大白菜YUCCA基因家族的鉴定与生物信息学分析
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摘要
生长素(IAA)是一种重要的植物内源激素,YUCCA基因作为IAA生物合成的限速酶编码基因,在植物生长发育过程中起着重要的调控作用。为深入研究大白菜YUCCA基因家族的功能,利用生物信息学分析对大白菜中YUCCA基因家族成员进行全基因组水平鉴定,并对其基因组信息、蛋白质生理生化特征、基因结构、保守结构域、系统进化树等方面进行研究。结果表明,在大白菜基因组中共鉴定出19个YUCCA基因,可以聚类到2个大的分支,CladeⅠ和CladeⅡ;YUCCA基因在大白菜10条染色体上呈不均匀分布,并有1对基因以串联重复现象在染色体上分布;基因结构分析表明大白菜YUCCA基因一般含有0～3个数量不等的内含子;对大白菜YUCCA蛋白质氨基酸序列多重比对的分析表明大白菜YUCCA蛋白质存在高度保守的FAD结合位点(一致序列为GAGPxG)和NADPH结合位点(一致序列为GxGNSG);通过MEME软件对大白菜YUCCA蛋白质模体(motif)的预测还发现12个比较保守的motif。上述研究结果为大白菜YUCCA基因功能的研究奠定了一定的基础。
引文
[1]Zhao Y D. Auxin biosynthesis and its role in plant development[J]. Annual Review of Plant Biology,2010,61(1):49-64.
[2]Mashiguchi K,Tanaka K,Sakai T,et al. The main auxin biosynthesis pathway in Arabidopsis[J]. Proceedings of the National Academy of Sciences,2011,108(45):18512-18517.
[3]Dai X H,Mashiguchi K,Chen Q G,et al. The biochemical mechanism of auxin biosynthesis by an Arabidopsis YUCCA flavin-containing monooxygenase[J]. Journal of Biological Chemistry,2013,288(3):1448-1457.
[4]Cheng Y F,Dai X H,Zhao Y D. Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis[J]. Genes & Development,2006,20(13):1790-1799.
[5]Cheng Y F,Dai X H,Zhao Y D. Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis[J]. Plant Cell,2007,19(8):2430-1439.
[6]Zhao Y D,Christensen S K,Fankhauser C,et al. A role for flavin monooxygenase-like enzymes in auxin biosynthesis[J]. Science,2001,291(5502):306-309.
[7]游小庆,桑贤春,赵芳明,等. 水稻窄叶突变体nal7(t)的遗传分析与基因定位[J]. 分子植物育种,2010,8(2):240-244.
[8]Kim J I,Baek D,Park H C,et al. Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit[J]. Molecular Plant,2013,6(2):337-349.
[9]Liu H,Xie W F,Zhang L,et al. Auxin biosynthesis by the YUCCA6 flavin monooxygenase gene in woodland strawberry[J]. Journal of Integrative Plant Biology,2014,56(4):350-363.
[10]Yamamoto Y,Kamiya N,Morinaka Y,et al. Auxin biosynthesis by the YUCCA genes in rice[J]. Plant Physiology,2007,143(3):1362-1371.
[11]Gallavotti A,Barazesh S,Malcomber S,et al. Sparse inflorescence 1 encodes a monocot-specific YUCCA-Like gene required for vegetative and reproductive development in maize[J]. Procnatlacadsciusa,2008,105(39):15196-15201.
[12]Ye X,Kang B G,Osburn L D,et al. Identification of the flavin-dependent monooxygenase-encoding YUCCA gene family in Populus trichocarpa and their expression in vegetative tissues and in response to hormone and environmental stresses[J]. Plant Cell,Tissue and Organ Culture,2009,97(3):271-283.
[13]郭庆东,李娜,惠文荣,等. 小麦TaYUC10基因种子特异表达载体构建及小麦遗传转化[C]. 全国小麦基因组学及分子育种大会, 2015.
[14]高玉龙,宋中邦,李文正,等. 两个烟草YUCCA6基因的克隆及分析[J]. 分子植物育种,2016,14(6):1376-1381.
[15]许菲,张颖,潘琪芳,等. 长春花黄素单加氧酶基因的克隆与组织表达分析[J]. 上海交通大学学报,2014,32(4):1-7.
