大豆Argonaute4的生物信息学分析
|
摘要
在RNA介导的DNA甲基化途径(RNA-directed DNA methylation pathway)中,Argonaute4(AGO4)蛋白是DNA被甲基化修饰的关键蛋白。研究大豆中Argonaute4蛋白能够为大豆甲基化研究奠定基础,本研究参考NCBI、Phyto-zome、Uni Prot KB等网站及数据库,对拟南芥的AGO4基因进行同源性分析,确定了大豆中AGO4蛋白及其基因序列,并对其进行分析预测。研究发现,大豆中AGO4包括3个基因Gm AGO4A、Gm AGO4B、Gm AGO4C,它们的一级结构、二级结构及理化性质都很相似,三级结构有差异,大豆AGO4C与拟南芥AGO4结构更相似。在302个野生大豆品系中对Gm AGO4的3个基因的外显子进行核酸及蛋白序列的分析,发现一些大豆品系的蛋白质由于突变三维结构发生了变化。对大豆中AGO4及其参与的甲基化途径的研究具有指导意义。
In the RNA-directed DNA methylation pathway,the Argonaute4(AGO4) protein plays a key role in DNA methyla-tion. In order to study Argonaute4 protein in soybean and lay a foundation for the study of methylation in soybean,in this pa-per,homology analysis of AGO4 gene in Arabidopsis thaliana was performed with NCBI,Phytozome,Uni Prot KB and otherwebsites,moreover,AGO4 protein and its gene sequence in soybean were confirmed and analyzed. The results indicate thatthere are three homologous genes of At AGO4 in soybean,Gm AGO4 A,Gm AGO4 B,Gm AGO4 C respectively,which primarystructures,secondary structures and physicochemical property are similar,but the tertiary structures are different,the tertiarystructures of Gm AGO4 C and Arabidopsis AGO4 are more similar. The nucleic acid and protein sequences of the three genes' exons were analyzed in 302 wild soybean lines,and it was found that the tertiary structures of some soybean lines changed dueto mutation. The results of this paper will be helpful for further study on the function of AGO4 in the methylation pathway insoybean.
In the RNA-directed DNA methylation pathway,the Argonaute4(AGO4) protein plays a key role in DNA methyla-tion. In order to study Argonaute4 protein in soybean and lay a foundation for the study of methylation in soybean,in this pa-per,homology analysis of AGO4 gene in Arabidopsis thaliana was performed with NCBI,Phytozome,Uni Prot KB and otherwebsites,moreover,AGO4 protein and its gene sequence in soybean were confirmed and analyzed. The results indicate thatthere are three homologous genes of At AGO4 in soybean,Gm AGO4 A,Gm AGO4 B,Gm AGO4 C respectively,which primarystructures,secondary structures and physicochemical property are similar,but the tertiary structures are different,the tertiarystructures of Gm AGO4 C and Arabidopsis AGO4 are more similar. The nucleic acid and protein sequences of the three genes' exons were analyzed in 302 wild soybean lines,and it was found that the tertiary structures of some soybean lines changed dueto mutation. The results of this paper will be helpful for further study on the function of AGO4 in the methylation pathway insoybean.
引文
[1] Song Q,Lu X,Li Q,et al. Genome-wide analysis of DNA methy-lation in soybean[J]. Molecular Plant,2013,6(6):1961-1974.
[2] Rodríguez-Leal D,Castillo-Cobián A,Rodríguez-Arévalo I,et al.A primary sequence analysis of the Argonaute protein family inplants[J]. Frontiers in Plant Science,2016,7:1347.
[3] Cho Y B,Jones S I,Vodkin L O. Mutations in Argonaute5 illumi-nate epistatic interactions of the K1 and I loci leading to saddleseed color patterns in Glycine max[J]. Plant Cell,2017,29(4):708-725.
[4] Bender J. DNA methylation and epigenetics[J]. Annual Reviewof Plant Biology,2004,55(1):41-68.
[5] Zhong X. Comparative epigenomics:A powerful tool to understandthe evolution of DNA methylation[J]. New Phytologist,2016,210(1):76-80.
