title: Direct comparison of small RNA and transcription factor signaling.
abstract: Small RNAs (sRNAs) and proteins acting as transcription factors (TFs) are the principal components of gene networks. These two classes of signaling molecules have distinct mechanisms of action; sRNAs control mRNA translation, whereas TFs control mRNA transcription. Here, we directly compare the properties of sRNA and TF signaling using mathematical models and synthetic gene circuits in Escherichia coli. We show the abilities of sRNAs to act on existing target mRNAs (as opposed to TFs, which alter the production of future target mRNAs) and, without needing to be first translated, have surprisingly little impact on the dynamics. Instead, the dynamics are primarily determined by the clearance rates, steady-state concentrations and response curves of the sRNAs and TFs; these factors determine the time delay before a target gene's expression can maximally respond to changes in sRNA and TF transcription. The findings are broadly applicable to the analysis of signaling in gene networks, and we demonstrate that they can be used to rationally reprogram the dynamics of synthetic circuits.
authors.affiliation: Department of Integrative Biology, University of California, 1005 Valley Life Sciences Building, Mail Code 3140, Berkeley, CA 94720-3140, USA.
authors.forename: Razika
authors.initials: R
authors.lastname: Hussein
authors.forename: Han N
authors.initials: HN
authors.lastname: Lim
mesh_terms: D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D014176:Protein Biosynthesis; D058727:RNA, Small Untranslated / Q000378:metabolism*; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D058727:RNA, Small Untranslated; D014157:Transcription Factors