Cloning and Expression of Antibiotic Production Genes

In silico tools for the analysis of antibiotic biosynthetic pathways

Natural products of bacteria and fungi are the most important source for antimicrobial drug leads. For decades, such compounds were exclusively found by chemical/bioactivity-guided screening approaches. The rapid progress in sequencing technologies only recently allowed the development of novel screening methods based on the genome sequences of potential producing organisms. The basic principle of such genome mining approaches is to identify genes, which are involved in the biosynthesis of such molecules, and to predict the products of the identified pathways. Thus, bioinformatics methods and tools are crucial for genome mining. In this review, a comprehensive overview is given on programs and databases for the identification and analysis of antibiotic biosynthesis gene clusters in genomic data.

Genetic improvement of processes yielding microbial products

Although microorganisms are extremely good in presenting us with an amazing array of valuable products, they usually produce them only in amounts that they need for their own benefit; thus, they tend not to overproduce their metabolites. In strain improvement programs, a strain producing a high titer is usually the desired goal. Genetics has had a long history of contributing to the production of microbial products. The tremendous increases in fermentation productivity and the resulting decreases in costs have come about mainly by mutagenesis and screening/selection for higher producing microbial strains and the application of recombinant DNA technology.

Development of recombinant Streptomyces for biotechnological and environmental uses

Recombinant DNA techniques for manipulation of genes in Streptomyces are well developed, and currently there is a high level of activity among researchers interested in applying molecular cloning and protoplast fusion techniques to strain development within this commercially important group of bacteria. A number of efficient plasmid and phage vector systems are being used for the molecular cloning of genes, primarily those encoding antibiotic biosynthesis enzymes, but also for a variety of other bioactive proteins and enzymes of known or potential commercial value. In addition, cloning aimed at constructing specialized bioconversion strains for use in the production of chemicals from organic carbon substrates is underway in numerous laboratories. This review discusses the current status of research involving recombinant DNA technologies applied to biotechnological applications using Streptomyces. The topic of potential environmental uses of recombinant Streptomyces is also reviewed, as is the status of current research aimed at assessing the fate and effects of recombinant Streptomyces in the environment. Also summarized is recent research that has confirmed that genetic exchange occurs readily among Streptomyces in the soil environment and which has shown the potential for exchange between recombinant Streptomyces and native soil bacteria.

Achievements in microbial technology

In 1973, recombinant DNA technology was born and the age of the "new biotechnology" came upon us. Today we are seeing the amazing results of recombinant DNA technology, hybridoma technology, enzyme engineering and protein engineering. These techniques are exerting major effects on basic research and on health care, diagnostics and agriculture and soon will bring about changes in other industries such as petroleum, mining, foods and chemicals. Entire pathways of primary and secondary metabolism have been cloned and expressed in foreign microorganisms. The development of recombinant DNA technology is having its major impact on the production of rare polypeptides such as mammalian enzymes, hormones, antibodies and biological response modifiers. In addition to natural polypeptides, analogs are being produced by recombinant DNA technology and this has added an extra dimension of excitement to the field. The future is thus insured for the expanded use of microorganisms in the biotechnological world and the continued improvement in microbial processes to reduce the cost of drugs, enzymes and specialty chemicals.

Exploiting the genetic potential of polyketide producing streptomycetes

Streptomycetes are the most important bacterial producers of bioactive secondary metabolites such as antibiotics or cytostatics. Due to the emerging resistance of pathogenic bacteria to all commonly used antibiotics, new and modified natural compounds are required for the development of novel drugs. In addition to the classical screening for natural compounds, genome driven approaches like combinatorial biosynthesis are permanently gaining relevance for the generation of new structures. This technology utilizes the combination of genes from different biosynthesis pathways resulting in the production of novel or modified metabolites. The basis for this strategy is the access to a significant number of genes and the knowledge about the activity and specificity of the enzymes encoded by them. A joint initiative was started to exploit the biosynthesis gene clusters from streptomycetes. In this publication, an overview of the strategy for the identification and characterization of numerous biosynthesis gene clusters for polyketides displaying interesting functions and particular structural features is given.

