玉米转录因子NF-YB基因家族的生物信息学分析
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摘要
为揭示玉米NF-YB基因家族的功能,本研究利用生物信息学手段,鉴定了玉米NF-YB基因家族,并系统的分析了该基因家族各蛋白的理化性质、基因的染色体定位、保守结构域、基因结构、系统进化、磷酸化位点、启动子和基因组织表达。结果表明:玉米基因组中含有21个NF-YB基因,所编码的蛋白质均位于细胞核,且不含有跨膜结构。这些基因不均匀地分布于玉米的9条染色体上,均含有高度保守的结构域CBFD_NFYB_HMF,系统进化分析将其分为3类。磷酸化位点分析表明,玉米NF-YB家族存在着大量的磷酸化位点。启动子分析表明,基因家族启动子区域均含有大量的逆境胁迫应答顺式作用元件。组织表达分析发现,至少有18个基因可以进行表达,其中有5个基因表现出组织特异性,不同基因在不同组织、不同时期的表达具有时序性。玉米NF-YB基因家族核心结构域的保守性、基因功能的分化、启动子序列中的大量逆境相关元件、基因表达的差异性,可能都是玉米更好调控自身生长发育和适应逆境的结果。研究结果为进一步解析玉米NF-YB基因家族的功能提供参考。
To reveal the function of NF-YB gene family in Zea mays, the NF-YB gene family was identified by bioinformatics method. The physicochemical properties of the proteins, gene position on chromosomes,conservative domain, gene structure, phylogenetic evolution, phosphorylation site, promoter and tissue expression of the gene family were systematically analyzed. The results showed that 21 NF-YB genes were identified in maize genome, and all the encoded protein located in nucleus without transmembrane domain. The genes were unevenly distributed on 9 chromosomes of maize, and all contained highly conserved structure domain CBFD_NFYB_HMF,which were classified into three types according to phylogenetic analysis. The phosphorylation site analysis indicated that there were abundant of phosphorylation sites in maize NF-YB family. Promoter analysis revealed that the promoter regions of gene family contained abundant cis-acting elements in stress response. Tissue expression analysis found that there are at least 18 g enes could be expressed, including 5 genes which showed tissue specificity, and the expression of different genes in different tissues and different periods was time-series.That conservatism of the core domain, the differentiation of gene function, the large number of adversity-related components in promoter sequence and the differential gene expression of maize NF-YB gene family might be resulted in better regulation of maize growth and development and adaptation to adversity. This study could provide reference for further study on the function of NF-YB gene family in maize.
To reveal the function of NF-YB gene family in Zea mays, the NF-YB gene family was identified by bioinformatics method. The physicochemical properties of the proteins, gene position on chromosomes,conservative domain, gene structure, phylogenetic evolution, phosphorylation site, promoter and tissue expression of the gene family were systematically analyzed. The results showed that 21 NF-YB genes were identified in maize genome, and all the encoded protein located in nucleus without transmembrane domain. The genes were unevenly distributed on 9 chromosomes of maize, and all contained highly conserved structure domain CBFD_NFYB_HMF,which were classified into three types according to phylogenetic analysis. The phosphorylation site analysis indicated that there were abundant of phosphorylation sites in maize NF-YB family. Promoter analysis revealed that the promoter regions of gene family contained abundant cis-acting elements in stress response. Tissue expression analysis found that there are at least 18 g enes could be expressed, including 5 genes which showed tissue specificity, and the expression of different genes in different tissues and different periods was time-series.That conservatism of the core domain, the differentiation of gene function, the large number of adversity-related components in promoter sequence and the differential gene expression of maize NF-YB gene family might be resulted in better regulation of maize growth and development and adaptation to adversity. This study could provide reference for further study on the function of NF-YB gene family in maize.
