基于转录组信息的黑果枸杞WD40蛋白质家族分析
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摘要
WD40蛋白质为真核生物中一种常见蛋白质,广泛参与植物生长发育的多种生物过程,在蛋白质-蛋白质及蛋白质-DNA的相互作用中发挥重要作用。为系统分析黑果枸杞WD40蛋白质家族成员,本研究以黑果枸杞青色期、转色期和成熟期3个发育时期的果实转录组测序数据为基础,结合Nr、Nt、Pfam、KOG/COG、Swiss-prot、KEGG及GO 7个数据库和NCBI网站,对黑果枸杞WD40蛋白质编码基因进行筛选注释。结果表明,共得到77个黑果枸杞WD40蛋白质家族成员,黑果枸杞WD40蛋白质结构域组成多样,且在不同物种间高度保守;亚细胞定位预测分析表明,黑果枸杞WD40蛋白质家族成员多位于细胞核及细胞质中;黑果枸杞和拟南芥WD40蛋白质共建的系统进化树可分为五个亚家族; WD40蛋白质家族成员编码基因随果实发育的表达模式表明,黑果枸杞WD40蛋白质家族成员可能参与了其果实花青素的变化调控。本研究结果为枸杞WD40蛋白质的分离及功能研究奠定了一定的理论基础。
WD40 protein is one of the most common transcription factor families in eukaryotes. It is widely involved in many biological processes and plays an important role in protein-protein and protein-DNA interactions. In order to systematically analyze the WD40 protein family members of Lycium ruthenicum Murr.,the transcriptome sequencing data of the fruit in the green,colouring,black periods of L. ruthenicum Murr.. was analyzed with the Nr、Nt、Pfam、KOG/COG、Swiss-prot、KEGG and GO database and NCBI website to screen and annotate the encoding genes of WD40 protein in L. ruthenicum Murr. We have screened 77 members of WD40 protein family in L. ruthenicum Murr.. The structural domain of WD40 protein in L. ruthenicum Murr. is diverse,and which is highly conserved among different species. The results of the subcellular localization demonstrated WD40 protein family in L. ruthenicum Murr. was mostly located in the nucleus and cytoplasm. The phylogenetic trees of WD40 protein family of L. ruthenicum Murr. and Arabidopsis thaliana showed that WD40 protein family of L. ruthenicum Murr. contained five subfamilies. The expression WD40 genes of L.ruthenicum Murr. dependent furit development indicated that WD40 protein family members of L. ruthenicum Murr. may be involved in the regulation of anthocyanin in their fruit. This study systematically analyzed the members of WD40 protein family of L. ruthenicum Murr.,which provide the basis for the study on the function and isolation of WD40 protein from Lycium barbarum Murr..
WD40 protein is one of the most common transcription factor families in eukaryotes. It is widely involved in many biological processes and plays an important role in protein-protein and protein-DNA interactions. In order to systematically analyze the WD40 protein family members of Lycium ruthenicum Murr.,the transcriptome sequencing data of the fruit in the green,colouring,black periods of L. ruthenicum Murr.. was analyzed with the Nr、Nt、Pfam、KOG/COG、Swiss-prot、KEGG and GO database and NCBI website to screen and annotate the encoding genes of WD40 protein in L. ruthenicum Murr. We have screened 77 members of WD40 protein family in L. ruthenicum Murr.. The structural domain of WD40 protein in L. ruthenicum Murr. is diverse,and which is highly conserved among different species. The results of the subcellular localization demonstrated WD40 protein family in L. ruthenicum Murr. was mostly located in the nucleus and cytoplasm. The phylogenetic trees of WD40 protein family of L. ruthenicum Murr. and Arabidopsis thaliana showed that WD40 protein family of L. ruthenicum Murr. contained five subfamilies. The expression WD40 genes of L.ruthenicum Murr. dependent furit development indicated that WD40 protein family members of L. ruthenicum Murr. may be involved in the regulation of anthocyanin in their fruit. This study systematically analyzed the members of WD40 protein family of L. ruthenicum Murr.,which provide the basis for the study on the function and isolation of WD40 protein from Lycium barbarum Murr..
