State-dependent promoter switching mediates integrase gene transcription in the integrative and conjugative element ICEKp1 of Klebsiella pneumoniae.

Integrative and conjugative elements (ICEs) are mobile genetic elements that widely disseminate adaptive traits among bacterial populations. Despite their prevalence, the regulatory mechanisms orchestrating ICE integration and excision remain poorly understood. Here, we investigate the transcriptional regulation of the integrase gene (int) in ICEKp1 of Klebsiella pneumoniae. Our results demonstrate that the integrated ICEKp1 exploits the adjacent host transfer RNA-asn promoter to drive int transcription, whereas the excised ICEKp1 switches to a 3'-end promoter. Remarkably, the messenger RNA stem-loops within the int 5'-UTR are organized as a potential terminator, attenuating the total amount of the full-length asn-int transcripts during ICEKp1's integration. Ligation of the 3' end and 5' end of ICEKp1 maintains the activity of the 3'-end promoter for the int transcription in the excised ICEKp1. This promoter switch of the integrase gene promotes a preference for ICEKp1 integration over excision. Furthermore, analogous regulatory mechanisms are observed in ICEclc and ICEEc1, suggesting evolutionary conservation of this regulatory strategy among diverse ICE families. These findings uncover a state-dependent int transcriptional regulatory mechanism that tends ICE toward the integrated state, highlighting the complex interplay between ICEs and their bacterial hosts.