地中海拟无枝菌酸菌U32染色体特性的脉冲场电泳分析

地中海拟无枝菌酸菌(Amycolatopsis mediterranei)U32是产力复霉素SV的工业生产菌株。采用脉冲场电泳分析发现,地中海拟无枝菌酸菌U32仅有一条约10 Mb的线性染色体, 没有内源性质粒。利用Southern杂交法,对11个编码力复霉素生物合成、相关初级、次级代谢关键酶以及调控蛋白的基因,在U32染色体DNA的PshBI酶切片段上进行了定位。分析发现在一条长度约700kb的PshBI酶切片段上,分别存在着力复霉素合成基因簇(rif)、氮代谢的亚硝酸还原酶小亚基基因(nasD)、衔接初级与次级代谢的甲基丙二酰变位酶基因(mcm)、脂肪酸代谢的乙酰辅酶A羧化酶生物素载体蛋白基因(accA)以及一套核糖体RNA转录单元。同时还发现U32至少有5套核糖体RNA转录单元。其余定位的基因均只出现单一杂交信号。     

力复霉素产生菌地中海拟无枝菌酸菌U32丙氨酸脱氢酶基因克隆及表达

丙氨酸脱氢酶(EC1411)可逆催化丙氨酸脱氨生成丙酮酸和NADH。它是生物体内的氨基酸代谢和氨同化途径的关键酶。在地中海拟无枝菌酸菌(Amycolatopsis mediterranei)U32中,丙氨酸脱氢酶的活力与力复霉素的生物合成有负相关现象,其活力受KNO3全局效应的调控。根据结核分枝杆菌(Mycobacterium tuberculosis)和天蓝链霉菌(Streptomyces coelicolor)的丙氨酸脱氢酶氨基酸的保守序列和地中海拟无枝菌酸菌U32对氨基酸密码子的使用偏好,设计一对简并PCR引物。以此引物从地中海拟无枝菌酸菌U32中扩增到一555bp的片段,并以此片段为探针从地中海拟无枝菌酸菌U32 基因组cosmid文库中成功的克隆到了丙氨酸脱氢酶结构基因(ald)。它编码了一个371个氨基酸的蛋白质,基因的GC含量为72.5％,符合链霉菌的基因结构特征。在起始密码子的上游6个碱基处,有一典型的链霉菌核糖体结合位点(RBS)：AGGAGG,第75位的氨基酸为赖氨酸,是丙酮酸结合位点。以pET28b为载体,在E.coli BL21(DE3)中高效表达了ald基因。用IPTG在22℃时诱导得到的丙氨酸脱氢酶活力最高。用HisTag柱纯化了表达的丙氨酸脱氢酶。酶学性质研究表明该酶专一性以LAla和NAD(H)为底物。     

地中海拟无枝菌酸菌U-32硝酸还原酶的基因克隆

outhern杂交分析表明在地中海拟无枝菌酸菌u－32染色体DNA和黑曲霉niaD(硝酸还原酶基因)之间存在着明显的同源性。利用异源niaD探针从地中海拟无枝菌酸菌u－32基因文库中筛选得到一个能与niaD杂交的5.0kb的Pst Ⅰ片段。该片段经同位素标记后能与地中海拟无枝菌酸菌u－32染色体上一个相同的Pst Ⅰ片段杂交,位于这一片段上的2．1kb sma Ⅰ—EcoR Ⅴ片段只能与以硝酸盐为唯一氮源的总RNA杂交,而不能与相同条件下以铵盐为唯一氮源的总RNA杂交,这些结果表明,所克隆到的5,0kb Pst Ⅰ DNA片段含有地中海拟无枝菌酸菌U-3z的硝酸还原酶基因。这是好氧细菌硝酸还原酶基因克隆的首次报道。由该酶蛋白分子量推测,其结构基因大小在1．5kb左右,进一步的杂交分析发现在5．0kb的Pstl片段中含有完整的NR基因。用20种限制酶对重组质粒pJLl进行了限制酶酶谱的构建。发现有10种酶在pJLl外源片段上无切点,6种酶为单切点,EcoR Ⅰ与Sma Ⅰ各有两个切点。     

