Streptomyces lincolnensis新遗传操作方法的建立以及lmbQ基因功能研究

以载体pSET152和pKC1139为出发质粒,通过供体菌大肠杆菌ET12567和S17-1转入林可链霉菌 (Streptomyces lincolnensis),建立和优化了接合转移体系.林可霉素生物合成基因簇中,lmbQ基因可能编码一个调控蛋白,构建了S.lincolnensis lmbQ基因中断载体,通过接合转移导入S.lincolnensis野生型菌株,筛选得到基因双交换突变株,通过PCR以及测序验证基因型正确,该突变株即为lmbQ同框敲除突变株.摇瓶发酵结果表明,lmbQ基因是一个正调控基因.     

苏云金素合成基因簇中非核糖体肽合成酶基因thu2功能的初步分析

对苏云金素生物合成基因簇中编码非核糖体肽合成酶基因thu2进行基因缺失插入失活的研究。用温敏型质粒pHT304-TS构建基因thu2的插入缺失质粒pEMB1434,电转化苏云金芽胞杆菌菌株CT-43后,通过抗性筛选和PCR验证得到thu2基因同源双交换基因敲除突变株CT-43-22。HPLC(高效液相色谱,High Performance Liquid Chromatography)检测发现CT-43-22没有苏云金素特征吸收峰;用pHT304构建得到含有完整thu2基因的回补质粒pEMB1435,电转化CT-43-22后得到互补重组菌CT-43-22b,发现其恢复了苏云金素的产生。显微镜观察突变株和互补重组菌均能产生正常的晶体和芽胞。thu2的基因敲除和基因互补实验证明,thu2基因为CT-43苏云金素生物合成的必需基因,但对晶体和芽胞的形成没有影响。     

柔红霉素产生菌SIPI-DM中dnmV的基因置换

dnmV基因编码柔红霉素生物合成途径中TDP-柔红糖胺C4酮基还原酶。阻断基因组上的dnmV基因并导入源于阿维菌素生物合成途径的aveBIV基因可构建得到表柔红霉素工程菌。本文从高产的柔红霉素产生菌SIPI-DM中分别扩增dnmV基因两侧同源交换臂, 并在两侧交换臂中插入aveBIV基因构建用于置换dnmV基因的同源双交换重组质粒。经筛选及验证得到aveBIV基因直接置换dnmV基因的表柔红霉素工程菌, 且该工程菌基因组上不引入抗性基因, 有利于进一步的基因改造。     

天蓝淡红链霉菌SIPI-1482中酮还原酶基因dnrU的阻断突变研究

目的：研究柔红霉素产生菌天蓝淡红链霉菌SIPI-1482中酮还原酶基因dnrU阻断后的产物（13s）-13-二氢柔红霉素及其他发酵产物的变化。方法：利用同源重组的原理,以大肠杆菌质粒pUC18为基础构建了dnrU基因交换质粒,通过在SIPI-1482染色体上的dnrU基因中插入安普霉素抗性基因来筛选dnrU的阻断突变株。结果和结论：PCR验证表明成功地阻断了dnrU基因。dnrU基因敲除后,重组菌发酵产物中（13s）-13-二氢柔红霉素消失,而其他发酵中间产物也有一定变化。     

卡西霉素生物合成调控基因calR2的功能

【背景】卡西霉素(Calcimycin)是由教酒链霉菌NRRL3882产生的吡咯聚醚类抗生素,结构独特且具有广泛的生物活性,但其生物合成调控机制尚不清楚。【目的】研究卡西霉素生物合成基因簇上编码LuxR家族同源蛋白的潜在调控基因calR2的功能。【方法】通过PCR-targeting的方法对卡西霉素基因簇上的calR2基因进行中断,HPLC对突变株及回补菌株的代谢产物进行分析。利用荧光定量RT-PCR分析ΔcalR2突变菌株和野生菌株的基因转录水平差异。【结果】calR2基因中断的突变株不能产生卡西霉素,回补菌株则恢复产生卡西霉素的能力。RT-PCR结果表明卡西霉素生物合成的一些重要骨架基因在ΔcalR2突变株中的转录水平明显降低。【结论】LuxR家族转录调控基因calR2在卡西霉素生物合成过程中起正调控作用。     

