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Series GSE158570 Query DataSets for GSE158570
Status Public on Mar 22, 2021
Title Genome-wide tracking of Escherichia coli DNA polymerase V to the lagging strand during the SOS response
Organism Escherichia coli
Experiment type Other
Summary Ribonucleotides are frequently incorporated into DNA and can be used as a marker of DNA replication enzymology. To investigate on a genome-wide scale, how E. coli pol V accesses undamaged chromosomal DNA during the SOS response, we mapped the location of ribonucleotides incorporated by steric gate variants of pol V across the entire E. coli genome. To do so, we used strains that are deficient in ribonucleotide excision repair (DrnhB), constitutively express all SOS-regulated genes [lexA(Def)] and constitutively “activated” RecA* (recA730). The strains also harbor two steric gate variants of E. coli pol V (Y11A or F10L), or a homolog of pol V, (pol VR391-Y13A). Ribonucleotides are frequently incorporated by the pol V-Y11A and pol VR391-Y13A variants, with a preference to the lagging strand. In contrast, the pol V-F10L variant incorporates less ribonucleotides and no strand preference was observed. Sharp transitions in strand specificity are observed at replication origin (oriC), while a gradient is observed at the termination region. To activate RecA* in a recA+ strain, we treated the strains with ciprofloxacin and genome-wide mapped the location of the incorporated ribonucleotides. Again, the polV-Y11A steric gate variant, exhibited a lagging strand preference. Our data is consistent with a specific role for pol V in lagging strand DNA synthesis across the entire E. coli genome during the SOS response.
 
Overall design Mapping ribonucleotides in DNA from E. coli that induced SOS-response in combination with various steric gate variants of polV that allow more ribonucleotides to be incororated with HydEn-seq (5´end sequencing of genomic fragments generated by alkaline hydrolysis).
 
Contributor(s) Faraz M, Woodgate R, Clausen AR
Citation(s) 33662762
Submission date Sep 25, 2020
Last update date Jul 09, 2021
Contact name Anders R. Clausen
E-mail(s) anders.r.clausen@hotmail.com
Organization name University of Gothenburg
Street address Box 440
City Göteborg
ZIP/Postal code 40530
Country Sweden
 
Platforms (1)
GPL21222 Illumina NextSeq 500 (Escherichia coli)
Samples (51)
GSM4803071 lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pGB2-replicate1
GSM4803072 lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pRW134-replicate1
GSM4803073 lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782 ::kan with pJM963-replicate3
Relations
BioProject PRJNA665690
SRA SRP285381

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE158570_RAW.tar 214.2 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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