小桐子CDPK及相关激酶基因家族的全基因组鉴定及表达分析
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摘要
基于小桐子基因组数据库,在全基因组水平对小桐子CDPK及相关激酶基因家族进行鉴定,并对其系统进化、基因结构、保守结构域、染色体定位以及器官与低温胁迫表达进行分析,为深入开展小桐子CDPK及相关激酶基因的功能鉴定及其在小桐子遗传改良中的应用提供依据。利用CDPK结构域的隐马尔可夫模型对小桐子蛋白质数据库进行相似性检索,经过Pfam与CDD在线工具的验证获得小桐子CDPK及相关激酶基因家族成员。利用不同的工具对CDPK及相关激酶基因进行生物信息学对比分析。通过小桐子器官与低温表达谱数据进行CDPK及相关激酶基因的表达分析。小桐子基因组中共检索到17个CDPK基因、5个CRK基因、2个PPCK基因、4个PEPRK基因以及1个CCaMK基因,各基因家族成员的基因长度、蛋白质等电点及亚细胞定位等理化参数具有家族特异性。序列比对与系统进化分析显示,5个基因家族都单独聚类,而CDPK与PEPRK基因家族又分别聚类为4个与2个亚族,且鉴定到小桐子CDPK家族成员的N-端可变区、激酶结构区、自抑区及EF-hand调控区4个保守结构域以及其他激酶成员的激酶结构域。同时,分别有21个与24个CDPK及相关激酶可能发生N-豆蔻酰化与N-十六烷酰化的修饰。染色体定位表明,小桐子CDPK及相关激酶基因不均匀地分布于10条染色体上,且存在JcCDPK7/JcCDPK9串联复制现象。转录组表达分析表明,29个CDPK及相关激酶基因中,有24个基因在叶片、根及种子中都有表达,而JcCDPK3、JcCDPK11、JcCRK3及JcCCaMK属于低温诱导高表达基因,与小桐子的抗冷性直接相关。
The plant-specific Calcium-dependent protein kinase(CDPK)is a Ser/Thr protein kinase and a sensors of Ca2+flux,which plays vital roles in Ca2+signaling transduction,plant growth,development,stress resistance and pathogen defense.The CDPK and its related kinase gene family were identified fromJatropha curcas based on the genome database,and then the phylogentic relationship,gene structure,conserved domains,chromosomal location,and organ &chilling stress expression were analyzed.This study might provide a significant foundation for further studies on the gene functions and genetic improvement of CDPKand its related kinase gene in J.curcas.Based on the Hidden Markov Model of conserved CDPKdomain,J.curcas protein database was searched by BLASTP,and then the CDPKand its related kinase genes family were obtained through Pfam and CDD verification.Contrast analysis for CDPKand its related kinase gene were conducted by various bioinformatics tools.Expression patterns of J.curcas CDPKand its related kinase genes in different organs and under chilling hardening were analyzed based on the Digital Gene Expression(DGE)data.The results showed that the J.curcas genome identified 17 CDPKs,five CRKs,two PPCKs,four PEPRKs,and one CCaMK,and all of the gene families owned family-specificity in genetic length,protein electrical points,and subcellular localization.Based on the sequence alignment and phylogenetic relationship,five CDPKand its related kinase gene families clustered individually,and the CDPK and PEPRK gene families were further classified into four and two subfamilies,respectively.Motif analysis revealed that all the CDPK contain N-variable region,kinase domain,auto-inhibitory domain,and EF-hand region from N-to C-terminal,and other CDPKrelated kinase contain kinase domain.Furthermore,21 CDPK and its related kinase had predicted N-myristoylation sites at their N-ternimal,and 24 members also had a nearby Cys residue that could serve as a site for N-palmitoylation.Chromosome mapping analysis indicated that J.curcas CDPKand its related kinase genes were distributed with different densities on10 chromosomes,and tandem duplication of JcCDPK7/JcCDPK9 was found on chromosome LG6.Transcription data revealed that the 24 of total 29 J.curcas CDPK and its related genes were expressed in all tissues of leaves,roots,and seeds.JcCDPK3,JcCDPK11,JcCRK3,and JcCCaMK were remarkably cold-induced expression in leaves,which is associated with J.curcas chilling resistance.The results of this study might lay a important foundation for further studies on the gene function and signaling transduction mechanism of CDPKand its related gene families in J.curcas.
