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

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 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. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. 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 polymerase or, vice versa, competing with inhibitors to activate transcription.

Protective Dps–DNA co‐crystallization in stressed cells: an in vitro structural study by small‐angle X‐ray scattering and cryo‐electron tomography

“…It is known that a high ordered Dps–DNA complex is not always formed. In our study we demonstrate that the co‐crystallization does not depend on the length of the DNA if it is longer than 3000 bp, and does not depend on the Dps/DNA ratio, although the most pronounced ordering is formed at the Dps/DNA ratio 1 Dps dodecamer to 66 bp of DNA, according to the previously published data . It is worth noting that our study was performed using Dps extracted from E. coli .…”

Excessive Promoters as Silencers of Genes Horizontally Acquired by Escherichia coli

“…The position weight matrices for motifs recognized by 82 transcription factors were built using aligned sequences of their binding sites collected in RegPrecise 4 (Novichkov et al, 2013). Matrices for 26 transcription factors, including H-NS, were taken from the Virtual Footprint collection 5 (Münch et al, 2005), while the matrix for the nucleoid protein Dps was obtained using original ChIP-seq data (Antipov et al, 2017). Sequence Logos for Supplementary Image 1 were generated by WebLogo 3 6 (Crooks et al, 2004).…”

Chromatinization ofEscherichia coliwith archaeal histones

“…Genomic regions bound by Fis and H-NS were obtained from (Kahramanoglou et al, 2011), regions bound by IHF from (Prieto et al, 2012), and regions bound by Dps from (Antipov et al, 2017). Differential histone occupancy was computed between regions bound by a given NAP and the unbound region immediately downstream.…”