three genes have increased significantly in growing periods of Ganoderma. Conclusion: These results provide basis for further understand the function of arginine methyltransferase and epigenetic regulation of Ganoderma.
引文
[1]Choudhuri S.From Waddington's epigenetic landscape to small noncoding RNA:Some important milestones in the history of epigenetics research[J].Toxicol Mech Methods,2011,21(4):252-274.
[2]康静婷,梁前进,梁辰,等.表观遗传学研究进展[J].科技导报,2013,31(19):66-74.
[3]Barski A,Cuddapah S,Cui K,et al.High-resolution profiling of histone methylations in the human genome[J].Cell,2007,129(4):823-837.
[4]王丽丽,朱祯,李霞.精氨酸甲基转移酶及其生物学功能研究进展[J].中国农学通报,2008,24(7):39-44.
[5]李想,张飞雄.组蛋白甲基化的研究进展[J].遗传,2004,26(2):244-248.
[6]侯毅枫,邓娴,陆天聪,等.蛋白质精氨酸甲基化参与基因转录后调控的研究进展[J].生命科学,2015,27(3):351-362.
[7]Bedford M T,Richard S.Arginine methylation:an emerging regulator of protein function[J].Mol Cell,2005,18(3):263-272.
[8]国家药典委员会.中华人民共和国药典.一部[S].北京:中国医药科技出版社,2015:188.
[9]Shiao M S.Natural products of the medicinal fungus Ganoderma lucidum:occurrence,biological activities,and pharmacological functions[J].Chem Rec,2003,3(3):172-180.
[10]Kimura Y,Taniguchi M,Baba K.Antitumor and antimetastatic effects on liver of triterpenoid fractions of Ganoderma lucidum:mechanism of action and isolation of an active substance[J].Anticancer Res,2001,22(6A):3309-3318.
[11]Shi M,Yang Y,Hu X,et al.Effect of ultrasonic extraction conditions on antioxidative and immunomodulatory activities of a Ganoderma lucidum polysaccharide originated from fermented soybean curd residue[J].Food Chem,2014,doi:10.1016/j.foodchem.2014.01.037.
[12]Chen S,Xu J,Liu C,et al.Genome sequence of the model medicinal mushroom Ganoderma lucidum[J].Nat Commun,2012,doi:10.1038/ncomms1923.
[13]程智逵,过倩萍,伍会健.组蛋白精氨酸甲基化修饰对基因转录的调控[J].生物化学与生物物理进展,2008,35(11):1225-1230.
[14]谢萍,田春艳,张令强,等.组蛋白甲基转移酶的研究进展[J].遗传,2007,29(9):1035-1041.
[15]Pei Y,Niu L,Lu F,et al.Mutations in the typeⅡprotein arginine methyltransferase At PRMT5 result in pleiotropic developmental defects in Arabidopsis[J].Plant Physiol,2007,144(4):1913-1923.
[16]Ahmad A,Dong Y,Cao X.Characterization of the PRMT gene family in rice reveals conservation of arginine methylation[J].PLo S One,2011,6(8):e22664.
[17]钱叶雄,徐士杰,张亚男,等.玉米精氨酸甲基转移酶蛋白家族生物信息学分析[J].生物技术进展,2014,4(1):22-29.
[18]查良平,袁媛,黄璐琦,等.厚朴MVA途径相关基因鉴定及生物信息学分析[J].中国中药杂志,2015,40(11):2077-2083.
[19]Bedford M T.Arginine methylation at a glance[J].J Cell Sci,2007,120(24):4243-4246.
[20]Boisvert F M,Chénard C A,Richard S.Protein interfaces in signaling regulated by arginine methylation[J].Sci Signal,2005,dio:10.1126/stke.2712005re2.
[21]Hang R,Liu C,Ahmad A,et al.Arabidopsis protein arginine methyltransferase 3 is required for ribosome biogenesis by affecting precursor ribosomal RNA processing[J].Proc Natl Acad Sci USA,2014,111(45):16190-16195.
[22]Deng X,Gu L,Liu C,et al.Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing[J].Proc Natl Acad Sci USA,2010,107(44):19114-19119.
[23]齐琳洁,袁媛,黄璐琦,等.金银花组蛋白甲基转移酶基因生物信息学及表达分析[J].中国中药杂志,2015,40(11):2062-2067.
