河八王分蘗基因NpD53克隆及其生物信息學分析
發(fā)布時間：2018-10-05 10:45
【摘要】：【目的】克隆河八王[Narenga porphyrocoma(Hance)Bor]分蘗基因NpD53,并分析其序列特征,為甘蔗野生種分蘗的分子機理研究提供理論參考�！痉椒ā恳院影送鯙樵囼灢牧�,提取其葉片總RNA,反轉錄獲得cDNA,通過RACE(cDNA末端快增)技術擴增NpD53基因,并采用生物信息學方法對其核苷酸序列及編碼蛋白的氨基酸序列進行分析�！窘Y果】NpD53基因(Gen Bank登錄號MF593461)的中間序列長度760 bp、5'端序列長度1497 bp、3'端序列長度1233 bp,拼接后其cDNA序列全長為2597 bp,包含1個2037 bp的開放閱讀框(ORF),編碼678個氨基酸,蛋白分子量75.02 k D,等電點6.59,親水性平均數(shù)-0.506,表明其為親水性蛋白,位于細胞核內(nèi)(可信度94.1%)。NpD53基因編碼蛋白(NpD53)存在P-loop_NTPase和Clp B_D2-small超家族核心序列,含有4個非特異性位點,與其他物種的D53蛋白均具有相同的保守結構域Clp B_D2-small;其二級結構僅有4種卷曲類型,以無規(guī)則卷曲最多,占42.77%,其次是α-螺旋,占35.55%,延伸鏈和β-轉角分別占15.34%和6.34%。NpD53蛋白的氨基酸序列同源性比對及系統(tǒng)進化樹分析結果顯示,河八王與禾本科物種(高粱和山羊草)的親緣關系較近,與海棗、油棕、芭蕉等物種的親緣關系較遠�！窘Y論】河八王分蘗基因NpD53編碼蛋白與其他物種的D53蛋白具有相同的保守結構域,且具有2個I類Clp ATP酶的非特異性位點,推測NpD53為一種分子伴侶,與河八王自身的耐熱性相關。
[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 偽 -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.
【作者單位】： 廣西甘蔗遺傳改良重點實驗室/農(nóng)業(yè)部廣西甘蔗生物技術與遺傳改良重點實驗室/中國農(nóng)業(yè)科學院甘蔗研究中心/廣西農(nóng)業(yè)科學院甘蔗研究所;云南省甘蔗遺傳改良重點實驗室;
【基金】：國家自然科學基金項目(31101195) 云南甘蔗遺傳改良重點實驗室項目(2015DG015-03) 廣西“八桂學者”和特聘專家專項項目([2013]3號) 廣西農(nóng)業(yè)科學院科技發(fā)展基金項目(桂農(nóng)科2016JM07)
【分類號】：S566.1
本文編號：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 偽 -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.
【作者單位】： 廣西甘蔗遺傳改良重點實驗室/農(nóng)業(yè)部廣西甘蔗生物技術與遺傳改良重點實驗室/中國農(nóng)業(yè)科學院甘蔗研究中心/廣西農(nóng)業(yè)科學院甘蔗研究所;云南省甘蔗遺傳改良重點實驗室;
【基金】：國家自然科學基金項目(31101195) 云南甘蔗遺傳改良重點實驗室項目(2015DG015-03) 廣西“八桂學者”和特聘專家專項項目([2013]3號) 廣西農(nóng)業(yè)科學院科技發(fā)展基金項目(桂農(nóng)科2016JM07)
【分類號】：S566.1
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