Production of 'hybrid' antibiotics by genetic engineering

The recent development of molecular cloning systems in Streptomyces has made possible the isolation of biosynthetic genes for some of the many antibiotics produced by members of this important genus of bacteria. Such clones can now be used to test the idea that novel antibiotics could arise through the transfer of biosynthetic genes between streptomycetes producing different antibiotics. The likelihood of a 'hybrid' compound being produced must depend on the substrate specificities of the biosynthetic enzymes, about which little is known. In attempts to demonstrate hybrid antibiotic production, we therefore began with strains producing different members of the same chemical class of compounds in order to maximize the chance of success. Here we report the production of novel compounds by gene transfer between strains producing the isochromanequinone antibiotics actinorhodin, granaticin and medermycin. These experiments were made possible by the recent cloning of the whole set of genes for the biosynthetic pathway of actinorhodin from Streptomyces coelicolor A3(2) (ref. 8). We believe that this represents the first report of the production of hybrid antibiotics by genetic engineering.     

Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes

A number of examples of circular plasmids with specific functions are known in both prokaryotes and eukaryotes. Several linear plasmids have also been identified, but these are all relatively small: large linear plasmids cannot be separated from chromosomal DNA by conventional techniques. There are several cases where the genetic evidence suggests that a character is encoded by a plasmid but no plasmid can be physically detected. This has been the case for antibiotic synthesis genes in Streptomyces; in particular a plasmid SCP1 in Streptomyces coelicolor has been shown to be involved in methylenomycin production by genetic evidence. We report here the application of orthogonal-field-alternation gel electrophoresis to the isolation of linear plasmids from Streptomyces. We have discovered a large linear plasmid of around 520 kilobases in Streptomyces lasaliensis and subsequently similar giant linear plasmids in other Streptomyces strains. We have confirmed that genes for methylenomycin biosynthesis are located on a series of giant linear plasmids in S. coelicolor. These observations may bear on the genetic variability and unstable genetic character of Streptomyces species.     

DNA cloning in Streptomyces: a bifunctional replicon comprising pBR322 inserted into a Streptomyces phage

The Gram-positive, mycelial, differentiating streptomycetes are responsible for the production of many important antibiotics. The availability of gene cloning systems in this microbial group would have many industrial applications besides allowing more penetrating study of the genetics of Streptomyces coelicolor A3(2) (which, as the best understood streptomycete genetically, serves as a model for much other Streptomyces genetics). Recent successes (see previous paper) in introducing Streptomyces DNA into S. coelicolor and Streptomyces lividans on plasmid vectors would be nicely complemented by the availability of Streptomyces bacteriophage vectors (discussed in ref. 5): for example, many phages have wide and easily defined host ranges; heat-inducible prophages might be used to give high copy number of cloned DNA; efficient phage promoters might be used to increase gene expression; there may be differential stabilities for particular DNA sequences cloned in plasmids vis-à-vis phages; selective insertion of DNA, utilizing packaging constraints, may be possible with phages; and in situ hybridization of radioactive probes to DNA in plaques is likely to be simple. We describe here the use of the moderately wide host range temperate phage, phi C31, for this purpose.     

A pair of two－component regulatory genes ecrA1／A2 in S. coelicolor

Two-component genes are kinds of genetic elements involved in regulation of antibiotic production in Streptomyces coelicolor. DNA microarray analysis revealed that ecrA1/A2, which mapped at distant sites from red locus and encode respectively the kinase and regulator, expressed coordinately with genes of Red specific biosynthetic pathway, ecrA1 and ecrA2 gene-disruptive mutants were constructed using homogenotisation by reciprocal double crossover. Fermentation data showed that the undecylprodigiosin (Red) level of production was lower than that of wild-type strain. However, the change of the actinorhodin (Act) production level was not significant compared with wild type. Thus, these experiment results confirmed that the two-component system ecrA 1/A2 was positive regulatory element for red gene cluster.     

DNA cloning in Streptomyces: resistance genes from antibiotic-producing species

The biochemical and morphological differentiation of actinomycetes makes them academically and economically interesting. Their secondary metabolites provide the majority of medically and agriculturally important antibiotics (streptomycete genes may also be the primary source of clinically important antibiotic resistance); their complex morphological developmental cycle involves a series of changes from vegetative mycelial growth to spore formation. Recombinant DNA technology would add a powerful new dimension to the analysis of these various aspects of actinomycete biology and would also facilitate the development of industrial strains with increased antibiotic yield, or capable of making new antibiotics. For most of these purposes, cloning of genes within and between actinomycetes is required to study the expression of particular genes in genetic backgrounds defined by mutations of the characters under study. To achieve this, we have now developed a method for molecular cloning involving the transfer of genes between unrelated streptomycetes.     

