Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA

Abstract

Bacterial small RNAs (sRNAs) are well established to regulate diverse cellular processes, but how they themselves are regulated is less understood. Recently, we identified a regulatory circuit wherein the GlmY and GlmZ sRNAs of Escherichia coli act hierarchically to activate mRNA glmS, which encodes glucosamine-6-phosphate (GlcN6P) synthase. Although the two sRNAs are highly similar, only GlmZ is a direct activator that base-pairs with the glmS mRNA, aided by protein Hfq. GlmY, however, does not bind Hfq and activates glmS indirectly by protecting GlmZ from RNA cleavage. This complex regulation feedback controls the levels of GlmS protein in response to its product, GlcN6P, a key metabolite in cell wall biosynthesis. Here, we reveal the molecular basis for the regulated turnover of GlmZ, identifying RapZ (RNase adaptor protein for sRNA GlmZ; formerly YhbJ) as a novel type of RNA-binding protein that recruits the major endoribonuclease RNase E to GlmZ. This involves direct interaction of RapZ with the catalytic domain of RNase E. GlmY binds RapZ through a secondary structure shared by both sRNAs and therefore acts by molecular mimicry as a specific decoy for RapZ. Thus, in analogy to regulated proteolysis, RapZ is an adaptor, and GlmY is an anti-adaptor in regulated turnover of a regulatory small RNA.

The Bacterial Phosphoenolpyruvate:Carbohydrate Phosphotransferase System: Regulation by Protein Phosphorylation and Phosphorylation-Dependent Protein-Protein Interactions

“…In most betaproteobacteria, such as R. eutropha and Neisseria meningitidis, the EIIA Man -encoding gene as well as ptsO and ptsP seem to form an operon, whereas ptsN and hprK are located in a second operon with hprK being followed by the rapZ (former yhbJ) gene (110). In E. coli, RapZ acts as adaptor protein allowing RNase E to degrade the small RNA GlmZ, which is required for the translation of the glucosamine-6-P synthase-encoding RNA (117). (28) and also the ␣-ketoglutarate/glutamine ratio (116) affect the phosphorylation states of these PTS proteins.…”

Allosteric Activation of Escherichia coli Glucosamine-6-Phosphate Deaminase (NagB) In Vivo Justified by Intracellular Amino Sugar Metabolite Concentrations

“…Since GlcN6P synthesized by GlmS during growth on glucose is the essential precursor of all cell wall PG and LPS amino sugar components, it is necessary to protect newly synthesized GlcN6P from degradation by NagB. This could be achieved by controlling GlmS activity (39,40).…”

“…Amino sugar homeostasis is achieved by a sophisticated posttranscriptional regulation of the expression of the glmS gene, encoding GlcN6P synthase. At high GlcN6P concentrations, expression of glmS is low, but when the GlcN6P concentration falls, a regulatory cascade is initiated, resulting in higher GlmS levels (40,43). This mechanism must maintain GlcN6P levels despite a potentially active deaminase (39).…”

Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli

“…As with the household 1 isolates, the proportion of mutations targeting TFs was significantly higher than expected for a random distribution based on the proportion of TFs among all protein-coding genes in JJ1886 (i.e., 2% versus 0.06%; P Ͻ 0.05). Also, 3 additional genes with nonsynonymous changes, cspE, degS, and rapZ, encoded other types of transcriptional regulators (28,35,36), while none of the 5 genes with synonymous changes did so. Notably, 2 of 4 intergenic SNPs also were found upstream of genes encoding transcriptional regulators: one directly in the promoter of the DNA-binding nucleoid protein Dps (37, 38) and shown (normalized mean score).…”