Fig. 3.

Salmonella sRNA interactome and identification of ProQ as a recurrent sRNA binder. (A) Grad-seq PCA plot of 238 Salmonella sRNAs. PC2 and PC3 are selected to visualize sRNA clusters with finer detail (Materials and Methods provides further information). Only Hfq- and CsrA-associated sRNAs are highlighted (SI Appendix, Fig. S4 shows a complete functional sRNA assignment). sRNAs selected for MS2 aptamer tagging and pull down are circled. (B and C) Pull down of the selected MS2 aptamer-tagged sRNAs from Salmonella lysates and identification of their binding partners. (B) Heat map showing proteins specifically copurified with each MS2 aptamer-tagged sRNA (most ribosomal proteins are omitted for clarity) and Spearman’s correlation coefficients of their sedimentation profiles with the Grad-seq profiles of the bait sRNAs. ProQ is a particularly frequent partner of the selected sRNAs and their sedimentation profiles match, suggesting a stable interaction. (C) ProQ is enriched in the MS2 aptamer-tagged sRNA pull downs, compared with control baits or no bait, as visualized with specific antibodies.