茶树CPP转录因子家族的全基因组鉴定及分析
|
摘要
CPP (cysteine-rich polycomb-like protein)转录因子广泛存在于动植物中,是一类成员数目较少的转录因子家族,在调控植物生长发育和响应非生物胁迫中起重要作用。该研究通过对茶树基因组系统的鉴定,获得10个CsCPP转录因子均具有典型的CXC结构域。系统发育分析将CsCPP家族成员分为4类(A～D),且大部分成员与葡萄在进化关系上更为接近。A类和C类成员的CXC结构域分布在蛋白序列的N端,而B类和D类成员分布在C端。茶树组织表达分析表明,CsCPP转录因子在生长活跃的顶芽和嫩叶中普遍高表达,不同组织的表达水平排序为:顶芽和嫩叶>根和茎>成熟叶和果>老叶和花。启动子分析发现了CsCPP家族成员的启动子区域存在大量的ABA和干旱响应元件;干旱处理下,6个CsCPP成员的表达水平均有不同程度上调,其中4个成员在ABA处理后表达迅速上调,表明CsCPP转录因子可能在ABA介导的干旱胁迫响应中起正调控作用;低温处理下,大部分CsCPP成员的表达均有轻微下调,而CsCPP2和CsCPP6的表达水平在6 h达到顶峰,表达量均超过2倍。研究结果为进一步发掘茶树CPP转录因子家族的功能奠定了基础。
The CPP(cysteine-rich polycomb-like protein) transcription factor family has a small number of members and is widely distributed in plants and animals. It plays an important role in regulating plant growth and development and responding to abiotic stress. In this study, 10 CsCPP transcription factors were obtained by systematic identification of the tea plant genome, all of which have typical CXC domains. The phylogenetic analysis divided the CsCPP family members into four categories(A-D), and most of the members were closer to the evolutionary relationship of the grapes. The CXC domains of class A and class C members were distributed at the N-terminus of the protein sequence, while the class B and class D members were distributed at the C-terminus. The expression analysis of tea plant tissues indicated that CsCPP transcription factors were highly expressed in the growing active apical buds and young leaves. The order of expression of different tissues was mainly: apical buds and young leaves> roots and stems> mature leaves and fruits> old leaves and flowers. Promoter analysis revealed a large number of ABA and drought response elements in the promoter region of the CsCPP family members. The expression levels of six CsCPP members under drought treatment increased to varying degrees. Four of them were up-regulated after ABA treatment, suggesting that CsCPP transcription factor may play a positive role in ABA-dependent drought stress response. The expression of most CsCPP members was slightly down-regulated under low temperature treatment, while the CsCPP2 and CsCPP6 reached more than 2-fold at 6 h. These results laid the foundation for further exploration of the function of tea plant CPP transcription factor family.
The CPP(cysteine-rich polycomb-like protein) transcription factor family has a small number of members and is widely distributed in plants and animals. It plays an important role in regulating plant growth and development and responding to abiotic stress. In this study, 10 CsCPP transcription factors were obtained by systematic identification of the tea plant genome, all of which have typical CXC domains. The phylogenetic analysis divided the CsCPP family members into four categories(A-D), and most of the members were closer to the evolutionary relationship of the grapes. The CXC domains of class A and class C members were distributed at the N-terminus of the protein sequence, while the class B and class D members were distributed at the C-terminus. The expression analysis of tea plant tissues indicated that CsCPP transcription factors were highly expressed in the growing active apical buds and young leaves. The order of expression of different tissues was mainly: apical buds and young leaves> roots and stems> mature leaves and fruits> old leaves and flowers. Promoter analysis revealed a large number of ABA and drought response elements in the promoter region of the CsCPP family members. The expression levels of six CsCPP members under drought treatment increased to varying degrees. Four of them were up-regulated after ABA treatment, suggesting that CsCPP transcription factor may play a positive role in ABA-dependent drought stress response. The expression of most CsCPP members was slightly down-regulated under low temperature treatment, while the CsCPP2 and CsCPP6 reached more than 2-fold at 6 h. These results laid the foundation for further exploration of the function of tea plant CPP transcription factor family.
引文
[1] WHEELER D S,WHEELER W J.The medicinal chemistry of tea[J].Drug Development Research,2010,61(2):45-65.
[2] LIU Y,WANG D,ZHANG S,et al.Global expansion strategy of Chinese herbal tea beverage[J].Advance Journal of Food Science and Technology,2015,7(9):739-745.
