Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria

Eric J N Helfrich,Adrien Y Burch,Marc G Chevrette,Franziska Hemmerling,Xiaowen Lu,Hannah A Minas,Stefan Leopold-Messer,Marnix H Medema,Jörn Piel,Reiko Ueoka,Steven E Lindow

doi:10.1038/s41467-021-21163-x

Abstract

Trans-acyltransferase polyketide synthases (trans-AT PKSs) are bacterial multimodular enzymes that biosynthesize diverse pharmaceutically and ecologically important polyketides. A notable feature of this natural product class is the existence of chemical hybrids that combine core moieties from different polyketide structures. To understand the prevalence, biosynthetic basis, and evolutionary patterns of this phenomenon, we developed transPACT, a phylogenomic algorithm to automate global classification of trans-AT PKS modules across bacteria and applied it to 1782 trans-AT PKS gene clusters. These analyses reveal widespread exchange patterns suggesting recombination of extended PKS module series as an important mechanism for metabolic diversification in this natural product class. For three plant-associated bacteria, i.e., the root colonizer Gynuella sunshinyii and the pathogens Xanthomonas cannabis and Pseudomonas syringae, we demonstrate the utility of this computational approach for uncovering cryptic relationships between polyketides, accelerating polyketide mining from fragmented genome sequences, and discovering polyketide variants with conserved moieties of interest. As natural combinatorial hybrids are rare among the more commonly studied cis-AT PKSs, this study paves the way towards evolutionarily informed, rational PKS engineering to produce chimeric trans-AT PKS-derived polyketides.

Highlights

Trans-acyltransferase polyketide synthases are bacterial multimodular enzymes that biosynthesize diverse pharmaceutically and ecologically important polyketides
Benchmarking on a set of 12 recently published trans-AT PKS assembly lines that were not part of the training set showed an accuracy of 81.2%, with regard to the chemistry associated with these functional clades (SI Dataset 1), which is on par with the results of the state-of-the-art algorithm for trans-AT PKS-derived polyketide structure prediction TransATor[17] (82.5%)
We found that 46 (94%) out of the 49 known trans-AT PKSs shared at least one contiguous pair of modules with another assembly line, and 34 (69%) shared at least two pairs; network analysis based on these data led to the identification of patterns of module sharing between various families of PKSs (Fig. 2a)

Summary

Introduction

Trans-acyltransferase polyketide synthases (trans-AT PKSs) are bacterial multimodular enzymes that biosynthesize diverse pharmaceutically and ecologically important polyketides. Biosynthetic basis, and evolutionary patterns of this phenomenon, we developed transPACT, a phylogenomic algorithm to automate global classification of trans-AT PKS modules across bacteria and applied it to 1782 trans-AT PKS gene clusters These analyses reveal widespread exchange patterns suggesting recombination of extended PKS module series as an important mechanism for metabolic diversification in this natural product class. Trans-acyltransferase polyketide synthases (trans-AT PKSs) are giant bacterial enzymes that assemble highly diverse and complex polyketide natural products. Some of these, such as mupirocin and virginiamycin, are used as antibiotics in human and veterinary medicine[1,2], and many others show promising drug-like bioactivities[3,4,5,6]. PKSs form hybrids with nonribosomal peptide synthetases (NRPSs) to produce hybrid polyketide–peptide backbones[13]

Methods

Results

Conclusion