[16]Wang X W,Wang H Z,Wang J,et al. The genome of the mesopolyploid crop species Brassica rapa[J]. Nature Genetics,2011,43(10):1035-1157.
[17]Saitou N,Nei M. The neighbor-joining method:a new method for reconstructing phylogenetic trees[J]. Molecular Biology and Evolution,1987,4(4):406-425.
[18]Blanc G,Wolfe K H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes[J]. Plant Cell,2004,16(7):1667-1678.
[19]Blanc G,Hokamp K,Wolfe K H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome[J]. Genome Research,2003,13(2):137-144.
[20]Lysak M A,Koch M A,Pecinka A,et al. Chromosome triplication found across the tribe Brassiceae[J]. Genome Research,2005,15(4):516-525.
[2]Mashiguchi K,Tanaka K,Sakai T,et al. The main auxin biosynthesis pathway in Arabidopsis[J]. Proceedings of the National Academy of Sciences,2011,108(45):18512-18517.
[3]Dai X H,Mashiguchi K,Chen Q G,et al. The biochemical mechanism of auxin biosynthesis by an Arabidopsis YUCCA flavin-containing monooxygenase[J]. Journal of Biological Chemistry,2013,288(3):1448-1457.
[4]Cheng Y F,Dai X H,Zhao Y D. Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis[J]. Genes & Development,2006,20(13):1790-1799.
[5]Cheng Y F,Dai X H,Zhao Y D. Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis[J]. Plant Cell,2007,19(8):2430-1439.
[6]Zhao Y D,Christensen S K,Fankhauser C,et al. A role for flavin monooxygenase-like enzymes in auxin biosynthesis[J]. Science,2001,291(5502):306-309.
[7]游小庆,桑贤春,赵芳明,等. 水稻窄叶突变体nal7(t)的遗传分析与基因定位[J]. 分子植物育种,2010,8(2):240-244.
[8]Kim J I,Baek D,Park H C,et al. Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit[J]. Molecular Plant,2013,6(2):337-349.
[9]Liu H,Xie W F,Zhang L,et al. Auxin biosynthesis by the YUCCA6 flavin monooxygenase gene in woodland strawberry[J]. Journal of Integrative Plant Biology,2014,56(4):350-363.
[10]Yamamoto Y,Kamiya N,Morinaka Y,et al. Auxin biosynthesis by the YUCCA genes in rice[J]. Plant Physiology,2007,143(3):1362-1371.
[11]Gallavotti A,Barazesh S,Malcomber S,et al. Sparse inflorescence 1 encodes a monocot-specific YUCCA-Like gene required for vegetative and reproductive development in maize[J]. Procnatlacadsciusa,2008,105(39):15196-15201.
[12]Ye X,Kang B G,Osburn L D,et al. Identification of the flavin-dependent monooxygenase-encoding YUCCA gene family in Populus trichocarpa and their expression in vegetative tissues and in response to hormone and environmental stresses[J]. Plant Cell,Tissue and Organ Culture,2009,97(3):271-283.
[13]郭庆东,李娜,惠文荣,等. 小麦TaYUC10基因种子特异表达载体构建及小麦遗传转化[C]. 全国小麦基因组学及分子育种大会, 2015.
[14]高玉龙,宋中邦,李文正,等. 两个烟草YUCCA6基因的克隆及分析[J]. 分子植物育种,2016,14(6):1376-1381.
[15]许菲,张颖,潘琪芳,等. 长春花黄素单加氧酶基因的克隆与组织表达分析[J]. 上海交通大学学报,2014,32(4):1-7.
[16]Wang X W,Wang H Z,Wang J,et al. The genome of the mesopolyploid crop species Brassica rapa[J]. Nature Genetics,2011,43(10):1035-1157.
[17]Saitou N,Nei M. The neighbor-joining method:a new method for reconstructing phylogenetic trees[J]. Molecular Biology and Evolution,1987,4(4):406-425.
[18]Blanc G,Wolfe K H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes[J]. Plant Cell,2004,16(7):1667-1678.
[19]Blanc G,Hokamp K,Wolfe K H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome[J]. Genome Research,2003,13(2):137-144.
[20]Lysak M A,Koch M A,Pecinka A,et al. Chromosome triplication found across the tribe Brassiceae[J]. Genome Research,2005,15(4):516-525.