[3] 王鹏杰,陈笛,林浥,等.8个茶树WRKY转录因子基因的克隆与表达分析[J].中草药,2019,50(3):685-693.WANG P J,CHEN D,LIN Y,et al.Cloning and expression analysis of eight WRKY genes in Camellia sinensis[J].Chinese Traditional and Herbal Drugs,2019,50(3):685-693.
[4] ANDERSEN S U,ALGREEN-PETERSEN R G,HOEDL M,et al.The conserved cysteine-rich domain of a tesmin/TSO1-like protein binds zinc in vitro and TSO1 is required for both male and female fertility in Arabidopsis thaliana[J].Journal of Experimental Botany,2007,58(13):3 657-3 670.
[5] CVITANICH C,PALLISGAARD N,NIELSEN K A,et al.CPP1,a DNA-binding protein involved in the expression of a soybean leghemoglobin c3 gene[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97(14):8 163-8 168.
[6] RIECHMANN J L,HEARD J,MARTIN G,et al.Arabidopsis transcription factors:genome-wide comparative analysis among eukaryotes[J].Science,2000,290(5 499):2 105-2 110.
[7] YANG Z F,GU S L,WANG X F,et al.Molecular evolution of the CPP-like gene family in plants:insights from comparative genomics of Arabidopsis and rice[J].Journal of Molecular Evolution,2008,67(3):266-277.
[8] ZHANG L,ZHAO H K,WANG Y M,et al.Genome-wide identification and expression analysis of the CPP-like gene family in soybean[J].Genetics and Molecular Research:GMR,2015,14(1):1 260-1 268.
[9] SONG X Y,ZHANG Y Y,WU F C,et al.Genome-wide analysis of the maize (Zea may L.) CPP-like gene family and expression profiling under abiotic stress[J].Genetics and Molecular Research:GMR,2016,15(3).
[10] ZHOU Y,HU L F,YE S F,et al.Genome-wide identification and characterization of cysteine-rich polycomb-like protein (CPP) family genes in cucumber (Cucumis sativus) and their roles in stress responses[J].Biologia,2018,73(4):425-435.
[11] SIJACIC P,WANG W,LIU Z.Recessive antimorphic alleles overcome functionally redundant loci to reveal TSO1 function in Arabidopsis flowers and meristems[J].PLoS Genetics,2011,7(11):e1002352.
[12] HAUSER B A,HE J Q,PARK S O,et al.TSO1 is a novel protein that modulates cytokinesis and cell expansion in Arabidopsis[J].Development,2000,127(10):2 219-2 226.
[13] WANG W P,SIJACIC P,XU P B,et al.Arabidopsis TSO1 and MYB3R1 form a regulatory module to coordinate cell proliferation with differentiation in shoot and root[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(13):E3 045-E3 054.
[14] 潘冉冉,位明明,王亚杰,等.巴西橡胶树HbCPP1基因的克隆与表达分析[J].植物生理学报,2018,54 (5):763-772.PAN R R,WEI M M,WANG Y J,et al.Cloning and expression analysis of HbCCP1 in rubber tree (Hevea brasiliensis) [J].Plant Physiology Journal,2018,54 (5):763-772.
[15] WEI C L,YANG H,WANG S B,et al.Draft genome sequence of Camellia sinensis var.sinensis provides insights into the evolution of the tea genome and tea quality[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(18):E4 151-E4 158.
[16] WANG P J,CHEN D,ZHENG Y C,et al.Identification and expression analyses of SBP-box genes reveal their involvement in abiotic stress and hormone response in tea plant (Camellia sinensis)[J].International Journal of Molecular Sciences,2018,19(11):E3 404.
[17] LETUNIC I,BORK P.20 years of the SMART protein domain annotation resource[J].Nucleic Acids Research,2018,46(D1):D493-D496.
[18] CROOKS G E,HON G,CHANDONIA J M,et al.WebLogo:a sequence logo generator[J].Genome Research,2004,14(6):1 188-1 190.
[19] HALL B G.Building phylogenetic trees from molecular data with MEGA.[J].Molecular Biology and Evolution,2013,30(5):1 229-1 235.
[20] HU B,JIN J P,GUO A Y,et al.GSDS 2.0:an upgraded gene feature visualization server[J].Bioinformatics (Oxford,England),2015,31(8):1 296-1 297.