引文
Ba llif J.,Endo S.,Kotani M.,Macadam J.,and Wu Y.J.,2011,Over-expression of HAP3b enhances primary root elongation in Arabidopsis,Plant Physiol.Biochem.,49(6):579-583
Brambilla V.,and Fornara F.,2016,Y flowering?Regulation and activity of CONSTANS and CCT-domain proteins in Arabidop-sis and crop species,Biochim.Biophys.Acta Gene Regul.Mech.,1860(5):655-660
Brown A.P.C.,Dunn M.A.,Goddard N.J.,and Hughes M.A.,2001,Identification of a novel low-temperature-response element in the promoter of the barley(Hordeum vulgare L.)gene blt101.1,Planta,213(5):770-780
Chen C.J.,Xia R.,Chen H.,and He Y.H.,2018,TBtools,a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface,Bio.Rxiv.,doi:https://doi.org/10.1101/289660
Ding H.X.,Liu F.,Zhang L.J.,Yu Y.X.,and Wei Q.,2017,The structure and function of NF-Y in plants,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(5):1691-1701(丁慧霞,刘凤,张利娟,余义勋,魏倩,2017,植物中NF-Y转录因子的结构和功能研究进展,分子植物育种,15(5):1691-1701)
Frontini M.,Imbriano C.,Manni I.,and Mantovani R.,2004,Cell-cycle regulation of NF-YC nuclear localization,Cell Cycle,3(2):217-222
Hackenberg D.,Wu Y.,Voigt A.,Adams R.,Schramm P.,and Grimm B.,2012,Studies on differential nuclear translocation mechanism and assembly of the three subunits of the Arabidopsis thaliana transcription factor NF-Y,Mol.Plant,5(4):876-888
Huang M.K.,Hu Y.L.,Liu X.,Li Y.,and Hou X.L.,2015a,Arabidopsis LEAFY COTYLEDON1 controls cell fate determination during post-embryonic development,Front.Plant Sci.,6:955
Huang M.,Hu Y.,Liu X.,Li Y.,and Hou X.,2015b,Arabidopsis leafy cotyledon1 mediates postembryonic development via interacting with Phytochrome-interacting factor 4,Plant Cell,27(11):3099-3111
Jeffares D.C.,Penkett C.J.,and Bahler J.,2008,Rapidly regulated genes are intron poor,Trends Genet.,24(8):375-378
Junker A.,Monke G.,Rutten T.,Keilwagen J.,Seifert M.,Thi T.M.N.,and Renou J.P.,Balzergue S.,Viehover P.,Hahnel U.,Ludwig-Müller J.,Altschmied L.,Conrad U.,Weisshaar B.,and Baumlein H.,2012,Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana,Plant J.,71(3):427-442
Le L.,Xu H.L.,Yang X.L.,Li L.X.,and Hu Y.K.,2011,Genomewide identification,classification and expression analysis of LEA gene family in soybean,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),44(19):3945-3954(李乐,许红亮,杨兴露,李雅轩,胡英考,2011,大豆LEA基因家族全基因组鉴定、分类和表达,中国农业科学,44(19):3945-3954)
Li S.,Li K.,Ju Z.,Cao D.Y.,Fu D.Q.,Zhu H.L.,Zhu B.Z.,and Luo Y.B.,2016,Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening,BMC Genomics,17(1):36
Li Y.L.,Liu J.H.,Zheng J.R.,and Hu J.G.,2013,Gene expression profile of sweet corn ears under heat stress,Zuowu Xuebao(Acta Agronomica Sinica),39(2):269-279(李余良,刘建华,郑锦荣,胡建广,2013,高温胁迫下甜玉米雌穗发育基因差异表达谱分析,作物学报,39(2):269-279)
Liang M.X.,Yin X.Z.,Lin Z.Y.,Zheng Q.S.,Liu G.H.,and Zhao G.M.,2014,Identification and characterization of NF-Ytranscription factor families in Canola(Brassica napus L.),Planta,239(1):107-126
Liu J.,Xu Z.Z.,Yuan N.,Guo Y.,Zhang B.L.,and Du J.C.,2016,Genome-wide analysis of NF-YB gene family in gossypium hirsutum l,Huabei Nongxuebao(Acta Agriculturae BorealiSinica),31(5):21-27(刘静,徐珍珍,袁娜,郭月,张保龙,杜建厂,2016,陆地棉NF-YB基因家族的全基因组分析,华北农学报,31(5):21-27)