[6] Movahedi A,Sun W,Zhang J,et al. RNA-directed DNA methyl-ation in plants[J]. Plant Cell Reports, 2015, 34(11):1857-1862.
[7] Pck A,Dennis E S,Wang M B. Analysis of Argonaute 4-associat-ed long non-coding RNA in Arabidopsis thaliana sheds novel in-sights into gene regulation through RNA-directed DNA methylation[J]. Genes,2017,8(8):198.
[8] Wang F,Axtell M J. AGO4 is specifically required for heterochro-matic siRNA accumulation at Pol V-dependent loci in Arabidopsisthaliana[J]. Plant Journal,2017,90(1):37-47.
[9] Lahmy S,Pontier D,Bies-Etheve N,et al. Evidence for Argo-naute4-DNA interactions in RNA-directed DNA methylation inplants[J]. Genes Development,2016,30(23):2565-2570.
[10] Xie M,Yu B. siRNA-directed DNA methylation in plants[J].Current Genomics,2015,16(1):23-31.
[11] Rodríguez-Leal D,Castillo-Cobián A,Rodríguez-Arévalo I,et al.A primary sequence analysis of the ARGONAUTE protein family inplants[J]. Frontiers in Plant Science,2016,7:1347.
[12] Jacobsen S E. Establishing,maintaining and modifying DNAmethylation patterns in plants and animals[J]. Nature ReviewsGenetics,2010,11(3):204-220.
[13] Zilberman D,Cao X,Jacobsen S E. Argonaute4 control of locus-specific siRNA accumulation and DNA and histone methylation[J]. Science,2003,299(5607):716-719.
[14] Pck A,Dennis E S,Wang M B. Analysis of Argonaute 4-associat-ed long non-coding RNA in Arabidopsis thaliana sheds novel in-sights into gene regulation through RNA-directed DNA methylation[J]. Genes,2017,8(8):198.
[15] Liu W,Duttke S H,Hetzel J,et al. RNA-directed DNA methyla-tion involves co-transcriptional small-RNA-guided slicing of poly-merase V transcripts in Arabidopsis[J]. Nature Plants,2018,4(3):181-188.
[16] Parida A P,Sharma A,Sharma A K. At MBD6,a methyl CpGbinding domain protein,maintains gene silencing in Arabidopsis byinteracting with RNA binding proteins[J]. Journal of Bioscience,2017,42(1):57-68.
[17] Córdoba-Caero D,Cognat V,Ariza R R,et al. Dual control ofROS1-mediated active DNA demethylation by DNA damage-bind-ing protein 2(DDB2)[J]. Plant Journal,2017,92(6):1181.
[18] Hernándezlagana E,Rodríguezleal D,Lúa J,et al. A multigenicnetwork of ARGONAUTE4 clade members controls early megasporeformation in Arabidopsis[J]. Genetics, 2016, 204(3):1045-1056.
[19] Oliver C,Santos J L,Pradillo M. Accurate chromosome segrega-tion at first meiotic division requires AGO4,a protein involved inRNA-dependent DNA methylation in Arabidopsis thaliana[J]. Ge-netics,2016,204(2):543-553.
[20] Kong W,Li B,Wang Q,et al. Analysis of the DNA methylationpatterns and transcriptional regulation of the NB-LRR-encodinggene family in Arabidopsis thaliana[J]. Plant Molecular Biology,2018,96(6):563-575.
[21] Cao J Y,Xu Y P,Li W,et al. Genome-wide identification ofDicer-like,Argonaute,and RNA-dependent RNA polymerase genefamilies in brassicaspecies and functional analyses of their Arabi-dopsis homologs in resistance to sclerotinia sclerotiorum[J]. Fron-tiers in Plant Science,2016,7:1614.
[22] Li S,Xia Q,Wang F,et al. Laser irradiation-induced DNA methyla-tion changes are heritable and accompanied with transpositional acti-vation of m Ping in rice[J]. Frontiers in Plant Science,2017,8:363.
[23] Schalk C,Molinier J. Global genome repair factors control DNAmethylation patterns in Arabidopsis[J]. Plant Signaling&Behav-ior,2016,11(12):e1253648.
