马铃薯CBL家族基因的鉴定及序列分析
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摘要
植物CBL家族基因在逆境胁迫应答中具有重要功能,但在马铃薯中鲜有报道。本研究通过生物信息学方法在马铃薯基因组中筛选出13个CBL基因,并鉴定了这些基因的染色体分布、理化性质、遗传进化、序列结构和顺式作用元件等。结果发现,马铃薯CBL基因在染色体上的分布是不均匀的,编码区长度在642～774 bp之间,外显子数除了StCBL1只含有一个以外,其余CBLs的外显子数多为7～9个;在遗传进化上,马铃薯CBL可分为两大组,且多与番茄CBL同源;通过对其编码蛋白序列进行比对,发现每个CBL均具有4个变异程度不等的EF-hand结构域;其含有的作用位点类型也有所差异,StCBL2/StCBL8/StCBL9的N端不含有常规的豆蔻酰化位点,其C端的核心基序FPSV中,缺失了可被CIPK磷酸化的关键丝氨酸残基;在马铃薯CBL基因的上游序列中发现了可以响应不同植物激素以及逆境胁迫的顺式作用元件。本研究对马铃薯CBL家族进行了鉴定与初步分析,可为进一步研究马铃薯CBL基因功能提供理论依据。
Plant CBL family genes have important functions in stress response, but they are rarely reported in potatoes. In this study, 13 CBL genes were screened in the potato genome by bioinformatics methods, and the chromosome distribution, physicochemical properties, genetic evolution, sequence structure and cis-acting elements of these genes were identified. The results showed that the distribution of CBL gene on the chromosome of potato was not uniform. The length of the coding region was between 642 bp and 774 bp, and the number of exons for StCBL1 was only one, while for others was 7 to 9. In genetic evolution, potato CBL could be divided into two groups, and most of them were homologous to tomato CBL. By comparing the sequence of its coding protein,it was found that each CBL had four EF-hand domains with varying degrees of variation. They contained different types of action sites. The N-terminus of StCBL2/StCBL8/StCBL9 did not contain a conventional myristoylation site,and the C-terminal core FPSV-motif lacked the key serine residues, which could be used for phosphorylation by CIPK(CBL-interacting protein kinases). Cis-acting elements responsive to different plant hormones and stress were found in the upstream sequence of potato CBL gene. In this study, potato CBL family was identified and preliminarily analyzed, which could provide theoretical basis for further study of potato CBL gene function.
Plant CBL family genes have important functions in stress response, but they are rarely reported in potatoes. In this study, 13 CBL genes were screened in the potato genome by bioinformatics methods, and the chromosome distribution, physicochemical properties, genetic evolution, sequence structure and cis-acting elements of these genes were identified. The results showed that the distribution of CBL gene on the chromosome of potato was not uniform. The length of the coding region was between 642 bp and 774 bp, and the number of exons for StCBL1 was only one, while for others was 7 to 9. In genetic evolution, potato CBL could be divided into two groups, and most of them were homologous to tomato CBL. By comparing the sequence of its coding protein,it was found that each CBL had four EF-hand domains with varying degrees of variation. They contained different types of action sites. The N-terminus of StCBL2/StCBL8/StCBL9 did not contain a conventional myristoylation site,and the C-terminal core FPSV-motif lacked the key serine residues, which could be used for phosphorylation by CIPK(CBL-interacting protein kinases). Cis-acting elements responsive to different plant hormones and stress were found in the upstream sequence of potato CBL gene. In this study, potato CBL family was identified and preliminarily analyzed, which could provide theoretical basis for further study of potato CBL gene function.
