烟草KNOX基因家族的结构与表达模式分析
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摘要
KNOX基因家族是具有同源异型盒结构域的转录因子,在植物形态建成、模式形成等过程中起重要调控作用。为明确烟草KNOX基因的结构及生物学功能,分别从普通烟草、林烟草和绒毛状烟草中鉴定出18、8和5个KNOX基因,并对其系统进化、基因结构、蛋白功能域及基因表达模式进行分析。结果表明,烟草KNOX基因可分为NtKNOXⅠ和NtKNOXⅡ两个亚类,两亚类又进一步分为5个进化分支。同一进化分支中烟草KNOX蛋白的功能域以及其编码序列在基因结构上的分布高度保守。基因表达分析表明,普通烟草中NtKNOXⅡ类基因在多个组织中表达,而且整体表达水平高于NtKNOXⅠ类基因。在林烟草和绒毛状烟草的根和叶中表达量最高的KNOX基因不同。
KNOX genes encode transcription factors with homeobox domains, which play important roles in plant morphogenesis and pattern formation. To explore the structure and functions of KNOX genes from tobacco,18, 8 and 5 KNOX genes were identified from Nicotiana tabacum, N. sylvestris and N. tomentosiformis,respectively. In addition, their phylogenetic, gene structure, protein functional domains and gene expression patterns were analyzed. The results showed that KNOX genes from tobacco could be divided into two subclasses:NtKNOX Ⅰ and NtKNOX Ⅱ, and the two subclasses were further divided into 5 evolutionary branches. In the same evolutionary branch, the functional domains of tobacco KNOX proteins and their coding sequences were highly conserved in gene structure. Expression analysis indicated that NtKNOX Ⅱ genes in N.tabacum were expressed in multiple tissues, and the overall expression level was higher than that of NtKNOX Ⅰgenes. The high expressed genes were different in roots and leaves of N. sylvestris and N. tomentosiformis.
KNOX genes encode transcription factors with homeobox domains, which play important roles in plant morphogenesis and pattern formation. To explore the structure and functions of KNOX genes from tobacco,18, 8 and 5 KNOX genes were identified from Nicotiana tabacum, N. sylvestris and N. tomentosiformis,respectively. In addition, their phylogenetic, gene structure, protein functional domains and gene expression patterns were analyzed. The results showed that KNOX genes from tobacco could be divided into two subclasses:NtKNOX Ⅰ and NtKNOX Ⅱ, and the two subclasses were further divided into 5 evolutionary branches. In the same evolutionary branch, the functional domains of tobacco KNOX proteins and their coding sequences were highly conserved in gene structure. Expression analysis indicated that NtKNOX Ⅱ genes in N.tabacum were expressed in multiple tissues, and the overall expression level was higher than that of NtKNOX Ⅰgenes. The high expressed genes were different in roots and leaves of N. sylvestris and N. tomentosiformis.
引文
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[3]Gehring W J,Affolter M,Burglin T.Homeodomain proteins[J].Annual Review of Biochemistry,1994,63(1):487-526.
[4]Chen H,Rosin F M,Prat S,et al.Interacting transcription factors from the three-amino acid loop extension superclass regulate tuber formation[J].Plant Physiology,2003,132(3):1391-1404.
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[7]Nadakuduti S S,Holdsworth W L,Klein C L,et al.KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN2-LIKEexpression in tomato[J].The Plant Journal,2014,78(6):1022-1033.
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[9]Ito Y,Eiguchi M,Kurata N.KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice[J].Genesis,2001,30(4):231-238.
[10]Yu H,Yang S H,Goh C J.DOH1,a class 1 knox gene,is required for maintenance of the basic plant architecture and floral transition in orchid[J].The Plant Cell,2000,12(11):2143-2160.
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[12]Magnani E,Hake S.KNOX lost the OX:the Arabidopsis KNATM gene defines a novel class of KNOX transcriptional regulators missing the homeodomain[J].The Plant Cell,2008,20(4):875-887.