S-丙二酰转移酶基因失活对地中海拟无枝酸菌产利福霉素的影响

为提高利福霉素的产量,构建了S-丙二酰转移酶基因失活的地中海拟无枝酸菌。利用融合PCR构建S-丙二酰转移酶基因的同源重组载体,通过电击转化导入到地中海拟无枝酸菌中,使之发生同源重组,以安普霉素为标记,筛选了S-丙二酰转移酶基因失活菌株,并对比了突变菌株与原始菌株的利福霉素SV产量。成功构建了S-丙二酰转移酶基因的同源重组载体,获得了地中海拟无枝酸菌突变株A.mediterranei △fab D,失活菌株的利福霉素SV产量为168.08 mg/L,比原始菌提高了9.94%。S-丙二酰转移酶基因的失活,弱化了突变菌株脂肪酸的合成,强化了利福霉素的合成。     

地中海拟无枝菌酸菌U-32硝酸还原酶的基因克隆

Southern杂交分析表明在地中海拟无枝菌酸菌U-32染色体DNA和黑曲霉niaD(硝酸还原酶基因)之间存在着明显的同源性。利用异源niaD探针从地中海拟无枝菌酸菌U-32基因文库中筛选得到一个能与niaD杂交的5.0kb的PstⅠ片段。该片段经同位素标记后能与地中海拟无枝菌酸菌U-32染色体上一个相同的PstⅠ片段杂交,位于这一片段上的2.1kb SmaⅠ-EcoR Ⅴ片段只能与以硝酸盐为唯一氮源的总RNA杂交,而不能与相同条件下以铵盐为唯一氮源的总RNA杂交,这些结果表明,所克隆到的5.0kb PstⅠDNA片段含有地中海拟无枝菌酸菌U-32的硝酸还原酶基因。这是好氧细菌硝酸还原酶基因克隆的首次报道。由该酶蛋白分子量推测,其结构基因大小在1.5kb左右,进一步的杂交分析发现在5.0kb的PstⅠ片段中含有完整的NR基因。用20种限制酶对重组质粒pJL1进行了限制酶酶谱的构建,发现有10种酶在pJL1外源片段上无切点,6种酶为单切点,EcoRⅠ与SmaⅠ各有两个切点。     

地中海拟无枝菌酸菌U32中amrC/amkC基因的序列分析及在大肠杆菌中的表达

从力复霉素SV产生菌——地中海拟无枝菌酸菌(Amycolatopsis mediterranei)U32的硝酸盐同化基因簇的上游克隆了一个2.6kb的Eco-RI—XhoI DNA片段并测定其序列。序列分析表明,该DNA片段编码两个完整的开放阅读框架(ORF),ORF2的起始密码子GTG与ORF1的终止密码子TGA在TG处重叠。ORF1编码一个含224个氨基酸的多肽,它同放线菌中典型的应答调节蛋白包括AfsQ1和MtrA有很高的同源性;ORF2编码一个含472个氨基酸的蛋白,它同包括AfsQ2和MtrB在内的组氨酸激酶同源。ORF1和ORF2有可能构成典型的双组份信号传导系统,分别命名为amrC和amkC。在T7启动子的控制下,完整的amrC和去除子N端一个可能的跨膜区的amkC在大肠杆菌中分别得到了高效表达,表达蛋白的分子量分别为30kD和46kD,与推测蛋白的分子量一致。     

林可链霉菌中的同源重组

为研究链霉菌中的同源整合频率和机制 ,采用不能在链霉菌中复制的大肠杆菌质粒转化链霉菌StreptomyceslincolnensisB48。质粒pYYE0 4a1上携带的被硫链丝菌素抗性基因灭活的林可霉素生物合成基因与染色体DNA上的同源基因发生重组 ,经过低抗筛选 ,得到两个突变子S .lincolnensisYY1和S .lincolnensisYY2。进一步以硫链丝菌素抗性基因为探针杂交染色体DNASmaⅠ片段 ,S .lincolnensisYY1和S .lincolnensisYY2都得到 1 5kb的阳性条带 ;而以缺失的lacZ基因为探针杂交染色体DNAHindⅢ和SmaⅠ联合酶切片段 ,只有S .lincolnensisYY2得到 4 4kb的阳性条带。Southern杂交结果表明S .lincolnensisYY1是由同源交换或二次重组产生的 ,而S .lincolnensisYY2为同源整合的结果。为验证同源整合子上大肠杆菌复制子和氨苄抗性基因的存在 ,用SphⅠ酶切染色体DNA后连接 ,连接液转化E .coliJM83感受态细胞 ,在氨苄抗性板上得到 2个转化子 ,命名为pSLE1。对…     