引文
Batistic O.,and Kudla J.,2012,Analysis of calcium signaling pathways in plants,Biochim.Biophys.Acta,1820(8):1283-1293
de la Torre F.,Gutiérrez-Beltrán E.,Pareja-Jaime Y.,Chakravarthy S.,Martin G.B.,and Del Pozo O.,2013,The tomato calcium sensor Cbl10 and its interacting protein kinase Cipk6 define a signaling pathway in plant immunity,Plant Cell,25(7):2748-2764
Fan H.,Ma Y.,Sun F.,Wang L.,and Huang X.M.,2012,Genomic analysis of CBL9 gene in potato,Shandong Nongye Kexue(Shandong Agricultural Sciences),44(8):10-12(范华,马妍,孙凡,王琳,黄晓明,2012,马铃薯CBL9基因的基因组解析,山东农业科学,44(8):10-12)
Hu B.,Jin J.P.,Guo A.Y.,Zhang H.,Luo J.C.,and Gao G.,2014,GSDS 2.0:an upgraded gene feature visualization server,Bioinformatics,31(8):1296-1297
Ishitani M.,Liu J.P.,Halfter U.,Kim C.S.,Shi W.M.,and Zhu J.K.,2000,SOS3 function in plant salt tolerance requires N-myristoylation and calcium binding,Plant Cell,12(9):1667-1677
Jacques S.,Ghesquière B.,De Bock P.J.,Demol H.,Wahni K.,Willems P.,Messens J.,Breusegem F.V.,and Gevaert K.,2015,Protein methionine sulfoxide dynamics in Arabidopsis thaliana under oxidative stress,Mol.Cell.Proteomics,14(5):1217-1229
Kolukisaoglu U.,Weinl S.,Blazevic D.,Bastistic O.,and Kudla J.,2004,Calcium sensors and their interacting protein kinases:genomics of the Arabidopsis and rice CBL-CIPK signaling networks,Plant Physiol.,134(1):43-58
Kumar S.,Stecher G.,and Tamura K.,2016,MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets,Mol.Biol.Evol.,33(7):1870-1874
Lewit-Bentley A.,and Réty S.,2000,EF-hand calcium-binding proteins,Curr.Opin.Struct.Biol.,10(6):637-643
Li X.J.,Liu H.B.,Lin X.Q.,Wu Z.D.,Xu C.H.,and Liu X.L.,2015,In silico cloning and bioinformatics analysis of KNOXgene in sugarcane(Sckn1),Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(1):136-142(李旭娟,刘洪博,林秀琴,吴转娣,徐超华,刘新龙,2015,甘蔗KNOX基因(Sckn1)的电子克隆及生物信息学分析,基因组学与应用生物学,34(1):136-142)
Liu P.,Duan Y.H.,Liu C.,Xue Q.H.,Guo J.,Qi T.,Kang Z.S.,and Guo J.,2018,The calcium sensor TaCBL4 and its interacting protein TaCIPK5 are required for wheat resistance to stripe rust fungus,J.Exp.Bot.,69(18):4443-4457
Liu S.M.,Wang S.H.,Liu M.Y.,Ji F.Q.,Li L.B.,and Hou L.X.,2015,Identification and characterization of CBL family genes in tomato,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),13(10):2268-2273(刘淑梅,王施慧,刘明毓,纪复勤,李利斌,侯丽霞,2015,番茄CBL家族基因的鉴定和遗传进化分析,分子植物育种,13(10):2268-2273)
Liu S.Y.,Huang H.F.,Wang X.D.,Gong C.,Song H.H.,Chen X.L.,and Wang A.X.,2017,Identification and characterization of CBL and CIPK genes in pepper,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(8):2977-2985(刘思源,黄海锋,王旭东,宫超,宋海慧,陈秀玲,王傲雪,2017,辣椒全基因组中CBL、CIPK基因家族的鉴定及特性分析,分子植物育种,15(8):2977-2985)
Nagae M.,Nozawa A.,Koizumi N.,Sano H.,Hashimoto H.,Sato M.,and Shimizu T.,2003,The crystal structure of the novel calcium binding protein At CBL2 from Arabidopsis thaliana,J.Biol.Chem.,278(43):42240-42246
Nuruzzaman M.,Manimekalai R.,Sharoni A.M.,Satoh K.,Kondoh H.,Ooka H.,and Kikuchi S.,2010,Genome-wide analysis of NAC transcription factor family in rice,Gene,465(1):30-44
