title: In vivo tests of thermodynamic models of transcription repressor function.
abstract: One emphasis of the Gibbs Conference on Biothermodynamics is the value of thermodynamic measurements for understanding behaviors of biological systems. In this study, the correlation between thermodynamic measurements of in vitro DNA binding affinity with in vivo transcription repression was investigated for two transcription repressors. In the first system, which comprised an engineered LacI/GalR homolog, mutational changes altered the equilibrium constant for binding DNA. Changes correlated with altered repression, but estimates of in vivo repressor concentration suggest a ≥25-fold discrepancy with in vitro conditions. In the second system, changes in ligand binding to BirA altered dimerization and subsequent DNA occupancy. Again, these changes correlate with altered in vivo repression, but comparison with in vitro measurements reveals a ~10-fold discrepancy. Further analysis of each system suggests that the observed discrepancies between in vitro and in vivo results reflect the contributions of additional equilibria to the transcription repression process.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States.
authors.forename: Sudheer
authors.initials: S
authors.lastname: Tungtur
authors.forename: Harlyn
authors.initials: H
authors.lastname: Skinner
authors.forename: Hongli
authors.initials: H
authors.lastname: Zhan
authors.forename: Liskin
authors.initials: L
authors.lastname: Swint-Kruse
authors.forename: Dorothy
authors.initials: D
authors.lastname: Beckett
mesh_terms: D001665:Binding Sites; D019731:Carbon-Nitrogen Ligases / Q000378:metabolism*; D004269:DNA, Bacterial / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D007763:Lac Operon; D056968:Lac Repressors / Q000235:genetics / Q000378:metabolism*; D008957:Models, Genetic; D016296:Mutagenesis; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; C050993:Galactose repressor proteins; D056968:Lac Repressors; D012097:Repressor Proteins; D019731:Carbon-Nitrogen Ligases; C058125:birA protein, E coli