Abstract
DNA mimicry is a direct and effective strategy by which the mimic competes with DNA for the DNA binding sites on other proteins. Until now, only about a dozen proteins have been shown to function via this strategy, including the DNA mimic protein DMP19 from Neisseria meningitides. We have shown previously that DMP19 dimer prevents the operator DNA from binding to the transcription factor NHTF. Here, we provide new evidence that DMP19 monomer can also interact with the Neisseria nucleoid-associated protein HU. Using BS3 crosslinking, gel filtration and isothermal titration calorimetry assays, we found that DMP19 uses its monomeric form to interact with the Neisseria HU dimer. Crosslinking conjugated mass spectrometry was used to investigate the binding mode of DMP19 monomer and HU dimer. Finally, an electrophoretic mobility shift assay (EMSA) confirmed that the DNA binding affinity of HU is affected by DMP19. These results showed that DMP19 is bifunctional in the gene regulation of Neisseria through its variable oligomeric forms.
Highlights
Protein-DNA interactions are very important to the control of cellular mechanisms such as gene regulation, DNA repair and recombination [1]
When we used BS3 crosslinking assays to search for new interactions between DNA mimic proteins and DNA binding proteins, we found that DMP19 could interact with Neisseria HU (Fig 1A)
Consistent with our previous reports [5,6], the observed molecular weights of both the DMP19 and Neisseria HU proteins were close to the theoretical molecular weights of their dimeric forms in the gel filtration analysis (Table 1)
Summary
Protein-DNA interactions are very important to the control of cellular mechanisms such as gene regulation, DNA repair and recombination [1]. DNA mimic proteins are one of the emerging control factors that affect these interactions by occupying the DNA binding sites on the proteins [1,2,3]. Control factors of this category usually present with DNA phosphate backbone-like negative surface charge distributions and DNA double helical groove-like shapes to deceive the DNA binding proteins [1,2,3]. Fewer than 20 DNA mimic proteins have been reported so far, and much more basic research is still needed to fully understand the novel mechanisms of these control factors [3].
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