[21] BAILEY T L,BODEN M,BUSKE F A,et al.MEME SUITE:tools for motif discovery and searching[J].Nucleic Acids Research,2009,37:W202-W208.
[22] LESCOT M,DéHAIS P,THIJS G,et al.PlantCARE,a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J].Nucleic Acids Research,2002,30(1):325-327.
[23] LIVAK K J,SCHMITTGEN T D.Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.[J].Methods,2001,25(4):402-408.
[24] XIA E H,ZHANG H B,SHENG J,et al.The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J].Molecular Plant,2017,10(6):866-877.
[25] WANG L,CAO H L,QIAN W J,et al.Identification of a novel bZIP transcription factor in Camellia sinensis as a negative regulator of freezing tolerance in transgenic Arabidopsis[J].Annals of Botany,2017,119(7):1 195-1 209.
[26] WANG P J,YUE C,CHEN D,et al.Genome-wide identification of WRKY family genes and their response to abiotic stresses in tea plant (Camellia sinensis)[J].Genes & Genomics,2019,41(1):17-33.
[27] SHEN W,LI H,TENG R M,et al.Genomic and transcriptomic analyses of HD-Zip family transcription factors and their responses to abiotic stress in tea plant (Camellia sinensis)[J].Genomics,2018,http://doi.org/10.1016/j.ygeno.2018.07.009.
[28] 王凯.拟南芥和水稻CPP转录因子家族的生物信息学分析[J].生物技术通报,2010,(2):76-84.WANG K.Bioinformatic analysis of the CPP transcription factors family in Arabidopsis and rice[J].Biotechnology Bulletin,2010,(2):76-84.
[29] LU T,DOU Y,ZHANG C.Fuzzy clustering of CPP family in plants with evolution and interaction;analyses[J].BMC Bioinformatics,2013,14(Suppl 13):S10.
[30] 吴耀荣,谢旗.ABA与植物胁迫抗性[J].植物学通报,2006,23(5):511-518.WU Y R,XIE Q.ABA and plant stress response[J].Chinese Bulletin of Botany,2006,23(5):511-518.
[2] LIU Y,WANG D,ZHANG S,et al.Global expansion strategy of Chinese herbal tea beverage[J].Advance Journal of Food Science and Technology,2015,7(9):739-745.
[3] 王鹏杰,陈笛,林浥,等.8个茶树WRKY转录因子基因的克隆与表达分析[J].中草药,2019,50(3):685-693.WANG P J,CHEN D,LIN Y,et al.Cloning and expression analysis of eight WRKY genes in Camellia sinensis[J].Chinese Traditional and Herbal Drugs,2019,50(3):685-693.
[4] ANDERSEN S U,ALGREEN-PETERSEN R G,HOEDL M,et al.The conserved cysteine-rich domain of a tesmin/TSO1-like protein binds zinc in vitro and TSO1 is required for both male and female fertility in Arabidopsis thaliana[J].Journal of Experimental Botany,2007,58(13):3 657-3 670.
[5] CVITANICH C,PALLISGAARD N,NIELSEN K A,et al.CPP1,a DNA-binding protein involved in the expression of a soybean leghemoglobin c3 gene[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97(14):8 163-8 168.
[6] RIECHMANN J L,HEARD J,MARTIN G,et al.Arabidopsis transcription factors:genome-wide comparative analysis among eukaryotes[J].Science,2000,290(5 499):2 105-2 110.
[7] YANG Z F,GU S L,WANG X F,et al.Molecular evolution of the CPP-like gene family in plants:insights from comparative genomics of Arabidopsis and rice[J].Journal of Molecular Evolution,2008,67(3):266-277.
[8] ZHANG L,ZHAO H K,WANG Y M,et al.Genome-wide identification and expression analysis of the CPP-like gene family in soybean[J].Genetics and Molecular Research:GMR,2015,14(1):1 260-1 268.
[9] SONG X Y,ZHANG Y Y,WU F C,et al.Genome-wide analysis of the maize (Zea may L.) CPP-like gene family and expression profiling under abiotic stress[J].Genetics and Molecular Research:GMR,2016,15(3).
[10] ZHOU Y,HU L F,YE S F,et al.Genome-wide identification and characterization of cysteine-rich polycomb-like protein (CPP) family genes in cucumber (Cucumis sativus) and their roles in stress responses[J].Biologia,2018,73(4):425-435.
