title: DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle.
abstract: The chromosomal DNA polymer constituting the cellular genetic material is primarily a device for coding information. Whilst the gene sequences comprise the digital (discontinuous) linear code, physiological alterations of the DNA superhelical density generate in addition analog (continuous) three-dimensional information essential for regulation of both chromosome compaction and gene expression. Insight into the relationship between the DNA analog information and the digital linear code is of fundamental importance for understanding genetic regulation. Our previous study in the model organism Escherichia coli suggested that the chromosomal gene order and a spatiotemporal gradient of DNA superhelicity associated with DNA replication determine the growth phase-dependent gene transcription. In this study we reveal a general gradient of DNA thermodynamic stability correlated with the polarity of chromosomal replication and manifest in the spatiotemporal pattern of gene transcription during the bacterial growth cycle. Furthermore, by integrating the physical and dynamic features of the transcribed sequences with their functional content we identify spatiotemporal domains of gene expression encompassing different functions. We thus provide both an insight into the organisational principle of the bacterial growth program and a novel holistic methodology for exploring chromosomal dynamics.
authors.affiliation: Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, D-28759 Bremen, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Sobetzko
authors.forename: Monika
authors.initials: M
authors.lastname: Glinkowska
authors.forename: Andrew
authors.initials: A
authors.lastname: Travers
authors.forename: Georgi
authors.initials: G
authors.lastname: Muskhelishvili
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D004278:DNA, Superhelical / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D013816:Thermodynamics
chemical_list: D004269:DNA, Bacterial; D004278:DNA, Superhelical