title: Distance matters: the impact of gene proximity in bacterial gene regulation.
abstract: Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system, we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences.
authors.affiliation: Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.
authors.forename: Otto
authors.initials: O
authors.lastname: Pulkkinen
authors.forename: Ralf
authors.initials: R
authors.lastname: Metzler
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001665:Binding Sites; D004269:DNA, Bacterial / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D008957:Models, Genetic; D013269:Stochastic Processes; D014157:Transcription Factors / Q000235:genetics*; D015533:Transcriptional Activation
chemical_list: D004269:DNA, Bacterial; D014157:Transcription Factors