DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli

• Published in: PLoS genetics Vol. 14; no. 1; p. e1007161
• Main Authors: Henrikus, Sarah S, Wood, Elizabeth A, McDonald, John P, Cox, Michael M, Woodgate, Roger, Goodman, Myron F, van Oijen, Antoine M, Robinson, Andrew
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 19-01-2018; Public Library of Science (PLoS)
• Subjects: Antibiotics; Binding Sites - genetics; Biochemistry; Biology and life sciences; Childrens health; Ciprofloxacin; Deoxyribonucleic acid; DNA; DNA biosynthesis; DNA damage; DNA Damage - genetics; DNA polymerase; DNA Polymerase beta - metabolism; DNA Polymerase beta - physiology; DNA polymerases; DNA repair; DNA Replication; DNA sequencing; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA-directed DNA polymerase; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins; Funding; Gene Expression Regulation, Bacterial; Gene Fusion; Genetic aspects; Genomes; Health aspects; Intermediates; Laboratories; Methods; Microscopy; Mutagenesis; Mutation; RecA protein; Recombination; Replication forks; Research and Analysis Methods; Single-stranded DNA; Software; SOS response; SOS Response, Genetics - genetics; Transcription; Ultraviolet radiation; Australia; United States > US; Maryland; Wisconsin
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1007161

In Escherichia coli, damage to the chromosomal DNA induces the SOS response, setting in motion a series of different DNA repair and damage tolerance pathways. DNA polymerase IV (pol IV) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DNA damage. The canonical view in the field is that pol IV primarily acts at replisomes that have stalled on the damaged DNA template. However, the results of several studies indicate that pol IV also acts on other substrates, including single-stranded DNA gaps left behind replisomes that re-initiate replication downstream of a lesion, stalled transcription complexes and recombination intermediates. In this study, we use single-molecule time-lapse microscopy to directly visualize fluorescently labelled pol IV in live cells. We treat cells with the DNA-damaging antibiotic ciprofloxacin, Methylmethane sulfonate (MMS) or ultraviolet light and measure changes in pol IV concentrations and cellular locations through time. We observe that only 5-10% of foci induced by DNA damage form close to replisomes, suggesting that pol IV predominantly carries out non-replisomal functions. The minority of foci that do form close to replisomes exhibit a broad distribution of colocalisation distances, consistent with a significant proportion of pol IV molecules carrying out postreplicative TLS in gaps behind the replisome. Interestingly, the proportion of pol IV foci that form close to replisomes drops dramatically in the period 90-180 min after treatment, despite pol IV concentrations remaining relatively constant. In an SOS-constitutive mutant that expresses high levels of pol IV, few foci are observed in the absence of damage, indicating that within cells access of pol IV to DNA is dependent on the presence of damage, as opposed to concentration-driven competition for binding sites.