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Series GSE150240 Query DataSets for GSE150240
Status Public on Aug 04, 2023
Title The Fur Pan-regulon in E. coli shows diversity in strain-specific sets of target genes
Organisms Escherichia coli; Salmonella enterica; Escherichia coli K-12; Escherichia coli O157:H7
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. Using ChIP-exo experiments, we performed a comprehensive study of Fur binding sites in nine Escherichia coli strains with different lifestyles. 79 of the 431 target genes (18%) found belong to Fur’s core regulon, comprising genes involved in ion transport and metabolism, energy production and conversion, and amino acid metabolism and transport. 179 of the target genes (42%) comprise the accessory regulon, most of which were related to cell wall structure and biogenesis, and virulence factor pathways. The remaining target genes (173 or 40%) were in the unique regulon, with gene functions that were largely unknown. Furthermore, deletion of the fur gene led to distinct phenotypes in growth, motility, antibiotic resistance, and siderophore production. These results provide a more complete understanding of how Fur regulates a set of target genes with surprising variation in closely related bacteria.
Overall design Identification of genome-wide bindings for nine different E. coli strains using ChIP-exo technology
Contributor(s) Gao Y
Citation(s) 37026477
Submission date May 11, 2020
Last update date Aug 05, 2023
Contact name Ye Gao
Organization name UCSD
Street address 9500 Gilman Dr.
City La Jolla
ZIP/Postal code 92093
Country USA
Platforms (4)
GPL21433 Illumina HiSeq 4000 (Escherichia coli)
GPL24377 Illumina HiSeq 4000 (Escherichia coli K-12)
GPL28511 Illumina HiSeq 4000 (Escherichia coli O157:H7)
Samples (36)
GSM4543902 W3110_Fur_Fe_1
GSM4543903 W3110_Fur_Fe_2
GSM4543904 W3110_Fur_DPD_1
BioProject PRJNA631626
SRA SRP261075

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
GSE150240_RAW.tar 1.4 Gb (http)(custom) TAR (of GFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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