title: Shaping the landscape of the Escherichia coli chromosome: replication-transcription encounters in cells with an ectopic replication origin.
abstract: Each cell division requires the unwinding of millions of DNA base pairs to allow chromosome duplication and gene transcription. As DNA replication and transcription share the same template, conflicts between both processes are unavoidable and head-on collisions are thought to be particularly problematic. Surprisingly, a recent study reported unperturbed cell cycle progression in Escherichia coli cells with an ectopic replication origin in which highly transcribed rrn operons were forced to be replicated opposite to normal. In this study we have re-generated a similar strain and found the doubling time to be twice that of normal cells. Replication profiles of this background revealed significant deviations in comparison to wild-type profiles, particularly in highly transcribed regions and the termination area. These deviations were alleviated by mutations that either inactivate the termination area or destabilise RNA polymerase complexes and allow their easier displacement by replication forks. Our data demonstrate that head-on replication-transcription conflicts are highly problematic. Indeed, analysis of the replication profile of the previously published E. coli construct revealed a chromosomal rearrangement that alleviates replication-transcription conflicts in an intriguingly simple way. Our data support the idea that avoiding head-on collisions has significantly contributed to shaping the distinct architecture of bacterial chromosomes.
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
authors.forename: Darja
authors.initials: D
authors.lastname: Ivanova
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
authors.forename: Toni
authors.initials: T
authors.lastname: Taylor
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Smith
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
authors.forename: Juachi U
authors.initials: JU
authors.lastname: Dimude
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Amy L
authors.initials: AL
authors.lastname: Upton
authors.affiliation: The Faculty of Health Sciences, Department of Cellular and Molecular Medicine, Copenhagen University, 2200 Copenhagen N, Denmark.
authors.forename: Mana M
authors.initials: MM
authors.lastname: Mehrjouy
authors.affiliation: Department of Science, Systems and Models, Roskilde University, DK-4000 Roskilde, Denmark.
authors.forename: Ole
authors.initials: O
authors.lastname: Skovgaard
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Sherratt
authors.affiliation: School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
authors.forename: Renata
authors.initials: R
authors.lastname: Retkute
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK christian.rudolph@brunel.ac.uk.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Rudolph
mesh_terms: D002876:Chromosomes, Bacterial; D004261:DNA Replication; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D018741:Replication Origin; D014158:Transcription, Genetic