植物串联CCCH锌指蛋白RR-TZF家族研究进展及生物信息学分析
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摘要
典型的串联CCCH型锌指结构蛋白(tandem CCCH zinc finger proteins, TZFs)含有由18个氨基酸分隔的二个串联CCCH motifs (C-X7-8-C-X5-C-X3-H、C-X5-C-X4-C-X3-H)。富含精氨酸的RR-TZF蛋白是植物特有,研究表明RR-TZF蛋白通过介导RNA的降解来调节基因的表达水平,影响植物的生长发育以及胁迫反应。本研究主要综述了植物RR-TZF蛋白在生长发育及胁迫反应中的功能及作用机制等;同时利用生物信息学手段对RR-TZF蛋白进行聚类分析,系统地分析了RR-TZF蛋白从低等植物到高等植物中的进化与保守性,并展望了未来可能的研究方向。为探究CCCH型锌指结构蛋白家族基因在作物中的具体功能及其应对非生物胁迫的分子机制研究提供了重要的理论依据。
The typical tandem CCCH zinc finger(TZF) protein contains two tandem CCCH motifs, C-X7-8-C-X5-C-X3-H and C-X5-C-X4-C-X3-H, which are spaced by 18 amino acids. Arginine-rich TZF(RR-TZF) proteins are specific in plant. Researches showed that the expression level of genes were regulated through mediating RNA degradation by RR-TZF protein, as well as affected the plant growth and stress response. This review mainly summarized the functions and reaction mechanisms of plant RR-TZF proteins during growth, development and stress responses. Besides, clustering analysis was performed on RR-TZF protein in combination with bioinformatics.The evolution and conservation of RR-TZF proteins from lower to higher plants was discussed and potential direction in future research was also proposed. The study would provide important theoretical basis for exploring the specific functions of CCCH zinc finger protein family gene in crops and revealing its molecular mechanisms in response to abiotic adversities.
The typical tandem CCCH zinc finger(TZF) protein contains two tandem CCCH motifs, C-X7-8-C-X5-C-X3-H and C-X5-C-X4-C-X3-H, which are spaced by 18 amino acids. Arginine-rich TZF(RR-TZF) proteins are specific in plant. Researches showed that the expression level of genes were regulated through mediating RNA degradation by RR-TZF protein, as well as affected the plant growth and stress response. This review mainly summarized the functions and reaction mechanisms of plant RR-TZF proteins during growth, development and stress responses. Besides, clustering analysis was performed on RR-TZF protein in combination with bioinformatics.The evolution and conservation of RR-TZF proteins from lower to higher plants was discussed and potential direction in future research was also proposed. The study would provide important theoretical basis for exploring the specific functions of CCCH zinc finger protein family gene in crops and revealing its molecular mechanisms in response to abiotic adversities.
引文
Albert S.,Després B.,Guilleminot J.,Bechtold N.,Pelletier G.,Delseny M.,and Devic M.,1999,The EMB506 gene encodes a novel ankyrin repeat containing protein that is essential for the normal development of Arabidopsis embryos,Plant J.Cell Mol.Biol.,17(2):169-179
Belostotsky D.A.,and Sieburth L.E.,2009,Kill the messenger:m RNA decay and plant development,Curr.Opin.Plant Biol.,12(1):96-102
Blackshear P.J.,Phillips R.S.,and Lai W.S.,2005,Tandem CCCH zinc finger proteins in m RNA binding,In:Shiro l.,and Natalie K.l.,Molecular Biology Intelligence Unit,Spinger-Verlag,Berlin Heidelberg,Germany,pp.80-90
Bogamuwa S.,and Jang J.C.,2013,The Arabidopsis tandem CCCH zinc finger proteins At TZF4,5 and 6 are involved in light-,abscisic acid-and gibberellic acid-mediated regulation of seed germination,Plant Cell Environ.,36(8):1507-1519
Bogamuwa S.P.,and Jang J.C.,2014,Tandem CCCH zinc finger proteins in plant growth,development and stress response,Plant Cell Physiol.,55(8):1367-1375
Brooks S.A.,and Blackshear P.J.,2013,Tristetraprolin(TTP):Interactions with m RNA and proteins,and current thoughts on mechanisms of action,BBA-Gene Regul.Mech.,1829(6-7):666-679
