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Multiple factors dictate target selection by Hfq‐binding small RNAs
Author(s) -
Beisel Chase L,
Updegrove Taylor B,
Janson Ben J,
Storz Gisela
Publication year - 2012
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1038/emboj.2012.52
Subject(s) - biology , base pair , pairing , binding site , transfer rna , genetics , rna , computational biology , dna , gene , physics , superconductivity , quantum mechanics
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.