Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host

The application of molecular cloning to antibiotic-producing microorganisms should lead to enhanced antibiotic productivity and to the biosynthesis of novel antibiotics by in vitro interspecific recombination. To allow such approaches, the genes for antibiotic synthesis must be isolated, analysed and perhaps modified. Certain Streptomyces species produce nearly two-thirds of the known natural antibiotics; the recent development of cloning systems in the genus makes it possible to isolate and analyse Streptomyces genes. However, antibiotics are metabolites which require sets of several enzymes for their synthesis and attempts to isolate the corresponding genes have so far yielded clones carrying either individual genes of the set, or only incomplete gene sets. We describe here the isolation of a large continuous segment of Streptomyces coelicolor DNA which apparently carries the complete genetic information required for synthesis of an antibiotic, actinorhodin , from simple primary metabolites. Not only can the cloned DNA 'complement' all available classes of actinorhodin non-producing mutants of S. coelicolor but, on introduction into a different host, Streptomyces parvulus , it directs the synthesis of the antibiotic. The tendency for the genes for antibiotic synthesis to be clustered together on the chromosomes of Streptomyces species and the availability of plasmid vectors which can carry stable inserts of DNA larger than 30 kilobase pairs (kb) and which can be introduced efficiently into Streptomyces protoplasts, suggest that the experiments described have general significance for this area of biotechnology.     

Recovery frequency of phages lambda and M13 from human and animal faeces

Derivatives of bacteriophages lambda and M13 are in common use as vectors in recombinant DNA RESEARCH. These laboratory-derived phages have been designed to allow cloning of DNA fragments, but to be unable to survive outside a defined laboratory and/or host-cell environment. To assess the availability of wild-type lambda or M13 phages in the environment which might potentially rescue debilitated derivative phages, we have now examined the frequency of these and other bacteriophages in human and animal faeces. We detected coliphage in over two-thirds of the faecal samples. Of these, 1.2% of the samples contained lambda-like phage and 3.5% had phage indistinguishable from M13.     

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.     

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.     

Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution

Interactions between bacterial hosts and their viruses (phages) lead to reciprocal genome evolution through a dynamic co-evolutionary process. Phage-mediated transfer of host genes--often located in genome islands--has had a major impact on microbial evolution. Furthermore, phage genomes have clearly been shaped by the acquisition of genes from their hosts. Here we investigate whole-genome expression of a host and phage, the marine cyanobacterium Prochlorococcus MED4 and the T7-like cyanophage P-SSP7, during lytic infection, to gain insight into these co-evolutionary processes. Although most of the phage genome was linearly transcribed over the course of infection, four phage-encoded bacterial metabolism genes formed part of the same expression cluster, even though they are physically separated on the genome. These genes--encoding photosystem II D1 (psbA), high-light inducible protein (hli), transaldolase (talC) and ribonucleotide reductase (nrd)--are transcribed together with phage DNA replication genes and seem to make up a functional unit involved in energy and deoxynucleotide production for phage replication in resource-poor oceans. Also unique to this system was the upregulation of numerous genes in the host during infection. These may be host stress response genes and/or genes induced by the phage. Many of these host genes are located in genome islands and have homologues in cyanophage genomes. We hypothesize that phage have evolved to use upregulated host genes, leading to their stable incorporation into phage genomes and their subsequent transfer back to hosts in genome islands. Thus activation of host genes during infection may be directing the co-evolution of gene content in both host and phage genomes.     

Retrovirus transfer of a bacterial gene into mouse haematopoietic progenitor cells

The haematopoietic system is made up of a hierarchy of cells with different developmental, functional and proliferative capacities. Although cellular diversity appears to arise from the commitment and maturation of stem cells, the molecular basis for this differentiation process is unknown. The introduction of cloned DNA sequences into haematopoietic progenitor cells would provide a novel approach for studying this differentiating in vivo system. One laboratory has reported DNA-mediated transfer of genes into mouse bone marrow cells. However, retroviruses offer a number of advantages over DNA-mediated gene transfer procedures, including high efficiency infection of a wide range of cell types in vitro and in vivo, stable and low copy integration into the host chromosome, and a defined integrated provirus structure. For these reasons recombinant DNA techniques have been utilized to construct high efficiency retrovirus vectors expressing foreign genes. We demonstrate here, using such a retrovirus vector, the transfer of a dominant selectable drug-resistance gene into defined classes of mouse haematopoietic progenitor cells. These observations should facilitate the development of molecular genetic approaches to fundamental and clinical problems in haematopoiesis.     

