title: RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA.
abstract: Base-pairing interactions between nucleic acids mediate target recognition in many biological processes. We developed a super-resolution imaging and modeling platform that enabled the in vivo determination of base pairing-mediated target recognition kinetics. We examined a stress-induced bacterial small RNA, SgrS, which induces the degradation of target messenger RNAs (mRNAs). SgrS binds to a primary target mRNA in a reversible and dynamic fashion, and formation of SgrS-mRNA complexes is rate-limiting, dictating the overall regulation efficiency in vivo. Examination of a secondary target indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other small RNA systems and other target search processes.
authors: Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA.
authors: Jingyi
authors: J
authors: Fei
authors: Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA.
authors: Digvijay
authors: D
authors: Singh
authors: Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA.
authors: Qiucen
authors: Q
authors: Zhang
authors: Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA.
authors: Seongjin
authors: S
authors: Park
authors: Department of Microbiology, University of Illinois, Urbana, IL, USA.
authors: Divya
authors: D
authors: Balasubramanian
authors: Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
authors: Ido
authors: I
authors: Golding
authors: Department of Microbiology, University of Illinois, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu.
authors: Carin K
authors: CK
authors: Vanderpool
authors: Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA. Carl R. Woese Institute for Genomic Biology, Howard Hughes Medical Institute, Urbana, IL, USA. Howard Hughes Medical Institute, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu.
authors: Taekjip
authors: T
authors: Ha
mesh_terms: D020029:Base Pairing; D004722:Endoribonucleases / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D057054:Molecular Imaging / Q000379:methods*; D009154:Mutation; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000235:genetics; D020871:RNA Stability; D012333:RNA, Messenger / Q000737:chemistry*; D058727:RNA, Small Untranslated / Q000737:chemistry*
chemical_list: D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C031629:phosphoenolpyruvate-glucose phosphotransferase; D004722:Endoribonucleases; C022537:ribonuclease E