The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli

Abstract

In Escherichia coli the glmS gene encoding glucosamine 6-phosphate (GlcN-6-P) synthase GlmS is feedback regulated by GlcN-6-P in a pathway that involves the small RNA GlmZ. Expression of glmS is activated by the unprocessed form of GlmZ, which accumulates when the intracellular GlcN-6-P concentration decreases. GlmZ stabilizes a glmS transcript that derives from processing. Overexpression of a second sRNA, GlmY, also activates glmS expression in an unknown way. Furthermore, mutations in two genes, yhbJ and pcnB, cause accumulation of full-length GlmZ and thereby activate glmS expression. The function of yhbJ is unknown and pcnB encodes poly(A) polymerase PAP-I known to polyadenylate and destabilize RNAs. Here we show that GlmY acts indirectly in a way that depends on GlmZ. When the intracellular GlcN-6-P concentration decreases, GlmY accumulates and causes in turn accumulation of full-length GlmZ, which finally activates glmS expression. In glmZ mutants, GlmY has no effect on glmS, whereas artificially expressed GlmZ can activate glmS expression also in the absence of GlmY. Furthermore, we show that PAP-I acts at the top of this regulatory pathway by polyadenylating and destabilizing GlmY. In pcnB mutants, GlmY accumulates and induces glmS expression by stabilizing full-length GlmZ. Hence, the data reveal a regulatory cascade composed of two sRNAs, which responds to GlcN-6-P and is controlled by polyadenylation.

The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq

“…The shorter GlmY* (z140 nt) is an exception, being the predominant RNA detected in the wild type. This has been previously observed as the full-length GlmY (z180 nt) is rapidly processed in the 39-end to originate the GlmY* species (Reichenbach et al 2008;Urban and Vogel 2008). Overexpression of PNPase in the hfq pnp strain was shown to reverse the accumulation of MicA* (Supplemental Fig.…”

“…This was also confirmed to be a consequence of the higher stabilization of GlmY* in the hfq pcnB mutant (data not shown). GlmY* is known to be highly polyadenylated in cells harboring Hfq (Reichenbach et al 2008;Urban and Vogel 2008). We have now shown that the lack of poly(A) polymerase I is an important factor affecting the sRNA decay in the absence of Hfq in stationary-phase cells.…”

The influence of Hfq and ribonucleases on the stability of the small non-coding RNA OxyS and its targetrpoSinE. coliis growth phase dependent

“…The half-life of OxyS in E. coli K12 wild type was reported to be 12-15 min, 14 the half-life in strain MC4100 can create new RNase cleavage sites 18,26 or protect from cleavage. 27,28 While RNase III preferentially cleaves double stranded RNA regions, RNase E recognizes single stranded AU rich segments. 29 To address the role of these RNases in OxyS decay we analyzed RNase deficient strains and compared OxyS stability in the isogenic wild type backgrounds.…”

Discovery and Validation of New Regulatory RNA Elements in Chlamydia trachomatis

“…Regulation of ncRNAs by polyadenylation was well characterized in the glmS/glmZ/glmY system (Kalamorz et al, 2007;Reichenbach et al, 2008). Translation of the glmS mRNA was normally weak since an internal hairpin structure containing the glmS Shine Dalgarno sequence limits ribosome access to the downstream glmS RBS and therefore GlmS synthesis (Kalamorz et al, 2007;Urban et al, 2008).…”

“…for gadY, , dsrA , and glmY (Reichenbach et al, 2008)) and is believed to involve post-transcriptional processing that is dependent on the balance between protection by RNA binding protein(s) and degradation by RNases. The functional significance has not been well-studied but, importantly, Davis and Waldor (Davis and Waldor, 2007) have shown that MicX of Vibrio cholerae can be detected as both an active precursor and a processed form and that the smaller, processed molecule is significantly more stable and abundant.…”