Cao H.,Glazebrook J.,Clarke J.D.,Volko S.,and Dong A.X.,1997,The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats,Cell,88(1):57-63
Chai G.,Hu R.,Zhang D.,Qi G.,Zuo R.,Cao Y.,Chen P.,Kong Y.,and Zhou G.,2012,Comprehensive analysis of CCCHzinc finger family in poplar(Populus trichocarpa),BMC Genomics,13(1):253-275
Dong H.K.,Yamaguchi S.,Lim S.,Oh E.,Park J.,Hanada A.,Kamiya Y.,and Choi G.,2008,SOMNUS,a CCCH-Type zinc finger protein in Arabidopsis,negatively regulates light-dependent seed germination downstream of PIL5,Plant Cell,20(5):1260-1277
Guo Y.H.,Yu Y.P.,Wang D.,Wu C.A.,Yang G.D.,Huang J.G.,and Zheng C.C.,2009,GhZFP1,a novel CCCH-type zinc finger protein from cotton,enhances salt stress tolerance and fungal disease resistance in transgenic tobacco by interacting with GZIRD21A and GZIPR5,New Phytol.,183(1):62-75
Huang P.,Ju H.W.,Min J.H.,Zhang X.,Chung J.S.,Cheong H.S.,and Kim C.S.,2012,Molecular and physiological characterization of the Arabidopsis thaliana oxidation-related zinc finger 2,a plasma membrane protein involved in ABA and salt stress response through the ABI2-mediated signaling pathway,Plant Cell Physiol.,53(1):193-203
Jan A.,Maruyama K.,Todaka D.,Kidokoro S.,Abo M.,Yoshimura E.,Shinozaki K.,Nakashima K.,and Yamaguchi-Shinozaki K.,2013,Os TZF1,a CCCH-tandem zinc finger protein,confers delayed senescence and stress tolerance in rice by regulating stress related genes,Plant Physiol.,161(3):1202-1216
Kedar V.P.,Zucconi B.E.,Wilson G.M.,and Blackshear P.J.,2012,Direct binding of specific AUF1 isoforms to tandem zinc finger domains of tristetraprolin(TTP)family proteins,J.Biol.Chem.,287(8):5459-5471
Kong Z.,Li M.,Yang W.,Xu W.,and Xue Y.,2006,Novel nuclear-localized CCCH-type zinc finger protein,Os DOS,is involved in delaying leaf senescence in rice,Plant Physiol.,141(4):1376-1388
Lee S.J.,Jung H.J.,Kang H.,and Kim S.Y.,2012,Arabidopsis zinc finger proteins At C3H49/At TZF3 and At C3H20/At TZF2are involved in ABA and JA responses,Plant Cell Physiol.,53(4):673-686
Lin P.C.,Pomeranz M.C.,Jikumaru Y.,Kang S.G.,Hah C.,Fujioka S.,Kamiya Y.,and Jang J.C.,2011,The Arabidopsis tandem zinc finger protein At TZF1 affects ABA-and GA-mediated growth,stress and gene expression responses,Plant J.Cell Mol.Biol.,65(2):253-268
Lykkeandersen J.,and Wagner E.,2005,Recruitment and activation of m RNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1,Gene.Dev.,19(3):351-361
Maldonadobonilla L.D.,Eschen-Lippold L.,Gago-Zachert S.,Tabassum N.,Bauer N.,Scheel D.,and Lee J.,2014,The Arabidopsis tandem zinc finger 9 protein binds RNA and mediates pathogenassociated molecular pattern-triggered immune responses,Plant Cell Physiol.,55(2):412-425
Niu Y.D.,Wang J.Q.,Xue Y.,Li N.N.,Li Y.,and Zhang F.,2016,Cloning and bioinformatics analysis of SKIP homologous gene cDNA from Medicago falcata L.,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(10):2794-2801(牛一丁,王佳琪,薛阳,李宁宁,李岩,张凤,2016,黄花苜蓿SKIP同源基因cDNA的克隆与生物信息学分析,基因组学与应用生物学,35(10):2794-2801)
Peng X.,Zhao Y.,Cao J.,Zhan W.,Jiang H.,Li X.,Ma Q.,Zhu S.,and Cheng B.,2012,CCCH-Type zinc finger family in maize:genome-wide identification,classification and expression profiling under abscisic acid and drought treatments,PLoS One,7(7):e40120-e40135
Piskurewicz U.,Jikumaru Y.,Kinoshita N.,Nambara E.,Kamiya Y.,and Lopez-Molina L.,2008,The Gibberellic acid signaling repressor RGL2 inhibits Arabidopsis seed germination by stimulating abscisic acid synthesis and ABI5 activity,Plant Cell,20(10):2729-2745
Pomeranz M.C.,Hah C.,Lin P.C.,Kang S.,Finer J.J.,Blackshear P.J.,and Jang J.C.,2010,The Arabidopsis tandem zinc finger protein At TZF1 traffics between the nucleus and cytoplasmic foci and binds both DNA and RNA,Plant Physiol.,152(2):151-165
