synthetic biology

Synthetic Biology for Actinomycetes

In Actinomycetes, the tools of Synthetic Biology comprise several strategies to build a chassis for high-yield producer strains of heterologously expressed biomolecules.

Reduced genomes by surgical deletion of several biosynthetic gene clusters and protein degrading machinery provides strains with lightened burden, without unnecessary metabolic routes for the bacterium function. Engineering of synthetic parts and cassettes, i.e. reshuffled, rewired and repurposed genetic elements and/or genes allow better control of expression. Improvement of transcription control by removing sigma factors helps to minimize maintenance efforts and increase product yields. Temporal and product-saving control of gene expression is reached through synthetic promoters and regulatory networks.

Synthetic biology new tools also allow EntreChem to increase the reach of Combinatorial biosynthesis:

  • The system developed in the yeast Saccharomyces cerevisiae called Transformation Assisted Recombination, TAR cloning, is particularly interesting. Using this method, it is possible to clone and mobilize fragments of DNA larger than 100 kbp to designer Streptomyces
  • Another particularly efficient method for the generation of mutants, either by deletion or substitution, is the use of the gene editing system CRISPR-Cas9 for Streptomyces. This method allows to generate clean mutants, that is, without the introduction of genetic material alien to the microorganism in question without the need for a negative selection process.

All combined, these tools generate Streptomyces hosts as a robust platform for biologically active natural products, both wild type or analogs obtained by genetic engineering and combinatorial biosynthesis.

How we make Drugs

Advances in bacterial recombinant DNA technology have enabled the cloning of gene clusters involved in the biosynthesis of many bioactive Natural Products, the detailed knowledge of their metabolic pathways, and the practice of combinatorial biosynthesis, complementary to chemical synthesis and biocatalysis, for the preparation of complex Natural Products and their analogs biosynthetically.
To learn more about EntreChem S.L. co-founders contribution to the field, see J Antibiot (Tokyo). 2011 Jan; 64(1): 51-7

Gene clusters encoding Natural Products have been cloned and characterized, and it is now possible to introduce structural alterations into a complex natural product by rational manipulation of its biosynthesis gene cluster. The resulting molecules can be produced in recombinant bacteria by established fermentation and downstream processes.

One particular aspect of our technology is the development of a series of “sugar plasmids”, able to direct the biosynthesis of rare sugars found on numerous bioactive compounds of interest in the clinical, agricultural or veterinary markets (see reviews by our co-founders here and here). These plasmids, combined with several flexible glycosyl transferases capable of recognizing and transferring different sugars that participate in biosynthesis of bioactive compounds, allow building focused libraries of analogs with altered carbohydrate profile. This is especially relevant, since sugar decorating domains are often considered responsible for the modulation of the drug interaction with biological targets.