Abstract
The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.
Highlights
In all domains of life, regulatory RNAs are versatile modulators of gene expression, and their actions are facilitated by protein chaperones with which they cooperate to achieve specificity and rapid response (Wagner and Romby 2015)
To further investigate the mechanism of small RNAs (sRNAs) binding by ProQ, mass spectrometry combined with hydrogen deuterium exchange experiments (HDX) was used to probe regions of ProQ that exhibit altered exchange profiles upon RNA binding
The results from the hydrogen–deuterium exchange (HDX) experiments are mapped as color-coded surfaces on the nuclear magnetic resonance (NMR) structures of the Nand C-terminal domains of ProQ (Fig. 7) and peptide coverage maps for these experiments are shown in Supplemental Figures S6 and S7
Summary
In all domains of life, regulatory RNAs are versatile modulators of gene expression, and their actions are facilitated by protein chaperones with which they cooperate to achieve specificity and rapid response (Wagner and Romby 2015). Ranging in size from 50–250 nucleotides (nt), sRNAs typically act by imperfectly base-pairing with their mRNA targets using a cognate seed region. This recognition can result in different downstream effects, depending on context. The sRNA:mRNA interaction can target the mRNA for rapid degradation, often by the multienzyme RNA degradosome assembly (Fei et al 2015; Wagner and Romby 2015). The sRNA:mRNA interaction can target the mRNA for rapid degradation, often by the multienzyme RNA degradosome assembly (Fei et al 2015; Wagner and Romby 2015). sRNAs can operate on actively transcribed genes by modulating the process of transcription termination (Sedlyarova et al 2016)
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