[24] Schalk C,Drevensek S,Kramdi A,et al. DNA DAMAGE BIND-ING PROTEIN 2(DDB2)shapes the DNA methylation landscape[J]. Plant Cell,2016,28(9):2043-2059.
[25] Jin X,Guo X,Zhu D,et al. miRNA profiling in the mice in re-sponse to Echinococcus multilocularis infection[J]. Acta Tropica,2017,166:39-44.
[26] Brosseau C,El O M,Adurogbangba A,et al. Antiviral defenseinvolves AGO4 in an Arabidopsis-potexvirus interaction[J]. Mo-lecular plant-microbe interactions,2016,29(11):878-888.
[27] Hamera S,Yan Y,Song X,et al. Expression of Cucumber mosaicvirus suppressor 2b alters FWA methylation and its siRNA accu-mulation in Arabidopsis thaliana[J]. Biology Open,2016,5(11):1727-1734.
[28]刘宇原,付爱根,徐敏.大豆转座子的研究现状及应用前景[J].大豆科学,2016,35(3):512-518.(Liu Y Y,Fu A G,Xu M. Research status and application prospects of soybean trans-poson[J]. Soybean Science,2016,35(3):512-518.)
[29] Song J J,Liu J,Tolia N H,et al. The crystal structure of the Argo-naute2 PAZ domain reveals an RNA binding motif in RNAi effectorcomplexes[J]. Nature Structural Biology, 2003, 10(12):1026-1032.
[30] Cerutti L,Mian N,Bateman A. Domains in gene silencing andcell differentiation proteins:The novel PAZ domain and redefini-tion of the Piwi domain[J]. Trends in Biochemical Sciences,2000,25(10):481.
[2] Rodríguez-Leal D,Castillo-Cobián A,Rodríguez-Arévalo I,et al.A primary sequence analysis of the Argonaute protein family inplants[J]. Frontiers in Plant Science,2016,7:1347.
[3] Cho Y B,Jones S I,Vodkin L O. Mutations in Argonaute5 illumi-nate epistatic interactions of the K1 and I loci leading to saddleseed color patterns in Glycine max[J]. Plant Cell,2017,29(4):708-725.
[4] Bender J. DNA methylation and epigenetics[J]. Annual Reviewof Plant Biology,2004,55(1):41-68.
[5] Zhong X. Comparative epigenomics:A powerful tool to understandthe evolution of DNA methylation[J]. New Phytologist,2016,210(1):76-80.
[6] Movahedi A,Sun W,Zhang J,et al. RNA-directed DNA methyl-ation in plants[J]. Plant Cell Reports, 2015, 34(11):1857-1862.
[7] Pck A,Dennis E S,Wang M B. Analysis of Argonaute 4-associat-ed long non-coding RNA in Arabidopsis thaliana sheds novel in-sights into gene regulation through RNA-directed DNA methylation[J]. Genes,2017,8(8):198.
[8] Wang F,Axtell M J. AGO4 is specifically required for heterochro-matic siRNA accumulation at Pol V-dependent loci in Arabidopsisthaliana[J]. Plant Journal,2017,90(1):37-47.
[9] Lahmy S,Pontier D,Bies-Etheve N,et al. Evidence for Argo-naute4-DNA interactions in RNA-directed DNA methylation inplants[J]. Genes Development,2016,30(23):2565-2570.
[10] Xie M,Yu B. siRNA-directed DNA methylation in plants[J].Current Genomics,2015,16(1):23-31.
[11] Rodríguez-Leal D,Castillo-Cobián A,Rodríguez-Arévalo I,et al.A primary sequence analysis of the ARGONAUTE protein family inplants[J]. Frontiers in Plant Science,2016,7:1347.
[12] Jacobsen S E. Establishing,maintaining and modifying DNAmethylation patterns in plants and animals[J]. Nature ReviewsGenetics,2010,11(3):204-220.
[13] Zilberman D,Cao X,Jacobsen S E. Argonaute4 control of locus-specific siRNA accumulation and DNA and histone methylation[J]. Science,2003,299(5607):716-719.
