Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation

Abstract

Hfq is a global regulator of gene expression in bacteria undergoing adaptation to changing environmental conditions. Its major function is to promote RNA-RNA interactions between regulatory small RNAs (sRNAs) and their target mRNAs. Previously, we demonstrated that Hfq binds many antisense RNAs (asRNAs) in vitro and hypothesized that Hfq may play a role in regulating gene expression via asRNAs. To investigate the E. coli Hfq-binding transcriptome in more detail, we co-immunoprecipitated and deep-sequenced RNAs bound to Hfq in vivo. We detected many new Hfq-binding sRNAs and observed that almost 300 mRNAs bind to Hfq. Among these, several are known to be sRNA targets. We identified 25 novel RNAs, which are transcribed from within protein coding regions and named them intragenic RNAs (intraRNAs). Furthermore, 67 asRNAs were co-immunoprecipitated with Hfq, demonstrating that Hfq binds antisense transcripts in vivo. Northern blot analyses confirmed the deep sequencing results and demonstrated that many of the novel Hfq-binding RNAs identified are regulated by Hfq.

Keywords: :

• Hfq
• Hfq co-immunoprecipitation
• Hfq aptamers
• sRNA
• asRNAs
• igRNAs
• intraRNAs

10.4161/rna.29299

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

We thank members of the Schroeder laboratory for thoughtful and critical readings of the manuscript, Maarja Lepamets for implementing the peak-calling algorithm, and Bojan Vilagos for assistance with graphical design in the manuscript preparation. We thank members of the Schroeder laboratory for useful discussion and Johanna Stranner for excellent technical assistance. This work was supported by the Austrian Science Fund FWF, grants no. I538 and F4301 to RS and the University of Vienna.