Polyketide Synthase Secrets Revealed

A new study solves long-standing mysteries about how bacterial natural-product-making factories are put together and how they work. The findings could accelerate efforts to engineer these workshops to produce novel bioactive agents for drug discovery.

Bacteria use huge multienzyme complexes called polyketide synthases (PKSs) to create a wide variety of polyketide natural products. A number of polyketides are approved drugs, including antibiotics such as erythromycin A, azithromycin, and tetracycline; the parasitic worm treatments avermectin and ivermectin; the anti­fungal drug amphotericin; the immunosuppressants tacrolimus (FK506) and sirolimus (rapamycin); and the cholesterol-lowering agent lovastatin.

Researchers have long tried to engineer PKSs to produce customized drug candidates. But successes have been few, and progress has been hampered by a lack of detailed understanding about how PKS systems look and work. Scientists have obtained X-ray structures of small PKS fragments and have proposed theoretical models of how they operate, but the structure and mechanism of a complete PKS module (working unit) had never been determined.

Now, after two years of effort, a University of Michigan group has obtained cryo-electron microscopy structures of one of the six modules in the PKS that assembles the core of the antibiotic pikromycin. The scientists captured the module at less than atomic resolution in five states of its catalytic cycle, enabling them to decipher its mechanism of action.

The work was carried out by Life Sciences Institute professors Georgios Skiniotis, Janet L. Smith, and David H. Sherman and chemistry professor Kristina Håkansson (Nature 2014, DOIs: 10.1038/nature13423 and 10.1038/nature13409).

The study is a milestone in the PKS field, says polyketide biosynthesis specialist Shiou-Chuan (Sheryl) Tsai of the University of California, Irvine. “Visualizing a modular PKS in action will have a profound influence in aiding the bioengineering of PKSs to produce new polyketides.”

The findings include surprising revelations. For example, earlier structures suggested that a penta­ketide substrate and a methylmalonyl extender unit combine after entering the module’s ketosynthase through a known entryway. The new work reveals that, although the substrate uses that door, the extender uses a previously completely unknown separate entryway.

The new structures show that the three pairs of enzyme domains in the dimeric PKS module adopt a horseshoe shape, which also wasn’t known before. In an open chamber inside the horseshoe, a component called acyl carrier protein (ACP) acts like a tiny FedEx truck by picking up and delivering substrates and products to the catalytic domains as needed.

And one of ACP’s movements is accompanied by a dramatic 180° rotation of the PKS module’s ketoreductase, to which ACP is tethered. “We have no idea how this flip is driven energetically, but it’s remarkable,” Skiniotis says.

With the structure and mechanism of a PKS module in hand, researchers will now want to learn more about ACP’s interactions with the enzyme domains by studying them at higher resolution, comments natural products biochemist Adrian T. Keatinge-Clay of the University of Texas, Austin. Such studies will “guide the engineering of synthases to produce designer polyketides valuable in synthesis, materials, and medicine,” he says.

Addressing still-open questions “will require further genetic, biochemical, and biophysical work,” notes PKS expert Peter F. Leadlay of the University of Cambridge in a Nature commentary. “Nonetheless, by showing that an intact module is much more than the sum of its parts, this elegant study has given fresh impetus to our search for the answers.”