ArticleBMC systems biology2010
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria.
Article in BMC systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- In Vivo Quantification of Surfactin Nonribosomal Peptide Synthetase Complexes inMicroorganisms · 2024Article
- Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity.Biophysical journal · 2022Article
- Accurate characterization of dynamic microbial gene expression and growth rate profiles.Synthetic biology (Oxford, England) · 2022Article
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- Article
- Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate.Journal of bacteriology · 2019Article
- WellInverter: a web application for the analysis of fluorescent reporter gene data.BMC bioinformatics · 2019Article
- Dynamic Modeling ofFrontiers in microbiology · 2018Article
- Quantitative Analysis of Intracellular Response Regulator Phosphatase Activity of Histidine Kinases.Methods in enzymology · 2018Article
- Glucose-Dependent Promoters for Dynamic Regulation of Metabolic Pathways.Frontiers in bioengineering and biotechnology · 2018Article
- The Long Hunt forJournal of bacteriology · 2017Article
- Genes on a Wire: The Nucleoid-Associated Protein HU Insulates Transcription Units in Escherichia coli.Scientific reports · 2016Article
- A Modular, Tn7-Based System for Making Bioluminescent or Fluorescent Salmonella and Escherichia coli Strains.Applied and environmental microbiology · 2016Article
- Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27.Journal of bacteriology · 2016Article
- Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection.PLoS computational biology · 2016Article
- Characterization of Intrinsic Properties of Promoters.ACS synthetic biology · 2016Article
- A synthetic growth switch based on controlled expression of RNA polymerase.Molecular systems biology · 2015Article
- Robust reconstruction of gene expression profiles from reporter gene data using linear inversion.Bioinformatics (Oxford, England) · 2015Article
- Inference of quantitative models of bacterial promoters from time-series reporter gene data.PLoS computational biology · 2015Article
- Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers.BMC biotechnology · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFluorescent and luminescent reporter genes have become popular tools for the real-time monitoring of gene expression in living cells. However, mathematical models are necessary for extracting biologically meaningful quantities from the primary data.
resultsWe present a rigorous method for deriving relative protein synthesis rates (mRNA concentrations) and protein concentrations by means of kinetic models of gene expression. We experimentally and computationally validate this approach in the case of the protein Fis, a global regulator of transcription in Escherichia coli. We show that the mRNA and protein concentration profiles predicted from the models agree quite well with direct measurements obtained by Northern and Western blots, respectively. Moreover, we present computational procedures for taking into account systematic biases like the folding time of the fluorescent reporter protein and differences in the half-lives of reporter and host gene products. The results show that large differences in protein half-lives, more than mRNA half-lives, may be critical for the interpretation of reporter gene data in the analysis of the dynamics of regulatory systems.
conclusionsThe paper contributes to the development of sound methods for the interpretation of reporter gene data, notably in the context of the reconstruction and validation of models of regulatory networks. The results have wide applicability for the analysis of gene expression in bacteria and may be extended to higher organisms.
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