Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators

• Published in: Cell reports (Cambridge) 2021-09, Vol.36 (13), p.109764-109764, Article 109764
• Main Authors: Reyer, Matthew A., Chennakesavalu, Shriram, Heideman, Emily M., Ma, Xiangqian, Bujnowska, Magda, Hong, Lu, Dinner, Aaron R., Vanderpool, Carin K., Fei, Jingyi
• Format: Article
• Language: English
• Subjects: Bacteria - genetics; Bacteria - metabolism; Bacterial Physiological Phenomena; bacterial small RNA; Escherichia coli - genetics; fluorescence microscopy; Gene Expression Regulation, Bacterial - genetics; gene regulation; mathematical modeling; Regulon - genetics; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Messenger - metabolism; RNA, Small Untranslated - genetics; RNA, Small Untranslated - metabolism
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2021.109764

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. [Display omitted] •SgrS and RyhB can regulate transcripts as soon as their binding sites exit the RNAP•Co-transcriptional regulation is promoted by Rho-dependent termination•Binding to the target mRNA is the primary determinant of hierarchical regulation•Co- and post-transcriptional level regulation all contribute to overall efficiency Reyer et al. use fluorescent microscopy and kinetic modeling to find that two sRNAs canonically described as post-transcriptional regulators can regulate their targets co-transcriptionally and determine the in vivo kinetic parameters that dictate differential regulation efficiency.