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

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.

Insights into azalomycin F assembly-line contribute to evolution-guided polyketide synthase engineering and identification of intermodular recognition

“…Recombination events are implicated in the evolution of modular PKS assembly-lines, especially in trans-AT PKS systems 32 , 33 , but there is less evidence for similar mechanisms in cis-AT PKS evolution 7 , 31 , 33 , 34 . In the light of the results of bioinformatics analysis of the AZL PKS assembly-line and the accelerated evolution via module recombination within the rapamycin and tylosin PKS systems 31 , we constructed a knockout mutant of azlB of the AZL PKS (Fig.…”

Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges

“…Indeed, several drugs which are used as antibiotics were identified as trans -AT PKS products (e.g., mupirocin, streptogramins) [ 78 , 79 ]. Many compounds from sponges and their symbionts are known to be biosynthesized by trans -AT PKS pathways (e.g., diffusomycin, psymberin, onnamide A, calyculin A, swinhoeiamide A, swinhodile A, clavosine A, geoetricin A, misakinolide A, oocydin A, and mycalamide A) [ 80 , 81 , 82 ]. The trans -AT PKS gene clusters detected in the sponge-associated bacteria metagenomes in our study had a best BLAST hit to gene clusters involved in the production of puwainaphycins and epothilones ( Tables S14–S16 ).…”

Insights into azalomycin F assembly-line contribute to evolution-guided polyketide synthase engineering and identification of intermodular recognition

“…Recombination events are implicated in the evolution of modular PKS assembly-lines, especially in trans-AT PKS systems 31,32 . but there is less evidence for similar mechanisms in cis-AT PKS evolution 7,30,32,33 .…”

“…Recombination events are implicated in the evolution of modular PKS assembly-lines, especially in trans-AT PKS systems 31,32 . but there is less evidence for similar mechanisms in cis-AT PKS evolution 7,30,32,33 . In the light of the results of bioinformatic analysis of the AZL PKS assembly-line and the accelerated evolution via module recombination within the rapamycin and tylosin PKS systems 30 , we constructed a knockout mutant of azlB of the AZL PKS (Fig.…”