引文
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[5]严莉,陈建伟,王翠平,乔改霞,李健.黑果枸杞WD40编码基因Lr AN11的克隆及表达分析[J].核农学报,2017,31(11):2103-2112
[6]Xu C,Min J.Structure and function of WD40 domain proteins[J].Protein&Cell,2011,2(3):202-214
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[14]Zhang C,Zhang F.The multifunctions of WD40 proteins in genome integrity and cell cycle progression[J].Journal of Genomics,2015,10(3):40-50
[15]Lee M H,Lee S H,Kim H,Jin J B,Kim D H,HwangⅠ.AWD40 repeat protein,Arabidopsis Sec13 homolog 1,may play a role in vacuolar trafficking by controlling the membrane association of At DRP2A[J].Molecules&Cells,2006,22(2):210-219
[16]Gachomo E W,Jimenez-Lopez J C,Baptiste L J,Kotchoni S O.GIGANTUS1(GTS1),a member of transducin/WD40 protein superfamily,controls seed germination,growth and biomass accumulation through ribosome-biogenesis protein interactions in Arabidopsis thaliana[J].BMC Plant Biology,2014,14(1):37-54
[17]Cheng Y,Zhu W,Chen Y,Ito S S,Asami T,Wang X L.Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-b HLH-WD40 complex by GSK3-like kinases[J].Elife,2014,3(3):69-76
[18]Beris D,Kapolas G,Livanos P,Roussis A,Milioni D,Haralampidis K.RNAi-mediated silencing of the Arabidopsis thaliana ULCS1 gene,encoding a WDR protein,results in cell wall modification impairment and plant infertility[J].Plant Science An International Journal of Experimental Plant Biology,2016,245(2):71-83
[19]Ge J,Li B,Dan S,Xie J Y,Long J Y,Dong H S.Tobacco TTG2regulates vegetative growth and seed production via the predominant role of ARF8 in cooperation with ARF17 and ARF19[J].BMC Plant Biology,2016,16(1):126-143
[20]Lee S,Lee J,Paek K H,Kwon S Y,Cho H S,Kim S J,Park J M.A novel WD40 protein,BnSWD1,is involved in salt stress in Brassica napus[J].Plant Biotechnology Reports,2010,4(2):165-172
[21]Guerriero G,Silvestrini L,Obersriebnig M,Hausman J F,Strauss J,EzcurraⅠ.A WDR gene is a conserved member of a chitin synthase gene cluster and influences the cell wall in aspergillus nidulans[J].International Journal of Molecular Sciences,2016,17(7):1031-1045
[22]赵秀玲.黑果枸杞生理活性成分研究进展[J].食品与生物技术学报,2016,35(6):561-568
[23]林丽,张裴斯,晋玲,贺正阳,高素芳.黑果枸杞的研究进展[J].中国药房,2013,24(47):4493-4497
[24]Feng C,Chen M,Xu C J,Bai L,Yin X R,Li X,Allan A C,Ferguson L B,Chen K S.Transcriptomic analysis of Chinese bayberry(Myrica rubra)fruit development and ripening using RNA-Seq[J].BMC Genomics,2012,13(1):13-19
[25]Ouyang Y,Huang X,Lu Z,Yao J L.Genomic survey,expression profile and co-expression network analysis of Os WD40 family in rice[J].BMC Genomics,2012,13(1):100-115
[26]An X H,Tian Y,Chen K Q,Wang X F,Hao Y J.The apple WD40protein Md TTG1 interacts with bHLH but not MYB proteins to regulate anthocyanin accumulation[J].Journal of Plant Physiology,2012,169(7):710-717
[27]Zhu Q,Li B,Mu S,Han B,Cui R.TTG2-regulated development is related to expression of putative auxin response factor genes in tobacco[J].BMC Genomics,2013,14(1):806-821
[2]Stirnimann C U,Petsalaki E,Russell R B,Müller C W.WD40proteins propel cellular networks[J].Trends in Biochemical Sciences,2010,35(10):565-574
[3]Wang Y,Jiang F,Zhuo Z,Wu X H,Wu Y D.A method for WD40repeat detection and secondary structure prediction[J].PLoS One,2013,8(6):e65705
[4]Wang C,Dong X,Han L,Su X D,Zhang Z.Identification of WD40 repeats by secondary structure-aided profile-profile alignment[J].Journal of Theoretical Biology,2016,398:122-129
[5]严莉,陈建伟,王翠平,乔改霞,李健.黑果枸杞WD40编码基因Lr AN11的克隆及表达分析[J].核农学报,2017,31(11):2103-2112
[6]Xu C,Min J.Structure and function of WD40 domain proteins[J].Protein&Cell,2011,2(3):202-214