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous bacteria responsible for producing most natural antibiotics used in human and veterinary medicine. Here we report the 8,667,507 base pair linear chromosome of this organism, containing the largest number of genes so far discovered in a bacterium. The 7,825 predicted genes include more than 20 clusters coding for known or predicted secondary metabolites. The genome contains an unprecedented proportion of regulatory genes, predominantly those likely to be involved in responses to external stimuli and stresses, and many duplicated gene sets that may represent 'tissue-specific' isoforms operating in different phases of colonial development, a unique situation for a bacterium. An ancient synteny was revealed between the central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering.     

Molecular regulation of development and differentiation inStreptomyces

Development and differentiation is an important and leading research field in modem biology. Streptomyces has a complicated life cycle of morphological differentiation including the spore germination, aerial mycelium and spore formation. Each developmental stage has a distinguished morphological feature which greatly facilitates the identification of developmental mutants, the complementary cloning and the spatial and temporal expression of the genes involved in differentiation. This characteristic of Streptomyces  is comparatively superior to other prokaryotic bacteria such as Escherichia coli, Bacillus subtilis and Myxococcus xanthus. Moreover, Streptomyces  also possesses a complicated physiological differentiation in which it produces a wide variety of secondary metabolites (more than half of the 12 000 or so known antibiotics), including many important antibiotics used in medicine, agriculture and industry. Studies on the molecular mechanism of antibiotic biosynthesis will be helpful in improving the antibiotic producer and developing some new medicines. In comparison with eukaryotic microorganism such as Asperillus nidulans,the structure of genetic material in Streptomyces  is simple,and it is linear and conkaryotes such as Streptomyces  cerevisiae. The large number of genes are the molecular basis of Streptomyces  differentiation,suggesting that the regulation mechanism of gene expression in differentiation and development may be complex^[1]     

RNA polymerase heterogeneity in Streptomyces coelicolor

Two forms of RNA polymerase holoenzyme have been identified in the filamentous differentiating bacterium Streptomyces coelicolor. They contain different species of sigma factor and are distinguishable by their ability to recognize different promoter classes. These and other holoenzyme forms may in part determine the selective expression of different gene sets in this morphologically-complex bacterium.     

Homology between Streptomyces genes coding for synthesis of different polyketides used to clone antibiotic biosynthetic genes

Many important antibiotics such as tetracyclines, erythromycin, adriamycin, monensin, rifamycin and avermectins are polyketides. In their biosynthesis, multifunctional synthases catalyse iterated condensation of thio-esters derived from acetate, propionate or butyrate to yield aliphatic chains of varying length and carrying different alkyl substituents. Subsequent modifications, including aromatic or macrolide ring closure or specific methylations or glycosylations, generate further chemical diversity. It has been suggested that, if different polyketide synthases had a common evolutionary origin, cloned DNA coding for one synthase might be used as a hybridization probe for the isolation of others. We show here that this is indeed possible. Study of a range of such synthase genes and their products should help to elucidate what determines the choice and order of condensation of different residues in polyketide assembly, and might yield, by in vitro recombination or mutagenesis, synthase genes capable of producing novel antibiotics. Moreover, because genes for entire antibiotic pathways are usually clustered in Streptomyces, cloned polyketide synthase genes are valuable in giving access to groups of linked biosynthetic genes.     

Gene expression in Pseudomonas aeruginosa biofilms.

Bacteria often adopt a sessile biofilm lifestyle that is resistant to antimicrobial treatment. Opportunistic pathogenic bacteria like Pseudomonas aeruginosa can develop persistent infections. To gain insights into the differences between free-living P. aeruginosa cells and those in biofilms, and into the mechanisms underlying the resistance of biofilms to antibiotics, we used DNA microarrays. Here we show that, despite the striking differences in lifestyles, only about 1% of genes showed differential expression in the two growth modes; about 0.5% of genes were activated and about 0.5% were repressed in biofilms. Some of the regulated genes are known to affect antibiotic sensitivity of free-living P. aeruginosa. Exposure of biofilms to high levels of the antibiotic tobramycin caused differential expression of 20 genes. We propose that this response is critical for the development of biofilm resistance to tobramycin. Our results show that gene expression in biofilm cells is similar to that in free-living cells but there are a small number of significant differences. Our identification of biofilm-regulated genes points to mechanisms of biofilm resistance to antibiotics.     

