牛樟芝倍半萜合酶基因克隆及在不同培养基中的表达

牛樟芝(Antrodia camphorata)是一种珍稀食药用菌,能产生具有抗癌活性的倍半萜类化合物。对牛樟芝基因组进行分析,获得倍半萜合酶基因序列并设计特异引物,提取在Glu培养基(麦芽浸粉6 g/L,酵母提取物3 g/L,葡萄糖40 g/L)上生长的牛樟芝菌丝体的RNA,利用RT-PCR技术克隆得到倍半萜合酶基因AcTPS1。AcTPS1基因c DNA全长为969 bp,编码323个氨基酸,根据系统进化树可知AcTPS1氨基酸序列与其他9种真菌倍半萜合酶聚为一类。AcTPS1拥有典型倍半萜合酶的结构域(RRSRSATAEAYACFIW),之后检测AcTPS1在不同培养基上的菌丝中的表达结果显示不同碳源中,只有葡萄糖作为碳源时该基因表达,不同氮源中,以番茄浸粉和酪蛋白胨为氮源时该基因表达。说明AcTPS1是一类诱导型表达的基因。为利用发酵培养以及异源表达手段获得牛樟芝活性化合物提供参考。     

牛樟芝非核糖体多肽合成酶基因(AcNRPS)的克隆与鉴定

胶霉毒素属于真菌天然次生代谢产物epipolythiodioxopiperazine(ETP)家族,具有免疫抑制剂、抗真菌等多种生物活性,是由非核糖体多肽合成酶(NRPSs)催化合成。从牛樟芝(Antrodia camphorata)基因组中挖掘出非核糖体多肽合成酶基因(AcNRPS,NCBI登录号为KX430967),克隆获取其全长cDNA,并对其进行生物信息学分析和表达谱分析。结果显示AcNRPS基因cDNA全长6 687 bp;与其DNA序列比对发现AcNRPS基因含有12个内含子;其开放阅读框编码2 229个氨基酸残基,BLAST比对发现其含有2个A-C-T结构域,底物需2个氨基酸;系统发育树结果显示AcNRPS与其他合成产物为胶霉毒素的NRPS基因聚为一类,其可合成胶霉毒素类化合物;表达谱分析显示,以葡萄糖和土豆蛋白胨作为碳、氮源的培养基能够有效促进牛樟芝NRPS基因的表达。     

牛樟芝非核糖体多肽合成酶基因(ＡcNRPS)的克隆与鉴定

胶霉毒素属于真菌天然次生代谢产物epipolythiodioxopiperazine (ETP)家族,具有免疫抑制剂、抗真菌等多种生物活性,是由非核糖体多肽合成酶(NRPSs)催化合成。从牛樟芝(Antrodia camphorata)基因组中挖掘出非核糖体多肽合成酶基因(AcNRPS,NCBI登录号为KX430967),克隆获取其全长cDNA,并对其进行生物信息学分析和表达谱分析。结果显示AcNRPS基因cDNA全长6 687 bp;与其DNA序列比对发现AcNRPS基因含有12 个内含子;其开放阅读框编码2 229 个氨基酸残基,BLAST比对发现其含有2 个A-C-T结构域,底物需2个氨基酸;系统发育树结果显示AcNRPS与其他合成产物为胶霉毒素的NRPS基因聚为一类,其可合成胶霉毒素类化合物;表达谱分析显示,以葡萄糖和土豆蛋白胨作为碳、氮源的培养基能够有效促进牛樟芝NRPS基因的表达。     

基于紫芝基因组的倍半萜合酶基因的发掘与功能鉴定

灵芝(Ganoderma lucidum)是目前研究最深入的药用真菌之一,也是作为研究天然产物生物合成的理想模式真菌.本研究通过对担子菌亚门灵芝属紫芝(Ganoderma sinense)基因组的数据挖掘发现两个倍半萜合酶基因.利用RT-PCR方法从紫芝菌丝体总RNA中扩增出两者的全长cDNA序列,将两个倍半萜合酶的编码序列克隆到表达载体中在大肠杆菌中进行异源表达,变性蛋白电泳显示两者都可以可溶性的形式在大肠杆菌中表达.顶空固相微萃取-气相色谱质谱法分析显示,重组紫芝萜类合酶具有明显的催化活性,可合成多个倍半萜类产物.本研究为进一步揭示真菌倍半萜合酶的结构与功能的相关性及其产物多样性形成机制奠定了基础.     

