甘蔗叶片和茎全长cDNA文库构建及表达序列标签（EST）分析
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摘要
甘蔗是世界上最重要的糖料作物,也是最重要的能源作物之一,主要用于生产蔗糖,还可用于生产糖醛、纤维、葡聚糖和绿色能源乙醇等,在国际上占据重要的经济地位。从事甘蔗生产的国家都十分重视对甘蔗的研究,其中基于分子生物学的甘蔗功能基因组学研究是从分子水平解析甘蔗各种机理的重要平台,而全长cDNA文库构建则是建立该平台的重要前提和基础之一。本研究以所构建的全长cDNA文库为基础,以EST测序和分析为主线,结合生物信息学方法、原核表达技术和实时荧光定量PCR技术对目标基因进行结构和表达分析,以期获得抗逆相关基因。主要结果如下:
(1)在引进、消化和吸收的基础上,通过对Oligo-capping文库构建法做的改进,形成了一套简便易行的技术体系,建立了甘蔗全长cDNA文库构建的技术平台,并利用该技术平台构建了甘蔗叶片和茎全长cDNA文库,经验证,文库质量较高,库容量分别为3.0×106cfu和2.5×106cfu,重组率分别为89.0%和91.0%,全长率分别为85.0%和88.9%,平均插入片段都为1.0 kb左右。
(2)对文库进行大规模测序,分别从甘蔗叶片和茎全长cDNA文库中获得228条和283条有效ESTs,平均长度分别为464 bp和459 bp,经DNAStar SeqmanⅡ聚类和拼接分别获得154和204个假定独立转录本(TUTs),冗余序列所占比例分别为32.4%、27.9%。利用blastn和blastx程序对获得的TUTs与GenBank中nr数据库进行分析,结果显示,甘蔗叶片和茎中分别有87个TUTs(含117条EST)和103个TUTs(含132条EST)与已知功能或假定功能的基因同源,结合拟南芥功能基因分类标准对这些TUTs进行分类,其中:来自叶片的TUTs可分为11类,以参与能量代谢的基因最多,其次为信号转导、蛋白质合成、转录、蛋白质降解及贮藏等类型的基因;来自蔗茎的TUTs可分为12类,以参与蛋白质合成的基因最多,其次为转录、细胞结构、蛋白质降解和贮藏、代谢等类型的基因。
(3)在EST测序和分析的基础上,从甘蔗叶片和茎全长cDNA文库中挑选7个抗逆相关候选基因cDNA全长,利用生物信息学软件对其进行序列特征分析和同源比对分析,推测这7个基因的表达产物分别为胚胎晚期丰富蛋白(LEA)、锰超氧化物歧化酶(MnSOD)、锌指蛋白(Zn)、S-腺苷蛋氨酸脱羧酶(SAMDC)、WRKY转录因子(WRKY)、谷胱甘肽硫转移酶(GST)及亲环蛋白(CyP)。分别将这7个基因命名为Sc-Lea、Sc-MnSOD、Sc-zf、Sc-SAMDC、Sc-WRKY、Sc-GST和Sc-CyP。
(4)根据载体pET29a(+)中酶切位点信息,从这7个基因开放读码框(ORF)两端设计特异引物,构建相应的原核表达载体,并将其转入大肠杆菌BL21(DE3),然后利用IPTG进行诱导培养,聚丙烯酰胺(SDS-PAGE)电泳显示,所表达的目的蛋白大小与它们各自推算的融合蛋白分子量大小基本相符,所有7个基因在BL21中成功表达。
(5)通过实时定量PCR技术,对Sc-Lea、Sc-MnSOD、Sc-zf、Sc-SAMDC、Sc-WRKY、Sc-GST和Sc-CyP这7个候选基因PEG、NaCl、SA、H2O2、甘蔗黑穗病菌(Ustilago scitaminea)外源胁迫下甘蔗幼苗中的表达情况进行检测,获得这7个候选基因在各种胁迫下的表达特性。
Sugarcane is not only the most important sugar crop, but also one of the most important energy crops in the world. It can be used in the production of cane sugar, fiber, dextran and green energy such as ethanol, so it occupies important economic position at the international level, all those countries engaging in the production of sugarcane pay great attention to the relevant research, and lots of them aims to study the functional genomics of sugarcane, among them the construction of full-length cDNA library is one of the prerequisites and foundations. In the present study, after sequencing, bioinformatics method, prokaryotic expression technology and Real-time PCR technique were all used to analyze the sequence characteristics and expression profile of the targeted genes and the aim of this study were to obtain some stress-related genes. The main results were as follows:
Basing on the conventional Oligo-capping method, we improved some of the steps and our own full-length cDNA construction platform was established. Then, using the improved Oligo-capping method, we have constructed two full-length cDNA libraries, one for sugarcane leaf and the other for sugarcane stem. Libraries check results indicated that the storage capacity of these two libraries were 3.0×106cfu and 2.5×106cfu, respectively; the recombination rates were 89.0% and 91.0%, respectively; the full-length rates were 85.0% and 88.9%, respectively; while the average insert size of both libraries was about 1.0 kb.