Qu J.,Kang S.G.,Wang W.,Musier-Forsyth K.,and Jang J.C.,2014,Arabidopsis thaliana tandem zinc finger 1(At TZF1)in RNA binding and decay,Plant J.,78(3):452-467
Sandler H.,Kreth J.,Timmers H.T.M.,and Stoecklin G.,2011,Not1 mediates recruitment of the deadenylase Caf1 to m R-NAs targeted for degradation by tristetraprolin,Nucleic Acids Res.,39(10):4373-4386
Wang D.,Guo Y.,Wu C.,Yang G.,Li Y.,and Zheng C.,2008,Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice,BMC Genomics,9(1):44-64
Wei L.J.,Zhou J.Y.,Chen S.,Wu L.M.,and Li D.P.,2009,Analysis on expression pattern of ankyrin ANK20 in Arabidopsis,Hunan Shifan Daxue Ziran Kexue Xuebao(Journal of Natural Science of Hunan Normal University),32(2):89-92(韦里俊,周继业,陈松,吴利明,李东屏,2009,拟南芥锚蛋白ANK20基因表达模式,湖南师范大学自然科学学报,32(2):89-92)
Xu J.,and Chua N.H.,2009,Arabidopsis decapping 5 is required for m RNA decapping,P-body formation,and translational repression during postembryonic development,Plant Cell,21(10):3270-3279
Yuan X.,Zhang S.,Qing X.,Sun M.,Liu S.,Su H.,Shu H.,and Li X.,2013,Superfamily of ankyrin repeat proteins in tomato,Gene,523(2):126-136
Zhou T.,Yang X.,Wang L.,Xu J.,and Zhang X.,2014,GhTZF1regulates drought stress responses and delays leaf senescence by inhibiting reactive oxygen species accumulation in transgenic Arabidopsis,Plant Mol.Biol.,85(1-2):163-177
Belostotsky D.A.,and Sieburth L.E.,2009,Kill the messenger:m RNA decay and plant development,Curr.Opin.Plant Biol.,12(1):96-102
Blackshear P.J.,Phillips R.S.,and Lai W.S.,2005,Tandem CCCH zinc finger proteins in m RNA binding,In:Shiro l.,and Natalie K.l.,Molecular Biology Intelligence Unit,Spinger-Verlag,Berlin Heidelberg,Germany,pp.80-90
Bogamuwa S.,and Jang J.C.,2013,The Arabidopsis tandem CCCH zinc finger proteins At TZF4,5 and 6 are involved in light-,abscisic acid-and gibberellic acid-mediated regulation of seed germination,Plant Cell Environ.,36(8):1507-1519
Bogamuwa S.P.,and Jang J.C.,2014,Tandem CCCH zinc finger proteins in plant growth,development and stress response,Plant Cell Physiol.,55(8):1367-1375
Brooks S.A.,and Blackshear P.J.,2013,Tristetraprolin(TTP):Interactions with m RNA and proteins,and current thoughts on mechanisms of action,BBA-Gene Regul.Mech.,1829(6-7):666-679
Cao H.,Glazebrook J.,Clarke J.D.,Volko S.,and Dong A.X.,1997,The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats,Cell,88(1):57-63
Chai G.,Hu R.,Zhang D.,Qi G.,Zuo R.,Cao Y.,Chen P.,Kong Y.,and Zhou G.,2012,Comprehensive analysis of CCCHzinc finger family in poplar(Populus trichocarpa),BMC Genomics,13(1):253-275
Dong H.K.,Yamaguchi S.,Lim S.,Oh E.,Park J.,Hanada A.,Kamiya Y.,and Choi G.,2008,SOMNUS,a CCCH-Type zinc finger protein in Arabidopsis,negatively regulates light-dependent seed germination downstream of PIL5,Plant Cell,20(5):1260-1277
Guo Y.H.,Yu Y.P.,Wang D.,Wu C.A.,Yang G.D.,Huang J.G.,and Zheng C.C.,2009,GhZFP1,a novel CCCH-type zinc finger protein from cotton,enhances salt stress tolerance and fungal disease resistance in transgenic tobacco by interacting with GZIRD21A and GZIPR5,New Phytol.,183(1):62-75
Huang P.,Ju H.W.,Min J.H.,Zhang X.,Chung J.S.,Cheong H.S.,and Kim C.S.,2012,Molecular and physiological characterization of the Arabidopsis thaliana oxidation-related zinc finger 2,a plasma membrane protein involved in ABA and salt stress response through the ABI2-mediated signaling pathway,Plant Cell Physiol.,53(1):193-203
Jan A.,Maruyama K.,Todaka D.,Kidokoro S.,Abo M.,Yoshimura E.,Shinozaki K.,Nakashima K.,and Yamaguchi-Shinozaki K.,2013,Os TZF1,a CCCH-tandem zinc finger protein,confers delayed senescence and stress tolerance in rice by regulating stress related genes,Plant Physiol.,161(3):1202-1216
