title: Characterization of Intrinsic Properties of Promoters.
abstract: Accurate characterization of promoter behavior is essential for the rational design of functional synthetic transcription networks such as logic gates and oscillators. However, transcription rates observed from promoters can vary significantly depending on the growth rate of host cells and the experimental and genetic contexts of the measurement. Furthermore, in vivo measurement methods must accommodate variation in translation, protein folding, and maturation rates of reporter proteins, as well as metabolic load. The external factors affecting transcription activity may be considered to be extrinsic, and the goal of characterization should be to obtain quantitative measures of the intrinsic characteristics of promoters. We have developed a promoter characterization method that is based on a mathematical model for cell growth and reporter gene expression and exploits multiple in vivo measurements to compensate for variation due to extrinsic factors. First, we used optical density and fluorescent reporter gene measurements to account for the effect of differing cell growth rates. Second, we compared the output of reporter genes to that of a control promoter using concurrent dual-channel fluorescence measurements. This allowed us to derive a quantitative promoter characteristic (ρ) that provides a robust measure of the intrinsic properties of a promoter, relative to the control. We imposed different extrinsic factors on growing cells, altering carbon source and adding bacteriostatic agents, and demonstrated that the use of ρ values reduced the fraction of variance due to extrinsic factors from 78% to less than 4%. This is a simple and reliable method to quantitatively describe promoter properties.
authors.affiliation: Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge CB2 3EA, United Kingdom.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Rudge
authors.affiliation: Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge CB2 3EA, United Kingdom.|Biological Computation Group, Microsoft Research , Cambridge CB1 2FB, United Kingdom.
authors.forename: James R
authors.initials: JR
authors.lastname: Brown
authors.affiliation: Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge CB2 3EA, United Kingdom.|Departamento de Genética Molecular y Microbiologia, Faculty de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile.
authors.forename: Fernan
authors.initials: F
authors.lastname: Federici
authors.affiliation: Biological Computation Group, Microsoft Research , Cambridge CB1 2FB, United Kingdom.
authors.forename: Neil
authors.initials: N
authors.lastname: Dalchau
authors.affiliation: Biological Computation Group, Microsoft Research , Cambridge CB1 2FB, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Phillips
authors.affiliation: Department of Pathology, University of Cambridge , Tennis Court Road, Cambridge CB2 1QP, United Kingdom.
authors.forename: James W
authors.initials: JW
authors.lastname: Ajioka
authors.affiliation: Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge CB2 3EA, United Kingdom.
authors.forename: Jim
authors.initials: J
authors.lastname: Haseloff
mesh_terms: D005453:Fluorescence; D017930:Genes, Reporter; D008164:Luminescent Proteins / Q000378:metabolism; D010957:Plasmids / Q000378:metabolism; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis
chemical_list: D008164:Luminescent Proteins
keywords: characterization; design; fluorescence; modeling; promoter; quantification; ratiometric; transcription