Aug 12, 2017

The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner

PloS One
Sergey S AntipovOlga N Ozoline

Abstract

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. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show 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 g...Continue Reading

Mentioned in this Paper

Rosaniline Dyes
Real-Time Polymerase Chain Reaction
Direct Repeat
Hematite
Gene Expression Regulation, Bacterial
Transcriptional Regulation
RHO gene
Deoxyribonuclease I
Bacterial Proteins
Molecular Helix

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