Glutamine synthetase mRNA releases sRNA from its 3’UTR to regulate carbon/nitrogen metabolic balance

Abstract

Glutamine synthetase is the key enzyme of nitrogen assimilation, which is encoded in the first cistron of glnALG operon and is induced under nitrogen limiting conditions through transcriptional activation by NtrBC in Salmonella and E. coli. 2-oxoglutarate serves as the carbon skeleton of glutamate and glutamine, but how 2-oxoglutarate fluctuation is controlled in response to nitrogen availability remained unknown. We show that the glnA mRNA produces an Hfq-dependent GlnZ sRNA from its 3′UTR through RNase E-mediated cleavage. Through a base-pairing mechanism, GlnZ primarily regulates sucA, encoding the E1o component of 2-oxoglutarate dehydrogenase. In the cells grown on glutamine as the nitrogen source, the endogenous GlnZ represses the expression of SucA to redirect the carbon flow from the TCA cycle to the nitrogen assimilation pathway. This study also clarifies that the release of GlnZ sRNA from the glnA mRNA by RNase E is essential for the post-transcriptional regulation of sucA, and thus the mRNA coordinates the two independent functions to balance the supply and demand of the fundamental metabolites.

A 3′ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria

“…Given the conservation of the seed sequence, we hypothesize that many mRNA targets are also conserved. Analysis of GlnZ targets in E. coli K-12, EHEC, and S. enterica in this study, and by Miyakoshi et al, support this hypothesis documenting regulation of sucA and glnP by the homologs (61). Additionally, recent RIL-seq analysis of Hfq-binding sRNAs in enteropathogenic E. coli (EPEC) identified a GlnZ sRNA derived from the 3´ UTR of glnA and predicted sucA and glnP as potential binding partners of GlnZ in EPEC (62).…”