罗中链霉菌中衣霉素基因簇的克隆及异源表达

衣霉素属于核苷类抗生素,具有抑制蛋白质N-糖基化的活性,是潜在的药物先导化合物.罗中链霉菌(Streptomyces luozzhongensis)TRM49605是一株产衣霉素的链霉菌属(Streptomyces)的新物种.本研究旨在探索TRM49605中衣霉素生物合成基因簇的生物学功能,为新型药物开发提供理论依据.通过antiSMASH预测发现TRM49605中衣霉素基因簇全长29.394 kb,由26个基因组成,采用Red/ET方法通过线线重组成功构建了含有衣霉素PartⅡ片段的质粒pTRM605-24-01以及含有完整衣霉素生物合成基因簇的质粒pTRM605-24-02.通过线环重组将接合转移元件插入pTRM605-24-02获得pTRM605-24-03质粒,通过属间接合转移将衣霉素生物合成基因簇整合至天蓝色链霉菌(S. coelicolor)M145中进行表达.成功克隆获得衣霉素生物合成基因簇并异源表达,为改造衣霉素生物合成基因簇提供理论依据.     

表达大肠杆菌谷氨酸-1-半醛氨基转移酶对红色荧光报告蛋白尿卟啉原Ⅲ甲基化酶的影响

谷氨酸-1-半醛氨基转移酶(Glutamate-1-semiadhyde aminotransferase,GSAT)是尿卟啉原Ⅲ生物合成上游途径的一个酶,尿卟啉原Ⅲ是红色荧光报告蛋白尿卟啉原Ⅲ甲基化酶(Uroporphyrinogen Ⅲ methyltransferase,UPMT)的底物。为了探明大肠杆菌共表达GSAT对UPMT荧光强度的影响,通过PCR扩增玉米upmt基因,将其插入pETDuet-1质粒中第2个顺反子中,构建的载体命名为pETU,表达UPMT的N端含有组氨酸标签;通过PCR扩增大肠杆菌编码GSAT的hemL基因,定点突变去除hemL基因中NcoⅠ序列,亚克隆至pET-51b质粒,再将获得的hemL基因插入pETU质粒的第一个顺反子中,构建pETeGU载体。表达GSAT的N端含有Strep标签。和单独表达upmt基因相比,表达2个基因后,蛋白印迹分析表明没有明显改变UPMT表达量,光谱扫描分析显示没有改变荧光物质的组成,但是增强了重组细胞的红色荧光物质三甲基咕啉的含量,该物质在354nm有特异吸收。用2mmol/L的GSAT抑制剂3-氨基-2,3二羟基苯甲酸处理后,表达两种酶的菌落荧光消失,表明重组GSAT可能增加内源尿卟啉原Ⅲ水平,从而增强重组UPMT催化产生的红色荧光。     

利用Duet系列共表达载体构建工程菌生物合成3-羟基丁酸(3HB)

通过PCR获得β-酮基硫解酶(PhaA)、乙酰乙酰辅酶A还原酶(PhaB)和硫酯酶(TesB)的基因phaA,phaB和tesB。以pACYCDuet-1、pRSFDuet-1、PET30a(+)为载体,以大肠杆菌表达型宿主E.coli BL21(DE3)为宿主茵,分别构建了两株表达体系不同的工程茵,建立了R-3-羟基丁酸(3HB)的代谢途径,实现3HB的生物合成。将两株工程茵分别进行诱导表达及发酵,结果表明,三个基因均可在表达型宿主BL21(DE3)中进行活性表达,通过三个酶的连续催化生物合成3HB,并且三个基因的均衡表达更有利于3HB的生物合成。将phaAB基因簇构建在ACYCDuet-1上,tesB基因构建在RSFDuet-1上,获得的工程茵BL21(AAB+RB),3HB产量可达到1.8 g/L。     