SOS response promotes horizontal dissemination of antibiotic resistance genes

Mobile genetic elements have a crucial role in spreading antibiotic resistance genes among bacterial populations. Environmental and genetic factors that regulate conjugative transfer of antibiotic resistance genes in bacterial populations are largely unknown. Integrating conjugative elements (ICEs) are a diverse group of mobile elements that are transferred by means of cell-cell contact and integrate into the chromosome of the new host. SXT is a approximately 100-kilobase ICE derived from Vibrio cholerae that encodes genes that confer resistance to chloramphenicol, sulphamethoxazole, trimethoprim and streptomycin. SXT-related elements were not detected in V. cholerae before 1993 but are now present in almost all clinical V. cholerae isolates from Asia. ICEs related to SXT are also present in several other bacterial species and encode a variety of antibiotic and heavy metal resistance genes. Here we show that SetR, an SXT encoded repressor, represses the expression of activators of SXT transfer. The 'SOS response' to DNA damage alleviates this repression, increasing the expression of genes necessary for SXT transfer and hence the frequency of transfer. SOS is induced by a variety of environmental factors and antibiotics, for example ciprofloxacin, and we show that ciprofloxacin induces SXT transfer as well. Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes.     

利迪链霉菌A02细菌人工染色体基因组文库的构建

 利迪链霉菌A02是从京郊森林土壤中分离筛选出的植物真菌病害高效生防菌,其活性产物为安全高效广谱的抗真菌剂纳他霉素。为了克隆纳他霉素生物合成基因簇和调控其表达相关的功能基因,通过基因改良的方式进行A02的定向分子改造,提高纳他霉素的效价和产量,提取了利迪链霉菌A02的基因组DNA,用Hind III和Bam HI部分酶解后,回收了97~194kb和48.5~97kb大小的高分子量DNA,与质粒载体Copycontrol pCC1BAC连接,分别构建了含有800个和1500个克隆的两个BAC文库。从文库中随机挑选20个克隆,酶切检测平均插入片段分别为133kb和65kb,空载率小于1%,假定利迪链霉菌的基因组有8×10⁶kb,计算文库基因组覆盖率分别为12.28倍和11.25倍。因此,从文库筛选到目的片段的概率达99.99%以上。     

广西北部湾海域表层海水细菌多样性及其潜在生物合成基因研究

本研究选取广西北部湾3处近海海域,以其表层海水作为研究对象进行细菌多样性分析,旨在挖掘潜在抗生素生物合成的菌株.选用传统稀释涂布法和基于16S rRNA基因序列的系统发育树分析海水中可培养细菌多样性,并对其基因组DNA进行抗生素生物合成基因聚酮合酶(PKS)基因、非核糖体肽合成酶(NRPS)基因及卤化酶(Halo)基因...     

基于转座子策略提高链霉菌中landomycin E产量的研究

【目的】对影响放线菌链霉菌Streptomyces globisporus产landomycin E(laE)的代谢网络进行研究,以提高次生代谢物的产量。【方法】通过构建含强启动子和抗性标记的转座子Tn7为基础的转座子,整合至S.globisporus的染色体产生突变库,筛选高产量的突变株并对其代谢网络进行研究分析。【结果】利用构建好的Tn7-转座子连续转化链霉菌S.globisporus,经过数轮的突变和筛选,得到6株产量有较大改变的突变株,对整合位点的亚克隆和测序结果表明,该位点整合导致编码类似细菌的某些调节因子如TetR和GntR家族的蛋白的基因失活。【结论】所构建的经过修饰的微型Tn7-转座子不仅带有抗性标记且有启动子,可插入链霉菌染色体产生突变,进而提高次生代谢物laE的产量,同时也证明,转座子基载体可应用于非模式菌链霉菌。     

Role of RNA transcripts in replication incompatibility and copy number control in antibiotic resistance plasmid derivatives

The genes required for autonomous replication and incompatibility in the antibiotic resistance plasmids R100 and R1 have been located within a 2.5-kilobase region of the 90-kilobase genome, within which the incompatibility gene occupies a 1.3-kilobase region excluding the replication origin. We now report that three RNA species are synthesized in vitro from the 2.5-kilobase region, which R100 and R1 have in common. One, a long RNA molecule which is transcribed in the direction of DNA replication, probably acts as a messenger or a protein required for plasmid replication. The second RNA species, only 91 nucleotides long, is transcribed in the opposite direction, from a region of the DNA entirely contained within the first and known to specify incompatibility and copy control functions. The third RNA species, 150 bases long, is transcribed from a region including the replication origin; it may be a primer of DNA synthesis or, in conjunction with the second of the three RNA species, an influence in the control of replication.     

