Circuitry Linking the Global Csr- and σ-Dependent Cell Envelope Stress Response Systems.

CsrA of is an RNA-binding protein that globally regulates a wide variety of cellular processes and behaviors, including carbon metabolism, motility, biofilm formation, and the stringent response. CsrB and CsrC are small RNAs (sRNAs) that sequester CsrA, thereby preventing CsrA-mRNA interaction. RpoE (σ) is the extracytoplasmic stress response sigma factor of Previous RNA sequencing (RNA-seq) studies identified mRNA as a CsrA target. Here, we explored the regulation of by CsrA and found that CsrA represses translation. Gel mobility shift, footprint, and toeprint studies identified three CsrA binding sites in the leader transcript, one of which overlaps the Shine-Dalgarno (SD) sequence, while another overlaps the translation initiation codon. Coupled transcription-translation experiments showed that CsrA represses translation by binding to these sites. We further demonstrate that σ indirectly activates the transcription of and , leading to increased sequestration of CsrA, such that repression of by CsrA is reduced. We propose that the Csr system fine-tunes the σ-dependent cell envelope stress response. We also identified a 51-amino-acid coding sequence whose stop codon overlaps the start codon and demonstrate that is translationally coupled with this upstream open reading frame (ORF51). The loss of coupling reduces translation by more than 50%. Identification of a translationally coupled ORF upstream of suggests that this previously unannotated protein may participate in the cell envelope stress response. In keeping with existing nomenclature, we named ORF51 , resulting in an operon arrangement of CsrA posttranscriptionally represses genes required for bacterial stress responses, including the stringent response, catabolite repression, and the RpoS (σ)-mediated general stress response. We show that CsrA represses the translation of , encoding the extracytoplasmic stress response sigma factor, and that σ indirectly activates the transcription of and , resulting in reciprocal regulation of these two global regulatory systems. These findings suggest that extracytoplasmic stress leads to derepression of translation by CsrA, and CsrA-mediated repression helps reset RpoE abundance to prestress levels once envelope damage is repaired. The discovery of an ORF, , translationally coupled with adds further complexity to translational control of .