基于转录组的荔枝XTH家族基因的鉴定及分析
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摘要
为了研究木葡聚糖内切葡聚糖酶/水解酶(xyloglucan endotransglucosylase/hydrolase, XTH)基因家族在荔枝花穗发育过程中的分布及表达情况,本研究基于‘妃子笑’荔枝花穗转录组数据,利用生物信息学研究方法,首次对‘妃子笑’荔枝XTH基因家族进行鉴定,包括基因的基本物理和化学特征,亚细胞定位,蛋白质保守结构域,进化关系和表达模式。结果表明:Lc XTH基因家族成员有29个,其蛋白长度范围在37～311 AA之间,对应的相对分子量范围在4.398～35.711 k D之间,等电点(pI)范围为4.39～9.46。此外,亚细胞定位分析显示所有LcXTH蛋白均位于细胞壁;Lc XTH含有2个相对保守的结构域(Glyco_hydro_16结构域和XET_C结构域);系统发育树分析表明LcXTH基因家族分为四组(Ⅰ～Ⅳ组),不同发育阶段LcXTHF基因的表达模式不同。本研究为进一步对XTH基因的功能研究提供理论依据。
In order to study the distribution and expression of Xyloglucan endotransglucosylase/hydrolase(XTH)gene family during the development of litchi spikes, based on the transcriptome data of 'Feizixiao' litchi flower panicles, the XTH gene family of 'Feizixiao' litchi was identified for the first time by using bioinformatics methods,including the basic physical and chemical characteristics of the gene, subcellular localization, protein conserved domain, evolutionary relationship and expression pattern. The results showed that there were 29 family members in LcXTH gene family, and the encoded proteins ranged from 37 to 311 aa in length. The relative molecular weight varied from 4.398 to 35.711 k D, and the isoelectric point(p I) was in the range of 4.39 to 9.46. In addition, subcellular localization analysis indicated that all of the Lc XTH proteins were located in the cell wall. LcXTH contained 2 relatively conservative domains(Glyco_hydro_16 domain and XET_C domain). Phylogenetic tree analysis revealed that LcXTH gene family was divided into four groups(groupⅠ～groupⅣ), and the expression patterns of LcXTHF gene were different at different developmental stages. This study could provide a theoretical basis for further functional study of XTH gene.
In order to study the distribution and expression of Xyloglucan endotransglucosylase/hydrolase(XTH)gene family during the development of litchi spikes, based on the transcriptome data of 'Feizixiao' litchi flower panicles, the XTH gene family of 'Feizixiao' litchi was identified for the first time by using bioinformatics methods,including the basic physical and chemical characteristics of the gene, subcellular localization, protein conserved domain, evolutionary relationship and expression pattern. The results showed that there were 29 family members in LcXTH gene family, and the encoded proteins ranged from 37 to 311 aa in length. The relative molecular weight varied from 4.398 to 35.711 k D, and the isoelectric point(p I) was in the range of 4.39 to 9.46. In addition, subcellular localization analysis indicated that all of the Lc XTH proteins were located in the cell wall. LcXTH contained 2 relatively conservative domains(Glyco_hydro_16 domain and XET_C domain). Phylogenetic tree analysis revealed that LcXTH gene family was divided into four groups(groupⅠ～groupⅣ), and the expression patterns of LcXTHF gene were different at different developmental stages. This study could provide a theoretical basis for further functional study of XTH gene.
