Multiple regulatory inputs including cell envelope stress orchestrate expression of the Escherichia coli rpoN operon

• Published in: Molecular microbiology Vol. 122; no. 1; pp. 11 - 28
• Main Authors: Sikora, Florian, Budja, Lara Veronika Perko, Milojevic, Olja, Ziemniewicz, Amelia, Dudys, Przemyslaw, Görke, Boris
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.07.2024
• Subjects: Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Carbon sources; E coli; Endoribonucleases; envelope stress; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Ethanol; Gene expression; Gene Expression Regulation, Bacterial; Genes; Glucosamine; Hibernation; LPS; mRNA processing; nitrogen‐related PTS; Operon - genetics; PhoP; Phosphotransferase; Promoter Regions, Genetic; Proteins; Regulatory mechanisms (biology); Ribonuclease E; rpoN operon; sigma E; Sigma factor; Sigma Factor - genetics; Sigma Factor - metabolism; Signal quality; Stress, Physiological - genetics; Transcription, Genetic; Transposon mutagenesis; nitrogen‐related PTS; envelope stress; PhoP; rpoN operon; sigma E; LPS
• ISSN: 0950-382X; 1365-2958; 1365-2958
• DOI: 10.1111/mmi.15280

The rpoN operon, an important regulatory hub in Enterobacteriaceae, includes rpoN encoding sigma factor σ54, hpf involved in ribosome hibernation, rapZ regulating glucosamine‐6‐phosphate levels, and two genes encoding proteins of the nitrogen‐related phosphotransferase system. Little is known about regulatory mechanisms controlling the abundance of these proteins. This study employs transposon mutagenesis and chemical screens to dissect the complex expression of the rpoN operon. We find that envelope stress conditions trigger read‐through transcription into the rpoN operon from a promoter located upstream of the preceding lptA‐lptB locus. This promoter is controlled by the envelope stress sigma factor E and response regulator PhoP is required for its full response to a subset of stress signals. σE also stimulates ptsN‐rapZ‐npr expression using an element downstream of rpoN, presumably by interfering with mRNA processing by RNase E. Additionally, we identify a novel promoter in the 3′ end of rpoN that directs transcription of the distal genes in response to ethanol. Finally, we show that translation of hpf and ptsN is individually regulated by the RNA chaperone Hfq, perhaps involving small RNAs. Collectively, our work demonstrates that the rpoN operon is subject to complex regulation, integrating signals related to envelope stress and carbon source quality. The E. coli rpoN operon encodes important regulatory proteins including sigma 54 and components of the nitrogen‐related PTS. Here we show that additional upstream and internally located promoters contribute to its transcription in response to distinct envelope stress conditions and carbon source quality. RNase E cleaves transcripts extensively upstream of ptsN, generating more stable mRNAs comprising the distal three genes. Translation of hpf and ptsN is individually regulated by the RNA chaperone Hfq.