河八王分蘖基因NpD53克隆及其生物信息学分析
发布时间：2018-10-05 10:45
【摘要】：【目的】克隆河八王[Narenga porphyrocoma(Hance)Bor]分蘖基因NpD53,并分析其序列特征,为甘蔗野生种分蘖的分子机理研究提供理论参考。【方法】以河八王为试验材料,提取其叶片总RNA,反转录获得cDNA,通过RACE(cDNA末端快增)技术扩增NpD53基因,并采用生物信息学方法对其核苷酸序列及编码蛋白的氨基酸序列进行分析。【结果】NpD53基因(Gen Bank登录号MF593461)的中间序列长度760 bp、5'端序列长度1497 bp、3'端序列长度1233 bp,拼接后其cDNA序列全长为2597 bp,包含1个2037 bp的开放阅读框(ORF),编码678个氨基酸,蛋白分子量75.02 k D,等电点6.59,亲水性平均数-0.506,表明其为亲水性蛋白,位于细胞核内(可信度94.1%)。NpD53基因编码蛋白(NpD53)存在P-loop_NTPase和Clp B_D2-small超家族核心序列,含有4个非特异性位点,与其他物种的D53蛋白均具有相同的保守结构域Clp B_D2-small;其二级结构仅有4种卷曲类型,以无规则卷曲最多,占42.77%,其次是α-螺旋,占35.55%,延伸链和β-转角分别占15.34%和6.34%。NpD53蛋白的氨基酸序列同源性比对及系统进化树分析结果显示,河八王与禾本科物种(高粱和山羊草)的亲缘关系较近,与海枣、油棕、芭蕉等物种的亲缘关系较远。【结论】河八王分蘖基因NpD53编码蛋白与其他物种的D53蛋白具有相同的保守结构域,且具有2个I类Clp ATP酶的非特异性位点,推测NpD53为一种分子伴侣,与河八王自身的耐热性相关。
[Abstract]:[objective] to clone the tiller gene NpD53, of Hebawang [Narenga porphyrocoma (Hance) Bor] and analyze its sequence characteristics, so as to provide a theoretical reference for the study of molecular mechanism of tillering in wild sugarcane species. [methods] Hebawang was used as the experimental material. The total RNA, reverse transcriptase was extracted from the leaves to obtain cDNA,. The NpD53 gene was amplified by RACE (cDNA terminal amplification technique. The nucleotide sequence and amino acid sequence of the protein were analyzed by bioinformatics method. [results] the intermediate length of NpD53 gene (Gen Bank accession number (MF593461) was 760 bp,5' terminal length 1497 bp,3' end length 1233 bp, sequence length. The cDNA sequence was 2597 bp, with an open reading frame (ORF),) of 2037 bp encoding 678 amino acids. The molecular weight of the protein is 75.02 KD, the isoelectric point is 6.59, and the hydrophilic average is -0.506, which indicates that it is a hydrophilic protein, which is located in the nucleus (reliability 94.1%) .NpD53 gene encoding protein (NpD53) contains P-loop_NTPase and Clp B_D2-small superfamily core sequences, and contains four nonspecific sites. D53 protein has the same conserved domain as other species, Clp BAC D2-small.The secondary structure of D53 protein has only four crimp types, the most of which is irregular crimp (42.7777), and the second is 伪 -helix. The results of homology analysis of amino acid sequence and phylogenetic tree of 6.34%.NpD53 protein showed that Hexiwang had close relationship with Gramineae species (sorghum and Leymus chinensis), and had close relationship with jujube and oil palm. [conclusion] the NpD53 encoding protein of Hebawang tiller gene has the same conserved domain as D53 protein of other species, and has two nonspecific sites of class I Clp ATP enzyme. It is assumed that NpD53 is a molecular chaperone, which is related to the heat resistance of Hebawang.
【作者单位】： 广西甘蔗遗传改良重点实验室/农业部广西甘蔗生物技术与遗传改良重点实验室/中国农业科学院甘蔗研究中心/广西农业科学院甘蔗研究所;云南省甘蔗遗传改良重点实验室;
【基金】：国家自然科学基金项目(31101195) 云南甘蔗遗传改良重点实验室项目(2015DG015-03) 广西“八桂学者”和特聘专家专项项目([2013]3号) 广西农业科学院科技发展基金项目(桂农科2016JM07)
【分类号】：S566.1
本文编号：2253088
[Abstract]:[objective] to clone the tiller gene NpD53, of Hebawang [Narenga porphyrocoma (Hance) Bor] and analyze its sequence characteristics, so as to provide a theoretical reference for the study of molecular mechanism of tillering in wild sugarcane species. [methods] Hebawang was used as the experimental material. The total RNA, reverse transcriptase was extracted from the leaves to obtain cDNA,. The NpD53 gene was amplified by RACE (cDNA terminal amplification technique. The nucleotide sequence and amino acid sequence of the protein were analyzed by bioinformatics method. [results] the intermediate length of NpD53 gene (Gen Bank accession number (MF593461) was 760 bp,5' terminal length 1497 bp,3' end length 1233 bp, sequence length. The cDNA sequence was 2597 bp, with an open reading frame (ORF),) of 2037 bp encoding 678 amino acids. The molecular weight of the protein is 75.02 KD, the isoelectric point is 6.59, and the hydrophilic average is -0.506, which indicates that it is a hydrophilic protein, which is located in the nucleus (reliability 94.1%) .NpD53 gene encoding protein (NpD53) contains P-loop_NTPase and Clp B_D2-small superfamily core sequences, and contains four nonspecific sites. D53 protein has the same conserved domain as other species, Clp BAC D2-small.The secondary structure of D53 protein has only four crimp types, the most of which is irregular crimp (42.7777), and the second is 伪 -helix. The results of homology analysis of amino acid sequence and phylogenetic tree of 6.34%.NpD53 protein showed that Hexiwang had close relationship with Gramineae species (sorghum and Leymus chinensis), and had close relationship with jujube and oil palm. [conclusion] the NpD53 encoding protein of Hebawang tiller gene has the same conserved domain as D53 protein of other species, and has two nonspecific sites of class I Clp ATP enzyme. It is assumed that NpD53 is a molecular chaperone, which is related to the heat resistance of Hebawang.
【作者单位】： 广西甘蔗遗传改良重点实验室/农业部广西甘蔗生物技术与遗传改良重点实验室/中国农业科学院甘蔗研究中心/广西农业科学院甘蔗研究所;云南省甘蔗遗传改良重点实验室;
【基金】：国家自然科学基金项目(31101195) 云南甘蔗遗传改良重点实验室项目(2015DG015-03) 广西“八桂学者”和特聘专家专项项目([2013]3号) 广西农业科学院科技发展基金项目(桂农科2016JM07)
【分类号】：S566.1
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