Different RNA recognition by ProQ and FinO depends on the sequence surrounding intrinsic terminator hairpins

<i>Escherichia coli</i> ProQ and FinO proteins both have RNA-binding FinO domains, which bind to intrinsic transcription terminators, but each protein recognizes distinct RNAs. To explore how ProQ and FinO discriminate between RNAs, we transplanted sequences surrounding terminator hairpins between RNAs specific for each protein, and compared their binding to ProQ, the isolated FinO domain of ProQ (ProQ^NTD), and FinO. The results showed that the binding specificity of chimeric RNAs toward ProQ, ProQ^NTD, or FinO was determined by the origin of the transplanted sequence. Further analysis showed that the sequence surrounding the terminator hairpin, including a purine-purine mismatch, in natural RNA ligands of FinO and in chimeric RNAs, weakened their binding by ProQ^NTD Overall, our studies suggest that RNA sequence elements surrounding the intrinsic terminator hairpin contribute to the discrimination between RNAs by ProQ and FinO.