title: The Consequences of Replicating in the Wrong Orientation: Bacterial Chromosome Duplication without an Active Replication Origin.
abstract: Chromosome replication is regulated in all organisms at the assembly stage of the replication machinery at specific origins. In Escherichia coli, the DnaA initiator protein regulates the assembly of replication forks at oriC. This regulation can be undermined by defects in nucleic acid metabolism. In cells lacking RNase HI, replication initiates independently of DnaA and oriC, presumably at persisting R-loops. A similar mechanism was assumed for origin-independent synthesis in cells lacking RecG. However, recently we suggested that this synthesis initiates at intermediates resulting from replication fork fusions. Here we present data suggesting that in cells lacking RecG or RNase HI, origin-independent synthesis arises by different mechanisms, indicative of these two proteins having different roles in vivo. Our data support the idea that RNase HI processes R-loops, while RecG is required to process replication fork fusion intermediates. However, regardless of how origin-independent synthesis is initiated, a fraction of forks will proceed in an orientation opposite to normal. We show that the resulting head-on encounters with transcription threaten cell viability, especially if taking place in highly transcribed areas. Thus, despite their different functions, RecG and RNase HI are both important factors for maintaining replication control and orientation. Their absence causes severe replication problems, highlighting the advantages of the normal chromosome arrangement, which exploits a single origin to control the number of forks and their orientation relative to transcription, and a defined termination area to contain fork fusions. Any changes to this arrangement endanger cell cycle control, chromosome dynamics, and, ultimately, cell viability.
  
  
  OBJECTIVE
  Cell division requires unwinding of millions of DNA base pairs to generate the template for RNA transcripts as well as chromosome replication. As both processes use the same template, frequent clashes are unavoidable. To minimize the impact of these clashes, transcription and replication in bacteria follow the same directionality, thereby avoiding head-on collisions. This codirectionality is maintained by a strict regulation of where replication is started. We have used Escherichia coli as a model to investigate cells in which the defined location of replication initiation is compromised. In cells lacking either RNase HI or RecG, replication initiates away from the defined replication origin, and we discuss the different mechanisms by which this synthesis arises. In addition, the resulting forks proceed in a direction opposite to normal, thereby inducing head-on collisions between transcription and replication, and we show that the resulting consequences are severe enough to threaten the viability of cells.
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.
authors.forename: Juachi U
authors.initials: JU
authors.lastname: Dimude
authors.affiliation: Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Center, Nottingham, United Kingdom.
authors.forename: Anna
authors.initials: A
authors.lastname: Stockum
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Midgley-Smith
authors.forename: Amy L
authors.initials: AL
authors.lastname: Upton
authors.affiliation: Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.
authors.forename: Helen A
authors.initials: HA
authors.lastname: Foster
authors.affiliation: Research Institute of Health, Life and Societies, Brunel University London, Uxbridge, United Kingdom.
authors.forename: Arshad
authors.initials: A
authors.lastname: Khan
authors.affiliation: Research Institute of Health, Life and Societies, Brunel University London, Uxbridge, United Kingdom.
authors.forename: Nigel J
authors.initials: NJ
authors.lastname: Saunders
authors.affiliation: School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom.
authors.forename: Renata
authors.initials: R
authors.lastname: Retkute
authors.affiliation: christian.rudolph@brunel.ac.uk.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Rudolph
mesh_terms: D058674:Chromosome Duplication; D002876:Chromosomes, Bacterial / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D050296:Microbial Viability; D018741:Replication Origin; D016914:Ribonuclease H / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; C071446:RecG protein, E coli; D016914:Ribonuclease H; C078856:ribonuclease HI