Analysis of the promoter region of saf, a Streptomyces griseus gene that increases production of extracellular enzymes

The product of the saf gene of Streptomyces griseus ATCC10137 mediated an increase in the production of several extracellular enzymes and retarded the formation of pigments and spores in Streptomyces [Daza et al., Mol. Gen. Genet. 222 (1990) 384-392]. A promoter upstream from saf was identified by subcloning a DNA fragment in the promoter probe pIJ486. Using the Escherichia coli-Brevibacterium lactofermentum promoter-probe shuttle vector, pULMJ51, we determined that the saf promoter region is also active in E. coli. The transcription start points (tsp) of the saf promoter in Streptomyces and E. coli have been determined using high-resolution S1 mapping. The tsp are at the same position in both microorganisms. Expression from the saf promoter region was negatively regulated by phosphate in Streptomyces, but not in E. coli. The amplification of the saf promoter lacking the saf coding region did not increase the production of extracellular enzymes and did not reduce sporulation or pigmentation in Streptomyces (i.e., it does not titrate out a putative repressor of the genes encoding extracellular enzymes). Several structural features of the saf promoter region and saf mRNA are studied in relation to the regulation of the saf gene expression.

Comparison of secretory expression in Escherichia coli and Streptomyces of Streptomyces subtilisin inhibitor (SSI) gene

To elucidate differences in the mechanism of gene expression between Streptomyces and Escherichia coli, the regulatory region for expression of the gene for a proteinaceous proteinase inhibitor, Streptomyces subtilisin inhibitor (SSI), was altered to express efficiently in E. coli. This was carried out by inserting a pre-SSI-encoding region downstream of the tac promoter and ribosome-binding site in a multi-copy plasmid. When the resultant plasmid pMKSI161-9 was introduced into E. coli JM105, SSI protein was found to be expressed and secreted into the periplasmic space by Western blot analysis. When introduced into 'leaky' E. coli strains, this protein was detected in the medium as well as in the periplasmic space in bacteria. NH2-terminal sequencing analysis of the SSI purified from E. coli JM105 indicated two processing sites, Ala(-4)/Ala(-3)-Pro(-2)-Gly and Ala(-4)-Ala-3/Pro(-2)-Gly-1, of pre-SII. These sites were different from those in Streptomyces albogriseolus S-3253 and Streptomyces lividans 66. The inhibitor activity of the processed protein toward subtilisin BPN' was almost the same as that of authentic SSI.

Cloning and characterization of a phosphate-regulated promoter involved in phosphate control of candicidin biosynthesis

Phosphate strongly repressed the formation of p-aminobenzoic acid (PABA) synthase, an enzyme involved in candicidin biosynthesis. Expression in Streptomyces lividans of the pabS gene (encoding PABA synthase) of Streptomyces griseus is repressed by phosphate at concentrations above 0.1 mM. However, expression of the pabS gene in Escherichia coli is not regulated by phosphate. Phosphate control of the expression of the pabS gene was observed in all plasmids containing the original 4.5-kb BamHI fragment, whereas no phosphate regulation was found when an upstream 1-kb fragment that carries the pabS promoter was deleted. Using the promoter-probe plasmid pIJ424, a '114-bp' promoter was cloned. Expression of the promoterless kanamycin phosphotransferase gene when fused to the '114-bp' promoter was strongly reduced by phosphate (90% at 5 mM concentration). The '114-bp' promoter has been sequenced and the first transcribed nucleotide identified by S1 mapping. The '114-bp' fragment is A + T-rich (54%), as compared to the Streptomyces genome (70-73% GC). The presence of a phosphate control sequence (pcs) in the upstream region of the pabS gene is proposed.