A novel peptide,selected from phage display library of random peptides,can efficiently target into human breast cancer cell

To develop a targeting vector for breast cancer biotherapy, MDA-MB-231 cell, a human breast cancer cell line, was co-cultured with pC89 （9 aa） phage display library of random peptides. In multiple inde-pendent peptide-presenting phage screening trials, subtilisin was used as a protease to inactivate extra-cellular phages. The internalized phages were collected by cell lysising and amplified in E. coli XLI-Blue. Through five rounds of selection, the pepUde-presenting phages which could be internalized in MDA-MB-231 cells were isolated. A comparison was made between internalization capacities of peptide-presenting phages isolated from MDA-MB-231 cells and RGD-integrin binding phage by coculturing them with other human tumor cell lines and normal cells. The nucleoUde sequences of isolated peptide-presenting phages were then determined by DNA sequencing. To uncover whether phage coat protein or amino acid order was required for the character of the pepUde to MDA-MB-231 cells, three peptides were synthesized. They are CASPSGALRSC, ASPSGALRS and CGVIFDHSVPC （the shifted sequence of CASPSGALRSC）, and after coculturing them with different cell lines, their targeting capacities to MDA-MB-231 cells were detected. These data suggested that the internalization process was highly selective, and capable of capturing a specific peptide from parent peptide variants. Moreover, the targeting internalization event of pepUdes was an amino acid sequence dependent manner. The results demonstrated the feasibility of using phage display library of random peptides to develop new targeting system for intracellular delivery of macromolecules, and the peptide we obtained might be modified as a targeting vector for breast cancer gene therapy.     

噬菌体展示禽流感病毒抗原变异性基因片段文库的构建

构建T7噬菌体展示禽流感病毒抗原变异性基因片段文库. 首先, 从Gene Bank中查找筛选禽流感病毒抗原变异性基因, 将其截短、 修饰、 简并后得到禽流感病毒抗原变异性基因微阵列. 其次, 将合成的禽流感病毒抗原变异性基因片段文库扩增、 酶切, 链接到双酶切后的T7噬菌体载体基因上, 构成重组噬菌体DNA. 最后, 重组噬菌体DNA经体外包装和扩增, 得到T7噬菌体展示文库, 并进行T7噬菌体展示文库滴度、 重组率和免疫活性测定. 实验结果表明, 从Gene Bank中查找、 筛选、 剪切和修饰共获得96 258条序列构建T7噬菌体展示文库, 原始文库滴度为3.6×107个菌落/mL, 重组率大于90%. 用禽流感病毒H5N1抗体进行捕获, 经聚合酶链式反应(PCR)鉴定, 得到理想目的条带, 证明噬菌体表面展示蛋白具有抗原活性, 可用于禽流感病毒感染患者的快速检测及抗原表位筛选.     

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.     

噬菌体展示禽流感病毒抗原变异性基因片段文库的构建

构建T7噬菌体展示禽流感病毒抗原变异性基因片段文库. 首先， 从Gene Bank中查找筛选禽流感病毒抗原变异性基因, 将其截短、 修饰、 简并后得到禽流感病毒抗原变异性基因微阵列. 其次， 将合成的禽流感病毒抗原变异性基因片段文库扩增、 酶切, 链接到双酶切后的T7噬菌体载体基因上, 构成重组噬菌体DNA. 最后， 重组噬菌体DNA经体外包装和扩增, 得到T7噬菌体展示文库, 并进行T7噬菌体展示文库滴度、 重组率和免疫活性测定. 实验结果表明, 从Gene Bank中查找、 筛选、 剪切和修饰共获得96 258条序列构建T7噬菌体展示文库, 原始文库滴度为3.6×107个菌落/mL, 重组率大于90%. 用禽流感病毒H5N1抗体进行捕获, 经聚合酶链式反应(PCR)鉴定, 得到理想目的条带, 证明噬菌体表面展示蛋白具有抗原活性, 可用于禽流感病毒感染患者的快速检测及抗原表位筛选.     

