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Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein.

Wang HC, Wu ML, Ko TP, Wang AH - Nucleic Acids Res. (2013)

Bottom Line: Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU.Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication.The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

ABSTRACT
DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

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Comparison of two DNA mimic proteins that bind to HU. (A) Comparison of the structure and charge distribution of Neisseria DMP12 monomer and Haemophilus HI1450 (protein data bank accession number: 1NNV). (B) Rooted phylogenetic tree of DMP12 and HI1450 homologs with branch lengths.
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gkt201-F6: Comparison of two DNA mimic proteins that bind to HU. (A) Comparison of the structure and charge distribution of Neisseria DMP12 monomer and Haemophilus HI1450 (protein data bank accession number: 1NNV). (B) Rooted phylogenetic tree of DMP12 and HI1450 homologs with branch lengths.

Mentions: DMP12 is not the only DNA mimic protein that targets bacterial HU protein. Parsons et al. (22, 33) reported Haemophilus HI1450 as another DNA mimic that interacts with bacterial HU. However, these two proteins have many different features. We are currently working to extend our understanding of how new DNA mimics might be identified, but in this case, we note that although the DMP12 and HI1450 core structures fold into four matching β-strands in antiparallel configuration with an RMSD (root mean square deviation) fit of 1.05 Å for 21 Cα atoms (Supplementary Figure 8A), no other significant similarities can be found between these two structures: both their charge distributions and their shapes are also different (Figure 6A and Supplementary Figure 8A). Phylogenetic analysis also shows that these two proteins are classified into two distinct groups (Figure 6B; Supplementary Figure 8B and C). All of this suggests that HI1450 and DMP12 probably interact with bacterial HU protein for different purposes. Moreover, the biological roles of both HU-bound DNA mimic proteins in the bacteria need to be further clarified. Until now, no biological function of HI1450 is proposed. The HI1450 homolog (yciU) knockout E. coli strain still maintains the normal cell shape, and it suggests this protein is not necessary for E. coli survival [National BioResource Project (NBRP); http://www.shigen.nig.ac.jp]. However, the increasing growth rate of DMP12 expressing E. coli suggests this protein may manipulate expression of bacterial genome to favor replication (Supplementary Figure S7), and it encourages more studies to understand this issue.Figure 6.


Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein.

Wang HC, Wu ML, Ko TP, Wang AH - Nucleic Acids Res. (2013)

Comparison of two DNA mimic proteins that bind to HU. (A) Comparison of the structure and charge distribution of Neisseria DMP12 monomer and Haemophilus HI1450 (protein data bank accession number: 1NNV). (B) Rooted phylogenetic tree of DMP12 and HI1450 homologs with branch lengths.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643605&req=5

gkt201-F6: Comparison of two DNA mimic proteins that bind to HU. (A) Comparison of the structure and charge distribution of Neisseria DMP12 monomer and Haemophilus HI1450 (protein data bank accession number: 1NNV). (B) Rooted phylogenetic tree of DMP12 and HI1450 homologs with branch lengths.
Mentions: DMP12 is not the only DNA mimic protein that targets bacterial HU protein. Parsons et al. (22, 33) reported Haemophilus HI1450 as another DNA mimic that interacts with bacterial HU. However, these two proteins have many different features. We are currently working to extend our understanding of how new DNA mimics might be identified, but in this case, we note that although the DMP12 and HI1450 core structures fold into four matching β-strands in antiparallel configuration with an RMSD (root mean square deviation) fit of 1.05 Å for 21 Cα atoms (Supplementary Figure 8A), no other significant similarities can be found between these two structures: both their charge distributions and their shapes are also different (Figure 6A and Supplementary Figure 8A). Phylogenetic analysis also shows that these two proteins are classified into two distinct groups (Figure 6B; Supplementary Figure 8B and C). All of this suggests that HI1450 and DMP12 probably interact with bacterial HU protein for different purposes. Moreover, the biological roles of both HU-bound DNA mimic proteins in the bacteria need to be further clarified. Until now, no biological function of HI1450 is proposed. The HI1450 homolog (yciU) knockout E. coli strain still maintains the normal cell shape, and it suggests this protein is not necessary for E. coli survival [National BioResource Project (NBRP); http://www.shigen.nig.ac.jp]. However, the increasing growth rate of DMP12 expressing E. coli suggests this protein may manipulate expression of bacterial genome to favor replication (Supplementary Figure S7), and it encourages more studies to understand this issue.Figure 6.

Bottom Line: Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU.Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication.The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

ABSTRACT
DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

Show MeSH
Related in: MedlinePlus