大豆PHD家族蛋白的全基因组鉴定及表达特征分析
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摘要
PHD(Plant Homeodomain Finger)基因家族编码一类锌指转录因子,广泛参与植物的生长发育和逆境应答过程。通过全基因组鉴定获得了95个大豆PHD家族蛋白。通过共线性分析、进化树构建、基因结构和功能结构域鉴定、GO注释分析、不同组织间和非生物胁迫下表达分析等,获得了大豆PHD家族基因复制、家族进化、保守结构域及基因表达等信息。结果表明,大豆PHD基因在家族进化、基因结构和保守结构域上存在较大变异,可能参与Zn2+结合、DNA结合及表观遗传调控等分子过程,参与调控植物生长发育和逆境应答。这些结果为进一步研究大豆PHD家族在生长发育和逆境应答中的生物学功能提供重要线索。
PHD(Plant Homeodomain Finger) family genes encode a class of zinc finger transcription factor proteins,which are widely involved in regulating plant growth and stress responses.In this study,through genome-wide analysis,we identified a total of 95 PHD family proteins in soybean proteome.We further performed the synteny analysis,constructed the phylogenic tree,identified the gene structures and functional domains,analyzed the gene ontology(GO) annotation,and investigated the expression patterns in different tissues and under abiotic stresses.These data provided comprehensive information regarding the gene duplication,family evolution,conserved domains and gene expression of the soybean PHD family.Our results presented in this study suggest that soybean PHD family displays a great divergence in family evolution,gene structure and conserved domain organization;possibly participates in different molecular processes,including Zn~(2+) binding,DNA binding and epigenetic regulation;and probably controls plant development and environmental stress responses.In summary,these findings will provide a crucial cue for further characterizing the biological function of soybean PHD family in plant growth and environmental stress responses.
PHD(Plant Homeodomain Finger) family genes encode a class of zinc finger transcription factor proteins,which are widely involved in regulating plant growth and stress responses.In this study,through genome-wide analysis,we identified a total of 95 PHD family proteins in soybean proteome.We further performed the synteny analysis,constructed the phylogenic tree,identified the gene structures and functional domains,analyzed the gene ontology(GO) annotation,and investigated the expression patterns in different tissues and under abiotic stresses.These data provided comprehensive information regarding the gene duplication,family evolution,conserved domains and gene expression of the soybean PHD family.Our results presented in this study suggest that soybean PHD family displays a great divergence in family evolution,gene structure and conserved domain organization;possibly participates in different molecular processes,including Zn~(2+) binding,DNA binding and epigenetic regulation;and probably controls plant development and environmental stress responses.In summary,these findings will provide a crucial cue for further characterizing the biological function of soybean PHD family in plant growth and environmental stress responses.
引文
[1]韩丹,王丕武,曲静,等.大豆C2H2型锌指蛋白基因SCTF-1转化及功能分析.中国油料作物学报,2016,38(3):307-312.
[2]Agarwal P,Arora R,Ray S,et al.Genome-wide identification of C2H2zinc-finger gene family in rice and their phylogeny and expression analysis.Plant Molecular Biology,2007,65(4):467-485.
[3]Hall T M.Multiple modes of RNA recognition by zinc finger proteins.Current Opinion in Structure Biology,2005,15(3):367-373.
[4]Arnaud D,Dejardin A,Leple J G,et al.Genome-wide analysis of LIMgene family in Populus trichocarpa,Arabidopsis thaliana,and Oryza sativa.DNA Research,2007,14(3):103-116.
[5]Takatsuji H.Zinc-finger transcription factors in plants.Cellular and Molecular Life Sciences,1998,54:582-596.
[6]Aasland R,Gibson T J,Stewart A F.The PHD finger:Implications for chromatin-mediated transcriptional regulation.Trends in Biochemical Sciences,1995,20:56-59.
[7]Borden K L B,Freemont S P.The ring finger domain:A recent example of a sequence-structure family.Current Opinion in Structural Biology,1996,6:395-401.
[8]Kaadige M R,Ayer D E.The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding.Journal of Biological Chemistry,2006,281(39):28831-28836.
[9]冯英,刘庆坡,薛庆中.水稻与拟南芥PHD-finger蛋白的系统分析.遗传学报,2004,31(11):1284-1293.
[10]Wang Q,Liu J,Wang Y,et al.Systematic analysis of the maize PHD-finger gene family reveals a subfamily involved in abiotic stress response.International Journal of Molecular Sciences,2015,16(10):23517-23544.
[11]Wu S,Wu M,Dong Q,et al.Genome-wide identification,classification and expression analysis of the PHD-finger protein family in Populus trichocarpa.Gene,2016,575(1):75-89.
[12]Sun M Z,Jia B W,Yang J K,et al.Genome-wide identification of the PHD-finger family genes and their responses to environmental stresses in Oryza sativa L.International Journal of Molecular Sciences,2017,18(9):2005.
[13]Chen X J,Sikandar H,Cheng Z H.Genome-wide identification and analysis of genes encoding PHD-finger protein in tomato.Pakistan Journal of Botany,2016,48(1):155-165.
