Changing the initiation unit of nonribosomal peptide synthetases to access underexplored biosynthetic potential

Abstract

Nonribosomal peptide synthases (NRPSs) are large multimodular enzymes, capable of synthesizing nonribosomal peptides (NRPs) with diverse structures and bioactivities. Genome sequencing revealed a large number of uncharacterized NRPS biosynthetic gene clusters (BGCs) and their products are underexplored. The majority of NRPSs remain silent potentially attributed to factors such as the low activity of the initiation unit or insufficient precursor supply. Exchanging the starter condensation (Cs) domains within initiation unit can change the length of acyl chains of NRPs, hinting at a promising strategy through swapping of a well-studied Cs domain to activate the initiation unit and harness primary metabolites as precursors, which may offer a new option to access silent BGCs. Here, we first pinpointed two highly efficient fusion sites for initiation unit exchanges. Subsequently, they were validated by replacing the initiation region of endopyrrole pathway with a Cs-containing initiation unit for generation of a lipo-endopyrrole derivate. We promptly leveraged this strategy of changing initiation unit to target six previously silent NRPS BGCs, three BGCs were successfully activated and five novel lipopeptides were identified, demonstrating its application to recover silent BGCs. Furthermore, we extended this strategy in more BGCs from different bacteria. Utilizing a heterologous Cs-containing unit to replace the initiation region of chitinimide biosynthetic pathway led to successful incorporation of N-terminal fatty acid chains into chitinimide to create artificial lipo-chitinimides. This study provides a feasible strategy to rationally recover silent BGCs and add fatty acid chains to NRPs, enriching the genome mining and combinatorial biosynthesis approach for bacterial natural products. SignificanceNonribosomal peptide synthetases (NRPSs) represent a valuable yet underexplored reservoir for bioactive natural products, but most of them are silent. This study introduces the concept that changing initiation unit to activate and optimize the functional expression of NRPSs, and successfully access three of six previously silent NRPS pathways, providing a feasible complement to the current genome mining approaches. Moreover, the N-terminal lipid chains are crucial for the activity of lipopeptides. We employed a heterologous Cs (starter condensation domain)-containing initiation unit to replace the original initiation region for creation of artificial nonribosomal lipopeptides, ultimately yielding three novel lipo-derivatives. This work presents a groundbreaking approach for activating and optimizing NRPSs and provides profound insight into the exploration of bacterial NRPS pathways.