Silencing of natural transformation by an RNA chaperone and a multitarget small RNA

Abstract

A highly conserved DNA uptake system allows many bacteria to actively import and integrate exogenous DNA. This process, called natural transformation, represents a major mechanism of horizontal gene transfer (HGT) involved in the acquisition of virulence and antibiotic resistance determinants. Despite evidence of HGT and the high level of conservation of the genes coding the DNA uptake system, most bacterial species appear non-transformable under laboratory conditions. In naturally transformable species, the DNA uptake system is only expressed when bacteria enter a physiological state called competence, which develops under specific conditions. Here, we investigated the mechanism that controls expression of the DNA uptake system in the human pathogen Legionella pneumophila. We found that a repressor of this system displays a conserved ProQ/FinO domain and interacts with a newly characterized trans-acting sRNA, RocR. Together, they target mRNAs of the genes coding the DNA uptake system to control natural transformation. This RNA-based silencing represents a previously unknown regulatory means to control this major mechanism of HGT. Importantly, these findings also show that chromosome-encoded ProQ/FinO domain-containing proteins can assist trans-acting sRNAs and that this class of RNA chaperones could play key roles in post-transcriptional gene regulation throughout bacterial species.natural transformation | RNA chaperone | non-coding RNA | Legionella pneumophila | ProQ/FinO

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein

“…Our discovery of a large class of ProQ-associated sRNAs opens the door for further studies of this potential domain of posttranscriptional control, which will likely reveal molecular mechanisms and physiological roles of RNA in bacteria. Indeed, a recent study in Legionella identified a ProQ-like protein as a matchmaker of sRNA-mRNA interactions in the regulation of bacterial competence (46).…”

Structure of the Escherichia coli ProQ RNA-binding protein

“…This region, delineated by residues R32, R69, R80, R100, K101, K107, and R114 (Fig. 2B, left panel) surrounds a surface patch identified on the homologous L. pneumophila RocC protein that is important for RNA binding and protein function (Attaiech et al 2016). This positively charged surface patch also maps to a conserved protected region in our HDX experiments, indicating this area is important for RNA binding.…”

“…However, ProQ has now emerged to function more broadly as a global sRNA binding protein in Salmonella, and a similar role is predicted for proteins containing ProQ/FinO domains found in divergent bacterial species (Smirnov et al 2016). In Legionella pneumophila, a ProQ/FinO domain protein has been shown to be required for regulation of an sRNA controlling natural competence (Attaiech et al 2016).…”

“…To date, a small number of proteins have been identified that specifically bind to sRNA molecules in numerous bacterial species, including Hfq, CsrA, and more recently FinO-like proteins (Romeo et al 2013;Wagner and Romby 2015;Attaiech et al 2016;Smirnov et al 2016Smirnov et al , 2017. The protein ProQ, a FinO family member, was originally identified as an osmoregulatory factor required for optimal expression of the proline channel protein ProP (Kunte et al 1999;Chaulk et al 2011;Kerr et al 2014).…”

Small Regulatory RNAs of Rickettsia conorii

“…Hypothetical proteins such as HP1334 in H. pylori and several other RNA binding proteins such as YbeY in Sinorhizobium meliloti have been implicated with chaperone activity5758. More recently, a ProQ/FinO domain containing protein Lpp0148 has been reported to function as a RNA chaperone in Legionella pneumophila 59. It is, therefore, possible that R. conorii proteins with unknown function may play a role in sRNA-mediated regulation.…”