引文
Berardini T.Z.,Mundodi S.,Reiser L.,Huala E.,Garcia-hernandez M.,Zhang P.F.,Mueller L.A.,Yoon J.,Doyle A.,Lander G.,Moseyko N.,Yoo D.,Xu I.,Zoeckler B.,Montoya M.,Miller N.,Weems D.,and Rhee S.Y.,2004,Functional annotation of the Arabidopsis genome using controlled vocabularies,Plant Physiol.,135(2):745-755
Campbell P.,and Braam J.,1998,Co-and/or post-translational modifications are critical for TCH4 XET activity,Plant J.,15(4):553-561
Chen C.,2017,Cloning and expression profiling of XTH family genes in ramie,Thesis for M.S.,Huazhong Agricultural University,Supervisor:Peng D.X.,pp.27-30(陈悰,2017,苎麻XTH家族基因克隆及表达分析,硕士学位论文,华中农业大学,导师:彭定祥,pp.27-30)
Chu P.,Liu H.J.,Yang L.,and Guan R.Z.,2014,Cloning and expression analysis of BnXTH1 gene from Brasscia napus,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),12(3):432-439)(楚璞,刘慧娟,杨力,管荣展,2014,甘蓝型油菜BnXTH1基因的克隆与表达分析,分子植物育种,12(3):432-439)
Dong J.L.,Jiang Y.Y.,Chen R.J.,Xu Z.J.,and Gao X.L.,2011,Isolation of a novel xyloglucan endotransglucosylase(OsX-ET9)gene from rice and analysis of the response of this gene to abiotic stresses,African Journal of Biotechnology,10(76):17424-17434
Geisler-Lee J.,Geisler M.,Coutinho P.M.,Segerman B.,Nishikubo N.,Takahashi J.,Aspeborg H.,Djerbi S.,Master E.,Andersson-Gunner覽s S.,Sundberg B.,Karpinski S.,Teeri T.T.,Kleczkowski L.A.,Henrissat B.,and Mellerowicz E.J.,2006,Poplar carbohydrate-active enzymes,Gene identifica tion and expression analyses,Plant Physiol.,140(3):946-962
Hong H.,Serraj R.,and Yang Q.,2009,Changes in Os XTH gene expression,ABA content,and peduncle elongation in rice subjected to drought at the reproductive stage,Acta Physiol.Plant.,31(4):749-756
Liu Y.,Liu D.,Zhang H.,Gao H.,Guo X.,Wang D.,Zhang X.,and Zhang A.,2007,Theα-andβ-expansin and xyloglucan endotransglucosylase/hydrolase gene families of wheat:Mo-lecular cloning,gene expression,and EST data mining,Genomics,90(4):516-529
Lu W.,Wang Y.,Jiang Y.,Li J.,Liu H.,Duan X.,and Song L.,2006,Differential expression of litchi XET genes in relation to fruit growth,Plant Physiol.Biochem.,44(11-12):707-713
Nishitani K.,and Tominaga R.,1992,Endo-xyloglucan transferase,a novel class of glycosyltransferase that catalyzes transfer of a segment of xyloglucan molecule to another xyloglucan molecule.,J.Biol.Chem.,267(29):21058-21064
Opazo M.C.,Figueroa C.R.,Henriquez J.,Herrera R.,Bruno C.,Valenzuela P.D.T.,and Moya-Leon M.A.,2010,Characterization of two divergent cDNAs encoding xyloglucan endotransglycosylase/hydrolase(XTH)expressed in Fragaria chiloensis fruit,Plant Sci.,179(5):479-488
Rose J.K.C.,Braam J.,Fry S.C.,and Nishitani K.,2002,The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis:current rerspectives and a new unifying nomenclature,Plant Cell Physiol.,43(12):1421-1435
SaladiéM.,Rose J.K.,Cosgrove D.J.,and CataláC.,2006,Characterization of a new xyloglucan endotransglucosylase/hydrolase(XTH)from ripening tomato fruit and implications for the diverse modes of enzymic action,Plant J.,47(2):282-295
Wang Y.S.,Nie F.,and Lin S.Q.,2015,The latest research progress in high-throughput sequencing of fruit tree,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(9):2034-2043(王云生,聂飞,林顺权,2015,果树高通量测序的最新研究进展,基因组学与应用生物学,34(9):2034-2043)
Xuan Y.,Zhou Z.S.,Li H.B.,and Yang Z.M.,2016,Identification of a group of XTHs genes responding to heavy metal mercury,salinity and drought stresses in Medicago truncatula,Ecotoxicol.Environ.Saf.,132:153-163
Yokoyama R.,Rose J.K.C.,and Nishitani K.,2004,A surprising diversity and abundance of xyloglucan endotransglucosylase/hydro/tion and expression analysis,Plant Physiol.,134(3):1088-1099
Yuan X.M.,He L.,Zhang K.Y.,Wu X.,Ma F.F.,Wang J.,and Han Y.H.,2017,Analysis of XTH genes that related to drought stress in foxtail millet,Shanxi Nongye Daxue Xuebao(Journal of Shanxi Agricultural University),37(1):1-6(元香梅,禾璐,张凯烨,武雪,马芳芳,王军,韩渊怀,2017,谷子XTH基因家族与抗旱相关基因的分析,山西农业大学学报,37(1):1-6)
