title: Spatial organization of transcription machinery and its  segregation from the replisome in fast-growing  bacterial cells.
abstract: In a fast-growing Escherichia coli cell, most RNA polymerase (RNAP) is allocated to rRNA synthesis forming transcription foci at clusters of rrn operons or bacterial nucleolus, and each of the several nascent nucleoids contains multiple pairs of replication forks. The composition of transcription foci has not been determined. In addition, how the transcription machinery is three-dimensionally organized to promote cell growth in concord with replication machinery in the nucleoid remains essentially unknown. Here, we determine the spatial and functional landscapes of transcription and replication machineries in fast-growing E. coli cells using super-resolution-structured illumination microscopy. Co-images of RNAP and DNA reveal spatial compartmentation and duplication of the transcription foci at the surface of the bacterial chromosome, encompassing multiple nascent nucleoids. Transcription foci cluster with NusA and NusB, which are the rrn anti-termination system and are associated with nascent rRNAs. However, transcription foci tend to separate from SeqA and SSB foci, which track DNA replication forks and/or the replisomes, demonstrating that transcription machinery and replisome are mostly located in different chromosomal territories to maintain harmony between the two major cellular functions in fast-growing cells. Our study suggests that bacterial chromosomes are spatially and functionally organized, analogous to eukaryotes.
authors.forename: Cedric
authors.initials: C
authors.lastname: Cagliero
authors.forename: Yan Ning
authors.initials: YN
authors.lastname: Zhou
authors.forename: Ding Jun
authors.initials: DJ
authors.lastname: Jin
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000032:analysis*; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000032:analysis; D020459:Genes, rRNA; D009097:Multienzyme Complexes / Q000032:analysis*; D010445:Peptide Elongation Factors / Q000032:analysis; D016601:RNA-Binding Proteins / Q000032:analysis; D014157:Transcription Factors / Q000032:analysis; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors; D000099272:Replisomes
chemical_list: D001426:Bacterial Proteins; D004259:DNA-Directed DNA Polymerase; D029968:Escherichia coli Proteins; D009097:Multienzyme Complexes; D010445:Peptide Elongation Factors; D016601:RNA-Binding Proteins; D014157:Transcription Factors; D035602:Transcriptional Elongation Factors; D000099272:Replisomes; C074952:NusB protein, E coli; C064872:antiterminator proteins, Bacteria; C068727:nusA protein, E coli