Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation

Abstract

Small noncoding RNAs (sRNA) can function as posttranscriptional activators of gene expression to regulate stress responses and metabolism. We here describe the mechanisms by which two sRNAs, GlmY and GlmZ, activate the Escherichia coli glmS mRNA, coding for an essential enzyme in amino-sugar metabolism. The two sRNAs, although being highly similar in sequence and structure, act in a hierarchical manner. GlmZ, together with the RNA chaperone, Hfq, directly activates glmS mRNA translation by an anti-antisense mechanism. In contrast, GlmY acts upstream of GlmZ and positively regulates glmS by antagonizing GlmZ RNA inactivation. We also report the first example, to our knowledge, of mRNA expression being controlled by the poly(A) status of a chromosomally encoded sRNA. We show that in wild-type cells, GlmY RNA is unstable due to 3′ end polyadenylation; whereas in an E. coli pcnB mutant defective in RNA polyadenylation, GlmY is stabilized and accumulates, which in turn stabilizes GlmZ and causes GlmS overproduction. Our study reveals hierarchical action of two well-conserved sRNAs in a complex regulatory cascade that controls the glmS mRNA. Similar cascades of noncoding RNA regulators may operate in other organisms.

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.…”

Regulating the regulator: an RNA decoy acts as an OFF switch for the regulation of an sRNA: Figure 1.

“…While GlmY and GlmZ sRNAs are homologous and positively regulate the translation of glmS, a gene encoding an enzyme of the biosynthesis pathway of amino sugars, only GlmZ pairs directly to its target. GlmY is also able to activate GlmS synthesis in vivo by counteracting a 39 RNA processing in GlmZ that otherwise inactivates it (Urban and Vogel 2008). Although the mechanism of this protection is unknown, one interesting possibility is that it involves RNA mimicry, with GlmY competing with the unidentified factors that direct GlmZ cleavage.…”

Discovery and Validation of New Regulatory RNA Elements in Chlamydia trachomatis

“…The RNA circularization protocol was previously developed to assess the poly-A status of RNAs (Urban and Vogel, 2008;Vogel and Hess, 2001). A schematic representation of the procedure is shown in Figure 4-1.…”

“…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). glmZ, an ncRNA, functions as an anti-antisense and melts this hairpin, allowing glmS translation.…”

“…glmY levels are controlled by polyadenylation and it was found that about 50% of glmY is polyadenylated. This regulatory hierarchy signifies the effect of polyadenylation on the function of glmS/glmZ/glmY (Urban et al, 2008) reviewed in (Gorke and Vogel, 2008).…”