Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

FopA is a global RBP that targets structured RNAs. (A) The major targeted RNA was the antisense RNA lnc, followed by STnc1590, mgtM, and STnc700 (log₂-fold change >4, n = 17). The RNA targetome of FopA was very different to ProQ recovered RNAs that were reanalyzed differently from Smirnov et al. (2016). (B) FopA targeted RNAs were analyzed for conservation motifs by the CMfinder algorithm. Homologs were searched by GLASSgo (1.5.0, Freiburg RNA tools [Lott et al. 2018]). The CMfinder algorithm determined RNA motifs (0.4.1.18 [Yao et al. 2005]), and R2R was used for visualization (1.0.6 [Weinberg and Breaker 2011]). (C) FopA-coIP read-coverage of the repZ locus. Inc is heavily enriched, together with the sparsely expressed repZ mRNA.