High-throught sequencing of clones from the sugarcane leaf and stem cDNA library from 5’end resulted in 228 and 283 effective ESTs sequences, respectively; The average length of these sequeces was 464 bp and 459 bp, respectively. 154 and 204 TUTs (tentative unique transcript, TUT) were obtained, respectively, after assembly by SeqmanⅡprogram of DNAStar software. The rates of the redundant sequence of both libraries were 32.4% and 27.9%, respectively. And then, these TUTs sequences were sent to GenBank for homologue search using blastn and blastx program. Out of these, 87 TUTs (including 117 ESTs) from leaf cDNA library and 103 TUTs (including 132 ESTs) from stem cDNA library had significant homology to genes with known function or putative function. These genes were classified according to the functional classification of Arabidopsis genes. Results indicated that genes from leaf cDNA library could be classfied into11 categories, among the largest category was genes related to energy metabolism, the function of the other genes were involved with signal transduction, protein synthesis, transcription, protein destination and storage etc; genes from stem cDNA library could be classfied into12 categories, among the largest category was genes related to protein synthesis, the others were transcription, cell structure, protein destination and storage, metabolism etc.
Seven full-length cDNAs of candidate stress-related genes were obtained from the two cDNA libraries through EST sequencing and the corresponding bioinformatics analysis. The analysis of their sequence characteristics and the homology were conducted by bioinformatics software. The coding proteins of the seven stress-related genes were as follows:late embryogenesis abundant protein(LEA), Mn-superoxide dismutase(MnSOD), Zinc finger protein(Zn), S-adenosylmethionine decarboxylase(SAMDC), WRKY transcription factor(WRKY), Glutathione S-transferase(GST) and cyclophilin. And these seven genes were named as Sc-Lea, Sc-MnSOD, Sc-zf, Sc-SAMDC, Sc-WRKY, Sc-GST, Sc-CyP, respectively.
The primers designed according to the ORFs sequence of these genes and the restriction enzyme cutting site information of the vector pET29a(+) were used to constructed their prokaryotic expression vectors. Then, the prokaryotic expression vectors containing the corresponding ORFs were successfully constructed and transformed into E.coil BL21 cells and their expression induced by IPTG. The results of SDS-PAGE indicated these genes could express the right targeted protein in E.coil BL21.
The sugarcane seedlings were treated by various exogenous chemicals, such as PEG, NaCl, SA, H2O2 and Ustilago scitaminea, and then the expression characters of the seven candidate genes were analyzed by Real-time PCR. The results showed that PEG could induce the expression of Sc-Lea, Sc-SAMDC, Sc-WRKY and Sc-CyP, but inhibit the expression of Sc-zf; NaCl could induce Sc-Lea, Sc-zf, Sc-SAMDC, Sc-WRKY and Sc-CyP; SA could induce the expression of Sc-WRKY and Sc-CyP, but inhibit the expression of Sc-SAMDC; H2O2 could induce the expression of Sc-GST and Sc-CyP,but inhibit the expression of Sc-Lea and Sc-SAMDC; Ustilago scitaminea could induce the expression of Sc-MnSOD, Sc-zf, Sc-WRKY and Sc-GST.