The plant-specific Calcium-dependent protein kinase(CDPK)is a Ser/Thr protein kinase and a sensors of Ca2+flux,which plays vital roles in Ca2+signaling transduction,plant growth,development,stress resistance and pathogen defense.The CDPK and its related kinase gene family were identified fromJatropha curcas based on the genome database,and then the phylogentic relationship,gene structure,conserved domains,chromosomal location,and organ &chilling stress expression were analyzed.This study might provide a significant foundation for further studies on the gene functions and genetic improvement of CDPKand its related kinase gene in J.curcas.Based on the Hidden Markov Model of conserved CDPKdomain,J.curcas protein database was searched by BLASTP,and then the CDPKand its related kinase genes family were obtained through Pfam and CDD verification.Contrast analysis for CDPKand its related kinase gene were conducted by various bioinformatics tools.Expression patterns of J.curcas CDPKand its related kinase genes in different organs and under chilling hardening were analyzed based on the Digital Gene Expression(DGE)data.The results showed that the J.curcas genome identified 17 CDPKs,five CRKs,two PPCKs,four PEPRKs,and one CCaMK,and all of the gene families owned family-specificity in genetic length,protein electrical points,and subcellular localization.Based on the sequence alignment and phylogenetic relationship,five CDPKand its related kinase gene families clustered individually,and the CDPK and PEPRK gene families were further classified into four and two subfamilies,respectively.Motif analysis revealed that all the CDPK contain N-variable region,kinase domain,auto-inhibitory domain,and EF-hand region from N-to C-terminal,and other CDPKrelated kinase contain kinase domain.Furthermore,21 CDPK and its related kinase had predicted N-myristoylation sites at their N-ternimal,and 24 members also had a nearby Cys residue that could serve as a site for N-palmitoylation.Chromosome mapping analysis indicated that J.curcas CDPKand its related kinase genes were distributed with different densities on10 chromosomes,and tandem duplication of JcCDPK7/JcCDPK9 was found on chromosome LG6.Transcription data revealed that the 24 of total 29 J.curcas CDPK and its related genes were expressed in all tissues of leaves,roots,and seeds.JcCDPK3,JcCDPK11,JcCRK3,and JcCCaMK were remarkably cold-induced expression in leaves,which is associated with J.curcas chilling resistance.The results of this study might lay a important foundation for further studies on the gene function and signaling transduction mechanism of CDPKand its related gene families in J.curcas.
引文
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[26]LI A L,ZHU Y F,TAN X M,et al.Evolutionary and functional study of the CDPK gene family in wheat(Triticum aestivum L.)[J].Plant Molecular Biology,2008,66(4):429-443.
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[28]SHEEN J.Ca2+-dependent protein kinase and stress signal transduction in plants[J].Science,1996,274(5294):1900-1902.
[2]ZHU L P,JIN X,XIE Q L,et al.Calcium-dependent protein kinase family genes involved in ethylene-induced natural rubber production in different Hevea brasiliensis cultivars[J].International Journal of Molecular Sciences,2018,19(4):947.
[3]LX Z,LI H Z,CHEN X X,et al.The role of calcium-dependent protein kinase in hydrogen peroxide,nitric oxide and ABA-dependent cold acclimation[J].Journal of Experimental Botany,2018,69(16):4127-4139.
[4]VALMONTE G R,ARTHUR K,HIGGINS C M,et al.Calcium-dependent protein kinases in plants:evolution,expression and function[J].Plant Cell Physiology,2014,55(3):551-569.
[5]SCHULZ P,HERDE M,ROMEIS T.Calcium-dependent protein kinases:hubs in plant stress signaling and development[J].Plant Physiology,2013,163(2):523-530.
[6]XIAO X H,YANG M,SUI J L,et al.The calcium-dependent protein kinase(CDPK)and CDPK-related kinase gene families in Hevea brasiliensis-comparison with five other plant species in structure,evolution,and expression[J].FEBS Open Bio,2017,7(1):4-24.
[7]ITO T,NAKATA M,ISHIDA S,et al.The mechanism of substrate recognition of Ca2+-dependent protein kinases[J].Plant Signaling&Behavior,2011,6(7):924-926.
[8]HRABAK E M,CHAN C W,GRIBSKOV M,et al.The Arabidopsis CDPK-SnRK superfamily of protein kinases[J].Plant Physiology,2003,132(2):666-680.
