Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators
Matthew A. Reyer,
Shriram Chennakesavalu,
Emily M. Heideman,
Xiangqian Ma,
Magda Bujnowska,
Lu Hong,
Aaron R. Dinner,
Carin K. Vanderpool,
Jingyi Fei
Affiliations
Matthew A. Reyer
Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
Shriram Chennakesavalu
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
Emily M. Heideman
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
Xiangqian Ma
Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
Magda Bujnowska
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
Lu Hong
Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
Aaron R. Dinner
Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
Carin K. Vanderpool
Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
Jingyi Fei
Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Corresponding author
Summary: Small RNAs (sRNAs) are important gene regulators in bacteria. Many sRNAs act post-transcriptionally by affecting translation and degradation of the target mRNAs upon base-pairing interactions. Here we present a general approach combining imaging and mathematical modeling to determine kinetic parameters at different levels of sRNA-mediated gene regulation that contribute to overall regulation efficacy. Our data reveal that certain sRNAs previously characterized as post-transcriptional regulators can regulate some targets co-transcriptionally, leading to a revised model that sRNA-mediated regulation can occur early in an mRNA’s lifetime, as soon as the sRNA binding site is transcribed. This co-transcriptional regulation is likely mediated by Rho-dependent termination when transcription-coupled translation is reduced upon sRNA binding. Our data also reveal several important kinetic steps that contribute to the differential regulation of mRNA targets by an sRNA. Particularly, binding of sRNA to the target mRNA may dictate the regulation hierarchy observed within an sRNA regulon.