[7]Yan S,Willis J.WD40-repeat protein WDR18 collaborates with Top BP1 to facilitate DNA damage checkpoint signaling[J].Biochemical&Biophysical Research Communications,2013,431(3):466-71
[8]Mishra A K,Puranik S,Prasad M.Structure and regulatory networks of WD40 protein in plants[J].Journal of Plant Biochemistry&Biotechnology,2012,21(1):32-39
[9]Mishra A K,Muthamilarasan M,Khan Y,Parida S K,Prasad M.Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet(Setaria italica L.)[J].PLoSOne,2014,9(1):e86852
[10]Hua Z,Vierstra R D.The cullin-RING ubiquitin-protein ligases[J].Annual Review of Plant Biology,2011,62(1):299-334
[11]Appleton B,Wu P C.The crystal structure of murine coronin-1:Aregulator of actin cytoskeletal dynamics in lymphocytes[J].Structure,2006,14(1):87-96
[12]Lim N R,Yeap Y C,Ang C S,Williamson N A,Bogoyevitch M A.Aurora A phosphorylation of WD40-repeat protein 62 in mitotic spindle regulation[J].Cell Cycle,2016,15(3):413-424
[13]Han Z,Guo L,Wang H,Shen Y,Deng X W.Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5[J].Molecular Cell,2006,22(1):137-144
[14]Zhang C,Zhang F.The multifunctions of WD40 proteins in genome integrity and cell cycle progression[J].Journal of Genomics,2015,10(3):40-50
[15]Lee M H,Lee S H,Kim H,Jin J B,Kim D H,HwangⅠ.AWD40 repeat protein,Arabidopsis Sec13 homolog 1,may play a role in vacuolar trafficking by controlling the membrane association of At DRP2A[J].Molecules&Cells,2006,22(2):210-219
[16]Gachomo E W,Jimenez-Lopez J C,Baptiste L J,Kotchoni S O.GIGANTUS1(GTS1),a member of transducin/WD40 protein superfamily,controls seed germination,growth and biomass accumulation through ribosome-biogenesis protein interactions in Arabidopsis thaliana[J].BMC Plant Biology,2014,14(1):37-54
[17]Cheng Y,Zhu W,Chen Y,Ito S S,Asami T,Wang X L.Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-b HLH-WD40 complex by GSK3-like kinases[J].Elife,2014,3(3):69-76
[18]Beris D,Kapolas G,Livanos P,Roussis A,Milioni D,Haralampidis K.RNAi-mediated silencing of the Arabidopsis thaliana ULCS1 gene,encoding a WDR protein,results in cell wall modification impairment and plant infertility[J].Plant Science An International Journal of Experimental Plant Biology,2016,245(2):71-83
[19]Ge J,Li B,Dan S,Xie J Y,Long J Y,Dong H S.Tobacco TTG2regulates vegetative growth and seed production via the predominant role of ARF8 in cooperation with ARF17 and ARF19[J].BMC Plant Biology,2016,16(1):126-143
[20]Lee S,Lee J,Paek K H,Kwon S Y,Cho H S,Kim S J,Park J M.A novel WD40 protein,BnSWD1,is involved in salt stress in Brassica napus[J].Plant Biotechnology Reports,2010,4(2):165-172
[21]Guerriero G,Silvestrini L,Obersriebnig M,Hausman J F,Strauss J,EzcurraⅠ.A WDR gene is a conserved member of a chitin synthase gene cluster and influences the cell wall in aspergillus nidulans[J].International Journal of Molecular Sciences,2016,17(7):1031-1045
[22]赵秀玲.黑果枸杞生理活性成分研究进展[J].食品与生物技术学报,2016,35(6):561-568
[23]林丽,张裴斯,晋玲,贺正阳,高素芳.黑果枸杞的研究进展[J].中国药房,2013,24(47):4493-4497
[24]Feng C,Chen M,Xu C J,Bai L,Yin X R,Li X,Allan A C,Ferguson L B,Chen K S.Transcriptomic analysis of Chinese bayberry(Myrica rubra)fruit development and ripening using RNA-Seq[J].BMC Genomics,2012,13(1):13-19
[25]Ouyang Y,Huang X,Lu Z,Yao J L.Genomic survey,expression profile and co-expression network analysis of Os WD40 family in rice[J].BMC Genomics,2012,13(1):100-115
[26]An X H,Tian Y,Chen K Q,Wang X F,Hao Y J.The apple WD40protein Md TTG1 interacts with bHLH but not MYB proteins to regulate anthocyanin accumulation[J].Journal of Plant Physiology,2012,169(7):710-717
[27]Zhu Q,Li B,Mu S,Han B,Cui R.TTG2-regulated development is related to expression of putative auxin response factor genes in tobacco[J].BMC Genomics,2013,14(1):806-821