Quan R.D.,Lin H.X.,Mendoza I.,Zhang Y.G.,Cao W.H.,Yang Y.Q.,Shang M.,Chen S.Y.,Pardo J.M.,and Guo Y.,2007,SCABP8/CBL10,a putative calcium sensor,interacts with the protein kinase SOS2 to protect Arabidopsis shoots from salt stress,Plant Cell,19(4):1415-1431
Roy S.W.,and Penny D.,2007,Patterns of intron loss and gain in plants:intron loss-dominated evolution and genome-wide comparison of O.sativa and A.thaliana,Mol.Biol.Evol.,24(1):171-181
Sun T.,Wang Y.,Wang M.,Li T.T.,Zhou Y.,Wang X.T.,Wei S.Y.,He G.Y.,and Yang G.X.,2015,Identification and comprehensive analyses of the CBL and CIPK gene families in wheat(Triticum aestivum L.),BMC Plant Biol.,15(1):269
Wang C.T.,Yuan Z.H.,Li S.P.,Wang W.,Xue R.L.,and Tai F.J.,2014,Characterization of eight CBL genes expressions in maize early seeding development,Acta Physiol.Plant.,36(12):3307-3314
Wang W.J.,2017,TOR regulated potassium absorption and photosynthetic growth via CIPK23 in potato and Arabidopsis,Thesis for M.S.,Southwest University,Supervisor:Zhang J.K.,pp.47-54(王婉晶,2017,TOR信号通路通过CIPK23调控马铃薯和拟南芥的钾离子吸收和生长,硕士学位论文,西南大学,导师:张建奎,pp.47-54)
Wang X.P.,Zhang H.L.,Gao H.C.,Wu Y.,and Wang Q.W.,2017,Research progress on the mechanism of CBL-CIPKsignaling pathways in response to abiotic stress,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(4):1295-1303(王晓彤,张海玲,高慧纯,吴杨,王全伟,2017,植物CBL-CIPK信号通路响应非生物胁迫作用机制的研究进展,分子植物育种,15(4):1295-1303)
Weinl S.,and Kudla J.,2009,The CBL-CIPK Ca2+-decoding signaling network:function and perspectives,New Phytologist,184(3):517-528
de la Torre F.,Gutiérrez-Beltrán E.,Pareja-Jaime Y.,Chakravarthy S.,Martin G.B.,and Del Pozo O.,2013,The tomato calcium sensor Cbl10 and its interacting protein kinase Cipk6 define a signaling pathway in plant immunity,Plant Cell,25(7):2748-2764
Fan H.,Ma Y.,Sun F.,Wang L.,and Huang X.M.,2012,Genomic analysis of CBL9 gene in potato,Shandong Nongye Kexue(Shandong Agricultural Sciences),44(8):10-12(范华,马妍,孙凡,王琳,黄晓明,2012,马铃薯CBL9基因的基因组解析,山东农业科学,44(8):10-12)
Hu B.,Jin J.P.,Guo A.Y.,Zhang H.,Luo J.C.,and Gao G.,2014,GSDS 2.0:an upgraded gene feature visualization server,Bioinformatics,31(8):1296-1297
Ishitani M.,Liu J.P.,Halfter U.,Kim C.S.,Shi W.M.,and Zhu J.K.,2000,SOS3 function in plant salt tolerance requires N-myristoylation and calcium binding,Plant Cell,12(9):1667-1677
Jacques S.,Ghesquière B.,De Bock P.J.,Demol H.,Wahni K.,Willems P.,Messens J.,Breusegem F.V.,and Gevaert K.,2015,Protein methionine sulfoxide dynamics in Arabidopsis thaliana under oxidative stress,Mol.Cell.Proteomics,14(5):1217-1229
Kolukisaoglu U.,Weinl S.,Blazevic D.,Bastistic O.,and Kudla J.,2004,Calcium sensors and their interacting protein kinases:genomics of the Arabidopsis and rice CBL-CIPK signaling networks,Plant Physiol.,134(1):43-58
Kumar S.,Stecher G.,and Tamura K.,2016,MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets,Mol.Biol.Evol.,33(7):1870-1874
Lewit-Bentley A.,and Réty S.,2000,EF-hand calcium-binding proteins,Curr.Opin.Struct.Biol.,10(6):637-643
