Synthetic biology enabling access to designer polyketides

Abstract

The full potential of polyketide discovery has yet to be reached due to a lack of suitable technologies and knowledge required to advance engineering of polyketide biosynthesis. Recent investigations on the discovery, enhancement, and non-natural utilization of these biosynthetic gene clusters via computational biology, metabolic engineering, structural biology, and enzymology-guided approaches have facilitated improved access to designer polyketides. Here, we discuss recent successes in gene cluster discovery, host strain engineering, precursor-directed biosynthesis, combinatorial biosynthesis, polyketide tailoring, and high-throughput synthetic biology, as well as challenges and outlooks for rapidly generating useful target polyketides.

Recent trends in biocatalysis

“…433 It is therefore not surprising that polyketides are also valuable to humans as pesticides (spinosyn A), antibiotics (erythromycin), antineoplastics (daunorubicin), immunosuppressants (FK506), antifungal (neoaureothin), antitumor (epothilone B), antiparasitic (avermectin), and cholesterollowering (lovastatin) drugs. 434 Most of this rich diversity is produced by the modular Type I or ''assembly-line'' polyketide synthases. 435 Polyketides are an excellent example of the central theme of this review, which is to demonstrate that it is still difficult to achieve the total enzymatic synthesis of natural products without the original host organism.…”

“…The modular Type I PKSs are commonly described as ''assembly-line'' complexes because each module sequentially adds a unit to the growing product so that the sequence of functional groups in the final polyketide depends on the sequence of PKS modules. 434,435,437,442 Each module of an assembly-line PKS consists of at least a ketosynthase, an acyltransferase, and an acyl-carrier protein domain (Fig. 4C).…”

“…435 Finally, a thioesterase domain cleaves the polyketide from the terminal acyl-carrier protein, often cyclizing the product to form a macrolactone. 434,437,442,443 The rich chemical and structural diversity of naturally occurring polyketides can often be enhanced by structural fine-tuning. 437,442 Chemical modification of natural polyketides is possible, but often inefficient, and selectivity is hard to achieve.…”

“…437,442 Chemical modification of natural polyketides is possible, but often inefficient, and selectivity is hard to achieve. 434 However, successful modification of the biosynthetic machinery itself would enable diversely modified analogues to be produced. Therefore, scientists have been trying to reprogram the modular architecture of assembly-line PKSs since they were discovered in the 1990s.…”

“…442 Not only should it be possible to produce targeted polyketide modifications, but libraries of 'unnatural natural products' could also be created and screened for novel activities, if only we could insert, delete, or swap out individual PKS modules at will. 434,445 Unfortunately, this combinatorial assembly approach is not straight forward since the chimeric assemblies are usually catalytically impaired and the production of structural analogues of medically relevant polyketides by genetic/protein engineering is still a major challenge. 434,442,446,447 Interactions between domains and modules seem to be as important to the activity and fidelity of assembly-line PKSs as enzyme-substrate interactions.…”