[24]刘凡,张建斌,贾彩红,等.香蕉Ma PRMT1基因的分离及表达分析[J].安徽农业科学,2008,36(27):11671-11673.
[2]康静婷,梁前进,梁辰,等.表观遗传学研究进展[J].科技导报,2013,31(19):66-74.
[3]Barski A,Cuddapah S,Cui K,et al.High-resolution profiling of histone methylations in the human genome[J].Cell,2007,129(4):823-837.
[4]王丽丽,朱祯,李霞.精氨酸甲基转移酶及其生物学功能研究进展[J].中国农学通报,2008,24(7):39-44.
[5]李想,张飞雄.组蛋白甲基化的研究进展[J].遗传,2004,26(2):244-248.
[6]侯毅枫,邓娴,陆天聪,等.蛋白质精氨酸甲基化参与基因转录后调控的研究进展[J].生命科学,2015,27(3):351-362.
[7]Bedford M T,Richard S.Arginine methylation:an emerging regulator of protein function[J].Mol Cell,2005,18(3):263-272.
[8]国家药典委员会.中华人民共和国药典.一部[S].北京:中国医药科技出版社,2015:188.
[9]Shiao M S.Natural products of the medicinal fungus Ganoderma lucidum:occurrence,biological activities,and pharmacological functions[J].Chem Rec,2003,3(3):172-180.
[10]Kimura Y,Taniguchi M,Baba K.Antitumor and antimetastatic effects on liver of triterpenoid fractions of Ganoderma lucidum:mechanism of action and isolation of an active substance[J].Anticancer Res,2001,22(6A):3309-3318.
[11]Shi M,Yang Y,Hu X,et al.Effect of ultrasonic extraction conditions on antioxidative and immunomodulatory activities of a Ganoderma lucidum polysaccharide originated from fermented soybean curd residue[J].Food Chem,2014,doi:10.1016/j.foodchem.2014.01.037.
[12]Chen S,Xu J,Liu C,et al.Genome sequence of the model medicinal mushroom Ganoderma lucidum[J].Nat Commun,2012,doi:10.1038/ncomms1923.
[13]程智逵,过倩萍,伍会健.组蛋白精氨酸甲基化修饰对基因转录的调控[J].生物化学与生物物理进展,2008,35(11):1225-1230.
[14]谢萍,田春艳,张令强,等.组蛋白甲基转移酶的研究进展[J].遗传,2007,29(9):1035-1041.
[15]Pei Y,Niu L,Lu F,et al.Mutations in the typeⅡprotein arginine methyltransferase At PRMT5 result in pleiotropic developmental defects in Arabidopsis[J].Plant Physiol,2007,144(4):1913-1923.
[16]Ahmad A,Dong Y,Cao X.Characterization of the PRMT gene family in rice reveals conservation of arginine methylation[J].PLo S One,2011,6(8):e22664.
[17]钱叶雄,徐士杰,张亚男,等.玉米精氨酸甲基转移酶蛋白家族生物信息学分析[J].生物技术进展,2014,4(1):22-29.
[18]查良平,袁媛,黄璐琦,等.厚朴MVA途径相关基因鉴定及生物信息学分析[J].中国中药杂志,2015,40(11):2077-2083.
[19]Bedford M T.Arginine methylation at a glance[J].J Cell Sci,2007,120(24):4243-4246.
[20]Boisvert F M,Chénard C A,Richard S.Protein interfaces in signaling regulated by arginine methylation[J].Sci Signal,2005,dio:10.1126/stke.2712005re2.
[21]Hang R,Liu C,Ahmad A,et al.Arabidopsis protein arginine methyltransferase 3 is required for ribosome biogenesis by affecting precursor ribosomal RNA processing[J].Proc Natl Acad Sci USA,2014,111(45):16190-16195.
[22]Deng X,Gu L,Liu C,et al.Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing[J].Proc Natl Acad Sci USA,2010,107(44):19114-19119.
[23]齐琳洁,袁媛,黄璐琦,等.金银花组蛋白甲基转移酶基因生物信息学及表达分析[J].中国中药杂志,2015,40(11):2062-2067.
[24]刘凡,张建斌,贾彩红,等.香蕉Ma PRMT1基因的分离及表达分析[J].安徽农业科学,2008,36(27):11671-11673.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |