Metabolic engineering--a genetic toolbox for small molecule organic synthesis

The antitumor antibiotic rebeccamycin-challenges and advanced approaches in production processes

Rebeccamycin is an antibiotic and antitumor substance isolated from the filamentous bacterium Lentzea aerocolonigenes. After its discovery, investigations of rebeccamycin focused on elucidating its structure, biological activity, and biosynthetic pathway. For potential medical application, a sufficient drug supply has to be ensured, meaning that the production process of rebeccamycin plays a major role. In addition to the natural production of rebeccamycin in L. aerocolonigenes, where the complex cell morphology is an important factor for a sufficient production, rebeccamycin can also be heterologously produced or chemically synthesized. Each of these production processes has its own challenges, and first approaches to production often lead to low final product concentrations, which is why process optimizations are performed. This review provides an overview of the production of rebeccamycin and the different approaches used for rebeccamycin formation including process optimizations.

Staurosporine Derivatives Generated by Pathway Engineering in a Heterologous Host and Their Cytotoxic Selectivity

Two new staurosporine derivatives, staurosporines M1 and M2 (4 and 5), in addition to five previously reported metabolites (1-3, 6, and 7), were generated by the heterologous expression of engineered spc gene clusters in Streptomyces coelicolor M1146. The structures of these derivatives were determined by a combination of spectroscopic methods and CD measurement. Compounds 1, 2, 4, and 5 showed effective activities against three tumor cell lines (HCT-116, K562, and Huh 7.5), and 3 was active against HCT-116 and K562 cells. In addition, compounds 3 and 5 showed undetectable toxicity up to 100 μM toward the normal hepatic cell line LO₂. Based on the IC₅₀ values, their structure and activity relationships are discussed.

Prediction of compounds' biological function (metabolic pathways) based on functional group composition

Efficient in silico screening approaches may provide valuable hints on biological functions of the compound-candidates, which could help to screen functional compounds either in basic researches on metabolic pathways or drug discovery. Here, we introduce a machine learning method (Nearest Neighbor Algorithm) based on functional group composition of compounds to the analysis of metabolic pathways. This method can quickly map small chemical molecules to the metabolic pathway that they likely belong to. A set of 2,764 compounds from 11 major classes of metabolic pathways were selected for study. The overall prediction rate reached 73.3%, indicating that functional group composition of compounds was really related to their biological metabolic functions.

Total synthesis approaches to natural product derivatives based on the combination of chemical synthesis and metabolic engineering

Secondary metabolites are an extremely diverse and important group of natural products with industrial and biomedical implications. Advances in metabolic engineering of both native and heterologous secondary metabolite producing organisms have allowed the directed synthesis of desired novel products by exploiting their biosynthetic potentials. Metabolic engineering utilises knowledge of cellular metabolism to alter biosynthetic pathways. An important technique that combines chemical synthesis with metabolic engineering is mutasynthesis (mutational biosynthesis; MBS), which advanced from precursor-directed biosynthesis (PDB). Both techniques are based on the cellular uptake of modified biosynthetic intermediates and their incorporation into complex secondary metabolites. Mutasynthesis utilises genetically engineered organisms in conjunction with feeding of chemically modified intermediates. From a synthetic chemist's point of view the concept of mutasynthesis is highly attractive, as the method combines chemical expertise with Nature's synthetic machinery and thus can be exploited to rapidly create small libraries of secondary metabolites. However, in each case, the method has to be critically compared with semi- and total synthesis in terms of practicability and efficiency. Recent developments in metabolic engineering promise to further broaden the scope of outsourcing chemically demanding steps to biological systems.

Advances in cloning, functional analysis and heterologous expression of fungal polyketide synthase genes

Fungal polyketides comprise a diverse group of secondary metabolites that play an important role for drug discovery, as pigments, and as mycotoxins. Their biosynthesis is governed by multidomain enzymes, so-called fungal type I polyketide synthases (PKS). Investigating the molecular basis of polyketide biosynthesis in fungi is of great importance for ecological and pharmacological reasons. In addition, cloning, functional analysis and expression of fungal PKS genes also set the basis for engineering the yet largely untapped biosynthetic potential.

