Context-dependent regulation of RpoS-dependent and RpoS-independent gene transcription by Crl during exponential growth in Escherichia coli

Abstract RpoS, an alternative sigma factor, directly regulates approximately 10% of gene transcription in E. coli . The small protein Crl functions as a partner that assists RpoS in exerting its regulatory role, particularly during the stationary phase. However, the coordinating role of Crl during the exponential phase remains unclear. In addition, whether Crl can regulate gene transcription independently of RpoS is still unknown. Therefore, in this study, we used the RpoS-dependent operon hdeAB and the RpoS-independent operon proVWX as model systems to investigate the transcriptional regulatory function of Crl using RT-qPCR and 3C-qPCR. Since the expression of both Crl and RpoS is modulated by environmental signals, we further examined the transcription of these operons under different pH and osmotic conditions. The results showed that Crl can regulate transcription independently of RpoS and exhibits environment-specific bidirectional regulation. Overall, this study improves our understanding of the regulatory mechanisms of Crl and highlights the complexity of transcriptional regulation.