[14] Pck A,Dennis E S,Wang M B. Analysis of Argonaute 4-associat-ed long non-coding RNA in Arabidopsis thaliana sheds novel in-sights into gene regulation through RNA-directed DNA methylation[J]. Genes,2017,8(8):198.
[15] Liu W,Duttke S H,Hetzel J,et al. RNA-directed DNA methyla-tion involves co-transcriptional small-RNA-guided slicing of poly-merase V transcripts in Arabidopsis[J]. Nature Plants,2018,4(3):181-188.
[16] Parida A P,Sharma A,Sharma A K. At MBD6,a methyl CpGbinding domain protein,maintains gene silencing in Arabidopsis byinteracting with RNA binding proteins[J]. Journal of Bioscience,2017,42(1):57-68.
[17] Córdoba-Caero D,Cognat V,Ariza R R,et al. Dual control ofROS1-mediated active DNA demethylation by DNA damage-bind-ing protein 2(DDB2)[J]. Plant Journal,2017,92(6):1181.
[18] Hernándezlagana E,Rodríguezleal D,Lúa J,et al. A multigenicnetwork of ARGONAUTE4 clade members controls early megasporeformation in Arabidopsis[J]. Genetics, 2016, 204(3):1045-1056.
[19] Oliver C,Santos J L,Pradillo M. Accurate chromosome segrega-tion at first meiotic division requires AGO4,a protein involved inRNA-dependent DNA methylation in Arabidopsis thaliana[J]. Ge-netics,2016,204(2):543-553.
[20] Kong W,Li B,Wang Q,et al. Analysis of the DNA methylationpatterns and transcriptional regulation of the NB-LRR-encodinggene family in Arabidopsis thaliana[J]. Plant Molecular Biology,2018,96(6):563-575.
[21] Cao J Y,Xu Y P,Li W,et al. Genome-wide identification ofDicer-like,Argonaute,and RNA-dependent RNA polymerase genefamilies in brassicaspecies and functional analyses of their Arabi-dopsis homologs in resistance to sclerotinia sclerotiorum[J]. Fron-tiers in Plant Science,2016,7:1614.
[22] Li S,Xia Q,Wang F,et al. Laser irradiation-induced DNA methyla-tion changes are heritable and accompanied with transpositional acti-vation of m Ping in rice[J]. Frontiers in Plant Science,2017,8:363.
[23] Schalk C,Molinier J. Global genome repair factors control DNAmethylation patterns in Arabidopsis[J]. Plant Signaling&Behav-ior,2016,11(12):e1253648.
[24] Schalk C,Drevensek S,Kramdi A,et al. DNA DAMAGE BIND-ING PROTEIN 2(DDB2)shapes the DNA methylation landscape[J]. Plant Cell,2016,28(9):2043-2059.
[25] Jin X,Guo X,Zhu D,et al. miRNA profiling in the mice in re-sponse to Echinococcus multilocularis infection[J]. Acta Tropica,2017,166:39-44.
[26] Brosseau C,El O M,Adurogbangba A,et al. Antiviral defenseinvolves AGO4 in an Arabidopsis-potexvirus interaction[J]. Mo-lecular plant-microbe interactions,2016,29(11):878-888.
[27] Hamera S,Yan Y,Song X,et al. Expression of Cucumber mosaicvirus suppressor 2b alters FWA methylation and its siRNA accu-mulation in Arabidopsis thaliana[J]. Biology Open,2016,5(11):1727-1734.
[28]刘宇原,付爱根,徐敏.大豆转座子的研究现状及应用前景[J].大豆科学,2016,35(3):512-518.(Liu Y Y,Fu A G,Xu M. Research status and application prospects of soybean trans-poson[J]. Soybean Science,2016,35(3):512-518.)
[29] Song J J,Liu J,Tolia N H,et al. The crystal structure of the Argo-naute2 PAZ domain reveals an RNA binding motif in RNAi effectorcomplexes[J]. Nature Structural Biology, 2003, 10(12):1026-1032.
[30] Cerutti L,Mian N,Bateman A. Domains in gene silencing andcell differentiation proteins:The novel PAZ domain and redefini-tion of the Piwi domain[J]. Trends in Biochemical Sciences,2000,25(10):481.