牛樟芝HMGR基因的克隆和表达分析

为研究牛樟芝(Antrodia camphorata)萜类生物合成MVA途径中关键酶3-羟-3-甲基戊二酸单酰辅酶A还原酶(3-hydroxy-3-methylglutary CoA reductase,HMGR)的调控机制,从牛樟芝基因组中分离并克隆出AcHMGR基因,对其进行生物信息学分析、不同碳氮源添加物对该基因的诱导表达情况进行分析。分析显示:AcHMGR基因含7个外显子、6个内含子;开放阅读框为3 402 bp,编码1 133个氨基酸残基组成蛋白质序列;AcHMGR包含HMGR典型的多肽位点,即2个HMG-CoA结合基序:PLG(Ⅰ/Ⅴ)AGPLK(Ⅰ/Ⅴ)DG和AEGTLVASTSRG,2个NADP结合基序:TGDAMGMNMI和IEVGT(Ⅰ/Ⅴ)GGGT;分子系统进化分析显示,AcHMGR蛋白序列与其他多孔菌科真菌的HMGR聚为一支;表达谱分析显示:碳源中的果糖、氮源中的酪蛋白胨诱导表达AcHMGR基因的能力最强。本研究为探讨牛樟芝萜类,尤其是三萜类化合物的生物合成及调控机理提供了帮助。     

遮阴对柠檬香茅中萜类化合物及其合成酶基因影响研究

为获取柠檬香茅(Cymbopogon citratus)中萜类化合物及其合成酶基因信息,以正常生长及遮阴下的柠檬香茅嫩叶为材料,进行代谢组学和转录组学结合q RT-PCR验证分析。代谢组分析结果表明,柠檬香茅所含萜类共23种,包括单萜4种、倍半萜4种、二萜8种、三萜3种和四萜4种。在遮阴下,柠檬香茅的二萜类银杏内酯C和四萜类虾青素相对含量更高。转录组测序结果表明,单萜生物合成涉及4类合成酶的24个基因,二萜生物合成涉及11类合成酶的49个基因,倍半萜和三萜生物合成涉及12类合成酶的58个基因,其中6类合成酶的8个基因在遮阴下的相对表达量显著提高,而前萘二烯加氧酶(c64786.0)基因正好相反。q RT-PCR分析表明,遮阴下4个FPKM值差异明显的萜类合成酶基因表达的变化趋势与转录组测序结果一致,但不同合成酶基因的差异表达量存在差异。因此,柠檬香茅所含4类共23种萜类化合物由27类合成酶共131个基因编码而来,不同光照强度影响9个合成酶基因的表达和2种萜类化合物含量。     

一个新型牛樟芝PR-PKS基因的克隆及表达分析

为了解牛樟芝中聚酮化合物的生物合成机理及聚酮合酶基因功能,从牛樟芝基因组挖掘并克隆得到一个部分还原型PKS(PR-PKS)基因(AcPKS3),并对其进行生物信息学分析及表达谱分析。结果显示,AcPKS3(GenBank登录号:MG988206)DNA全长8 286 bp,有22个内含子,其外显子共编码2 285个氨基酸;结构域依次为KS-AT-KR-ACP-SDR,各结构域的活性保守位点为β-酮基合成酶(DTACSS)、酰基转移酶(GHSAGETA)、酮基还原酶(YLLVGGIG)、酰基转移酶(YGLDSITSA)、短链醇脱氢酶与NAD(P)H结合的N端保守序列(ITGTTGSFG)及活性保守位点(YTESK);AcPKS3与6-甲基水杨酸合成酶的亲缘关系较近;不同碳源中葡萄糖,不同氮源中牛肉浸粉、酪蛋白胨、土豆蛋白胨可促进AcPKS3基因表达。本研究为牛樟芝聚酮合酶功能研究及牛樟芝基因资源利用提供参考。     