Nelson D.E.,Repetti P.P.,Adams T.R.,Creelman R.A.,Wu J.,Warner D.C.,Anstrom D.C.,Bensen R.J.,and Heard J.E.,2007,Plant nuclear factor Y(NF-Y)B subunits confer drought tolerance and lead to improved corn yields on water-limited acres,Proc.Natl.Acad.Sci.USA,104(42):16450-16455
Qin F.,Li J.,Zhang G.Y.,Zhao J.,Chen S.Y.,and Liu Q.,2003,Isolation and structural analysis of DRE-binding transcription factor from maize(Zea mays L.),Acta Botanica Sinica,45(3):331-339
Quach T.N.,Nguyen H.T.M.,Valliyodan B.,Joshi T.,Xu D.,and Nguyen H.T.,2015,Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response,Mol.Genet.Genomics,290(3):1095-1115
Riechmann J.L.,and Ratcliffe O.J.,2000,A genomic perspective on plant transcription factors,Curr.Opin.Plant Biol.,3(5):423-434
Siefers N.,Dang K.K.,Kumimoto R.W.,Bynum W.E.I.,Tayrose G.,and Holt B.F.I.,2009,Tissue-specific expression patterns of Arabidopsis NF-Y transcription factors suggest potential for extensive combinatorial complexity,Plant Physiol.,149(2):625-641
Stephenson T.J.,Mcintyre C.L.,Collet C.,and Xue G.P.,2011,TaNF-YB3 is involved in the regulation of photosynthesis genes in Triticum aestivum,Funct.Integr.Genomics,11(2):327-340
Stephenson T.J.,Mcintyre C.L.,Collet C.,and Xue G.P.,2007,Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum,Plant Mol.Biol.,65(1-2):77-92
Sun X.L.,Li Y.,Cai H.,Bai X.,Wei J.,Ji Z.J.,and Zhu Y.M.,2011,Arabidopsis bZIP1 transcription factor binding to AB-RE cis-element regulates abscisic acid signal transduction,Zuowu Xuebao(Acta Agronomica Sinica),37(4):612-619(孙晓丽,李勇,才华,柏锡,纪巍,季佐军,朱延明,2011,拟南芥b ZIP1转录因子通过与ABRE元件结合调节ABA信号传导,作物学报,37(4):612-619)
Wei X.J.,Xu J.F.,Guo H.N.,Jiang L.,Chen S.H.,Yu C.Y.,Zhou Z.L.,Hu P.S.,Zhai H.Q.,and Wan J.M.,2010,DTH8 suppresses flowering in rice,influencing plant height and yield potential simultaneously,Plant Physiol.,153(4):1747-1758
Yang W.J.,Lu Z.H.,Xiong Y.F.,and Yao J.L.,2016,Genome-wide identification and co-expression network analysis of the OsNF-Y gene family in rice,Crop J.,5(1):21-31
Zhang T.,Zhang D.,Liu Y.J.,Luo C.B.,Zhou Y.N.,and Zhang L.Y.,2015,Overexpression of a NF-YB3 transcription factor from Picea wilsonii confers tolerance to salinity and drought stress in transformed Arabidopsis thaliana,Plant Physiol.Biochem.,94:153-164
Zhao F.C.,Jing L.Q.,Yan F.B.,Lei D.L.,Wang G.Y.,and Lu W.P.,2013,Effects of heat stress during grain filling on sugar accumulation and enzyme activity associated with sucrose metabolism in sweet corn,Zuowu Xuebao(Acta Agronomica Sinica),39(9):1644-1651(赵福成,景立权,闫发宝,陆大雷,王桂跃,陆卫平,2013,灌浆期高温胁迫对甜玉米籽粒糖分积累和蔗糖代谢相关酶活性的影响,作物学报,39(9):1644-1651)
Zhao H.,Wu D.,Kong F.Y.,Lin K.,Zhang H.S.,and Li G.,2016,The Arabidopsis thaliana nuclear factor Y transcription factors,Front.Plant Sci.,7:2045
Zhaxybayeva O.,and Gogarten J.P.,2003,Spliceosomal introns:new insights into their evolution,Curr.Biol.,13(19):764-766
Zheng W.J.,Xu Z.S.,Feng Z.J.,Li L.C.,Chen M.,Chai S.C.,and Ma Y.Z.,2012,Genome-wide identification,classification,and expression of NF-YB gene family in soybean,Zuowu Xuebao(Acta Agronomica Sinica),38(9):1570-1582(郑炜君,徐兆师,冯志娟,李连城,陈明,柴守诚,马有志,2012,大豆NF-YB家族全基因组鉴定、分类和表达,作物学报,38(9):1570-1582)