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[14]Johnson A D.Molecular mechanisms of cell-type determination in budding yeast[J].Current Opinion in Genetics&Development,1995,5(5):552-558.
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[16]Sakakibara K,Nishiyama T,Deguchi H,et al.Class 1KNOX genes are not involved in shoot development in the moss Physcomitrella patens but do function in sporophyte development[J].Evolution&Development,2008,10(5):555-566.
[17]Sakakibara K,Ando S,Yip H K,et al.KNOX2 genes regulate the haploid-to-diploid morphological transition in land plants[J].Science,2013,339(6123):1067-1070.
[18]Tsuda K,Ito Y,Sato Y,et al.Positive autoregulation of a KNOX gene is essential for shoot apical meristem maintenance in rice[J].The Plant Cell,2011,23(12):4368-4381.
[19]Vollbrecht E,Reiser L,Hake S.Shoot meristem size is dependent on inbred background and presence of the maize homeobox gene,knotted[J].Development,2000,127(14):3161-3172.
[20]Bharathan G,Goliber T E,Moore C,et al.Homologies in leaf form inferred from KNOXI gene expression during development[J].Science,2002,296(5574):1858-1860.
[21]Alakonya A,Kumar R,Koenig D,et al.Interspecific RNA interference of SHOOT MERISTEMLESS-like disrupts Cuscuta pentagona plant parasitism[J].The Plant Cell,2012,24(7):3153-3166.
[22]Li Y,Pi L M,Huang H,et al.ATH1 and KNAT2proteins act together in regulation of plant inflorescence architecture[J].Journal of Experimental Botany,2012,63(3):1423-1433.
[23]Hay A,Tsiantis M.A KNOX family TALE[J].Current Opinion in Plant Biology,2009,12(5):593-598.
[24]Furumizu C,Alvarez J P,Sakakibara K,et al.Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication[J].PLoS Genetics,2015,11(2):e1004980.
[25]Li E Y,Bhargava A,Qiang W Y,et al.The Class IIKNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus[J].New Phytologist,2012,194(1):102-115.
[26]Gong S Y,Huang G Q,Sun X,et al.Cotton KNL1,encoding a class II KNOX transcription factor,is involved in regulation of fibre development[J].Journal of Experimental Botany,2014,65(15):4133-4147.
[27]Li E Y,Wang S C,Liu Y Y,et al.OVATE FAMILYPROTEIN4(OFP4)interaction with KNAT7 regulates secondary cell wall formation in Arabidopsis thaliana[J].The Plant Journal,2011,67(2):328-341.
[28]Sakamoto T,Kamiya N,Ueguchi-Tanaka M,et al.KNOX homeodomain protein directly suppresses the expression of a gibberellin biosynthetic gene in the tobacco shoot apical meristem[J].Genes&Development,2001,15(5):581-590.
[29]Bolduc N,Hake S.The maize transcription factor KNOTTED1 directly regulates the gibberellin catabolism gene ga2ox1[J].The Plant Cell,2009,21(6):1647-1658.
[30]Townsley B T,Sinha N R,Kang J L.KNOX1 genes regulate lignin deposition and composition in monocots and dicots[J].Frontiers in Plant Science,2013,4:121.
[31]Yanai O,Shani E,Dolezal K,et al.Arabidopsis KNOXIproteins activate cytokinin biosynthesis[J].Current Biology,2005,15(17):1566-1571.
[32]Sakamoto T,Sakakibara H,Kojima M,et al.Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice[J].Plant Physiology,2006,142(1):54-62.
[33]谢小东,王晨,罗朝鹏,等.烟草同源异型盒转录因子NtKNATM1基因的克隆及表达分析[J].烟草科技,2017,50(7):1-6,13.XIE Xiaodong,WANG Chen,LUO Zhaopeng,et al.Cloning and expression analysis of transcription factor gene NtKNATM1 from Nicotiana tabacum[J].Tobacco Science&Technology,2017,50(7):1-6,13.
[34]Livak K J,Schmittgen T D.Analysis of relative gene expression data using real-time quantitative PCR and the 2-△△CTmethod[J].Methods,2001,25(4):402-408.
