Hexuronates influence the oligomeric form of the Dps structural protein of bacterial nucleoid and its ability to bind to linear DNA fragments

Bessonova, Tatiana A.; Shumeiko, S. A.; Purtov, Yuri A.; Antipov, S.S.; Preobrazhenskaya, Elena V.; Tutukina, Maria N.; Ozoline, Olga N.

doi:10.1134/s0006350916060075

Cited by 8 publications

(10 citation statements)

References 18 publications

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“…Some nutrients can fulfill this role during the exit from starvation. We recently found, for instance, that D-galacturonate and D-glucuronate, but not glucose, are capable of altering the oligomeric form of Dps [ 82 ], which may be crucial for remodeling. In any case, it became clear that interacting with genomic DNA Dps can affect expression of some genes.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2017

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2017

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“…Therefore, it is not surprising that iron ions affect the structure of the protein, which naturally interacts with them and plays a decisive role in the protective packaging of the bacterial chromosome. Data from both electrophoretic fractionation and gel filtration experiments are extremely convincing ( Figure 1 B,D), but the most important observation made in this study is the opposite effect of iron ions on the oligomeric state of Dps compared to hexuronates [ 14 ]. Since during the fasting, when almost the entire genome is covered with Dps [ 2 , 3 , 4 ], the concentration of iron ions in the bacterial cells is lower than in the rapidly growing culture [ 39 ], whereas the number of Dps molecules is ~15–30-fold greater [ 2 , 3 , 4 ], it is clear that the Dps particles cannot be saturated with iron and should be relatively unstable.…”

Section: Discussionmentioning

confidence: 79%

“…In AFM experiments, all our protein samples were fairly homogenous, usually containing less than 20% of particles smaller than dodecamers [ 18 ]; sedimentation experiments yielded ~10% of putative dimers [ 20 ], whereas dynamic light scattering revealed only one peak corresponding to dodecamers [ 20 ]. Using freshly prepared Dps, we did not observe small oligomers upon electrophoretic fractionation [ 14 ], but detected them with the addition of glucoronate or galacturonate [ 14 ]. Once we had found an opposite dependence on iron ions, we used a protein sample that contained both smaller oligomers and larger aggregates to show this.…”

Section: Resultsmentioning

confidence: 99%

“…That is why, it was reasonable to assume that the DNA-binding capacity of Dps can be modulated by components with a physiologically dependent presence in bacterial cells. Recently, two such ligands from the metabolic pathway, which are more energetically effective than glycolysis ( d -glucuronate and d -galacturonate) have been found [ 14 ]. By destabilizing the dodecameric form of Dps, they provide the bacteria with a mechanism that, in response to the appearance of nutrients, can stop Dps-mediated condensation of the genome, and consequently, restore its lost functionality.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, the integrity of the Dps globule may depend on the size and configuration of the particles formed at the centers of nucleation, and on the filling level of the inner cavity of the protein. The recently discovered dependence of the Dps oligomeric form on the presence of d -glucoronate and d -galacturonate, which causes the dissociation of dodecamers—while the d -glucose did not affect them—indicates a specific dependence of Dps on some low-molecular weight ligands [ 14 ]. The aim of this study is to understand whether the natural “internal ligands” of Dps can also affect its structural state.…”

Section: Introductionmentioning

confidence: 99%

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The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions

et al. 2017

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The Dps protein of Escherichia coli, which combines ferroxidase activity and the ability to bind DNA, is effectively used by bacteria to protect their genomes from damage. Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides; however, the diversity of its oligomeric forms has only been studied fragmentarily. Here, we show that iron ions stabilize the dodecameric form of Dps. This was found by electrophoretic fractionation and size exclusion chromatography, which revealed several oligomers in highly purified protein samples and demonstrated their conversion to dodecamers in the presence of 1 mM Mohr’s salt. The transmission electron microscopy data contradicted the assumption that the stabilizing effect is given by the optimal core size formed in the inner cavity of Dps. The charge state of iron ions was evaluated using Mössbauer spectroscopy, which showed the presence of Fe3O4, rather than the expected Fe2O3, in the sample. Assuming that Fe2+ can form additional inter-subunit contacts, we modeled the interaction of FeO and Fe2O3 with Dps, but the binding sites with putative functionality were predicted only for Fe2O3. The question of how the dodecameric form can be stabilized by ferric oxides is discussed.

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Dps Is a Universally Conserved Dual-Action DNA-Binding and Ferritin Protein

Orban

Finkel

2022

J Bacteriol

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Hexuronates influence the oligomeric form of the Dps structural protein of bacterial nucleoid and its ability to bind to linear DNA fragments

Cited by 8 publications

References 18 publications

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

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

The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions

Dps Is a Universally Conserved Dual-Action DNA-Binding and Ferritin Protein

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