牛樟芝中一个新型还原型聚酮合酶基因的克隆及表达分析

为了研究牛樟芝中PKS基因与化合物之间的关系,该研究通过对牛樟芝基因组分析获得牛樟芝聚酮合酶基因,以此序列为模板设计含有起始密码子和终止密码子的特异引物并以牛樟芝c DNA为模板克隆获得一个高度还原型PKS(HR-PKS)基因全长,命名为AcPKS2;对AcPKS2基因进行生物信息学分析,并比较该基因在不同培养基上的表达量。结果表明:AcPKS2全长7 842 bp,有24个内含子,其外显子共编码2 613个氨基酸,该蛋白的相对分子质量为293.5 kDa,理论等电点pI为5.78。用CDD分析其结构域显示,该基因属于HR-PKS,其结构域组织排列为KS-AT-DH-MT-ER-KR-ACP-TE,8个结构域其活性位点分别为β-酮基合成酶(DTACSSSL)、酰基转移酶(GHSIGETA)、脱水酶(RNDGSTSPL)、甲基转移酶(SFDIITAFDV)、烯酰还原酶(HAGVSSPAA)、酮基还原酶(GSPGQANYTAA)、酰基转移酶(YGLDSLTSVRL)、硫酯酶(KQPNGPY)。系统发育树显示AcPKS2与其他化合物未知的HR-PKS蛋白聚为一支,结构域和系统进化树分析显示该基因可能编码一种新的含TE结构域高度还原型聚酮合酶;表达分析结果显示葡萄糖和果糖能够诱导该基因的表达。     

维药新塔花(Ziziphora bungena)zbHDS基因克隆及组织表达分析

对维药新塔花(Ziziphora bungena)萜类化合物生物合成途径中,关键酶1-羟基-2甲基-2-(E)-丁烯基-4-二磷酸合成酶HDS基因克隆,进行组织表达特异性分析,为研究新塔花萜类化合物生物合成途径与基因调控提供基础。结合新塔花转录组数据库,根据编码区序列设计引物,通过RT-PCR方法对Z. bungena基因HDS (zbHDS)的编码区cDNA进行克隆,对其进行相关生物信息学分析,通过Real-Time进一步分析其组织表达特异性。RT-PCR扩增了一个长2 465 bp的zbHDS (登录号:MG065856)基因片段,含一个2 229 bp的开放阅读框,编码742个氨基酸。进化树分析结果显示,与丹参(Salvia miltiorrhiza)具有较近的亲缘关系。Real-Time PCR结果显示zbHDS基因在各器官中均有表达,在茎和叶中表达量较高,根和花中表达量相对较低。本研究首次从新塔花中克隆HDS基因并获得其编码区序列,zbHDS基因具有组织表达特异性,为进一步研究新塔花中萜类化合物生物合成途径提供数据支持。     

冬凌草1-脱氧-D-木酮糖-5-磷酸合成酶基因克隆与表达分析

1-脱氧-D-木酮糖-5-磷酸合成酶(1-deoxy-D-xylulose 5-phosphate synthase,DXS)是植物萜类代谢通路中2-C-甲基-D-赤藓糖醇-4-磷酸(MEP)途径的第一个关键酶,在植物萜类物质的生物合成中发挥重要的作用.为了研究该基因在冬凌草二萜类成分合成中的作用,该研究在冬凌草转录组测序结果的基础上设计一对特异性引物,采用RT-PCR方法得到冬凌草IrDXS基因cDNA全长序列,并对其蛋白进行理化性质分析、信号肽预测、亚细胞定位预测、蛋白质二级结构、三级结构预测分析及跨膜域分析等生物信息学分析,同时利用实时荧光定量PCR的方法检测IrDXS基因在冬凌草不同部位中的表达情况.结果表明:从冬凌草叶片中分离得到了一条编码DXS的全长基因,通过生物信息学软件分析发现,该基因编码全长2169 bp,编码722个氨基酸,分子量为77.7 kD.多序列比对发现该基因编码的蛋白和其他植物中已知的DXS蛋白序列具有较高的同源性,N端均包含了一段质体转运肽序列,并均具有一个保守的焦磷酸硫胺素结构域和与吡啶结合相关的DRAG结构域.序列进化树分析显示,IrDXS基因属于植物DXS2家族.DXS基因在冬凌草根中表达量最高、愈伤组织中最低.该研究首次获得了IrDXS基因的全长cDNA序列,并揭示了其在不同组织中的表达差异,为后续的深入研究IrDXS基因在冬凌草二萜类成分合成途径中的功能奠定了基础.     