柔红霉素产生菌SIPI-1482中dnmV基因功能的阻断及恢复

dnmV基因产物为柔红霉素生物合成途径中TDP-6-脱氧己糖C4酮基还原酶,破坏该基因能阻断柔红糖胺的合成,进而阻断柔红霉素的产生。从天蓝淡红链霉菌(S. coeruleorubidus)SIPI-1482基因组DNA中经PCR扩增出dnmV及其上游dnmU基因片段,并由此构建了用于阻断dnmV基因的同源重组质粒pYG817,转化SIPI-1482菌株后成功地破坏了dnmV基因,发酵结果显示阻断突变株不再代谢产生柔红霉素,为引入新的基因来改变代谢产物的糖基结构打下了基础。通过导入dnmV基因表达质粒可重建该突变株的生物合成途径,恢复产生柔红霉素,但产量比出发菌株要低。     

卡西霉素生物合成基因簇中调控基因calR1的功能

【背景】卡西霉素(calcimycin)是重要的离子载体抗生素,其生物合成基因簇已从教酒链霉菌NRRL3882的基因组DNA中成功克隆,但基因簇内的部分生物合成基因及调控基因的功能有待研究。【目的】研究卡西霉素产生菌教酒链霉菌NRRL3882中编码TylR家族同源转录调控蛋白的calR1基因的功能。【方法】通过PCR-targeting的方法,构建calR1基因敲除突变株及回补菌株,对突变菌株及回补菌株进行发酵,通过HPLC分析其代谢产物。利用荧光定量PCR检测ΔcalR1突变菌株和野生菌株的生物合成基因转录水平。【结果】calR1基因敲除突变株丧失产生卡西霉素的能力,但仍有中间产物噻唑霉素的积累,回补菌株中卡西霉素的产量有一定程度的恢复。RT-qPCR结果表明,卡西霉素合成相关的一些重要基因calC、calG、calU3等基因的表达量明显改变。【结论】TylR家族转录调控基因calR1是卡西霉素生物合成的调控基因。     

Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends

The 387 kb linear plasmid pPZG101 of Streptomyces rimosus R6 can integrate into the chromosome or form a prime plasmid carrying the oxytetracycline biosynthesis cluster. The integration of plasmid pPZG101 into the linear chromosome of S. rimosus R6-501 in mutant MV25 was shown to be due to a single cross-over at a 4 bp common sequence. pPZG101 had integrated into a 250 kb DNA sequence that was reiterated at a low level. This sequence includes the oxytetracycline biosynthesis cluster, so that homologous recombination generated a mixed population carrying different copy numbers of the region. The 1 Mb linear plasmid pPZG103 in mutant MV17 had also arisen from a cross-over between pPZG101 and the chromosome, so that one end of pPZG103 consists of c . 850 kb of chromosomal sequence including the oxytetracycline biosynthesis cluster. The plasmid pPZG101 was shown to consist of a unique central region of about 30 kb flanked by terminal inverted repeats of about 180 kb. Analysis of a presumed ancestor plasmid pPZG102 suggested that the long terminal repeats had arisen by a recombination event during the strain development programme.     

阴沟肠杆菌B8拮抗活性基因‘admA’及上游调控序列的克隆与功能鉴定

为了阐明水稻白叶枯病拮抗菌阴沟肠杆菌B8的作用机理,文章采用转座子标签法和染色体步移技术克隆到突变株B8B中Tn5插入位点周边拮抗活性相关片段,并通过基因敲除验证了获得的拮抗相关片段admA’上游调控序列的功能。以转座子中Kan抗性基因为标签,克隆了B8B菌株中Tn5插入位点左侧2 608 bp序列,经两次染色体步移得到Tn5插入位点右侧的2 354 bp序列。序列拼接后获得B8菌株拮抗相关序列4 611 bp的Bcontig。生物信息学分析显示该序列含有7个ORF,分别对应于3-磷酸甘油醛脱氢酶(GADPH)基因的部分编码区、2个LysR家族转录调控因子、弧菌假设蛋白VSWAT3-20465及成团泛菌(Pantoea agglomerans)andrimid生物合成基因簇的admA、admB和部分admC基因序列。B8B菌株Tn5插入分别位于同源于弧菌假设蛋白的anrPORF及‘admA’基因上游200 bp和894 bp处。通过同源重组技术,借助敲除质粒pMB-BG,获得拮抗活性消失的突变株B-1和B-3。结果表明B8B突变株中Tn5的插入可能影响了anrP蛋白的转录和表达,进而调控拮抗物质编码基因簇的生物合成。B8菌株中拮抗物质相关基因是类似于andrimid生物合成基因簇的基因家族,其上游调控区对该抗生素的生物合成具有重要的作用。     

