河八王分蘖基因NpD53克隆及其生物信息学分析
【目的】克隆河八王［Narengaporphyrocoma（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（GenBank登录号MF593461）的中间序列长度760bp、5'端序列长度1497bp、3'端序列长度1233bp，拼接后其cDNA序列全长为2597bp，包含1个2037bp的开放阅...
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| Published in | 南方农业学报 Vol. 48; no. 9; pp. 1554 - 1559 |
|---|---|
| Main Author | |
| Format | Journal Article |
| Language | Chinese |
| Published |
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,南宁530007
2017
云南省甘蔗遗传改良重点实验室,云南开远661600%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,南宁,530007%云南省甘蔗遗传改良重点实验室,云南开远,661600 |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2095-1191 |
| DOI | 10.3969/j.issn.2095-1191.2017.09.03 |
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| Abstract | 【目的】克隆河八王［Narengaporphyrocoma（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（GenBank登录号MF593461）的中间序列长度760bp、5'端序列长度1497bp、3'端序列长度1233bp，拼接后其cDNA序列全长为2597bp，包含1个2037bp的开放阅读框（ORF），编码678个氨基酸，蛋白分子量75.02kD，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ClpB_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ClpB_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ClpATP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。 |
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| AbstractList | S566.1; [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(GenBank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1233bp,拼接后其cDNA序列全长为2597 bp,包含1个2037 bp的开放阅读框(ORE),编码678个氨基酸,蛋白分子量75.02kD,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ClpB_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ClpB_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. 【目的】克隆河八王［Narengaporphyrocoma（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（GenBank登录号MF593461）的中间序列长度760bp、5'端序列长度1497bp、3'端序列长度1233bp，拼接后其cDNA序列全长为2597bp，包含1个2037bp的开放阅读框（ORF），编码678个氨基酸，蛋白分子量75.02kD，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ClpB_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ClpB_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ClpATP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_FL | [Objective] This research was aimed to clone tillering-related gene NpD53 from Narenga porphyrocoma(Hance) Bor,and analyze the sequence characteristics of NpD53 and provide theoretical basis for the study on molecular mechanism of wild sugarcane tillering.[Method]Total RNA was isolated from the leaves ofN.porphyrocoma and the cDNA was obtained by reverse transcription.NpD53 was amplified by RACE (rapid amplification of cDNA end) and its nucleotide sequence and amino acid sequence of encoding protein were analyzed by bioinformatics methods.[Result]The cloned Gene NpD53 (GeneBank accession No.MF593461) contained midregion sequence of 760 bp,5'terminal sequence of 1497 bp,3'terminal sequence of 1233 bp.Combining the three parts,its cDNA sequence full-length was 2597 bp.It contained an open reading frame(ORF) of 2037 bp,encoded 678 amino acids with molecular mass of 75.02 KD,pI of 6.59,and average hydrophilicity of-0.506,which meant it was a hydrophilic protein.The protein was situated in cell nucleus (94.1％ confidence).The encoding protein (NpD53) of NpD53 had two super family core sequences,namely P-loop_NT-Pase and ClpB_D2-small,with four non-specific sites,and shared the same ClpB_D2-small conserved domain with D53 protein of other species.Its secondary structure had only four coil types,among which random coils were in the majority,accounting for 42.77％,followed by alpha helix,accounting for 35.55％,while extended strand and beta turn accounted for 15.34％ and 6.34％ respectively.According to the homology comparison and phylogenetic tree analysis for amino acid sequences of NpD53 protein,N.porphyrocoma had a close phylogenetic relationship with gramineous plants(Sorghum bicolor andAegilops tauschii),and had a distant phylogenetic relationship with Phoenix dactylifera,Elaeis guineensis and Musa acuminate.[Conclusion] The encoding protein of tillering-related gene NpD53 from N.porphyrocoma shares the same conserved domain with D53 protein of other species,and has two non-specific sites of class-Ⅰ Clp ATPase.It is predicted that NpD53 may be a molecular chaperone,and is related to heat resistance ofN.porphyrocoma. |
| Author | 刘昔辉;张荣华;桂意云;张小秋;韦金菊;周会;区惠平;刘新龙 |
| AuthorAffiliation | 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,南宁530007;云南省甘蔗遗传改良重点实验室,云南开远661600 |
| AuthorAffiliation_xml | – name: 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,南宁530007;云南省甘蔗遗传改良重点实验室,云南开远661600%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,南宁,530007%云南省甘蔗遗传改良重点实验室,云南开远,661600 |
| Author_FL | OU Hui-ping ZHANG Rong-hua ZHANG Xiao-qiu ZHOU Hui LIU Xin-long GUI Yi-yun WEI Jin-ju LIU Xi-hui |
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| Author_xml | – sequence: 1 fullname: 刘昔辉;张荣华;桂意云;张小秋;韦金菊;周会;区惠平;刘新龙 |
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| DocumentTitleAlternate | Cloning and bioinformatics analysis of tillering-related gene NpD53from Narenga porphyrocoma(Hance)Bor |
| DocumentTitle_FL | Cloning and bioinformatics analysis of tillering-related gene NpD53 from Narenga porphyrocoma(Hance) Bor |
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| Keywords | NpD53基因 河八王 克隆 RACE 序列分析 gene NpD53 sequence analysis Narenga porphyrocoma(Hance) Bor cloning |
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| Notes | Narenga porphyrocoma(Hance)Bor;gene NpD53;cloning;sequence analysis;RACE 45-1381/S Objective】This research was aimed to clone tillering-related gene NpD53from Narenga porphyrocoma(Hance)Bor,and analyze the sequence characteristics of NpD53and provide theoretical basis for the study on molecular mechanism of wild sugarcane tillering.【Method】Total RNAwas isolated from the leaves of N.porphyrocoma and the cDNA was obtained by reverse transcription.NpD53was amplified by RACE(rapid amplification of cDNA end)and its nucleotide sequence and amino acid sequence of encoding protein were analyzed by bioinformatics methods.【Result】The cloned Gene NpD53(GeneBank accession No.MF593461)contained midregion sequence of760bp,5'terminal sequence of1497bp,3'terminal sequence of1233bp.Combining the three parts,its cDNA sequence full-length was2597bp.It containedan open reading frame(ORF)of2037bp,encoded678amino acids with molecular mass of75.02KD,pI of6.59,and average hydrophilicity of-0.506,which meant it was a hydrophi |
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| PublicationTitle | 南方农业学报 |
| PublicationTitleAlternate | Journal of Southern Agriculture |
| PublicationTitle_FL | Journal of Southern Agriculture |
| PublicationYear | 2017 |
| Publisher | 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,南宁530007 云南省甘蔗遗传改良重点实验室,云南开远661600%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,南宁,530007%云南省甘蔗遗传改良重点实验室,云南开远,661600 |
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| Snippet | 【目的】克隆河八王［Narengaporphyrocoma（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... S566.1; [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... |
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| SubjectTerms | 河八王;NpD53基因;克隆;序列分析;RACE |
| Title | 河八王分蘖基因NpD53克隆及其生物信息学分析 |
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