[14]Wu X J,Li M Y,Que F,et al.Genome-wide analysis of PHD family transcription factors in carrot(Daucus carota L.)reveals evolution and response to abiotic stress.Acta Physiologiae Plantarum,2016,38(3):2049-2061.
[15]张帆,杨仲南,张森.拟南芥PHD-finger-蛋白家族的全基因组分析.云南植物研究,2009,31(3):227-238.
[16]Ye Y,Gong Z,Lu X,et al.Germostatin resistance locus 1 encodes a PHD finger protein involved in auxin-mediated seed dormancy and germination.Plant Journal,2016,85(1):3-15.
[17]Kim D H,Sung S.The binding specificity of the PHD-finger domain of VIN3 moderates vernalization response.Plant Physiology,2017,173(2):1258-1268.
[18]Fernandez Gomez J,Wilson Z A.A barley PHD finger transcription factor that confers male sterility by affecting tapetal development.Plant Biotechnology Journal,2014,12(6):765-777.
[19]Lopez-Gonzalez L,Mouriz A,Narro-Diego L,et al.Chromatindependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins.The Plant Cell,2014,26(10):3922-3938.
[20]Wei W,Huang J,Hao Y J,et al.Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants.PLoS ONE,2009,4(9):e7209.
[21]Wu T,Pi E X,Tsai S N,et al.GmPHD5 acts as an important regulator for crosstalk between histone H3K4 di-methylation and H3K14 acetylation in response to salinity stress in soybean.BMCPlant Biology,2011,11:178.
[22]Zhang H,Meltzer P,Davis S.RCircos:an R package for Circos 2Dtrack plots.BMC Bioinformatics,2013,14:244.
[23]李晓旭,刘成,李伟,等.番茄WOX转录因子家族的鉴定及进化、表达分析.遗传,2016,38(5):444-460.
[24]Schmutz J,Cannon S B,Schlueter J,et al.Genome sequence of the palaeopolyploid soybean.Nature,2010,463:178-183.
[25]Winicov I.Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa.Planta,2000,210(3):416-422.
[26]Winicov I I,Bastola D R.Transgenic overexpression of the transcription factor alfin1 enhances expression of the endogenous MsPRP2 gene in alfalfa and improves salinity tolerance of the plants.Plant Physiology,1999,120(2):473-480.
[27]Robert-Seilaniantz A,Grant M,Jones J D.Hormone crosstalk in plant disease and defense:more than just jasmonate-salicylate antagonism.Annual Review of Phytopathology,2011,49:317-343.
[28]Callebaut I,Courvalin J C,Mornon J P.The BAH(bromo-adjacent homology)domain:a link between DNA methylation,replication and transcriptional regulation.FEBS Letters,1999,446(1):189-193.
[29]Oliver A W,Jones S A,Roe S M,et al.Crystal structure of the proximal BAH domain of the polybromo protein.Biochemical Journal,2005,389(3):657-664.
[30]Baumbusch L O,Thorstensen T,Krauss V,et al.The Arabidopsis thaliana genome contains at least 29 active genes encoding SETdomain proteins that can be assigned to four evolutionarily conserved classes.Nucleic Acids Research,2001,29(21):4319-4333.
[31]Cui X,De Vivo I,Slany R,et al.Association of SET domain and myotubularin-related proteins modulates growth control.Nature Genetics,1998,18(4):331-337.
[32]Stec I,Nagl S B,van Ommen G J,et al.The PWWP domain:a potential protein-protein interaction domain in nuclear proteins influencing differentiation.FEBS Letters,2000,473(1):1-5.
[33]Qin S,Min J R.Structure and function of the nucleosome-binding PWWP domain.Trends in Biochemical Sciences,2014,39(11):536-547.
[34]Molitor A M,Bu Z Y,Yu Y,et al.Arabidopsis AL PHD-PRC1complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes.PLoS Genetics,2014,10(1):e1004091.
[2]Agarwal P,Arora R,Ray S,et al.Genome-wide identification of C2H2zinc-finger gene family in rice and their phylogeny and expression analysis.Plant Molecular Biology,2007,65(4):467-485.
[3]Hall T M.Multiple modes of RNA recognition by zinc finger proteins.Current Opinion in Structure Biology,2005,15(3):367-373.
[4]Arnaud D,Dejardin A,Leple J G,et al.Genome-wide analysis of LIMgene family in Populus trichocarpa,Arabidopsis thaliana,and Oryza sativa.DNA Research,2007,14(3):103-116.
[5]Takatsuji H.Zinc-finger transcription factors in plants.Cellular and Molecular Life Sciences,1998,54:582-596.
[6]Aasland R,Gibson T J,Stewart A F.The PHD finger:Implications for chromatin-mediated transcriptional regulation.Trends in Biochemical Sciences,1995,20:56-59.
[7]Borden K L B,Freemont S P.The ring finger domain:A recent example of a sequence-structure family.Current Opinion in Structural Biology,1996,6:395-401.