将一株原红霉素链霉菌转入拟无枝菌酸菌属的分类学研究

对保藏的红霉素链霉菌AS4.894、AS4.198的化学分类研究表明,它们的胞壁类型为IV/A型,不属于胞壁为Ⅱ型的链霉菌属。菌株AS4.198与已由Labeda(1987)转入糖多孢菌属(Saccharopolyspora),定名为Saccharopolyspora erythreus的菌株相似;菌株AS4.894虽然胞壁型与糖多孢菌相似,但磷酸类脂为PⅡ型,应转入拟无枝菌酸菌属(Amycolatopsis Lechevalier,1986)。通过与红霉素糖多孢菌(Saccharopolyspora erythreus)和白色拟无枝菌酸菌(Amycolatopsis alba,A83850~T)进行比较,菌株AS4.894的生长Ph范围广泛,耐盐和耐50℃高温,DNA G+C mol％高,区别于拟无枝菌酸菌属中的任何已知种,而建议命名为新种——红霉素拟无枝菌酸菌(Amycolatopsis erythreus comb.nov.)。     

同源重组法构建多功能农药降解基因工程菌研究

构建遗传稳定的多功能农药降解基因工程菌可以为农药污染的生物修复提供良好的菌种资源,然而,构建遗传稳定且不带入外源抗性的基因工程菌是一个难点。通过以受体菌的16S rDNA为同源重组指导序列、sacB基因为双交换正筛选标记构建同源重组载体,二亲结合的方法将甲基对硫磷水解酶基因（mpd）整合到呋喃丹降解菌Sphingomonas sp.CDS1染色体的16S rDNA位点,分别成功构建了含1个和2个mpd基因插入到rDNA位点且不带入外源抗性的基因工程菌株CDSmpd和CDS-2mpd。同源重组单交换的效率为3.7×10^－7～6.8×10^－7。通过PCR和Southern杂交的方法验证了同源重组事件。基因工程菌遗传稳定,能同时降解甲基对硫磷和呋喃丹。甲基对硫磷水解酶（MPH）的比活在各生长时期均高于原始出发菌株,比活最高达6.22 mu/μg。     

Construction of shuttle cloning vectors for Bacteroides fragilis and use in assaying foreign tetracycline resistance gene expression

Shuttle vectors capable of replication in both Escherichia coli and Bacteroides fragilis have been developed. Conjugal transfer of these plasmids from E. coli to B. fragilis is facilitated by inclusion of the origin of transfer of the IncP plasmid RK2. The vectors pDK1 and pDK2 provide unique sites for cloning selectable markers in Bacteroides. pOA10 is a cosmid vector containing the replication region of pCP1 necessary for maintenance in Bacteroides. pDK3, pDK4.1, and pDK4.2 contain the Bacteroides clindamycin resistance gene allowing selection and maintenance in B. fragilis of plasmids containing inserted DNA fragments. pDK3 was used to test the expression in B. fragilis of five foreign tetracycline resistance (TcR) genes. The tetA, -B, and -C markers from facultative gram-negative bacteria, as well as a TcR determinant from Clostridium perfringens, did not express TcR in B. fragilis. The tetM gene, originally described in streptococci, encoded a small but reproducible increase of TcR in Bacteroides. These studies demonstrate the utility of shuttle vectors for introducing cloned genes into Bacteroides and underscore the differences in gene expression in these anaerobes.     

