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Escherichia coli str. K-12 substr. MG1655

ABSTRACT: The Nucleoid Protein Dps Binds Genomic DNA of Escherichia coli in a Non-random Manner

PROVIDER: PRJNA396582 | ENA |

REPOSITORIES: ENA

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The Nucleoid Protein Dps Binds Genomic DNA of Escherichia coli in a Non-random Manner

Project description: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.

2017-08-10 | GSE102091 | GEO

RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

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RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

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exoRNA-mediated Cell-to-cell Communications in E. coli are Supported by Dps Mobility

Project description:Being a ferroxidase and a structural factor of the Escherichia coli nucleoid, Dps protein was recently encountered in the outer membrane and attracted attention as a potential partner for bacterial RNAs. Here, we show the first images visualizing Dps on the surface of bacteria and demonstrate that Dps produced by E. coli K-12 MG1655 or BL21(DE3) cells can cross bacteria-impermeable membrane and attach to the cell surface of a dps-null mutant. Using RNAseq and pull-down assays, we identified RNAs with specifically reduced secretion in the mutant and witnessed preferential interaction of Dps with tRNA and sRNA fragments. Upon analysis of their deviations from the genomic sequences, we selected one circular and six linear oligonucleotides with different folding as model RNAs and showed their ability to affect the growth of bacteria via Dps-dependent internalization by cells. This assumes Dps involvement in intercellular signal transduction within a bacterial population through participation in RNA secretion

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Escherichia coli str. K-12 substr. MG1655

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YAMAT-seq of mature tRNA pools in the bacterium Escherichia coli str. K-12 substr. MG1655 and derivatives

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Project description:Characterisation of Modular Reponse of non-pathogenic E.coli K12 MG1655 Response to acid adaptation, part A

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