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Interactions of archaeal chromatin proteins Alba1 and Alba2 with nucleic acids.

Črnigoj M, Podlesek Z, Zorko M, Jerala R, Anderluh G, Ulrih NP - PLoS ONE (2013)

Bottom Line: Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT).The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures.Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

View Article: PubMed Central - PubMed

Affiliation: Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

ABSTRACT

Background: Architectural proteins have important roles in compacting and organising chromosomal DNA. There are two potential histone counterpart peptide sequences (Alba1 and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823).

Methodology/principal findings: THESE TWO PEPTIDES WERE EXPRESSED AND THEIR INTERACTIONS WITH VARIOUS DNAS WERE STUDIED USING A COMBINATION OF VARIOUS EXPERIMENTAL TECHNIQUES: surface plasmon resonance, UV spectrophotometry, circular dichroism-spectropolarimetry, gel-shift assays, and isothermal titration calorimetry.

Conclusions/significance: Our data indicate that there are significant differences in the properties of the Alba1 and Alba2 proteins. Both of these Alba proteins can thermally stabilise DNA polynucleotides, as seen from UV melting curves. Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT). Surface plasmon resonance sensorgrams for binding of Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 to DNA oligonucleotides show different binding patterns. Circular dichroism indicates that Alba2 has a less-ordered secondary structure than Alba1. The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures. Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

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CD spectra of Alba2.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba2 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). Molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).
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pone-0058237-g008: CD spectra of Alba2.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba2 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). Molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).

Mentions: The intensity of the far-UV CD spectra of Alba2 (Figure 8a) did not change significantly with temperature, as was observed for Alba1. The calculated amount of secondary structure elements for Alba2 from the CD spectra were 11% α-helices, 60% β-sheet, and 29% β-turns. These data would suggest that the Alba2 protein does not change in secondary structure according to temperature, in the temperature range studied. In the presence of CT-DNA (at a molar ratio of 1∶5) (Figure 8b), as with Alba1, Alba2 also adopted a more ordered structure as the temperature increased from 25°C to 90°C. In the presence of AT-DNA (at a molar ratio of 1∶5), the molar ellipticity of the far-UV CD spectra of Alba2 was lower, representing a less-ordered structure (Figure 8c), although the molar ellipticity increased with temperature. In the presence of GC-DNA (at the molar ratio of 1∶5), the far-UV CD spectra of Alba2 at 25°C showed spectral characteristics typical of a disordered structure. As the temperature increased, the structure became more ordered, with a higher content of β-strands. When the temperature approached 90°C, the structure became less ordered again, similar to that at 25°C (Figure 8d). Again, the explanation for these structural changes might be related to the equilibrium of dsDNA↔ 2× ssDNA (Table 1).


Interactions of archaeal chromatin proteins Alba1 and Alba2 with nucleic acids.

Črnigoj M, Podlesek Z, Zorko M, Jerala R, Anderluh G, Ulrih NP - PLoS ONE (2013)

CD spectra of Alba2.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba2 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). Molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585288&req=5

pone-0058237-g008: CD spectra of Alba2.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba2 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). Molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).
Mentions: The intensity of the far-UV CD spectra of Alba2 (Figure 8a) did not change significantly with temperature, as was observed for Alba1. The calculated amount of secondary structure elements for Alba2 from the CD spectra were 11% α-helices, 60% β-sheet, and 29% β-turns. These data would suggest that the Alba2 protein does not change in secondary structure according to temperature, in the temperature range studied. In the presence of CT-DNA (at a molar ratio of 1∶5) (Figure 8b), as with Alba1, Alba2 also adopted a more ordered structure as the temperature increased from 25°C to 90°C. In the presence of AT-DNA (at a molar ratio of 1∶5), the molar ellipticity of the far-UV CD spectra of Alba2 was lower, representing a less-ordered structure (Figure 8c), although the molar ellipticity increased with temperature. In the presence of GC-DNA (at the molar ratio of 1∶5), the far-UV CD spectra of Alba2 at 25°C showed spectral characteristics typical of a disordered structure. As the temperature increased, the structure became more ordered, with a higher content of β-strands. When the temperature approached 90°C, the structure became less ordered again, similar to that at 25°C (Figure 8d). Again, the explanation for these structural changes might be related to the equilibrium of dsDNA↔ 2× ssDNA (Table 1).

Bottom Line: Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT).The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures.Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

View Article: PubMed Central - PubMed

Affiliation: Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

ABSTRACT

Background: Architectural proteins have important roles in compacting and organising chromosomal DNA. There are two potential histone counterpart peptide sequences (Alba1 and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823).

Methodology/principal findings: THESE TWO PEPTIDES WERE EXPRESSED AND THEIR INTERACTIONS WITH VARIOUS DNAS WERE STUDIED USING A COMBINATION OF VARIOUS EXPERIMENTAL TECHNIQUES: surface plasmon resonance, UV spectrophotometry, circular dichroism-spectropolarimetry, gel-shift assays, and isothermal titration calorimetry.

Conclusions/significance: Our data indicate that there are significant differences in the properties of the Alba1 and Alba2 proteins. Both of these Alba proteins can thermally stabilise DNA polynucleotides, as seen from UV melting curves. Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT). Surface plasmon resonance sensorgrams for binding of Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 to DNA oligonucleotides show different binding patterns. Circular dichroism indicates that Alba2 has a less-ordered secondary structure than Alba1. The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures. Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

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