Molecular characterization of a cDNA clone encoding glutamine synthetase from a gymnosperm,Pinus sylvestris

A full-length cDNA clone (pGSP114) encoding glutamine synthetase was isolated from a gt11 library of the gymnosperm Pinus sylvestris. Nucleotide sequence analysis showed that pGSP114 contains an open reading frame encoding a protein of 357 amino acid residues with a calculated molecular mass of 39.5 kDa. The derived amino acid sequence was more homologous to cytosolic (GS1) (78–82%) than to chloroplastic (GS2) (71–75%) glutamine synthetase in angiosperms. The lack of N-terminal presequence and C-terminal extension which define the primary structure of GS2, also supports that the isolated cDNA encodes cytosolic GS. Southern blot analysis of genomic DNA from P. sylvestris and P. pinaster suggests that GS may be encoded by a small gene family in pine. GS mRNA was more abundant in cotyledons and stems than in roots of both Scots and maritime pines. Western blot analysis in P. sylvestris seedlings showed that only one GS polypeptide, similar in size to GS1 in P. pinaster, could be detected in several different tissues. Our results suggest that cytosolic GS is mainly responsible for glutamine biosynthesis in pine seedlings.This paper is dedicated to the memory of Dr. Jesús S. Olavarría.     

Molecular cloning, in vitro expression and characterization of a plant squalene synthetase cDNA

Squalene synthetase (farnesyl-diphosphate:farnesyl-diphosphate farnesyltransferase, EC 2.5.1.21) catalyzes the first committed step for sterol biosynthesis and is thought to play an important role in the regulation of isoprenoid biosynthesis in eukaryotes. Using degenerate oligonucleotides based on a conserved region found in yeast and human squalene synthetase genes, a cDNA was cloned from the plant Nicotiana benthamiana. The cloned cDNA contained an open reading frame of 1234 bp encoding a polypeptide of 411 amino acids (M _r 47002). Northern blot analysis of, poly(A)⁺ mRNA from N. benthamiana and N. tabacum cv. MD609 revealed a single band of ca. 1.6 kb in both Nicotiana species. The identity and functionality of the cloned plant squalene synthetase cDNA was further confirmed by expression of the cDNA in Escherichia coli and in a squalene synthetase-deficient erg9 mutant of Saccharomyces cerevisiae. Antibodies raised against a truncated form of the protein recognized an endogenous plant protein of appropriate size as well as the full-length bacterially expressed protein as detected by western analysis. Comparison of the deduced primary amino acid sequences of plant, yeast, rat and human squalene synthetase revealed regions of conservation that may indicate similar functions within each polypeptide.     

Cloning,expression in yeast,and functional characterization of CYP71D14, a root-specific cytochrome P450 from <Emphasis Type="Italic">Petunia hybrida</Emphasis>

Alkaloids, which are naturally occurring amines, are biosynthesized and accumulated in plant tissues such as roots, leaves, and stems. Many alkaloids have pharmacological effects on humans and animals. Cytochrome P450 (P450 or CYP) monooxygenases are known to play key roles in the biosynthesis of alkaloids in higher plants. A cDNA clone encoding a P450 protein consisting of 502 amino acids was isolated from Petunia hybrida. The deduced amino acid sequence of the cDNA clone showed a high level of similarity with the other P450 species in the CYP71D family; hence, this novel P450 was named CYP71D14. Among plant P450 species, CYP71D14 had 45.7% similarity in its amino acid sequence to CYP71D12, which is involved in the biosynthesis of the indole alkaloids vinblastine and vincristine. Expression of CYP71D14 mRNA in Petunia plants was examined by Northern blot analysis by using a full-length cDNA of CYP71D14 as a probe. CYP71D14 mRNA was expressed most abundantly in the roots. The nucleotide sequence of CYP71D14 has been submitted to the DDBJ, EMBL, and GenBank nucleotide databases under the accession number AB028462. An erratum to this article can be found at     