Microbial Isoprenoid Production: An Example of Green Chemistry through Metabolic Engineering

Saving energy, cost efficiency, producing less waste, improving the biodegradability of products, potential for producing novel and complex molecules with improved properties, and reducing the dependency on fossil fuels as raw materials are the main advantages of using biotechnological processes to produce chemicals. Such processes are often referred to as green chemistry or white biotechnology. Metabolic engineering, which permits the rational design of cell factories using directed genetic modifications, is an indispensable strategy for expanding green chemistry. In this chapter, the benefits of using metabolic engineering approaches for the development of green chemistry are illustrated by the recent advances in microbial production of isoprenoids, a diverse and important group of natural compounds with numerous existing and potential commercial applications. Accumulated knowledge on the metabolic pathways leading to the synthesis of the principal precursors of isoprenoids is reviewed, and recent investigations into isoprenoid production using engineered cell factories are described.

Combinatorial biosynthesis of antitumor indolocarbazole compounds

Rebeccamycin and staurosporine are natural products with antitumor properties, which belong to the family of indolocarbazole alkaloids. An intense effort currently exists for the generation of indolocarbazole derivatives for the treatment of several diseases, including cancer and neurodegenerative disorders. Here, we report a biological process based on combinatorial biosynthesis for the production of indolocarbazole compounds (or their precursors) in engineered microorganisms as a complementary approach to chemical synthesis. We have dissected and reconstituted the entire biosynthetic pathway for rebeccamycin in a convenient actinomycete host, Streptomyces albus. This task was achieved by coexpressing different combinations of genes isolated from the rebeccamycin-producing microorganism. Also, a gene (staC) was identified in staurosporine-producing microbes and was shown to have a key role to differentiate the biosynthetic pathways for the two indolocarbazoles. Last, incorporation of the pyrH and thal genes, encoding halogenases from different microorganisms, resulted in production of derivatives with chlorine atoms at novel positions. We produced >30 different compounds by using the recombinant strains generated in this work.

Large-scale synthesis of globotriose derivatives through recombinant E. coli

The carbohydrate chains decorating cell membranes and secreted proteins participate in a range of important biological processes. However, their ultimate significance and possible therapeutic potential have not been fully explored due to the lack of economical methods for their production. This study is an example of the use of a genetically engineered bacterial strain in the preparation of diverse oligosaccharides. Based on an ex vivo biosynthetic pathway, an artificial gene cluster was constructed by linking the genes of five associated enzymes on a plasmid vector. This plasmid was inserted into the E. coli NM522 strain to form globotriose-producing cells ('superbug' pLDR20-CKTUF). The specific strain was conveniently applied to the synthesis of globotriose trisaccharide and its derivatives, as potential neutralizers for Shiga toxin. This work demonstrates a novel and economical method for generating ligand diversity for carbohydrate drug development.

Comment: 2004’s fastest organic and biomolecular chemistry!

In January 2003, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC)--a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?

Comment: 2004’s fastest organic and biomolecular chemistry!

In January 2004, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC) - a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?

Comment: 2004’s fastest organic and biomolecular chemistry!

In January 2003, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC)--a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?

Diversity of polyketide synthase gene sequences in Aspergillus species

Fungal polyketide synthases are responsible for the biosynthesis of several mycotoxins and other secondary metabolites. The aim of our work was to investigate the diversity of polyketide synthases in Aspergillus species using two approaches: PCR amplification using oligonucleotide primers, and bioinformatics. Ketosynthase domain probes amplified DNA fragments of about 700 bp in each examined isolate. Sequences of these domains were aligned and analyzed by phylogenetic methods. The ketosynthase domain sequences were highly diverse indicating that they most probably represent polyketide synthases responsible for different functions. A. albertensis and A. niger ketosynthase domain sequences clustered together with sequences of genes required for pigment biosynthesis (wA) in A. nidulans and P. patulum, while the ketosynthase domain sequence of A. muricatus was most closely related to an A. parasiticus wA type domain sequence, and those of the A. ochraceus isolates formed a distinct clade on the tree. These sequences were highly homologous to an A. terreus naphthopyrone synthase gene. An Aspergillus fumigatus genomic database was also searched for ketosynthase domain sequences, which have been included in the phylogenetic analysis. Altogether 14 putative ketosynthase domain sequences were identified. Clustering of the ketosynthase domain sequences correlated well with the type of metabolites produced by the corresponding polyketide synthases. At least 8 clusters with putative ketosynthase domain sequences of unknown function have been identified. Further studies are in progress to clarify the role of some of the identified polyketide synthase genes.

Evidence from engineered gene fusions for the repeated use of a module in a modular polyketide synthase

Functional evidence for programmed loss of co-linearity on the borrelidin modular polyketide synthase (PKS) is presented.