(1)在引进、消化和吸收的基础上,通过对Oligo-capping文库构建法做的改进,形成了一套简便易行的技术体系,建立了甘蔗全长cDNA文库构建的技术平台,并利用该技术平台构建了甘蔗叶片和茎全长cDNA文库,经验证,文库质量较高,库容量分别为3.0×106cfu和2.5×106cfu,重组率分别为89.0%和91.0%,全长率分别为85.0%和88.9%,平均插入片段都为1.0 kb左右。
(2)对文库进行大规模测序,分别从甘蔗叶片和茎全长cDNA文库中获得228条和283条有效ESTs,平均长度分别为464 bp和459 bp,经DNAStar SeqmanⅡ聚类和拼接分别获得154和204个假定独立转录本(TUTs),冗余序列所占比例分别为32.4%、27.9%。利用blastn和blastx程序对获得的TUTs与GenBank中nr数据库进行分析,结果显示,甘蔗叶片和茎中分别有87个TUTs(含117条EST)和103个TUTs(含132条EST)与已知功能或假定功能的基因同源,结合拟南芥功能基因分类标准对这些TUTs进行分类,其中:来自叶片的TUTs可分为11类,以参与能量代谢的基因最多,其次为信号转导、蛋白质合成、转录、蛋白质降解及贮藏等类型的基因;来自蔗茎的TUTs可分为12类,以参与蛋白质合成的基因最多,其次为转录、细胞结构、蛋白质降解和贮藏、代谢等类型的基因。
(3)在EST测序和分析的基础上,从甘蔗叶片和茎全长cDNA文库中挑选7个抗逆相关候选基因cDNA全长,利用生物信息学软件对其进行序列特征分析和同源比对分析,推测这7个基因的表达产物分别为胚胎晚期丰富蛋白(LEA)、锰超氧化物歧化酶(MnSOD)、锌指蛋白(Zn)、S-腺苷蛋氨酸脱羧酶(SAMDC)、WRKY转录因子(WRKY)、谷胱甘肽硫转移酶(GST)及亲环蛋白(CyP)。分别将这7个基因命名为Sc-Lea、Sc-MnSOD、Sc-zf、Sc-SAMDC、Sc-WRKY、Sc-GST和Sc-CyP。
(4)根据载体pET29a(+)中酶切位点信息,从这7个基因开放读码框(ORF)两端设计特异引物,构建相应的原核表达载体,并将其转入大肠杆菌BL21(DE3),然后利用IPTG进行诱导培养,聚丙烯酰胺(SDS-PAGE)电泳显示,所表达的目的蛋白大小与它们各自推算的融合蛋白分子量大小基本相符,所有7个基因在BL21中成功表达。
(5)通过实时定量PCR技术,对Sc-Lea、Sc-MnSOD、Sc-zf、Sc-SAMDC、Sc-WRKY、Sc-GST和Sc-CyP这7个候选基因PEG、NaCl、SA、H2O2、甘蔗黑穗病菌(Ustilago scitaminea)外源胁迫下甘蔗幼苗中的表达情况进行检测,获得这7个候选基因在各种胁迫下的表达特性。
Sugarcane is not only the most important sugar crop, but also one of the most important energy crops in the world. It can be used in the production of cane sugar, fiber, dextran and green energy such as ethanol, so it occupies important economic position at the international level, all those countries engaging in the production of sugarcane pay great attention to the relevant research, and lots of them aims to study the functional genomics of sugarcane, among them the construction of full-length cDNA library is one of the prerequisites and foundations. In the present study, after sequencing, bioinformatics method, prokaryotic expression technology and Real-time PCR technique were all used to analyze the sequence characteristics and expression profile of the targeted genes and the aim of this study were to obtain some stress-related genes. The main results were as follows:
Basing on the conventional Oligo-capping method, we improved some of the steps and our own full-length cDNA construction platform was established. Then, using the improved Oligo-capping method, we have constructed two full-length cDNA libraries, one for sugarcane leaf and the other for sugarcane stem. Libraries check results indicated that the storage capacity of these two libraries were 3.0×106cfu and 2.5×106cfu, respectively; the recombination rates were 89.0% and 91.0%, respectively; the full-length rates were 85.0% and 88.9%, respectively; while the average insert size of both libraries was about 1.0 kb.