Characterization of DNA sequences required for the CcrAB-mediated integration of staphylococcal cassette chromosome mec, a Staphylococcus aureus genomic island

The mobile element staphylococcal cassette chromosome mec (SCCmec), which carries mecA, the gene responsible for methicillin resistance in staphylococci, inserts into the chromosome at a specific site, attB, mediated by serine recombinases, CcrAB and CcrC, encoded on the element. This study sought to determine the sequence specificity for CcrB DNA binding in vitro and for CcrAB-mediated SCCmec insertion in vivo. CcrB DNA binding, as assessed in vitro by electrophoretic mobility shift assay (EMSA), revealed that a 14-bp sequence (CGTATCATAAGTAA; the terminal sequence of the orfX gene) was the minimal requirement for binding, containing an invariant sequence (TATCATAA) found in all chromosomal (attB) and SCCmec (attS) integration sites. The sequences flanking the minimal attB and attS binding sites required for insertion in vivo were next determined. A plasmid containing only 37 bp of attS and flanking sequences was required for integration into the attB site at 92% efficiency. In contrast, at least 200 bp of sequence within orfX, 5' to the attB core, and 120 bp of specific sequence 3' to the orfX stop site and attB core were required for the highest insertion frequency. Finally, an attS-containing plasmid was inserted into wild-type Staphylococcus aureus strains without integrated SCCmec (methicillin susceptible) at various frequencies which were determined both by sequences flanking the att site and by the presence of more than one att site on either the chromosome or the integration plasmid. This sequence specificity may play a role in the epidemiology of SCCmec acquisition.     

Characterization of the Micromonospora rosaria pMR2 plasmid and development of a high G+C codon optimized integrase for site-specific integration

pMR2, an 11.1 kb plasmid was isolated from Micromonospora rosaria SCC2095, NRRL3718, and its complete nucleotide sequence determined. Analysis revealed 13 ORFs including homologs of a KorSA regulatory protein and TraB plasmid transfer protein found on other actinomycete plasmids. pMR2 contains att/int functions consisting of an integrase, an excisionase, and a putative plasmid attachment site (attP). The integrase gene contained a high frequency of codons rarely used in high G+C actinomycete coding regions. The gene was codon optimized for actinomycete codon usage to create the synthetic gene int-OPT. pSPRX740, containing an rpsL promoter and the att/int-OPT region, was introduced into Micromonospora halophytica var. nigra ATCC33088. Analysis of DNA flanking the pSPRX740 integration site confirmed site-specific integration into a tRNA(Phe) gene in the M. halopytica var. nigra chromosome. The pMR2 attP element and chromosomal attachment (attB) site contain a 63 bp region of sequence identity overlapping the 3' end of the tRNA(Phe) gene. Plasmids comprising the site-specific att/int-OPT functions of pMR2 can be used to integrate genes into the chromosome of actinomycetes with an appropriate tRNA gene. The development of an integrative system for Micromonospora will expand our ability to study antibiotic biosynthesis in this important actinomycete genus.     

Site-specific topoisomerase I-mediated DNA cleavage induced by nogalamycin: a potential role of ligand-induced DNA bending at a distal site

