title: Multiple factors dictate target selection by Hfq-binding small RNAs.
abstract: Hfq-binding small RNAs (sRNAs) in bacteria modulate the stability and translational efficiency of target mRNAs through limited base-pairing interactions. While these sRNAs are known to regulate numerous mRNAs as part of stress responses, what distinguishes targets and non-targets among the mRNAs predicted to base pair with Hfq-binding sRNAs is poorly understood. Using the Hfq-binding sRNA Spot 42 of Escherichia coli as a model, we found that predictions using only the three unstructured regions of Spot 42 substantially improved the identification of previously known and novel Spot 42 targets. Furthermore, increasing the extent of base-pairing in single or multiple base-pairing regions improved the strength of regulation, but only for the unstructured regions of Spot 42. We also found that non-targets predicted to base pair with Spot 42 lacked an Hfq-binding site, folded into a secondary structure that occluded the Spot 42 targeting site, or had overlapping Hfq-binding and targeting sites. By modifying these features, we could impart Spot 42 regulation on non-target mRNAs. Our results thus provide valuable insights into the requirements for target selection by sRNAs.
authors.affiliation: Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA. cbeisel@ncsu.edu
authors.forename: Chase L
authors.initials: CL
authors.lastname: Beisel
authors.forename: Taylor B
authors.initials: TB
authors.lastname: Updegrove
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Janson
authors.forename: Gisela
authors.initials: G
authors.lastname: Storz
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D004926:Escherichia coli / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000378:metabolism*; D035683:MicroRNAs / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017421:Sequence Analysis
chemical_list: D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D035683:MicroRNAs