[11] SIJACIC P,WANG W,LIU Z.Recessive antimorphic alleles overcome functionally redundant loci to reveal TSO1 function in Arabidopsis flowers and meristems[J].PLoS Genetics,2011,7(11):e1002352.
[12] HAUSER B A,HE J Q,PARK S O,et al.TSO1 is a novel protein that modulates cytokinesis and cell expansion in Arabidopsis[J].Development,2000,127(10):2 219-2 226.
[13] WANG W P,SIJACIC P,XU P B,et al.Arabidopsis TSO1 and MYB3R1 form a regulatory module to coordinate cell proliferation with differentiation in shoot and root[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(13):E3 045-E3 054.
[14] 潘冉冉,位明明,王亚杰,等.巴西橡胶树HbCPP1基因的克隆与表达分析[J].植物生理学报,2018,54 (5):763-772.PAN R R,WEI M M,WANG Y J,et al.Cloning and expression analysis of HbCCP1 in rubber tree (Hevea brasiliensis) [J].Plant Physiology Journal,2018,54 (5):763-772.
[15] WEI C L,YANG H,WANG S B,et al.Draft genome sequence of Camellia sinensis var.sinensis provides insights into the evolution of the tea genome and tea quality[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(18):E4 151-E4 158.
[16] WANG P J,CHEN D,ZHENG Y C,et al.Identification and expression analyses of SBP-box genes reveal their involvement in abiotic stress and hormone response in tea plant (Camellia sinensis)[J].International Journal of Molecular Sciences,2018,19(11):E3 404.
[17] LETUNIC I,BORK P.20 years of the SMART protein domain annotation resource[J].Nucleic Acids Research,2018,46(D1):D493-D496.
[18] CROOKS G E,HON G,CHANDONIA J M,et al.WebLogo:a sequence logo generator[J].Genome Research,2004,14(6):1 188-1 190.
[19] HALL B G.Building phylogenetic trees from molecular data with MEGA.[J].Molecular Biology and Evolution,2013,30(5):1 229-1 235.
[20] HU B,JIN J P,GUO A Y,et al.GSDS 2.0:an upgraded gene feature visualization server[J].Bioinformatics (Oxford,England),2015,31(8):1 296-1 297.
[21] BAILEY T L,BODEN M,BUSKE F A,et al.MEME SUITE:tools for motif discovery and searching[J].Nucleic Acids Research,2009,37:W202-W208.
[22] LESCOT M,DéHAIS P,THIJS G,et al.PlantCARE,a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J].Nucleic Acids Research,2002,30(1):325-327.
[23] LIVAK K J,SCHMITTGEN T D.Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.[J].Methods,2001,25(4):402-408.
[24] XIA E H,ZHANG H B,SHENG J,et al.The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J].Molecular Plant,2017,10(6):866-877.
[25] WANG L,CAO H L,QIAN W J,et al.Identification of a novel bZIP transcription factor in Camellia sinensis as a negative regulator of freezing tolerance in transgenic Arabidopsis[J].Annals of Botany,2017,119(7):1 195-1 209.
[26] WANG P J,YUE C,CHEN D,et al.Genome-wide identification of WRKY family genes and their response to abiotic stresses in tea plant (Camellia sinensis)[J].Genes & Genomics,2019,41(1):17-33.
[27] SHEN W,LI H,TENG R M,et al.Genomic and transcriptomic analyses of HD-Zip family transcription factors and their responses to abiotic stress in tea plant (Camellia sinensis)[J].Genomics,2018,http://doi.org/10.1016/j.ygeno.2018.07.009.
[28] 王凯.拟南芥和水稻CPP转录因子家族的生物信息学分析[J].生物技术通报,2010,(2):76-84.WANG K.Bioinformatic analysis of the CPP transcription factors family in Arabidopsis and rice[J].Biotechnology Bulletin,2010,(2):76-84.
[29] LU T,DOU Y,ZHANG C.Fuzzy clustering of CPP family in plants with evolution and interaction;analyses[J].BMC Bioinformatics,2013,14(Suppl 13):S10.
[30] 吴耀荣,谢旗.ABA与植物胁迫抗性[J].植物学通报,2006,23(5):511-518.WU Y R,XIE Q.ABA and plant stress response[J].Chinese Bulletin of Botany,2006,23(5):511-518.