Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

Abstract

Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are “carved out” from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.

Feedback regulation of small RNA processing by the cleavage product

“…Indeed, additional presence of GlmZ* in the assay inhibited GlmZ cleavage when supplied at concentrations of ≥16 nM (Figure 2(b), lanes 7-9). Inhibition of GlmZ cleavage by GlmZ* was less efficient as compared to GlmY, which impeded GlmZ processing already at a concentration of ≥8 nM (Figure 2(b), lanes [10][11][12][13][14]. Taken together, GlmZ* competes with full-length GlmZ for RapZ binding, thereby counteracting GlmZ processing in vitro, but with a somewhat lower efficiency than observed for GlmY.…”

“…However, RNase E also has important roles for sRNA biogenesis and maturation. Several sRNAs are known to be produced from the 3ʹ region of protein coding genes, either through usage of an internal promoter or by RNase E catalyzed mRNA processing [11][12][13], and regulatory roles for sRNAs generated through the latter mechanism were demonstrated in various species including E. coli and Salmonella [14][15][16][17]. An additional class of sRNAs is autonomously transcribed, but undergoes maturation.…”

Genome‐wide screen and functional analysis in Xanthomonas reveal a large number of mRNA‐derived sRNAs, including the novel RsmA‐sequester RsmU

“…The majority of bacterial sRNAs so far identified are encoded within IGRs and are independently transcribed (Vogel et al ., 2003; Kawano et al ., 2005; Loh et al ., 2009; Chao et al ., 2012; Chao and Vogel, 2016; Dar and Sorek 2018). Nevertheless, a few 3′‐UTR‐derived sRNAs (Kawano et al ., 2005; Kim et al ., 2014; Chao and Vogel, 2016; Chao et al ., 2017; Eisenhardt et al ., 2018; Miyakoshi et al ., 2019), 5′‐UTR‐derived sRNAs (Kawano et al ., 2005; Drecktrah et al ., 2018), and protein coding region‐derived sRNAs (called decay‐generated noncoding RNAs [decRNAs]) (Dar and Sorek, 2018) have been reported in different bacterial species. Surprisingly, our study demonstrated that, in Xcc, mRNA processing is the primary source of cellular sRNA, suggesting a close link between sRNA biogenesis and mRNA decay.…”

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

“…These can be transcribed from promoters internal to the coding sequence or cleaved from the longer mRNA. There also are hints of sRNAs being derived from 5′ UTRs (11,20) and possibly even from within coding sequences (90). To generate the specific small transcript in these cases, there need to be promoters, terminators, or ribonuclease cleavage sites internal or adjacent to the coding sequence.…”