Brambilla V.,and Fornara F.,2016,Y flowering?Regulation and activity of CONSTANS and CCT-domain proteins in Arabidop-sis and crop species,Biochim.Biophys.Acta Gene Regul.Mech.,1860(5):655-660
Brown A.P.C.,Dunn M.A.,Goddard N.J.,and Hughes M.A.,2001,Identification of a novel low-temperature-response element in the promoter of the barley(Hordeum vulgare L.)gene blt101.1,Planta,213(5):770-780
Chen C.J.,Xia R.,Chen H.,and He Y.H.,2018,TBtools,a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface,Bio.Rxiv.,doi:https://doi.org/10.1101/289660
Ding H.X.,Liu F.,Zhang L.J.,Yu Y.X.,and Wei Q.,2017,The structure and function of NF-Y in plants,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(5):1691-1701(丁慧霞,刘凤,张利娟,余义勋,魏倩,2017,植物中NF-Y转录因子的结构和功能研究进展,分子植物育种,15(5):1691-1701)
Frontini M.,Imbriano C.,Manni I.,and Mantovani R.,2004,Cell-cycle regulation of NF-YC nuclear localization,Cell Cycle,3(2):217-222
Hackenberg D.,Wu Y.,Voigt A.,Adams R.,Schramm P.,and Grimm B.,2012,Studies on differential nuclear translocation mechanism and assembly of the three subunits of the Arabidopsis thaliana transcription factor NF-Y,Mol.Plant,5(4):876-888
Huang M.K.,Hu Y.L.,Liu X.,Li Y.,and Hou X.L.,2015a,Arabidopsis LEAFY COTYLEDON1 controls cell fate determination during post-embryonic development,Front.Plant Sci.,6:955
Huang M.,Hu Y.,Liu X.,Li Y.,and Hou X.,2015b,Arabidopsis leafy cotyledon1 mediates postembryonic development via interacting with Phytochrome-interacting factor 4,Plant Cell,27(11):3099-3111
Jeffares D.C.,Penkett C.J.,and Bahler J.,2008,Rapidly regulated genes are intron poor,Trends Genet.,24(8):375-378
Junker A.,Monke G.,Rutten T.,Keilwagen J.,Seifert M.,Thi T.M.N.,and Renou J.P.,Balzergue S.,Viehover P.,Hahnel U.,Ludwig-Müller J.,Altschmied L.,Conrad U.,Weisshaar B.,and Baumlein H.,2012,Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana,Plant J.,71(3):427-442
Le L.,Xu H.L.,Yang X.L.,Li L.X.,and Hu Y.K.,2011,Genomewide identification,classification and expression analysis of LEA gene family in soybean,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),44(19):3945-3954(李乐,许红亮,杨兴露,李雅轩,胡英考,2011,大豆LEA基因家族全基因组鉴定、分类和表达,中国农业科学,44(19):3945-3954)
Li S.,Li K.,Ju Z.,Cao D.Y.,Fu D.Q.,Zhu H.L.,Zhu B.Z.,and Luo Y.B.,2016,Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening,BMC Genomics,17(1):36
Li Y.L.,Liu J.H.,Zheng J.R.,and Hu J.G.,2013,Gene expression profile of sweet corn ears under heat stress,Zuowu Xuebao(Acta Agronomica Sinica),39(2):269-279(李余良,刘建华,郑锦荣,胡建广,2013,高温胁迫下甜玉米雌穗发育基因差异表达谱分析,作物学报,39(2):269-279)
Liang M.X.,Yin X.Z.,Lin Z.Y.,Zheng Q.S.,Liu G.H.,and Zhao G.M.,2014,Identification and characterization of NF-Ytranscription factor families in Canola(Brassica napus L.),Planta,239(1):107-126
Liu J.,Xu Z.Z.,Yuan N.,Guo Y.,Zhang B.L.,and Du J.C.,2016,Genome-wide analysis of NF-YB gene family in gossypium hirsutum l,Huabei Nongxuebao(Acta Agriculturae BorealiSinica),31(5):21-27(刘静,徐珍珍,袁娜,郭月,张保龙,杜建厂,2016,陆地棉NF-YB基因家族的全基因组分析,华北农学报,31(5):21-27)
