Unveiling the regulatory network controlling natural transformation in lactococci
Lactococcus lactis is a lactic acid bacterium of major importance for food fermentation and biotechnological applications. The ability to manipulate its genome quickly and easily through competence for DNA transformation would accelerate its general use as a platform for a variety of applications. Natural transformation in this species requires the activation of the master regulator ComX. However, the growth conditions that lead to spontaneous transformation, as well as the regulators that control ComX production, are unknown. Here, we identified the carbon source, nitrogen supply, and pH as key factors controlling competence development in this species. Notably, we showed that these conditions are sensed by three global regulators (i.e., CcpA, CodY, and CovR), which repress comX transcription directly. Furthermore, our systematic inactivation of known signaling systems suggests that classical pheromone-sensing regulators are not involved. Finally, we discovered that the ComX-degrading MecA-ClpCP machinery plays a predominant role based on the identification of a single amino-acid substitution in the adaptor protein MecA of a highly transformable strain. Contrasting with closely-related streptococci, the master competence regulator in L. lactis is regulated both proximally by general sensors and distantly by the Clp degradation machinery. This study not only highlights the diversity of regulatory networks for competence control in Gram-positive bacteria, but it also paves the way for the use of natural transformation as a tool to manipulate this biotechnologically important bacterium. Overall design: To investigate the effects of CodY and CovRS inactivation on the transcription of competence genes, codY- and covRS-deletion mutants were generated and cultured in their respective competence-activating medium. Cells were harvested during competence activation (glucose-maltose diauxic shift). Total RNA was extracted and sequenced. The transcriptomes of the mutants were compared to those of the wild-type strain grown in the same medium and conditions.To highlight the set of late competence genes, we also compared the  transcriptomes of a WT strain carrying an empty vector with a WT strain overexpressing the master comptence regulator ComX .