Li X.J.,Liu H.B.,Lin X.Q.,Wu Z.D.,Xu C.H.,and Liu X.L.,2015,In silico cloning and bioinformatics analysis of KNOXgene in sugarcane(Sckn1),Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(1):136-142(李旭娟,刘洪博,林秀琴,吴转娣,徐超华,刘新龙,2015,甘蔗KNOX基因(Sckn1)的电子克隆及生物信息学分析,基因组学与应用生物学,34(1):136-142)
Liu P.,Duan Y.H.,Liu C.,Xue Q.H.,Guo J.,Qi T.,Kang Z.S.,and Guo J.,2018,The calcium sensor TaCBL4 and its interacting protein TaCIPK5 are required for wheat resistance to stripe rust fungus,J.Exp.Bot.,69(18):4443-4457
Liu S.M.,Wang S.H.,Liu M.Y.,Ji F.Q.,Li L.B.,and Hou L.X.,2015,Identification and characterization of CBL family genes in tomato,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),13(10):2268-2273(刘淑梅,王施慧,刘明毓,纪复勤,李利斌,侯丽霞,2015,番茄CBL家族基因的鉴定和遗传进化分析,分子植物育种,13(10):2268-2273)
Liu S.Y.,Huang H.F.,Wang X.D.,Gong C.,Song H.H.,Chen X.L.,and Wang A.X.,2017,Identification and characterization of CBL and CIPK genes in pepper,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(8):2977-2985(刘思源,黄海锋,王旭东,宫超,宋海慧,陈秀玲,王傲雪,2017,辣椒全基因组中CBL、CIPK基因家族的鉴定及特性分析,分子植物育种,15(8):2977-2985)
Nagae M.,Nozawa A.,Koizumi N.,Sano H.,Hashimoto H.,Sato M.,and Shimizu T.,2003,The crystal structure of the novel calcium binding protein At CBL2 from Arabidopsis thaliana,J.Biol.Chem.,278(43):42240-42246
Nuruzzaman M.,Manimekalai R.,Sharoni A.M.,Satoh K.,Kondoh H.,Ooka H.,and Kikuchi S.,2010,Genome-wide analysis of NAC transcription factor family in rice,Gene,465(1):30-44
Quan R.D.,Lin H.X.,Mendoza I.,Zhang Y.G.,Cao W.H.,Yang Y.Q.,Shang M.,Chen S.Y.,Pardo J.M.,and Guo Y.,2007,SCABP8/CBL10,a putative calcium sensor,interacts with the protein kinase SOS2 to protect Arabidopsis shoots from salt stress,Plant Cell,19(4):1415-1431
Roy S.W.,and Penny D.,2007,Patterns of intron loss and gain in plants:intron loss-dominated evolution and genome-wide comparison of O.sativa and A.thaliana,Mol.Biol.Evol.,24(1):171-181
Sun T.,Wang Y.,Wang M.,Li T.T.,Zhou Y.,Wang X.T.,Wei S.Y.,He G.Y.,and Yang G.X.,2015,Identification and comprehensive analyses of the CBL and CIPK gene families in wheat(Triticum aestivum L.),BMC Plant Biol.,15(1):269
Wang C.T.,Yuan Z.H.,Li S.P.,Wang W.,Xue R.L.,and Tai F.J.,2014,Characterization of eight CBL genes expressions in maize early seeding development,Acta Physiol.Plant.,36(12):3307-3314
Wang W.J.,2017,TOR regulated potassium absorption and photosynthetic growth via CIPK23 in potato and Arabidopsis,Thesis for M.S.,Southwest University,Supervisor:Zhang J.K.,pp.47-54(王婉晶,2017,TOR信号通路通过CIPK23调控马铃薯和拟南芥的钾离子吸收和生长,硕士学位论文,西南大学,导师:张建奎,pp.47-54)
Wang X.P.,Zhang H.L.,Gao H.C.,Wu Y.,and Wang Q.W.,2017,Research progress on the mechanism of CBL-CIPKsignaling pathways in response to abiotic stress,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(4):1295-1303(王晓彤,张海玲,高慧纯,吴杨,王全伟,2017,植物CBL-CIPK信号通路响应非生物胁迫作用机制的研究进展,分子植物育种,15(4):1295-1303)
Weinl S.,and Kudla J.,2009,The CBL-CIPK Ca2+-decoding signaling network:function and perspectives,New Phytologist,184(3):517-528