Open Access Research article

The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues

José M Eirín-López1, Rodrigo González-Romero1, Deanna Dryhurst2, Toyotaka Ishibashi2 and Juan Ausió2*

Author Affiliations

1 Departamento de Biología Celular y Molecular, Universidade da Coruña, E15071 A Coruña, Spain

2 Department of Biochemistry and Microbiology, University of Victoria, V8W 3P6 Victoria, BC, Canada

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BMC Evolutionary Biology 2009, 9:31  doi:10.1186/1471-2148-9-31

Published: 4 February 2009

Additional files

Additional File 1:

GenBank Accession numbers for the histone H2A sequences used in the present work. The data provided represent the accession numbers for H2A sequences used in this work, including canonical H2A genes and the variants H2A.Bbd, macro H2A, and H2A.X. The ANNOTATION field denotes: gene sequences newly isolated from draft genomes (In silico), and gene sequences predicted as H2A, H2A.Bbd and H2A.X from databases and draft/complete genomes data (PRED).

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Additional File 2:

GenBank Accession numbers for the histone variants H2A.Z-1, H2A.Z-2 and H2A.Z-e used in the present work. The data provided include the accession numbers for the H2A.Z variants used in this work. The ANNOTATION field denotes: gene sequences newly isolated from draft genomes (In silico), gene sequences predicted as H2A, H2A.Z-1 and H2A.Z-2 from databases and draft/complete genomes data (PRED), sequences defined either as H2A.Z-1 or H2A.Z-2 by the present analyses (a), sequences defined as H2A by the present analyses (b) and sequences whose annotation either as H2A.Z-1 or H2A.Z-2 has been corrected by the present work (c).

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Additional File 3:

Phylogenetic neighbor-joining tree showing the phylogenetic relationships among histone H2A.Z-1 and H2A.Z-2 protein forms. The reconstruction was carried out by calculating theee evolutionary amino acid p-distances from the H2A sequences of all the organisms analyzed (see Additional file 2). Histone H2A.Z-1 variants are indicated in pink, H2A.Z-2 variants are indicated in purple and H2A.Z-e sequences from early chordates are indicated in brown. Histone variants from protostomes, plants and fungi/protists are indicated in blue, while the root of the tree is labeled in black. Variant sequences predicted from databases and complete/draft genomes data are indicated by PRED near the species name. Numbers for interior nodes indicate BP/CP confidence values. Numbers in colored boxes and in boldface account for the bootstrap values obtained in the reconstruction of the maximum parsimony trees using all the informative positions in the alignment. Confidence values were based on 1000 replications and are only shown if at least one of the values is >50%.

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Additional File 4:

Graphical representation of the amino acid variation between H2A.Z-1 and H2A.Z-2 variants. A Protein logos representation of the overall amino acid variation at each position of the alignment of H2A.Z-1 and H2A.Z-2 variants from vertebrates. The size of the bars is proportional to the frequency for a given amino acid and the overall height is proportional to the conservation of the sites. Colors were assigned to amino acids according to their physical and chemical structural characteristics (red, acidic; blue, basic; green, polar uncharged; purple, nonpolar hydrophobic). B Tertiary structures modeled for H2A.Z-1, H2A.Z-2 and H2A.Z-e from early chordates are shown below the protein logos representation, indicating the quality of the modeling process based on amino acid energies (gromos) and the compatibility of the 3D atomic models with the corresponding protein sequences (verify3d) at each amino acid position. Residues encompassing variation in the energy environment of the atomic model, including polymorphic positions between H2A.Z-1/H2A.Z-2 and H2A.Z-e from early chordates (indicated below in red) are highlighted in the 3D figures as well as in the nearby graphs.

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Additional File 5:

Electrostatic distances and potentials in different H2A.Z proteins. A Electrostatic distances calculated from the similarity indices for the electrostatic potentials of histone H2A variants represented in a color coded matrix (heat map). The distance between similarity indices (SI) of two molecules (a and b) is defined as <a onClick="popup('http://www.biomedcentral.com/1471-2148/9/31/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2148/9/31/mathml/M1">View MathML</a>. The color code, as well as the number of comparisons for each distance interval are indicated in the key/histogram. The tree along the side of the image assembles the proteins into groups of similar electrostatic potentials (epogram), with discontinuous black lines delimiting three different groups of similarity with respect to human H2A.Z-1. B Representation of the electrostatic potentials for three representative H2A molecules belonging to different groups of similarity as defined in the epogram. Negatively charged surfaces are red and positively charged surfaces are blue, colors were assigned to amino acids according to their physical and chemical structural characteristics as in Supplementary Figure 2. The residue occupying the second position in the triresidue is indicated in each case.

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Additional File 6:

Genomic GC content, amino acid composition and A+G content at first codon positions and fourfold degenerate positions in the H2A.Z-1 genes analyzed. The data provided was used for gauging the presence of selection acting on H2A.Z-1 genes.

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Additional File 7:

Genomic GC content, amino acid composition and A+G content at first codon positions and fourfold degenerate positions in the H2A.Z-2 genes analyzed. The data provided was used for gauging the presence of selection acting on H2A.Z-2 genes.

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