MinD-RNase E interplay controls localization of polar mRNAs in E. coli

Abstract

The E. coli transcriptome at the cell’s poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.

Synopsis

A subset of E. coli transcripts localizes to the cell poles via an unknown mechanism. Here, the interaction of MinD and RNase E is shown to prevent site-specific degradation of polar mRNAs, thus favoring their enrichment in the cell poles.

• Candidate approach and proteomic analysis identify MinD and RNase E as regulators of polar mRNA localization.

• MinD interacts with a short peptide within the membrane-targeting sequence of RNase E.

• In the absence of MinD, RNase E transiently accumulates at cell poles.

• Polar accumulation of RNase E in ΔminCDE cells destabilizes polar mRNAs, resulting in their elimination from the poles and potentially affecting localization of the encoded proteins.

Abstract

The polar transcriptome of E. coli is regulated by MinD-dependent inhibition of RNase E recruitment to the cell pole.