An unusually large multifunctional polypeptide in the erythromycin-producing polyketide synthase of Saccharopolyspora erythraea

Erythromycin A, a clinically important polyketide antibiotic, is produced by the Gram-positive bacterium Saccharopolyspora erythraea. In an arrangement that seems to be generally true of antibiotic biosynthetic genes in Streptomyces and related bacteria like S. erythraea, the ery genes encoding the biosynthetic pathway to erythromycin are clustered around the gene (ermE) that confers self-resistance on S. erythraea. The aglycone core of erythromycin A is derived from one propionyl-CoA and six methylmalonyl-CoA units, which are incorporated head-to-tail into the growing polyketide chain, in a process similar to that of fatty-acid biosynthesis, to generate a macrolide intermediate, 6-deoxyerythronolide B. 6-Deoxyerythronolide B is converted into erythromycin A through the action of specific hydroxylases, glycosyltransferases and a methyltransferase. We report here the analysis of about 10 kilobases of DNA from S. erythraea, cloned by chromosome 'walking' outwards from the erythromycin-resistance determinant ermE, and previously shown to be essential for erythromycin biosynthesis. Partial sequencing of this region indicates that it encodes the synthase. Our results confirm this, and reveal a novel organization of the erythromycin-producing polyketide synthase, which provides further insight into the mechanism of chain assembly.     

Tertiary structural similarity between a class A beta-lactamase and a penicillin-sensitive D-alanyl carboxypeptidase-transpeptidase

beta-Lactam antibiotics--the penicillins, cephalosporins and related compounds--act by inhibiting enzymes that catalyse the final stages of the synthesis of bacterial cell walls. Recent crystallographic studies of representative enzymes are beginning to reveal the structural bases of antibiotic specificity and mechanism of action, while intensive efforts are being made to understand the beta-lactamase enzymes that are largely responsible for bacterial resistance to these antibiotics. It has been suggested that the beta-lactamases and beta-lactam target enzymes may be evolutionarily related and some similarity of amino-acid sequence around a common active-site serine residue supports this idea. We present here the first evidence from a comparison of three-dimensional structures in support of this hypothesis: the structure of beta-lactamase I from Bacillus cereus is similar to that of the penicillin-sensitive D-alanyl-D-alanine carboxypeptidase-transpeptidase from Streptomyces R61.     

铜绿假单胞菌鞭毛运动相关基因的研究

建立优化的转化条件,将M u转座复合物电转化到临床分离的一株铜绿假单胞菌(P seud om onasaerug inosa)PA 68中,最高转化效率达3.66×104CFU/μg DNA.通过表型筛选,得到三株鞭毛运动能力缺陷的突变子,Sourn thern杂交证实转座子为单点插入.经基因克隆、核苷酸测序研究,证明转座子分别插入到uvrD、phzF 1、zw f三个基因中,这是首次在国际上将M u转座重组技术应用到鞭毛运动相关基因的研究中.由于人工M u转座技术具有随机单点插入的优点,克服了传统转座子能在染色体上迁移的缺点,为进一步研究P.aerug inosa的鞭毛运动机理及致病性奠定基础.     

植物基因分离的方法

总结了目前植物基因分离的方法．概括出四大类植物基因分离的方法，即序列克隆法，功能克隆法。作图克隆法。表型差异克隆法，并对其特点和适用范围进行了评述。     

复数小波变换在天蓝色链霉菌凝胶图像压缩中的应用

小波变换等多分辨分析方法能够处理图像配准中图像的全局和局部变形，小波变换在配准的同时还可以进行图像压缩，作为新近发展起来的多分辨分析方法，复数小波变换提供了移动不变性和方向选择性滤波器，在压缩比为40：1时，复数小波变换所实现的天蓝色链霉菌蛋白组凝胶图像压缩结果与离散小波变换结果十分接近。