[8]Kaadige M R,Ayer D E.The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding.Journal of Biological Chemistry,2006,281(39):28831-28836.
[9]冯英,刘庆坡,薛庆中.水稻与拟南芥PHD-finger蛋白的系统分析.遗传学报,2004,31(11):1284-1293.
[10]Wang Q,Liu J,Wang Y,et al.Systematic analysis of the maize PHD-finger gene family reveals a subfamily involved in abiotic stress response.International Journal of Molecular Sciences,2015,16(10):23517-23544.
[11]Wu S,Wu M,Dong Q,et al.Genome-wide identification,classification and expression analysis of the PHD-finger protein family in Populus trichocarpa.Gene,2016,575(1):75-89.
[12]Sun M Z,Jia B W,Yang J K,et al.Genome-wide identification of the PHD-finger family genes and their responses to environmental stresses in Oryza sativa L.International Journal of Molecular Sciences,2017,18(9):2005.
[13]Chen X J,Sikandar H,Cheng Z H.Genome-wide identification and analysis of genes encoding PHD-finger protein in tomato.Pakistan Journal of Botany,2016,48(1):155-165.
[14]Wu X J,Li M Y,Que F,et al.Genome-wide analysis of PHD family transcription factors in carrot(Daucus carota L.)reveals evolution and response to abiotic stress.Acta Physiologiae Plantarum,2016,38(3):2049-2061.
[15]张帆,杨仲南,张森.拟南芥PHD-finger-蛋白家族的全基因组分析.云南植物研究,2009,31(3):227-238.
[16]Ye Y,Gong Z,Lu X,et al.Germostatin resistance locus 1 encodes a PHD finger protein involved in auxin-mediated seed dormancy and germination.Plant Journal,2016,85(1):3-15.
[17]Kim D H,Sung S.The binding specificity of the PHD-finger domain of VIN3 moderates vernalization response.Plant Physiology,2017,173(2):1258-1268.
[18]Fernandez Gomez J,Wilson Z A.A barley PHD finger transcription factor that confers male sterility by affecting tapetal development.Plant Biotechnology Journal,2014,12(6):765-777.
[19]Lopez-Gonzalez L,Mouriz A,Narro-Diego L,et al.Chromatindependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins.The Plant Cell,2014,26(10):3922-3938.
[20]Wei W,Huang J,Hao Y J,et al.Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants.PLoS ONE,2009,4(9):e7209.
[21]Wu T,Pi E X,Tsai S N,et al.GmPHD5 acts as an important regulator for crosstalk between histone H3K4 di-methylation and H3K14 acetylation in response to salinity stress in soybean.BMCPlant Biology,2011,11:178.
[22]Zhang H,Meltzer P,Davis S.RCircos:an R package for Circos 2Dtrack plots.BMC Bioinformatics,2013,14:244.
[23]李晓旭,刘成,李伟,等.番茄WOX转录因子家族的鉴定及进化、表达分析.遗传,2016,38(5):444-460.
[24]Schmutz J,Cannon S B,Schlueter J,et al.Genome sequence of the palaeopolyploid soybean.Nature,2010,463:178-183.
[25]Winicov I.Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa.Planta,2000,210(3):416-422.
[26]Winicov I I,Bastola D R.Transgenic overexpression of the transcription factor alfin1 enhances expression of the endogenous MsPRP2 gene in alfalfa and improves salinity tolerance of the plants.Plant Physiology,1999,120(2):473-480.
[27]Robert-Seilaniantz A,Grant M,Jones J D.Hormone crosstalk in plant disease and defense:more than just jasmonate-salicylate antagonism.Annual Review of Phytopathology,2011,49:317-343.
[28]Callebaut I,Courvalin J C,Mornon J P.The BAH(bromo-adjacent homology)domain:a link between DNA methylation,replication and transcriptional regulation.FEBS Letters,1999,446(1):189-193.
[29]Oliver A W,Jones S A,Roe S M,et al.Crystal structure of the proximal BAH domain of the polybromo protein.Biochemical Journal,2005,389(3):657-664.
[30]Baumbusch L O,Thorstensen T,Krauss V,et al.The Arabidopsis thaliana genome contains at least 29 active genes encoding SETdomain proteins that can be assigned to four evolutionarily conserved classes.Nucleic Acids Research,2001,29(21):4319-4333.
[31]Cui X,De Vivo I,Slany R,et al.Association of SET domain and myotubularin-related proteins modulates growth control.Nature Genetics,1998,18(4):331-337.
[32]Stec I,Nagl S B,van Ommen G J,et al.The PWWP domain:a potential protein-protein interaction domain in nuclear proteins influencing differentiation.FEBS Letters,2000,473(1):1-5.
[33]Qin S,Min J R.Structure and function of the nucleosome-binding PWWP domain.Trends in Biochemical Sciences,2014,39(11):536-547.
[34]Molitor A M,Bu Z Y,Yu Y,et al.Arabidopsis AL PHD-PRC1complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes.PLoS Genetics,2014,10(1):e1004091.