Many DNA binding ligands (e.g., nogalamycin, actinomycin D, terbenzimidazoles, indolocarbazoles, nitidine, and coralyne) and various types of DNA lesions (e.g., UV dimers, DNA mismatches, and abasic sites) are known to stimulate topoisomerase I-mediated DNA cleavage. However, the mechanism(s) by which these covalent and noncovalent DNA interactions stimulate topoisomerase I-mediated DNA cleavage remains unclear. Using nogalamycin as a model, we have studied the mechanism of ligand-induced topoisomerase I-mediated DNA cleavage. We show by both mutational and DNA footprinting analyses that the binding of nogalamycin to an upstream site (from position -6 to -3) can induce highly specific topoisomerase I-mediated DNA cleavage. Substitution of this nogalamycin binding site with a DNA bending sequence (A(5)) stimulated topoisomerase I-mediated DNA at the same site in the absence of nogalamycin. Replacement of the A(5) sequence with a disrupted DNA bending sequence (A(2)TA(2)) significantly reduced the level of topoisomerase I-mediated DNA cleavage. These results, together with the known DNA bending property of nogalamycin, suggest that the nogalamycin-DNA complex may provide a DNA structural bend to stimulate topoisomerase I-mediated DNA cleavage.     

The entire nogalamycin biosynthetic gene cluster of Streptomyces nogalater: characterization of a 20-kb DNA region and generation of hybrid structures

Fragments spanning 20 kb of Streptomyces nogalater genomic DNA were characterized to elucidate the molecular genetic basis of the biosynthetic pathway of the anthracycline antibiotic nogalamycin. Structural analysis of the products obtained by expression of the fragments in S. galilaeus and S. peucetius mutants producing aclacinomycin and daunomycin metabolites, respectively, revealed hybrid compounds in which either the aglycone or the sugar moiety was modified. Subsequent sequence analysis revealed twenty ORFs involved in nogalamycin biosynthesis, of which eleven could be assigned to the deoxysugar pathway, four to aglycone biosynthesis, while the remaining five express products with unknown function. On the basis of sequence similarity and experimental data, the functions of the products of the newly discovered genes were determined. The results suggest that the entire biosynthetic gene cluster for nogalamycin is now known. Furthermore, the compounds obtained by heterologous expression of the genes show that it is possible to use the genes in combinatorial biosynthesis to create novel chemical structures for drug screening purposes.     

Right 25 bp terminus sequence of the nopaline T-DNA is essential for and determines direction of DNA transfer from agrobacterium to the plant genome

We have determined which sequences at the right border of the T-DNA region of the nopaline C58 Ti plasmid are required for transfer and/or integration of the T-DNA into the plant cell genome. The results indicate that the 25 bp T-DNA terminus repeat sequence, TGACAGGATATATTGGCGGGTAAAC, is directly responsible for T-DNA transfer; furthermore, this sequence is directional in its mode of action. A transfer-negative nononcogenic Ti plasmid derivative, pGV3852, was constructed, in which 3 kb covering the right T-DNA border region was substituted for by pBR322 sequences. The pBR322 sequences in pGV3852 provide a site for homologous recombination with pBR-derived plasmids containing sequences to assay for transfer activity. First, a 3.3 kb restriction fragment overlapping the deleted region in pGV3852 was shown to restore transfer activity. Second, a sequence of only 25 bp, the T-DNA terminus sequence, was shown to be sufficient to restore normal transfer activity. The transfer-promoting sequences are most active when reinserted in one orientation, that normally found in the Ti plasmid.     

Gene conversion associated with site-specific recombination in yeast plasmid pSR1.

A circular DNA plasmid, pSR1, isolated from Zygosaccharomyces rouxii has a pair of inverted repeats consisting of completely homologous 959-base pair (bp) sequences. Intramolecular recombination occurs frequently at the inverted repeats in cells of Saccharomyces cerevisiae, as well as in Z. rouxii, and is catalyzed by a protein encoded by the R gene of its own genome. The recombination is, however, independent of the RAD52 gene of the host genome. A site for initiation of the intramolecular recombination in the S. cerevisiae host was delimited into, at most, a 58-bp region in the inverted repeats by using mutant plasmids created by linker insertion. The 58-bp region contains a pair with 14-bp dyad symmetry separated by a 3-bp spacer sequence. The recombination initiated at this site was accompanied by a high frequency of gene conversion (3 to 50% of the plasmid clones examined). Heterogeneity created by the linker insertion or by a deletion (at most 153 bp so far tested) at any place on the inverted repeats was converted to a homologous combination by the gene conversion, even in the rad52-1 mutant host. A mechanism implying branch migration coupled with DNA replication is discussed.