[9]ASANO T,TANAKA N,YANG G,et al.Genome-wide identification of the rice calciumdependent protein kinase and its closely related kinase gene families:comprehensive analysis of the CDPKs gene family in rice[J].Plant Cell Physiology,2005,46(2):356-366.
[10]KONG X,LV W,JIANG S,et al.Genome-wide identification and expression analysis of calcium-dependent protein kinase in maize[J].BMC Genomics,2013,14:433.
[11]ZUO R,HU R,CHAI G,et al.Genome-wide identification,classification,and expression analysis of CDPK and its closely related gene families in poplar(Populus trichocarpa)[J].Molecular Biology Reports,2013,40(3):2645-2662.
[12]CHENG S H,WILLMANN M R,CHEN H C,et al.Calcium signaling through protein kinases.The Arabidopsis calcium-dependent protein kinase gene family[J].Plant Physiology,2002,129(2):469-485.
[13]WANG J P,XU Y P,MUNYAMPUNDU J P,et al.Calcium-dependent protein kinase(CDPK)and CDPK-related kinase(CRK)gene families in tomato:genome-wide identification and functional analyses in disease resistance[J].Molecular Genetics and Genomics,2016,291(2):661-676.
[14]SATO S,HIRAKAWA H,ISOBE S,et al.Sequence analysis of the genome of an oil-bearing tree,Jatropha curcas L[J].DNA Research,2011,18(1):65-76.
[15]WU P Z,ZHOU C P,CHENG S F,et al.Integrated genome sequence and linkage map of physic nut(Jatropha curcas L.),a biodiesel plant[J].The Plant Journal,2015,81(5):810-821.
[16]WANG H B,ZOU Z R,WANG S S,et al.Deep sequencing-based transcriptome analysis of the oil-bearing plant Physic Nut(Jatropha curcas L.)under cold treatments[J].Plant Omics,2014,7(3):178-187.
[17]WANG H B,ZOU Z R,WANG S S,et al.Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcus L[J].Plos ONE,2013,8(12):e82817.
[18]THOEN P A,ARIYUREK Y,THYGESEN H H,et al.Deep sequencing-based expression analysis shows major advances in robustness,resolution and inter-lab portability over five microarray platforms[J].Nucleic Acids Research,2008,36(21):e141.
[19]MORRISSY A S,MORIN R D,DELANEY A,et al.Nextgeneration tag sequencing for cancer gene expression profiling[J].Genome Research,2009,19(10):1825-1835.
[20]MOHANTA T K,MOHANTA N,MOHANTA Y K,et al.Genome-wide identification of calcium dependent protein kinase gene family in plant lineage shows presence of novel D-x-D and D-E-L motifs in EF-hand domain[J].Frontiers in Plant Science,2015,6:e1146.
[21]CHEN F,FASOLII M,TORNIELLI G B,et al.The evolutionary history and diverse physiological of the grapevine calcium-dependent protein gene family[J].Plos ONE,2013,8(12):e80818.
[22]SHULAEV V,SARGENT D J,CROWHURST R N,et al.The genome of woodland strawberry(Fragaria vesca)[J].Nature Genetics,2011,43(2):109-116.
[23]VERDE I,ABBOTT A G,SSALABRIN S,et al.The highquality draft genome of peach(Prunus persica)identifies unique patterns of genetic diversity,domestication and genome evolution[J].Nature Genetics,2013,45(5):487-494.
[24]CANNON S B,MITRA A,BAUMGARTEN A.The roles of segmental and tandem duplication in the evolution of large gene families in Arabidopsis thaliana[J].BMCPlant Biology,2004,20(3):116-124.
[25]YOON G M,CHO H S,HA H J,et al.Characterization of NtCDPK1,a calcium-dependent protein kinase gene in Nicotiana tabacum,and the activity of its encoded protein[J].Plant Molecular Biology,1999,39(5):991-1001.
[26]LI A L,ZHU Y F,TAN X M,et al.Evolutionary and functional study of the CDPK gene family in wheat(Triticum aestivum L.)[J].Plant Molecular Biology,2008,66(4):429-443.
[27]LIU G S,CHEN J,WANG X C.VfCPK1,agene encoding calcium-dependent protein kinase fromVicia faba,is induced by drought and abscisic acid[J].Plant,Cell and Environment,2006,29(11):2091-2099.
[28]SHEEN J.Ca2+-dependent protein kinase and stress signal transduction in plants[J].Science,1996,274(5294):1900-1902.