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Series GSE100657 Query DataSets for GSE100657
Status Public on Sep 13, 2018
Title A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication
Organism Caulobacter vibrioides NA1000
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary When DNA is unwound during replication, it becomes overtwisted and forms positive supercoils in front of the translocating DNA polymerase. Unless removed or dissipated, this superhelical tension can impede replication elongation. Topoisomerases, including gyrase and topoisomerase IV in bacteria, are required to relax positive supercoils ahead of DNA polymerase, but may not be sufficient for replication. Here, we find that GapR, a chromosome structuring protein in Caulobacter crescentus, is required to complete DNA replication. GapR associates in vivo with positively supercoiled chromosomal DNA, and our biochemical and structural studies demonstrate that GapR forms a dimer-of-dimers that fully encircles overtwisted DNA. Further, we show that GapR stimulates gyrase and topo IV to relax positive supercoils, thereby enabling DNA replication. Analogous chromosome structuring proteins that locate to the overtwisted DNA in front of replication forks may be present in other organisms, similarly helping to recruit and stimulate topoisomerases during DNA replication.
Overall design Sequencing experiments from Caulobacter crescentus CB15N wild-type, GapR-3xFLAG, and GapR-depleted cells. (i) RNA-seq after GapR depletion, (ii) GapR-3xFLAG ChIP-seq, (iii) cell-cycle DNA-seq after GapR depletion.
Contributor(s) Guo MS, Haakonsen DL, Zeng W, Schumacher MA, Laub MT
Citation(s) 30220456
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM082899 Cell cycle regulation and chromosome organization in Caulobacter crescentus MASSACHUSETTS INSTITUTE OF TECHNOLOGY Michael Laub
R01 GM115563 Assembly and partition mechanism of Walker-box based segregation machinery DUKE UNIVERSITY Maria Schumacher
Submission date Jun 29, 2017
Last update date Jul 25, 2021
Contact name Monica S Guo
Organization name University of Washington
Department Microbiology
Lab Guo
Street address 750 Republican St
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
Platforms (2)
GPL18276 Illumina HiSeq 2000 (Caulobacter crescentus NA1000)
GPL20784 Illumina MiSeq (Caulobacter crescentus NA1000)
Samples (21)
GSM2690549 Negative control ChIP-seq
GSM2690550 GapR-3xFLAG ChIP-seq
GSM2690551 Rif treated GapR-3xFLAG ChIP-seq
BioProject PRJNA392436
SRA SRP110755

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Supplementary file Size Download File type/resource
GSE100657_RAW.tar 282.0 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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