title: Genome scale patterns of supercoiling in a bacterial chromosome.
abstract: DNA in bacterial cells primarily exists in a negatively supercoiled state. The extent of supercoiling differs between regions of the chromosome, changes in response to external conditions and regulates gene expression. Here we report the use of trimethylpsoralen intercalation to map the extent of supercoiling across the Escherichia coli chromosome during exponential and stationary growth phases. We find that stationary phase E. coli cells display a gradient of negative supercoiling, with the terminus being more negatively supercoiled than the origin of replication, and that such a gradient is absent in exponentially growing cells. This stationary phase pattern is correlated with the binding of the nucleoid-associated protein HU, and we show that it is lost in an HU deletion strain. We suggest that HU establishes higher supercoiling near the terminus of the chromosome during stationary phase, whereas during exponential growth DNA gyrase and/or transcription equalizes supercoiling across the chromosome.
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India.
authors.forename: Avantika
authors.identifier: http://orcid.org/0000-0002-5827-0826
authors.initials: A
authors.lastname: Lal
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.
authors.forename: Amlanjyoti
authors.initials: A
authors.lastname: Dhar
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.
authors.forename: Andrei
authors.initials: A
authors.lastname: Trostel
authors.affiliation: Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.
authors.forename: Fedor
authors.initials: F
authors.lastname: Kouzine
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India.
authors.forename: Aswin S N
authors.initials: AS
authors.lastname: Seshasayee
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.
authors.forename: Sankar
authors.initials: S
authors.lastname: Adhya
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D002876:Chromosomes, Bacterial / Q000235:genetics*; D027081:DNA Gyrase / Q000378:metabolism; D004278:DNA, Superhelical / Q000235:genetics*; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics; D005363:Ficusin / Q000494:pharmacology; D016680:Genome, Bacterial; D006918:Hydroxyurea / Q000494:pharmacology; D011485:Protein Binding / Q000187:drug effects; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D001426:Bacterial Proteins; D004278:DNA, Superhelical; D027081:DNA Gyrase; D005363:Ficusin; D006918:Hydroxyurea