Nelson D.E.,Repetti P.P.,Adams T.R.,Creelman R.A.,Wu J.,Warner D.C.,Anstrom D.C.,Bensen R.J.,and Heard J.E.,2007,Plant nuclear factor Y(NF-Y)B subunits confer drought tolerance and lead to improved corn yields on water-limited acres,Proc.Natl.Acad.Sci.USA,104(42):16450-16455
Qin F.,Li J.,Zhang G.Y.,Zhao J.,Chen S.Y.,and Liu Q.,2003,Isolation and structural analysis of DRE-binding transcription factor from maize(Zea mays L.),Acta Botanica Sinica,45(3):331-339
Quach T.N.,Nguyen H.T.M.,Valliyodan B.,Joshi T.,Xu D.,and Nguyen H.T.,2015,Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response,Mol.Genet.Genomics,290(3):1095-1115
Riechmann J.L.,and Ratcliffe O.J.,2000,A genomic perspective on plant transcription factors,Curr.Opin.Plant Biol.,3(5):423-434
Siefers N.,Dang K.K.,Kumimoto R.W.,Bynum W.E.I.,Tayrose G.,and Holt B.F.I.,2009,Tissue-specific expression patterns of Arabidopsis NF-Y transcription factors suggest potential for extensive combinatorial complexity,Plant Physiol.,149(2):625-641
Stephenson T.J.,Mcintyre C.L.,Collet C.,and Xue G.P.,2011,TaNF-YB3 is involved in the regulation of photosynthesis genes in Triticum aestivum,Funct.Integr.Genomics,11(2):327-340
Stephenson T.J.,Mcintyre C.L.,Collet C.,and Xue G.P.,2007,Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum,Plant Mol.Biol.,65(1-2):77-92
Sun X.L.,Li Y.,Cai H.,Bai X.,Wei J.,Ji Z.J.,and Zhu Y.M.,2011,Arabidopsis bZIP1 transcription factor binding to AB-RE cis-element regulates abscisic acid signal transduction,Zuowu Xuebao(Acta Agronomica Sinica),37(4):612-619(孙晓丽,李勇,才华,柏锡,纪巍,季佐军,朱延明,2011,拟南芥b ZIP1转录因子通过与ABRE元件结合调节ABA信号传导,作物学报,37(4):612-619)
Wei X.J.,Xu J.F.,Guo H.N.,Jiang L.,Chen S.H.,Yu C.Y.,Zhou Z.L.,Hu P.S.,Zhai H.Q.,and Wan J.M.,2010,DTH8 suppresses flowering in rice,influencing plant height and yield potential simultaneously,Plant Physiol.,153(4):1747-1758
Yang W.J.,Lu Z.H.,Xiong Y.F.,and Yao J.L.,2016,Genome-wide identification and co-expression network analysis of the OsNF-Y gene family in rice,Crop J.,5(1):21-31
Zhang T.,Zhang D.,Liu Y.J.,Luo C.B.,Zhou Y.N.,and Zhang L.Y.,2015,Overexpression of a NF-YB3 transcription factor from Picea wilsonii confers tolerance to salinity and drought stress in transformed Arabidopsis thaliana,Plant Physiol.Biochem.,94:153-164
Zhao F.C.,Jing L.Q.,Yan F.B.,Lei D.L.,Wang G.Y.,and Lu W.P.,2013,Effects of heat stress during grain filling on sugar accumulation and enzyme activity associated with sucrose metabolism in sweet corn,Zuowu Xuebao(Acta Agronomica Sinica),39(9):1644-1651(赵福成,景立权,闫发宝,陆大雷,王桂跃,陆卫平,2013,灌浆期高温胁迫对甜玉米籽粒糖分积累和蔗糖代谢相关酶活性的影响,作物学报,39(9):1644-1651)
Zhao H.,Wu D.,Kong F.Y.,Lin K.,Zhang H.S.,and Li G.,2016,The Arabidopsis thaliana nuclear factor Y transcription factors,Front.Plant Sci.,7:2045
Zhaxybayeva O.,and Gogarten J.P.,2003,Spliceosomal introns:new insights into their evolution,Curr.Biol.,13(19):764-766
Zheng W.J.,Xu Z.S.,Feng Z.J.,Li L.C.,Chen M.,Chai S.C.,and Ma Y.Z.,2012,Genome-wide identification,classification,and expression of NF-YB gene family in soybean,Zuowu Xuebao(Acta Agronomica Sinica),38(9):1570-1582(郑炜君,徐兆师,冯志娟,李连城,陈明,柴守诚,马有志,2012,大豆NF-YB家族全基因组鉴定、分类和表达,作物学报,38(9):1570-1582)