Cloning and expression of transaldolase from potato

We have isolated a cDNA encoding transaldolase, an enzyme of the pentose-phosphate pathway, from potato (Solanum tuberosum). The 1.5 kb cDNA encodes a protein of 438 amino acid residues with a molecular mass of 47.8 kDa. When the potato cDNA was expressed in Escherichia coli a 45 kDa protein with transaldolase activity was produced. The first 62 amino acids of the deduced amino acid sequence represent an apparent plastid transit sequence. While the potato transaldolase has considerable similarity to the enzyme from cyanobacteria and Mycobacterium leprae, similarity to the conserved transaldolase enzymes from humans, E. coli and Saccharomyces cerevisiae is more limited. Northern analysis indicated that the transaldolase mRNA accumulated in tubers in response to wounding. Probing the RNA from various potato tissues indicated that the transaldolase mRNA accumulation to higher levels in the stem of mature potato plants than in either leaves or tubers. These data are consistent with a role for this enzyme in lignin biosynthesis.     

丹参环阿屯醇合酶基因克隆及表达分析

以丹参cDNA为模板,克隆了丹参环阿屯醇合酶(cycloartenol synthase,CAS)基因的cDNA序列(SmCAS),对其序列进行生物信息学分析,并采用实时荧光定量PCR方法研究了该基因在丹参不同器官及不同胁迫处理下的表达模式。结果显示:该基因全长2 346bp,包含2 271bp开放阅读框,编码756个氨基酸。预测其编码蛋白分子量为86.16kD,具有氧化鲨烯环化酶超家族典型的DCTAE结构域和QW结构域。该基因推测的氨基酸序列与人参、田七、积雪草、甘草、拟南芥的相似性分别为83%、84%、83%、81%和80%。SmCAS基因在丹参根、茎、叶、花中均有表达,在花中表达量最高;而且SmCAS基因能够响应ABA、低温和干旱的诱导。     

Structure and expression of the lignin O-methyltransferase gene from Zea mays L.

The isolation and characterization of cDNA and homologous genomic clones encoding the lignin O-methyltransferase (OMT) from maize is reported. The cDNA clone has been isolated by differential screening of maize root cDNA library. Southern analysis indicates that a single gene codes for this protein. The genomic sequence contains a single 916 bp intron. The deduced protein sequence from DNA shares significant homology with the recently reported lignin-bispecific caffeic acid/5-hydroxyferulic OMTs from alfalfa and aspen. It also shares homology with OMTs from bovine pineal glands and a purple non-sulfur photosynthetic bacterium. The mRNA of this gene is present at different levels in distinct organs of the plant with the highest accumulation detected in the elongation zone of roots. Bacterial extracts from clones containing the maize OMT cDNA show an activity in methylation of caffeic acid to ferulic acid comparable to that existing in the plant extracts. These results indicate that the described gene encodes the caffeic acid 3-O-methyltransferase (COMT) involved in the lignin biosynthesis of maize.     

罗汉果色氨酸转氨酶基因SgTAR2的克隆及表达分析

色氨酸转氨酶基因家族,是直接参与植物生长素生物合成途径的关键酶基因。该研究在罗汉果转录组测序的基础上,结合RACE技术克隆罗汉果色氨酸转氨酶基因SgTAR2的全长cDNA序列和DNA序列;并对其进行生物信息学分析和时空表达分析。结果表明:克隆所得SgTAR2的cDNA全长序列2078bp,最长ORF为1332bp,编码443个氨基酸,Gen Bank登录号为KU949381,其编码蛋白具有2个蒜氨酸酶保守结构域和多个5'-PLP结合位点,推测其可能参与催化色氨酸转氨基作用、化学防御作用、生长素生物合成等生物学过程;SgTAR2基因DNA长为4103bp,含有4个内含子和5个外显子,其内含子具有多个高水平转录调控因子和多个与激素、环境等胁迫响应相关的作用元件,暗示SgTAR2基因内含子协同调控罗汉果生长素合成、抗胁迫反应、形态发育等生物学过程。实时荧光定量结果显示,SgTAR2基因在罗汉果各组织器官均有表达,在雌蕊和15d幼果期表达量较高,暗示该基因参与罗汉果果实早期发育。该研究结果表明SgTAR2参与了生长素介导的罗汉果不同生长发育过程,特别对幼果及花的起始发育和器官形态建成等具有重要意义。