Feedback regulation of small RNA processing by the cleavage product

ABSTRACT

Many bacterial small RNAs (sRNAs) are processed resulting in variants with roles potentially distinct from the primary sRNAs. In Enterobacteriaceae sRNA GlmZ activates expression of glmS by base-pairing when the levels of glucosamine-6-phosphate (GlcN6P) are low. GlmS synthesizes GlcN6P, which is required for cell envelope biosynthesis. When dispensable, GlmZ is cleaved by RNase E in the base-pairing sequence. Processing requires protein RapZ, which binds GlmZ and recruits RNase E by interaction. Cleavage is counteracted by the homologous sRNA GlmY, which accumulates upon GlcN6P scarcity and sequesters RapZ. Here, we report a novel role for a processed sRNA. We observed that processing of GlmZ is never complete in vivo. Even upon RapZ overproduction, a fraction of GlmZ remains full-length, while the 5ʹ cleavage product (GlmZ*) accumulates. GlmZ* retains all elements required for RapZ binding. Accordingly, GlmZ* can displace full-length GlmZ from RapZ and counteract processing in vitro. To mimic GlmZ* in vivo, sRNA chimeras were employed consisting of foreign 3ʹ ends including a terminator fused to the 3ʹ end of GlmZ*. In vitro, these chimeras perform indistinguishable from GlmZ*. Expression of the chimeras in vivo inhibited processing of endogenous GlmZ, causing moderate upregulation of GlmS synthesis. Hence, accumulation of GlmZ* prevents complete GlmZ turnover. This mechanism may serve to adjust a robust glmS basal expression level that is buffered against fluctuations in RapZ availability.

KEYWORDS:

• Small RNA GlmZ
• RNase E
• adaptor protein RapZ
• RNA processing
• feedback regulation

Acknowledgments

We thank Isabella Moll for providing S2 antiserum and plasmid pACA-RNA43^SD, Bernard Badet for the GlmS antiserum and Yvonne Göpel for construction of plasmid pYG135. We are grateful to Eliane Hajnsdorf for the gift of strain JC357 and to Muna A. Khan for construction of strain Z946. This work was supported by the ‘Austrian Science Fund’ (FWF) through the Special Research Program RNA-REG F43 under grant number F4317 (to B.G) and the Doktoratskolleg RNA Biology W1207-B09.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplemental material

Supplementary data for this article can be accessed here

Additional information

Funding

This work was supported by the Austrian Science Fund [Doktoratskolleg RNA Biology W1207-B09]; Austrian Science Fund [RNA-REG F43; F4317].