title: Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus.
abstract: The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180° on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Tamas
authors.initials: T
authors.lastname: Gaal
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Bratton
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Sanchez-Vazquez
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sliwicki
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Kristine
authors.initials: K
authors.lastname: Sliwicki
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Vegel
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Pannu
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Gourse
mesh_terms: D002876:Chromosomes, Bacterial / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D009697:Nucleolus Organizer Region; D009876:Operon / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D011938:Rec A Recombinases / Q000378:metabolism
chemical_list: D012329:RNA, Bacterial; D011938:Rec A Recombinases
keywords: ParB-CFP and YFP fusions; bacterial chromosome structure; long-distance chromosomal interactions; nucleolus; rRNA operons