Physical and functional mapping of two cointegrate plasmids derived from RP4 and TOL plasmid pDK1

Cointegrate plasmids were formed in vivo between the broad-host-range R-plasmid RP4 and two catabolic plasmids derived from Pseudomonas putida HS1. One of these was the wild-type plasmid pDK1 encoding the complete inducible toluene/xylene (TOL) catabolic pathway and one was pDKT1, a deletion derivative of pDK1 selected after growth of HS1 on benzoate and supporting growth on only toluene. The two plasmids formed, pDK2 and pDKT2 respectively, each consisted of a complete RP4 replicon in which was an insert of the parent plasmid DNA respectively 40 and 20 kbp in size. The detailed restriction maps of the two plasmids were determined and many of the catabolic genes were located by subcloning and enzyme assay of recombinant plasmids in Escherichia coli and Pseudomonas hosts. The insert in pDK2 contained both operons of the catabolic pathway, the 'upper pathway' operon (xylCAB) and the meta pathway operon (xylDLEGF(I,J,K)H), and a region identified as having the function of the regulator gene xylS. The insert in pDKT2 contained only the upper pathway operon and the regulatory region. Within each of the three coding regions there was great similarity with the same regions on TOL plasmids pWW0 and pWW53-4 apparent (a) by the same order of the genes, (b) by a similar pattern of restriction sites and (c) by hybridization studies. However, the order and orientations of the three coding regions differed from those previously described for both pWW0 and pWW53-4. The significance of these findings to the evolution of TOL plasmids is discussed.     

L-asparaginase genes in Escherichia coli: isolation of mutants and characterization of the ansA gene and its protein product

Mutants of Escherichia coli have been isolated which are resistant to beta-aspartyl hydroxamate, a lethal substrate of asparaginase II in fungi and a substrate for asparaginase II in E. coli. Among the many phenotypic classes observed, a single mutant (designated GU16) was found with multiple defects affecting asparaginases I and II and aspartase. Other asparaginase II-deficient mutants have also been derived from an asparaginase I-deficient mutant. The mutant strain, GU16, was unable to utilize asparagine and grew poorly on aspartate as the sole source of carbon; transformation of this strain with an E. coli recombinant plasmid library resulted in a large recombinant plasmid which complemented both these defects. Two subclones were isolated, designated pDK1 and pDK2; the former complemented the partial defect in the utilization of aspartate, although its exact function was not established. pDK2 encoded the asparaginase I gene (ansA), the coding region of which was further defined within a 1.7-kilobase fragment. The ansA gene specified a polypeptide, identified in maxicells, with a molecular weight of 43,000. Strains carrying recombinant plasmids encoding the ansA gene overproduced asparaginase I approximately 130-fold, suggesting that the ansA gene might normally be under negative regulation. Extracts from strains overproducing asparaginase I were electrophoresed, blotted, and probed with asparaginase II-specific antisera; no cross-reaction of the antisera with asparaginase I was observed, indicating that asparaginases I and II are not appreciably related immunologically. When a DNA fragment containing the ansA gene was used to probe Southern blots of restriction endonuclease-digested E. coli chromosomal DNA, no homologous sequences were revealed other than the expected ansA-containing fragments. Therefore, the genes encoding asparaginases I and II are highly sequence related.     

Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1

In contrast to the high accumulation in sequence data for hyperthermophilic archaea, methodology for genetically manipulating these strains is still at an early stage. This study aimed to develop a gene disruption system for the hyperthermophilic euryarchaeon Thermococcus kodakaraensis KOD1. Uracil-auxotrophic mutants with mutations in the orotidine-5'-monophosphate decarboxylase gene (pyrF) were isolated by positive selection using 5-fluoroorotic acid (5-FOA) and used as hosts for further transformation experiments. We then attempted targeted disruption of the trpE locus in the host strain by homologous recombination, as disruption of trpE was expected to result in tryptophan auxotrophy, an easily detectable phenotype. A disruption vector harboring the pyrF marker within trpE was constructed for double-crossover recombination. The host cells were transformed with the exogenous DNA using the CaCl(2) method, and several transformants could be selected based on genetic complementation. Genotypic and phenotypic analyses of a transformant revealed the unique occurrence of targeted disruption, as well as a phenotypic change of auxotrophy from uracil to tryptophan caused by integration of the wild-type pyrF into the host chromosome at trpE. As with the circular plasmid, gene disruption with linear DNA was also possible when the homologous regions were relatively long. Shortening these regions led to predominant recombination between the pyrF marker in the exogenous DNA and the mutated allele on the host chromosome. In contrast, we could not obtain trpE disruptants by insertional inactivation using a vector designed for single-crossover recombination. The gene targeting system developed in this study provides a long-needed tool in the research on hyperthermophilic archaea and will open the way to a systematic, genetic approach for the elucidation of unknown gene function in these organisms.     