不同荧光蛋白基因标记利迪链霉菌

 利迪链霉菌（Streptomyces lydicus）A01 是一株分离自北京郊区对植物病原真菌具有广谱抑制作用的放线菌,在植物真菌病害防治中具有良好的应用前景。为了检测红霉素启动子在利迪链霉菌A01 中的活性,为后期对菌株A01 进行遗传改造提供技术支持,同时对生防菌A01 进行遗传标记以研究和阐明其在生态环境中的生物学行为规律,本实验采用两亲本接合的方法,将增强绿色荧光蛋白（EGFP）和红色荧光蛋白（RFP）基因片段克隆到携带红霉素启动子（ermE^*）的链霉菌表达载体pIB139 中,成功构建了以egfp 和rfp 为报告基因的重组载体pIB139-EGFP 和pIB139-RFP,并转化利迪链霉菌A01,突变株在荧光显微镜下观察到较强的绿色荧光和红色荧光,同时PCR 鉴定结果正确。这表明重组载体pIB139-EGFP 和pIB139-RFP 成功转入菌株A01,并且ermE^*启动子成功启动egfp 和rfp 基因表达。     

Phage antibodies: filamentous phage displaying antibody variable domains

New ways of making antibodies have recently been demonstrated using gene technology. Immunoglobulin variable (V) genes are amplified from hybridomas or B cells using the polymerase chain reaction, and cloned into expression vectors. Soluble antibody fragments secreted from bacteria are then screened for binding activities. Screening of V genes would, however, be revolutionized if they could be expressed on the surface of bacteriophage. Phage carrying V genes that encode binding activities could then be selected directly with antigen. Here we show that complete antibody V domains can be displayed on the surface of fd bacteriophage, that the phage bind specifically to antigen and that rare phage (one in a million) can be isolated after affinity chromatography.     

Photosynthesis genes in marine viruses yield proteins during host infection

Cyanobacteria, and the viruses (phages) that infect them, are significant contributors to the oceanic 'gene pool'. This pool is dynamic, and the transfer of genetic material between hosts and their phages probably influences the genetic and functional diversity of both. For example, photosynthesis genes of cyanobacterial origin have been found in phages that infect Prochlorococcus and Synechococcus, the numerically dominant phototrophs in ocean ecosystems. These genes include psbA, which encodes the photosystem II core reaction centre protein D1, and high-light-inducible (hli) genes. Here we show that phage psbA and hli genes are expressed during infection of Prochlorococcus and are co-transcribed with essential phage capsid genes, and that the amount of phage D1 protein increases steadily over the infective period. We also show that the expression of host photosynthesis genes declines over the course of infection and that replication of the phage genome is a function of photosynthesis. We thus propose that the phage genes are functional in photosynthesis and that they may be increasing phage fitness by supplementing the host production of these proteins.     

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.     

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。     

The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage

Toxic shock syndrome (TSS) is a complex of generalized symptoms caused by a local staphylococcal infection, and a circulating toxin is thought to be involved. Indeed, nearly 100% of TSS isolates produce an exoprotein, TSSE, that is thought to have an aetiological role on the basis of positive animal tests (refs 1,2 and F. Quimby, personal communication) and human serological data. Although the precise role of TSSE in TSS remains unclear (E. Kass, personal communication), no other staphylococcal factor has been implicated. Our preliminary studies of the genetics of TSSE production failed to demonstrate plasmid or phage involvement or linkage with known chromosomal genes (ref. 4 and B.N.K. et al., unpublished data); however, Schutzer et al. have found that most TSS strains harbour prophages with common plating characteristics and suggest that the toxin(s) involved in TSS are transmitted by lysogenic conversion. We show here that TSSE is not demonstrably transferred by lysogeny; moreover, we have cloned the gene and found that the cloned product is serologically and biologically indistinguishable from the native protein, and that the TSSE determinant is associated with a larger DNA segment that is absent or rearranged in TSSE- strains.     

Capsid modification of adeno-associated virus and tumor targeting gene therapy

Targeting is critical for successful tumor gene therapy. The adeno-associated virus （AAV） has aroused wide concern due to its excellent advantages over other viral vectors in gene therapy. AAV has a broad infection spectrum, which also results in poor specificity towards tissues or cells and low transduction efficiency. Therefore, it is imperative to improve target and transduction efficiency in AAV-mediated gene therapy. Up to now, researchers have developed many strategies to modify AAV capsids for im- proving targeting or retargeting only desired cells. These strategies include not only traditional chemical modification, phage display technology, modification of AAV capsid genome, chimeric vectors and so on, but also many novel strategies involved in marker rescue strategy, direct evolution of capsid proteins, direct display random peptides on AAV capsid, AAVP （AAV-Phage）, and etc. This review will summarize the advances of researches on the capsid modification of AAV to target malignant cells.     

宿主细胞DNA损伤反应与重组腺相关病毒载体基因表达

文中主要讨论细胞DNA修复机制与重组腺相关病毒(recombinant adeno-associated virus,rAAV)载体的相互关系,探讨通过调节宿主细胞DNA修复机制,提高rAAV载体表达及基因打靶效率的方法,进而提高rAAV载体基因表达的可能性.     

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.