Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators
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 kineti...
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doaj-e691deedae4c409898c5742a69ce88c42021-10-01T04:57:39ZengElsevierCell Reports2211-12472021-09-013613109764Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulatorsMatthew A. Reyer0Shriram Chennakesavalu1Emily M. Heideman2Xiangqian Ma3Magda Bujnowska4Lu Hong5Aaron R. Dinner6Carin K. Vanderpool7Jingyi Fei8Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USADepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USADepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USADepartment of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USADepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USAGraduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USAGraduate 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, USADepartment of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USAGraduate 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 authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2211124721012183bacterial small RNAgene regulationfluorescence microscopymathematical modeling |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Matthew A. Reyer Shriram Chennakesavalu Emily M. Heideman Xiangqian Ma Magda Bujnowska Lu Hong Aaron R. Dinner Carin K. Vanderpool Jingyi Fei |
spellingShingle |
Matthew A. Reyer Shriram Chennakesavalu Emily M. Heideman Xiangqian Ma Magda Bujnowska Lu Hong Aaron R. Dinner Carin K. Vanderpool Jingyi Fei Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators Cell Reports bacterial small RNA gene regulation fluorescence microscopy mathematical modeling |
author_facet |
Matthew A. Reyer Shriram Chennakesavalu Emily M. Heideman Xiangqian Ma Magda Bujnowska Lu Hong Aaron R. Dinner Carin K. Vanderpool Jingyi Fei |
author_sort |
Matthew A. Reyer |
title |
Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators |
title_short |
Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators |
title_full |
Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators |
title_fullStr |
Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators |
title_full_unstemmed |
Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators |
title_sort |
kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional srna regulators |
publisher |
Elsevier |
series |
Cell Reports |
issn |
2211-1247 |
publishDate |
2021-09-01 |
description |
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. |
topic |
bacterial small RNA gene regulation fluorescence microscopy mathematical modeling |
url |
http://www.sciencedirect.com/science/article/pii/S2211124721012183 |
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