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Replication of the E scherichia coli chromosome in RN ase HI ‐deficient cells: multiple initiation regions and fork dynamics
Author(s) -
Maduike Nkabuije Z.,
Tehranchi Ashley K.,
Wang Jue D.,
Kreuzer Kenneth N.
Publication year - 2014
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.12440
Subject(s) - biology , dnaa , ter protein , dna replication , rnase p , pre replication complex , genetics , origin of replication , origin recognition complex , control of chromosome duplication , seqa protein domain , microbiology and biotechnology , eukaryotic dna replication , dna , gene , rna
Summary DNA replication in E scherichia coli is normally initiated at a single origin, oriC , dependent on initiation protein DnaA . However, replication can be initiated elsewhere on the chromosome at multiple ectopic oriK sites. Genetic evidence indicates that initiation from oriK depends on RNA‐DNA hybrids ( R ‐loops), which are normally removed by enzymes such as RN ase HI to prevent oriK from misfiring during normal growth. Initiation from oriK sites occurs in RN ase HI ‐deficient mutants, and possibly in wild‐type cells under certain unusual conditions. Despite previous work, the locations of oriK and their impact on genome stability remain unclear. We combined 2 D gel electrophoresis and whole genome approaches to map genome‐wide oriK locations. The DNA copy number profiles of various RN ase HI ‐deficient strains contained multiple peaks, often in consistent locations, identifying candidate oriK sites. Removal of RN ase HI protein also leads to global alterations of replication fork migration patterns, often opposite to normal replication directions, and presumably eukaryote‐like replication fork merging. Our results have implications for genome stability, offering a new understanding of how RN ase HI deficiency results in R ‐loop‐mediated transcription‐replication conflict, as well as inappropriate replication stalling or blockage at T er sites outside of the terminus trap region and at ribosomal operons.