Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9

<div><p>Sox9 plays an important role in a large variety of developmental pathways in vertebrates. It is composed of three domains: high-mobility group box (HMG box), dimerization (DIM) and transactivation (TAD). One of the main processes for regulation and variability of the pathways involving Sox9 is the self-gene expression regulation of Sox9. However, the subsequent roles of the Sox9 domains can also generate regulatory modulations. Studies have shown that TADs can bind to different types of proteins and its function seems to be influenced by DIM. Therefore, we hypothesized that both domains are directly associated and can be responsible for the functional variability of Sox9. We applied a method based on a broad phylogenetic context, using sequences of the HMG box domain, to ensure the homology of all the Sox9 copies used herein. The data obtained included 4,921 sequences relative to 657 metazoan species. Based on coevolutionary and selective pressure analyses of the Sox9 sequences, we observed coevolutions involving DIM and TADs. These data, along with the experimental data from literature, indicate a functional relationship between these domains. Moreover, DIM and TADs may be responsible for the functional plasticity of Sox9 because they are more tolerant for molecular changes (higher Ka/Ks ratio than the HMG box domain). This tolerance could allow a differential regulation of target genes or promote novel targets during transcriptional activation. In conclusion, we suggest that DIM and TADs functional association may regulate differentially the target genes or even promote novel targets during transcription activation mediated by Sox9 paralogs, contributing to the subfunctionalization of Sox9a and Sox9b in teleosts.</p></div

Evolutionary relationships among the <i>Sox9</i> vertebrate sequences.

<p>(A) Phylogeny of the Sox9 multiple sequence alignment using the maximum likelihood method from the PhyML program. The aLRT (SH-like) values of branch support are shown. The corresponding clades for <i>Sox9</i> (blue), <i>Sox9a</i> (green) and <i>Sox9b</i> (orange) are indicated. The database entries (accession numbers from GenBank or Ensembl) are shown with their corresponding annotations in the database in parenthesis. The single asterisks (*) indicates the divergences between our results and the gene annotation in the corresponding database entry, whereas the double asterisks (**) indicates the sequence obtained from the genome walking technique. The scale bar below the phylogenetic tree indicates the average number of nucleotides substitutions per site. (B) Dendogram of the synteny analysis, based on the closest genetic markers: the clades corresponding to <i>Sox9</i> (blue), <i>Sox9a</i> (green) and <i>Sox9b</i> (orange) were obtained from the hierarchical manhattan clustering method, implemented in the R software.</p

Schematic representation of the interactions observed in the Imp<i>α</i>-NplNLS interface.

<p>(A) The major (P2–P5) and minor (P1’-P2’) sites and the linker region are indicated in the sequence of the NplNLS. (B) The standard MD (300 ns ensemble) and (C) NM-displacement (ensemble from reference structures 67,730 ps, 207,080 ps and 274,970 ps) interaction scheme is shown with salt bridges (red) and hydrogen bonds (green) as dashed-lines, and hydrophobic contacts are shown as arcs with radiating spokes. The important tryptophan residues that mediate the hydrophobic contacts are depicted in the scheme as black sticks. The main chain of the NplNLS is represented as a gray horizontal line with its respective amino acid sequences, together with side chains shown as perpendicular lines. Only interactions that had an occupancy rate ≥50% of the analyzed trajectories are indicated in the scheme.</p

The starting structure of Imp<i>α</i>-NplNLS for MD simulations.

<p>(A) The Imp<i>α</i> as a cartoon diagram colored based on each ARM repeat as a rainbow spectrum from N-terminal (blue) to C-terminal (red) and the NplNLS as a cyan cartoon diagram positioned in an antiparallel configuration compared to Imp<i>α</i>. (B) The surface representation of Imp<i>α</i> with the NplNLS as a cyan stick diagram, indicating both major (blue) and minor (orange) binding sites. (C) The major site zoom indicating positions P2–P5 and (D) the minor site zoom in P1’ and P2’. In both sites, the positively charged side chains are positioned in the main pockets of the Imp<i>α</i> binding core.</p

Geometric analysis of the bending and twisting motions of Imp<i>α</i>.

<p>(A) The bending motion was quantitatively characterized by the radius of curvature along NM7 (solid line) and PC1 (dashed line) for Imp<i>α</i> -NplNLS and along NM7 for Apo Imp<i>α</i> (dotted line), whereas (B) the twisting motion was quantitatively characterized by the average values for the angles between helices along NM9 (solid line) and PC3 (dashed line) for Imp<i>α</i> -NplNLS and along NM9 for Apo Imp<i>α</i> (dotted line).</p

Schematic representation of the interactions observed in the Imp<i>α</i>-NplNLS interface.

<p>(A) The major (P2–P5) and minor (P1’-P2’) sites and the linker region are indicated in the sequence of the NplNLS. (B) The standard MD (300 ns ensemble) and (C) NM-displacement (ensemble from reference structures 67,730 ps, 207,080 ps and 274,970 ps) interaction scheme is shown with salt bridges (red) and hydrogen bonds (green) as dashed-lines, and hydrophobic contacts are shown as arcs with radiating spokes. The important tryptophan residues that mediate the hydrophobic contacts are depicted in the scheme as black sticks. The main chain of the NplNLS is represented as a gray horizontal line with its respective amino acid sequences, together with side chains shown as perpendicular lines. Only interactions that had an occupancy rate ≥50% of the analyzed trajectories are indicated in the scheme.</p

Main motions observed from NM analysis of Imp<i>α</i> -NplNLS.

<p>Imp<i>α</i> (cartoon model) is shown as a rainbow spectrum from N-terminal (blue) to C-terminal (red), and NplNLS (cyan cartoon model) is positioned in an antiparallel configuration compared to Imp<i>α</i>. The vector arrows for NM7–9 are shown with the correspondent description of the motion that they described. NM7 is shown in a front view, whereas NM8 and NM9 are shown in an upper view (90° rotation in the X-axis).</p