[35]Sheen S J.Isozymic evidence bearing on the origin of Nicotiana tabacum L.[J].Evolution;International Journal of Organic Evolution,1972,26(1):143-154.
[36]Kerstetter R,Vollbrecht E,Lowe B,et al.Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes[J].The Plant Cell,1994,6(12):1877-1887.
[37]Woody J L,Shoemaker R C.Gene expression:sizing it all up[J].Frontiers in Genetics,2011,2:70.
[38]李方正,杨素欣,吴春霞,等.大豆KNOX基因家族的结构和表达分析[J].植物学报,2012,47(3):236-247.LI Fangzheng,YANG Suxin,WU Chunxia,et al.Structure and expression analysis of KNOX gene family in soybean[J].Bulletin of Botany,2012,47(3):236-247.
[2]Williams R W.Plant homeobox genes:many functions stem from a common motif[J].BioEssays,1998,20(4):280-282.
[3]Gehring W J,Affolter M,Burglin T.Homeodomain proteins[J].Annual Review of Biochemistry,1994,63(1):487-526.
[4]Chen H,Rosin F M,Prat S,et al.Interacting transcription factors from the three-amino acid loop extension superclass regulate tuber formation[J].Plant Physiology,2003,132(3):1391-1404.
[5]Hay A,Tsiantis M.KNOX genes:versatile regulators of plant development and diversity[J].Development,2010,137(19):3153-3165.
[6]Vollbrecht E,Veit B,Sinha N,et al.The developmental gene Knotted-1 is a member of a maize homeobox gene family[J].Nature,1991,350(6315):241-243.
[7]Nadakuduti S S,Holdsworth W L,Klein C L,et al.KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN2-LIKEexpression in tomato[J].The Plant Journal,2014,78(6):1022-1033.
[8]Di Giacomo E,Sestili F,Iannelli M A,et al.Characterization of KNOX genes in Medicago truncatula[J].Plant Molecular Biology,2008,67(1/2):135-150.
[9]Ito Y,Eiguchi M,Kurata N.KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice[J].Genesis,2001,30(4):231-238.
[10]Yu H,Yang S H,Goh C J.DOH1,a class 1 knox gene,is required for maintenance of the basic plant architecture and floral transition in orchid[J].The Plant Cell,2000,12(11):2143-2160.
[11]Tsuda K,Hake S.Diverse functions of KNOXtranscription factors in the diploid body plan of plants[J].Current Opinion in Plant Biology,2015,27:91-96.
[12]Magnani E,Hake S.KNOX lost the OX:the Arabidopsis KNATM gene defines a novel class of KNOX transcriptional regulators missing the homeodomain[J].The Plant Cell,2008,20(4):875-887.
[13]Kimura S,Koenig D,Kang J L,et al.Natural variation in leaf morphology results from mutation of a novel KNOX gene[J].Current Biology,2008,18(9):672-677.
[14]Johnson A D.Molecular mechanisms of cell-type determination in budding yeast[J].Current Opinion in Genetics&Development,1995,5(5):552-558.
[15]Kües U,Richardson W V,Tymon A M,et al.The combination of dissimilar alleles of the Aαand Aβgene complexes,whose proteins contain homeo domain motifs,determines sexual development in the mushroom Coprinus cinereus[J].Genes&Development,1992,6(4):568-577.
[16]Sakakibara K,Nishiyama T,Deguchi H,et al.Class 1KNOX genes are not involved in shoot development in the moss Physcomitrella patens but do function in sporophyte development[J].Evolution&Development,2008,10(5):555-566.
[17]Sakakibara K,Ando S,Yip H K,et al.KNOX2 genes regulate the haploid-to-diploid morphological transition in land plants[J].Science,2013,339(6123):1067-1070.
[18]Tsuda K,Ito Y,Sato Y,et al.Positive autoregulation of a KNOX gene is essential for shoot apical meristem maintenance in rice[J].The Plant Cell,2011,23(12):4368-4381.