High-throught sequencing of clones from the sugarcane leaf and stem cDNA library from 5’end resulted in 228 and 283 effective ESTs sequences, respectively; The average length of these sequeces was 464 bp and 459 bp, respectively. 154 and 204 TUTs (tentative unique transcript, TUT) were obtained, respectively, after assembly by SeqmanⅡprogram of DNAStar software. The rates of the redundant sequence of both libraries were 32.4% and 27.9%, respectively. And then, these TUTs sequences were sent to GenBank for homologue search using blastn and blastx program. Out of these, 87 TUTs (including 117 ESTs) from leaf cDNA library and 103 TUTs (including 132 ESTs) from stem cDNA library had significant homology to genes with known function or putative function. These genes were classified according to the functional classification of Arabidopsis genes. Results indicated that genes from leaf cDNA library could be classfied into11 categories, among the largest category was genes related to energy metabolism, the function of the other genes were involved with signal transduction, protein synthesis, transcription, protein destination and storage etc; genes from stem cDNA library could be classfied into12 categories, among the largest category was genes related to protein synthesis, the others were transcription, cell structure, protein destination and storage, metabolism etc.
Seven full-length cDNAs of candidate stress-related genes were obtained from the two cDNA libraries through EST sequencing and the corresponding bioinformatics analysis. The analysis of their sequence characteristics and the homology were conducted by bioinformatics software. The coding proteins of the seven stress-related genes were as follows:late embryogenesis abundant protein(LEA), Mn-superoxide dismutase(MnSOD), Zinc finger protein(Zn), S-adenosylmethionine decarboxylase(SAMDC), WRKY transcription factor(WRKY), Glutathione S-transferase(GST) and cyclophilin. And these seven genes were named as Sc-Lea, Sc-MnSOD, Sc-zf, Sc-SAMDC, Sc-WRKY, Sc-GST, Sc-CyP, respectively.
The primers designed according to the ORFs sequence of these genes and the restriction enzyme cutting site information of the vector pET29a(+) were used to constructed their prokaryotic expression vectors. Then, the prokaryotic expression vectors containing the corresponding ORFs were successfully constructed and transformed into E.coil BL21 cells and their expression induced by IPTG. The results of SDS-PAGE indicated these genes could express the right targeted protein in E.coil BL21.
The sugarcane seedlings were treated by various exogenous chemicals, such as PEG, NaCl, SA, H2O2 and Ustilago scitaminea, and then the expression characters of the seven candidate genes were analyzed by Real-time PCR. The results showed that PEG could induce the expression of Sc-Lea, Sc-SAMDC, Sc-WRKY and Sc-CyP, but inhibit the expression of Sc-zf; NaCl could induce Sc-Lea, Sc-zf, Sc-SAMDC, Sc-WRKY and Sc-CyP; SA could induce the expression of Sc-WRKY and Sc-CyP, but inhibit the expression of Sc-SAMDC; H2O2 could induce the expression of Sc-GST and Sc-CyP,but inhibit the expression of Sc-Lea and Sc-SAMDC; Ustilago scitaminea could induce the expression of Sc-MnSOD, Sc-zf, Sc-WRKY and Sc-GST.
引文
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