Kedar V.P.,Zucconi B.E.,Wilson G.M.,and Blackshear P.J.,2012,Direct binding of specific AUF1 isoforms to tandem zinc finger domains of tristetraprolin(TTP)family proteins,J.Biol.Chem.,287(8):5459-5471
Kong Z.,Li M.,Yang W.,Xu W.,and Xue Y.,2006,Novel nuclear-localized CCCH-type zinc finger protein,Os DOS,is involved in delaying leaf senescence in rice,Plant Physiol.,141(4):1376-1388
Lee S.J.,Jung H.J.,Kang H.,and Kim S.Y.,2012,Arabidopsis zinc finger proteins At C3H49/At TZF3 and At C3H20/At TZF2are involved in ABA and JA responses,Plant Cell Physiol.,53(4):673-686
Lin P.C.,Pomeranz M.C.,Jikumaru Y.,Kang S.G.,Hah C.,Fujioka S.,Kamiya Y.,and Jang J.C.,2011,The Arabidopsis tandem zinc finger protein At TZF1 affects ABA-and GA-mediated growth,stress and gene expression responses,Plant J.Cell Mol.Biol.,65(2):253-268
Lykkeandersen J.,and Wagner E.,2005,Recruitment and activation of m RNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1,Gene.Dev.,19(3):351-361
Maldonadobonilla L.D.,Eschen-Lippold L.,Gago-Zachert S.,Tabassum N.,Bauer N.,Scheel D.,and Lee J.,2014,The Arabidopsis tandem zinc finger 9 protein binds RNA and mediates pathogenassociated molecular pattern-triggered immune responses,Plant Cell Physiol.,55(2):412-425
Niu Y.D.,Wang J.Q.,Xue Y.,Li N.N.,Li Y.,and Zhang F.,2016,Cloning and bioinformatics analysis of SKIP homologous gene cDNA from Medicago falcata L.,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(10):2794-2801(牛一丁,王佳琪,薛阳,李宁宁,李岩,张凤,2016,黄花苜蓿SKIP同源基因cDNA的克隆与生物信息学分析,基因组学与应用生物学,35(10):2794-2801)
Peng X.,Zhao Y.,Cao J.,Zhan W.,Jiang H.,Li X.,Ma Q.,Zhu S.,and Cheng B.,2012,CCCH-Type zinc finger family in maize:genome-wide identification,classification and expression profiling under abscisic acid and drought treatments,PLoS One,7(7):e40120-e40135
Piskurewicz U.,Jikumaru Y.,Kinoshita N.,Nambara E.,Kamiya Y.,and Lopez-Molina L.,2008,The Gibberellic acid signaling repressor RGL2 inhibits Arabidopsis seed germination by stimulating abscisic acid synthesis and ABI5 activity,Plant Cell,20(10):2729-2745
Pomeranz M.C.,Hah C.,Lin P.C.,Kang S.,Finer J.J.,Blackshear P.J.,and Jang J.C.,2010,The Arabidopsis tandem zinc finger protein At TZF1 traffics between the nucleus and cytoplasmic foci and binds both DNA and RNA,Plant Physiol.,152(2):151-165
Qu J.,Kang S.G.,Wang W.,Musier-Forsyth K.,and Jang J.C.,2014,Arabidopsis thaliana tandem zinc finger 1(At TZF1)in RNA binding and decay,Plant J.,78(3):452-467
Sandler H.,Kreth J.,Timmers H.T.M.,and Stoecklin G.,2011,Not1 mediates recruitment of the deadenylase Caf1 to m R-NAs targeted for degradation by tristetraprolin,Nucleic Acids Res.,39(10):4373-4386
Wang D.,Guo Y.,Wu C.,Yang G.,Li Y.,and Zheng C.,2008,Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice,BMC Genomics,9(1):44-64
Wei L.J.,Zhou J.Y.,Chen S.,Wu L.M.,and Li D.P.,2009,Analysis on expression pattern of ankyrin ANK20 in Arabidopsis,Hunan Shifan Daxue Ziran Kexue Xuebao(Journal of Natural Science of Hunan Normal University),32(2):89-92(韦里俊,周继业,陈松,吴利明,李东屏,2009,拟南芥锚蛋白ANK20基因表达模式,湖南师范大学自然科学学报,32(2):89-92)
Xu J.,and Chua N.H.,2009,Arabidopsis decapping 5 is required for m RNA decapping,P-body formation,and translational repression during postembryonic development,Plant Cell,21(10):3270-3279
Yuan X.,Zhang S.,Qing X.,Sun M.,Liu S.,Su H.,Shu H.,and Li X.,2013,Superfamily of ankyrin repeat proteins in tomato,Gene,523(2):126-136
Zhou T.,Yang X.,Wang L.,Xu J.,and Zhang X.,2014,GhTZF1regulates drought stress responses and delays leaf senescence by inhibiting reactive oxygen species accumulation in transgenic Arabidopsis,Plant Mol.Biol.,85(1-2):163-177