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Series GSE71860 Query DataSets for GSE71860
Status Public on Aug 06, 2016
Title Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (ChIP-seq)
Organism Caulobacter vibrioides NA1000
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism.
Overall design An allele of phoB bearing a C-terminal 3x-flag tag was integrated at its native locus, and ChIP followed by deep sequencing on Illumina MiSeq was performed on samples grown in rich medium, phosphate-limited medium, and in a pstS::Tn5 mutant background in rich medium.
Contributor(s) Laub MT, Lubin EA
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Submission date Aug 07, 2015
Last update date May 15, 2019
Contact name Michael Laub
Organization name MIT
Street address 31 Ames St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (1)
GPL20784 Illumina MiSeq (Caulobacter crescentus NA1000)
Samples (6)
GSM1847005 PYE_control
GSM1847006 PYE_treat
GSM1847007 M5G_control
This SubSeries is part of SuperSeries:
GSE71961 Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus
BioProject PRJNA292618
SRA SRP062286

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Supplementary file Size Download File type/resource
GSE71860_RAW.tar 7.1 Mb (http)(custom) TAR (of WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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