[19]Vollbrecht E,Reiser L,Hake S.Shoot meristem size is dependent on inbred background and presence of the maize homeobox gene,knotted[J].Development,2000,127(14):3161-3172.
[20]Bharathan G,Goliber T E,Moore C,et al.Homologies in leaf form inferred from KNOXI gene expression during development[J].Science,2002,296(5574):1858-1860.
[21]Alakonya A,Kumar R,Koenig D,et al.Interspecific RNA interference of SHOOT MERISTEMLESS-like disrupts Cuscuta pentagona plant parasitism[J].The Plant Cell,2012,24(7):3153-3166.
[22]Li Y,Pi L M,Huang H,et al.ATH1 and KNAT2proteins act together in regulation of plant inflorescence architecture[J].Journal of Experimental Botany,2012,63(3):1423-1433.
[23]Hay A,Tsiantis M.A KNOX family TALE[J].Current Opinion in Plant Biology,2009,12(5):593-598.
[24]Furumizu C,Alvarez J P,Sakakibara K,et al.Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication[J].PLoS Genetics,2015,11(2):e1004980.
[25]Li E Y,Bhargava A,Qiang W Y,et al.The Class IIKNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus[J].New Phytologist,2012,194(1):102-115.
[26]Gong S Y,Huang G Q,Sun X,et al.Cotton KNL1,encoding a class II KNOX transcription factor,is involved in regulation of fibre development[J].Journal of Experimental Botany,2014,65(15):4133-4147.
[27]Li E Y,Wang S C,Liu Y Y,et al.OVATE FAMILYPROTEIN4(OFP4)interaction with KNAT7 regulates secondary cell wall formation in Arabidopsis thaliana[J].The Plant Journal,2011,67(2):328-341.
[28]Sakamoto T,Kamiya N,Ueguchi-Tanaka M,et al.KNOX homeodomain protein directly suppresses the expression of a gibberellin biosynthetic gene in the tobacco shoot apical meristem[J].Genes&Development,2001,15(5):581-590.
[29]Bolduc N,Hake S.The maize transcription factor KNOTTED1 directly regulates the gibberellin catabolism gene ga2ox1[J].The Plant Cell,2009,21(6):1647-1658.
[30]Townsley B T,Sinha N R,Kang J L.KNOX1 genes regulate lignin deposition and composition in monocots and dicots[J].Frontiers in Plant Science,2013,4:121.
[31]Yanai O,Shani E,Dolezal K,et al.Arabidopsis KNOXIproteins activate cytokinin biosynthesis[J].Current Biology,2005,15(17):1566-1571.
[32]Sakamoto T,Sakakibara H,Kojima M,et al.Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice[J].Plant Physiology,2006,142(1):54-62.
[33]谢小东,王晨,罗朝鹏,等.烟草同源异型盒转录因子NtKNATM1基因的克隆及表达分析[J].烟草科技,2017,50(7):1-6,13.XIE Xiaodong,WANG Chen,LUO Zhaopeng,et al.Cloning and expression analysis of transcription factor gene NtKNATM1 from Nicotiana tabacum[J].Tobacco Science&Technology,2017,50(7):1-6,13.
[34]Livak K J,Schmittgen T D.Analysis of relative gene expression data using real-time quantitative PCR and the 2-△△CTmethod[J].Methods,2001,25(4):402-408.
[35]Sheen S J.Isozymic evidence bearing on the origin of Nicotiana tabacum L.[J].Evolution;International Journal of Organic Evolution,1972,26(1):143-154.
[36]Kerstetter R,Vollbrecht E,Lowe B,et al.Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes[J].The Plant Cell,1994,6(12):1877-1887.
[37]Woody J L,Shoemaker R C.Gene expression:sizing it all up[J].Frontiers in Genetics,2011,2:70.
[38]李方正,杨素欣,吴春霞,等.大豆KNOX基因家族的结构和表达分析[J].植物学报,2012,47(3):236-247.LI Fangzheng,YANG Suxin,WU Chunxia,et al.Structure and expression analysis of KNOX gene family in soybean[J].Bulletin of Botany,2012,47(3):236-247.