Red recombinase assisted gene replacement in Klebsiella pneumoniae

The Red recombinase system, the most convenient genetic tool applied in Escherichia coli and other bacteria, was introduced for gene replacement in Klebsiella pneumoniae. The novel K. pneumoniae gene replacement system comprised the Red and FLP recombinases expression vector pDK6-red and pDK6-flp, and linear DNA fragments which encompassed a selective marker gene with target gene flanking extensions; the latter were PCR amplified using a plasmid DNA template obtained by in vivo recombination in E. coli. In this study, dhak1 gene, encoding a subunit of dihydroxyacetone kinase II, was deleted markerlessly at a transformation ratio of 260 CFU/μg DNA, i.e., 1,000-fold higher than that achieved in the native way. Our studies provide an efficient method with detailed protocol to perform gene replacement in K. pneumoniae and has great potential to be developed as a routine genetic approach for this important industrial microorganism.     

Requirement of duplicated operons for maximal metabolism of phthalate by Rhodococcus sp. strain DK17

The operons encoding the transformation of phthalate to protocatechuate are duplicated and present on two different megaplasmids [pDK2 (330 kb) and pDK3 (750 kb)] in Rhodococcus sp. strain DK17. RT-PCR experiments using gene-specific primers showed that both the pDK2- and the pDK3-encoded dihydroxyphthalate decarboxylase genes are simultaneously expressed during growth on phthalate. The doubling time of the pDK2-cured mutant strain DK176 in minimal liquid medium with 5mM phthalate is 52.5% of that of the wild-type strain DK17. The data indicate that both copies of the phthalate operon are equally functional in DK17, and gene dosage is the main reason for slower growth of DK176 on phthalate.     

Delineation of the viral products of recombination in vaccinia virus-infected cells.

Plasmids containing the vaccinia virus thymidine kinase gene, its flanking DNA sequences, and the Escherichia coli beta-galactosidase gene were used in conjunction with a thymidine kinase-deficient virus to examine the viral products of recombination. Progeny derived from single-crossover events could be distinguished from those generated by gene conversion or double-crossover events when the beta-galactosidase gene was separated from the thymidine kinase gene by the flanking sequences. Using methotrexate to select for recombinant virus and a chromogenic indicator to detect beta-galactosidase, the generation of viral recombinants was measured over a 48-h period. Recombinant progeny were first observed at 12 h and increased to a maximum of 2.5% at 48 h. Single-crossover products, as determined by beta-galactosidase expression, reached a maximum of 57% of the recombinant population at 24 h and thereafter declined. DNA hybridization analysis was used to examine genomic structures of the progeny of the initial viral plaques, plaques purified three times, and those subject to a 10(4)-fold amplification. These analyses confirmed that single-crossover events within either the 5'- or 3'-homologous flanking sequences generated unstable recombinant structures. These structures were shown to contain a single copy of the intact thymidine kinase gene within the corresponding copy of the duplicated thymidine kinase flanking sequences, separated by the beta-galactosidase gene and plasmid DNA. Significantly, these duplicated structures could undergo further recombination to produce repeats of either the intact or the deleted thymidine kinase sequences. These intermediate structures ultimately degenerated to produce either the parental thymidine kinase-deleted or the wild-type genome. The wild-type genome was also shown to be generated directly by gene conversion or double-crossover events.     

A model system for the study of repair of DNA double-strand breaks in Saccharomyces cerevisiae

The efficiency of "LiCl transformation" in Saccharomyces cerevisiae haploid cells by an autonomously replicating pLL12 plasmid carrying yeast LEU2 and LYS2 genes is increased (by an order or more) when the plasmid is linearized by the restriction endonuclease XhoI cleavage of a unique site in LYS2 gene. Transformants were selected on the medium lacking leucine. This phenomenon has been shown to be a result of recombinational repair of double-strand breaks (DSB) of plasmid DNA stimulated by a restriction endonuclease. The kinetic data have shown the process of plasmid DNA DSB repair to consist of two phases. The completion of the first phase occurs during an hour and the second phase occurs in 14-18 hours. DNA double-strand gaps (the deleted sequences of plasmid LYS2 gene in DSB region) with maximal length of 2-2.5 kb are repaired with the same efficiency as DSB. The genetic control of the recombinational repair of plasmid DNA DSB has been studied.