Two functional acyl-CoA ligases affect free fatty acid metabolism to block biosynthesis of an antifungal antibiotic in Lysobacter enzymogenes.

In Lysobacter enzymogenes (Le), Le RpfB1 and Le RpfB2 were predicted to encode acyl-CoA ligases. RpfB1 is located in the Rpf gene cluster. Interestingly, we found an RpfB1 homolog (RpfB2) outside of this canonical gene cluster, and nothing is known about its functionality or mechanism. Here, we report that Le rpfB1 and Le rpfB2 can functionally replace EcFadD in the Escherichia colifadD mutant JW1794. RpfB activates long-chain fatty acids (n-C16:0 and n-C18:0) for the corresponding fatty acyl-CoA ligase (FCL) activity in vitro, and Glu-361 plays critical roles in the catalytic mechanism of RpfB1 and RpfB2. Deletion of rpfB1 and rpfB2 resulted in significantly increased HSAF production, and overexpression of rpfB1 or rpfB2 completely suppressed HSAF production. Deletion of rpfB1 and rpfB2 resulted in increased LeDSF3 synthesis in L. enzymogenes. Overall, our results showed that changes in intracellular free fatty acid levels significantly altered HSAF production. Our report shows that intracellular free fatty acids are required for HSAF production and that RpfB affects HSAF production via FCL activity. The global transcriptional regulator Clp directly regulated the expression of rpfB1 and rpfB2. In conclusion, these findings reveal new roles of RpfB in antibiotic biosynthesis in L. enzymogenes. IMPORTANCE Understanding the biosynthetic and regulatory mechanisms of HSAF could improve the yield in L. enzymogenes. Here, we report that Le RpfB1 and Le RpfB2 encode acyl-CoA ligases. Our research shows that Le RpfB1 and Le RpfB2 affect free fatty acid metabolism via FCL activity to reduce the substrate for HSAF synthesis and thereby block HSAF production in L. enzymogenes. Furthermore, these findings reveal new roles for the fatty acyl-CoA ligases Le RpfB1 and Le RpfB2 in antibiotic biosynthesis in L. enzymogenes. Importantly, the novelty of this work is the finding that RpfB2 lies outside the Rpf gene cluster and plays a key role in HSAF production, which has not been reported in other DSF/Rpf-producing bacteria.