Zhang L.,Niu X.L.,Zhang H.Y.,and Liu Y.S.,2012,Functional analysis via overexpressing xyloglucan endotransglycosylase gene OsXTH11 in rice,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(16):3231-3239(张黎,牛向丽,张惠莹,刘永胜,2012,水稻木葡聚糖内糖基转移酶基因OsXTH-11过表达的作用分析,中国农业科学,45(16):3231-3239)
Campbell P.,and Braam J.,1998,Co-and/or post-translational modifications are critical for TCH4 XET activity,Plant J.,15(4):553-561
Chen C.,2017,Cloning and expression profiling of XTH family genes in ramie,Thesis for M.S.,Huazhong Agricultural University,Supervisor:Peng D.X.,pp.27-30(陈悰,2017,苎麻XTH家族基因克隆及表达分析,硕士学位论文,华中农业大学,导师:彭定祥,pp.27-30)
Chu P.,Liu H.J.,Yang L.,and Guan R.Z.,2014,Cloning and expression analysis of BnXTH1 gene from Brasscia napus,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),12(3):432-439)(楚璞,刘慧娟,杨力,管荣展,2014,甘蓝型油菜BnXTH1基因的克隆与表达分析,分子植物育种,12(3):432-439)
Dong J.L.,Jiang Y.Y.,Chen R.J.,Xu Z.J.,and Gao X.L.,2011,Isolation of a novel xyloglucan endotransglucosylase(OsX-ET9)gene from rice and analysis of the response of this gene to abiotic stresses,African Journal of Biotechnology,10(76):17424-17434
Geisler-Lee J.,Geisler M.,Coutinho P.M.,Segerman B.,Nishikubo N.,Takahashi J.,Aspeborg H.,Djerbi S.,Master E.,Andersson-Gunner覽s S.,Sundberg B.,Karpinski S.,Teeri T.T.,Kleczkowski L.A.,Henrissat B.,and Mellerowicz E.J.,2006,Poplar carbohydrate-active enzymes,Gene identifica tion and expression analyses,Plant Physiol.,140(3):946-962
Hong H.,Serraj R.,and Yang Q.,2009,Changes in Os XTH gene expression,ABA content,and peduncle elongation in rice subjected to drought at the reproductive stage,Acta Physiol.Plant.,31(4):749-756
Liu Y.,Liu D.,Zhang H.,Gao H.,Guo X.,Wang D.,Zhang X.,and Zhang A.,2007,Theα-andβ-expansin and xyloglucan endotransglucosylase/hydrolase gene families of wheat:Mo-lecular cloning,gene expression,and EST data mining,Genomics,90(4):516-529
Lu W.,Wang Y.,Jiang Y.,Li J.,Liu H.,Duan X.,and Song L.,2006,Differential expression of litchi XET genes in relation to fruit growth,Plant Physiol.Biochem.,44(11-12):707-713
Nishitani K.,and Tominaga R.,1992,Endo-xyloglucan transferase,a novel class of glycosyltransferase that catalyzes transfer of a segment of xyloglucan molecule to another xyloglucan molecule.,J.Biol.Chem.,267(29):21058-21064
Opazo M.C.,Figueroa C.R.,Henriquez J.,Herrera R.,Bruno C.,Valenzuela P.D.T.,and Moya-Leon M.A.,2010,Characterization of two divergent cDNAs encoding xyloglucan endotransglycosylase/hydrolase(XTH)expressed in Fragaria chiloensis fruit,Plant Sci.,179(5):479-488
Rose J.K.C.,Braam J.,Fry S.C.,and Nishitani K.,2002,The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis:current rerspectives and a new unifying nomenclature,Plant Cell Physiol.,43(12):1421-1435
SaladiéM.,Rose J.K.,Cosgrove D.J.,and CataláC.,2006,Characterization of a new xyloglucan endotransglucosylase/hydrolase(XTH)from ripening tomato fruit and implications for the diverse modes of enzymic action,Plant J.,47(2):282-295
Wang Y.S.,Nie F.,and Lin S.Q.,2015,The latest research progress in high-throughput sequencing of fruit tree,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(9):2034-2043(王云生,聂飞,林顺权,2015,果树高通量测序的最新研究进展,基因组学与应用生物学,34(9):2034-2043)
Xuan Y.,Zhou Z.S.,Li H.B.,and Yang Z.M.,2016,Identification of a group of XTHs genes responding to heavy metal mercury,salinity and drought stresses in Medicago truncatula,Ecotoxicol.Environ.Saf.,132:153-163
Yokoyama R.,Rose J.K.C.,and Nishitani K.,2004,A surprising diversity and abundance of xyloglucan endotransglucosylase/hydro/tion and expression analysis,Plant Physiol.,134(3):1088-1099
Yuan X.M.,He L.,Zhang K.Y.,Wu X.,Ma F.F.,Wang J.,and Han Y.H.,2017,Analysis of XTH genes that related to drought stress in foxtail millet,Shanxi Nongye Daxue Xuebao(Journal of Shanxi Agricultural University),37(1):1-6(元香梅,禾璐,张凯烨,武雪,马芳芳,王军,韩渊怀,2017,谷子XTH基因家族与抗旱相关基因的分析,山西农业大学学报,37(1):1-6)
Zhang L.,Niu X.L.,Zhang H.Y.,and Liu Y.S.,2012,Functional analysis via overexpressing xyloglucan endotransglycosylase gene OsXTH11 in rice,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(16):3231-3239(张黎,牛向丽,张惠莹,刘永胜,2012,水稻木葡聚糖内糖基转移酶基因OsXTH-11过表达的作用分析,中国农业科学,45(16):3231-3239)