title: Quantitative characterization of gene regulation by Rho dependent transcription termination.
abstract: Rho factor dependent transcription termination (RTT) is common within the coding sequences of bacterial genes and it acts to couple transcription and translation levels. Despite the importance of RTT for gene regulation, its effects on mRNA and protein concentrations have not been quantitatively characterized. Here we demonstrate that the exogenous cfp gene encoding the cyan fluorescent protein can serve as a model for gene regulation by RTT. This was confirmed by showing that Psu and bicyclomycin decrease RTT and increase full length cfp mRNAs (but remarkably they have little effect on protein production). We then use cfp to characterize the relationship between its protein and full length mRNA concentrations when the translation initiation rate is varied by sequence modifications of the translation initiation region (TIR). These experiments reveal that the fold change in protein concentration (RP) and the fold change in full length mRNA concentration (Rm) have the relationship RP≈Rm(b), where b is a constant. The average value of b was determined from three separate data sets to be ~3.6. We demonstrate that the above power law function can predict how altering the translation initiation rate of a gene in an operon will affect the mRNA concentrations of downstream genes and specify a lower bound for the associated changes in protein concentrations. In summary, this study defines a simple phenomenological model to help program expression from single genes and operons that are regulated by RTT, and to guide molecular models of RTT.
authors.affiliation: Department of Integrative Biology, 3040 Valley Life Sciences Building, Mail code 3140, University of California Berkeley, Berkeley, CA 94720-3140, USA.
authors.forename: Razika
authors.initials: R
authors.lastname: Hussein
authors.affiliation: Department of Integrative Biology, 3040 Valley Life Sciences Building, Mail code 3140, University of California Berkeley, Berkeley, CA 94720-3140, USA.
authors.forename: Tiffany Y
authors.initials: TY
authors.lastname: Lee
authors.affiliation: Department of Integrative Biology, 3040 Valley Life Sciences Building, Mail code 3140, University of California Berkeley, Berkeley, CA 94720-3140, USA. Electronic address: hanlim@berkeley.edu.
authors.forename: Han N
authors.initials: HN
authors.lastname: Lim
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D019086:Bridged Bicyclo Compounds, Heterocyclic / Q000494:pharmacology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000235:genetics*; D007763:Lac Operon / Q000235:genetics; D008957:Models, Genetic; D012234:Rho Factor / Q000502:physiology*; D013728:Terminator Regions, Genetic; D061806:Transcription Termination, Genetic / Q000187:drug effects
chemical_list: D000900:Anti-Bacterial Agents; D019086:Bridged Bicyclo Compounds, Heterocyclic; C485182:Cyan Fluorescent Protein; D012234:Rho Factor; D049452:Green Fluorescent Proteins; C024504:bicozamycin
keywords: Allometric scaling; RNase E; Rho factor dependent transcription termination; Synthetic biology; Transcription–translation coupling; mRNA degradation