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Status |
Public on Aug 10, 2017 |
Title |
The Nucleoid Protein Dps Binds Genomic DNA of Escherichia coli in a Non-random Manner |
Organism |
Escherichia coli str. K-12 substr. MG1655 |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. Ferroxidase activity of Dps is rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. Using the ChIP-seq data presented here, we found a non-random distribution of Dps binding sites in the bacterial chromosome of exponentially growing cells and showed their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. The transcription activity of several Dps-targeted genes evaluated by qRT-PCR, showed dependence on the presence of Dps. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA or, vice versa, competing with inhibitors to activate transcription.
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Overall design |
ChIP-Seq for Dps from Escherichia coli K12 MG1655
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Contributor(s) |
Antipov SS, Tutukina MN, Preobrazhenskaya EV, Kondrashov FA, Patrushev MV, Toshchakov SV, Dominova I, Shvyreva US, Vrublevskaya VV, Morenkov OS, Sukharicheva NA, Panyukov VV, Ozoline ON |
Citation(s) |
28800583 |
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Submission date |
Jul 31, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Olga N Ozoline |
E-mail(s) |
[email protected]
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Organization name |
Institute of Cell Biophysics of Russian Academy of Sciences
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Department |
Functional Genomics and Cellular Stress
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Lab |
Functional Genomics and Cellular Stress
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Street address |
Institutskaya
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City |
Pushchino |
State/province |
Moscow Region |
ZIP/Postal code |
142290 |
Country |
Russia |
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Platforms (2) |
GPL15010 |
Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655) |
GPL17439 |
Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655) |
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Samples (4)
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Relations |
BioProject |
PRJNA396582 |
SRA |
SRP114473 |