engleski

Modelling of homologous recombination in modular polyketide synthases combined with synthetic biology as a strategy for producing biologically active lead compounds

Modular polyketide synthases (PKS) are an attractive target for synthetic biology approaches with the possibility of reusing synthesized components in many constructs. A major stumbling block in the reprogramming of PKS has been the low product yield after most manipulations. Homologous recombination probably plays a major role in the natural evolution of modular PKS and would occur in regions of high sequence similarity, which may well favour better product yield compared to junctions typically selected for in vitro manipulation. However, it is not clear whether recombination between existing clusters can cover a comparable chemical space compared to a fully combinatorial approach. We decided to model homologous recombination between pairs of PKS clusters to determine the potential to generate novel chemical entities. The recombination model assumed a core of sequence identity in a region of high sequence similarity. The ClustScan annotation program developed a data format for modular PKSs that links DNA sequence to module architecture and the chemical structure of the polyketide backbone. This format was used to develop an algorithm to determine whether a recombinant would produce a polyketide product and predict the chemical structure. For ease of use, this was implemented as a program (CompGen) with a graphical user interface. Recombination between 47 well-characterised clusters was modeled. This yielded 20, 187 recombinants that were predicted to produce a product and 11, 796 unique chemical entities. The details of the recombinants were entered into a database (http://bioserv.pbf.hr/cms/). The chemical structures can be exported in a standard SMILE format. These were used to calculate the molecular weights and degree of reduction of the predicted products. These data showed that they covered a significant region of chemical space. The large number of recombinants and their chemical diversity indicate that this is an attractive target for synthetic biology to produce novel lead compounds.

Modular polyketide synthases; gene clusters; homeologous recombination; synthetic biology

nije evidentirano