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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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Sequence composition of the Alba proteins.The amino-acid sequences of Alba1 (APE1832.1–APA1) and Alba2 (APE1823–APA2) from A. pernix was aligned with those of the homologous proteins from Sulfolobus shibitae Alba1 (P60849– SSA1) and S. solfataricus Alba2 (Q97ZF4–SSA2). The positively charged amino acids (R and K), phenylalanine (F), tyrosine (Y) and cysteine (C) are marked.
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pone-0058237-g012: Sequence composition of the Alba proteins.The amino-acid sequences of Alba1 (APE1832.1–APA1) and Alba2 (APE1823–APA2) from A. pernix was aligned with those of the homologous proteins from Sulfolobus shibitae Alba1 (P60849– SSA1) and S. solfataricus Alba2 (Q97ZF4–SSA2). The positively charged amino acids (R and K), phenylalanine (F), tyrosine (Y) and cysteine (C) are marked.

Mentions: Alba2 is expressed at 5% to 10% of the Alba 1 protein levels [8]. The fact that Alba2 forms heterodimers with Alba1, which behave similarly to Alba2 based on our SPR and UV melting curves (thermal stabilisation of AT sequences, precipitation of GC sequences), and differently than Alba1 might provide a mechanism for the control of chromatin packaging in this organism, as was suggested for the Alba1/Alba2 heterodimer from S. solfataricus[8], [24]. However, a functionally crucial difference between the S. solfataricus Alba1 and Alba2 proteins is the presence of an F60 residue in Alba1, which is not conserved in Alba2, while in Alba2 from A. pernix, a phenylalanine is at position 58 (Figure 12). It appears that the Aeropyrum homologues both contain the equivalent of this residue, and are thus both Alba1-type proteins. This might mean that potential heterodimer formation does not have such distinct effects on DNA binding as seen with the Sulfolobus proteins [24], [27].


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)

Sequence composition of the Alba proteins.The amino-acid sequences of Alba1 (APE1832.1–APA1) and Alba2 (APE1823–APA2) from A. pernix was aligned with those of the homologous proteins from Sulfolobus shibitae Alba1 (P60849– SSA1) and S. solfataricus Alba2 (Q97ZF4–SSA2). The positively charged amino acids (R and K), phenylalanine (F), tyrosine (Y) and cysteine (C) are marked.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585288&req=5

pone-0058237-g012: Sequence composition of the Alba proteins.The amino-acid sequences of Alba1 (APE1832.1–APA1) and Alba2 (APE1823–APA2) from A. pernix was aligned with those of the homologous proteins from Sulfolobus shibitae Alba1 (P60849– SSA1) and S. solfataricus Alba2 (Q97ZF4–SSA2). The positively charged amino acids (R and K), phenylalanine (F), tyrosine (Y) and cysteine (C) are marked.
Mentions: Alba2 is expressed at 5% to 10% of the Alba 1 protein levels [8]. The fact that Alba2 forms heterodimers with Alba1, which behave similarly to Alba2 based on our SPR and UV melting curves (thermal stabilisation of AT sequences, precipitation of GC sequences), and differently than Alba1 might provide a mechanism for the control of chromatin packaging in this organism, as was suggested for the Alba1/Alba2 heterodimer from S. solfataricus[8], [24]. However, a functionally crucial difference between the S. solfataricus Alba1 and Alba2 proteins is the presence of an F60 residue in Alba1, which is not conserved in Alba2, while in Alba2 from A. pernix, a phenylalanine is at position 58 (Figure 12). It appears that the Aeropyrum homologues both contain the equivalent of this residue, and are thus both Alba1-type proteins. This might mean that potential heterodimer formation does not have such distinct effects on DNA binding as seen with the Sulfolobus proteins [24], [27].

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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