Abstract
The modular organization of the type I polyketide synthases (PKSs) would seem propitious for rational engineering of desirable analogous. However, despite decades of efforts, such experiments remain largely inefficient. Here, we combined multiple, state-of-the-art approaches including modification of docking domains, use of modules of varying domain composition, alternative interdomain fusion sites, and targeted adaptation of key domain-domain interfaces, to reprogram the stambomycin PKS by deleting seven internal modules – the most substantial modification to an intact system reported to date. One such system produced the target 37-membered mini-stambomycin metabolites, a reduction in chain length of 14 carbons relative to the 51-membered parental compounds, but also substantial quantities of shunt metabolites released from the multienzyme subunit upstream of the newly-installed junction. Our data also provide evidence for an unprecedented off-loading mechanism of such stalled intermediates involving the C-terminal thioesterase domain acting on chains located four modules upstream. The yields of all metabolites were substantially reduced compared to the wild type compounds, likely reflecting the poor tolerance to the non-native substrates of the modules downstream of the introduced interfaces. Taken together, our data demonstrate that even ‘optimized’ PKS engineering strategies remain inadequate for efficient production of target polyketide derivatives, and highlight several areas for future investigation.