Putative nuclear export signals.

<p>The signals according to Wada et al. (1998) have been identified manually. Sequences in brackets had too weak characteristics to define them as explicit nuclear export signals.</p

Structural homology among the <i>D. discoideum</i> Arps.

<p>The sequences were modeled in comparison to the Act8-type actin (upper left). Whereas Arps 1, 2 and 3 show high similarity to the three-dimensional structure of actin, Arp 5, 6 and 11 are clearly different. Attempts to model Arps 4 and 8 failed due to low structural homology and the absence of available templates. Filactin (Fia, lower right) shows high structural homology in the actin domain. Modeling was done using the Swiss Model Server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002654#pone.0002654-Schwede1" target="_blank">[58]</a>, graphics were generated with the YASARA molecular visualization software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002654#pone.0002654-Kalay1" target="_blank">[59]</a>.</p

The <i>D. discoideum</i> actinome.

<p>41 members of the actinome were identified according to their actin sequence profile. 17 conventional actins share identical amino acid sequences but are encoded by 17 distinct genes (Act8 group, right panel). 17 actins share high homologies to conventional actin but are different in their protein sequences (left panel, #1, 3–17). Nine members of the actinome are conserved actin-related proteins (Arps, #18–25).</p

Occurrence of Arps in model organisms. (* assembly).

<p>Occurrence of Arps in model organisms. (* assembly).</p

Actin pseudogenes in the <i>D. discoideum</i> genome (aa: amino acids).

<p>Actin pseudogenes in the <i>D. discoideum</i> genome (aa: amino acids).</p

Motif logos from Act8 homologues across species.

<p>The five structural actin motifs are summarized as sequence logos which reflect the structural, functional and evolutionary significance of specific amino acids at a particular position. In difference to the variability of the motif profiles in <i>D. discoideum</i> only (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002654#pone-0002654-g006" target="_blank">Fig. 6</a>), the homologies in conventional actins throughout evolution are extremely high. The following actins have been compared: <i>Arabidopsis thaliana</i>, Q541W9_ARATH - <i>Caenorhabditis elegans</i>, ACT2_CAEEL - <i>Dictyostelium discoideum</i>, Act8, DDB0216213 - <i>Drosophila melanogaster</i>, ACT1_DROME(Act5C) - <i>Entamoeba histolytica</i>, Q51B76_ENTHI - <i>Gallus gallus</i>, ACTB_CHICK (beta-actin) - <i>Homo sapiens</i>, ACTG_HUMAN (gamma-actin) - <i>Mus musculus</i>, ACTG_MOUSE (gamma-actin) - <i>Saccharomyces cerevisiae</i>, ACT_YEAST - <i>Takifugu rubripes</i>, ACT1_FUGRU, (beta-actin1) - <i>Xenopus laevis</i>, ACTB_XENLA (beta-actin).</p

Phylogenetic comparison of the <i>D. discoideum</i> (blue) and <i>D. fasciculatum</i> (red) actinomes.

<p>Both genomes code for many conventional actins which, however, form distinct groups. In contrast, the Arps from both organisms are in all cases closely related and form branched pairs.</p

Putative duplications of actin genes.

<p>The presence of 17 identical conventional actins, each one encoded by a distinct gene, suggests a series of gene duplications. Most of these genes are clustered on chromosome 2 (blue, underlined) and chromosome 5 (red, bold). An analysis of the corresponding genomic DNA implies 5 consecutive duplication events. The tree was generated with the programme DNAML 3.5c.</p

Alignment of <i>D. discoideum</i> Arps with Act8.

<p>The alignment was done with the programme BioEdit (version 7.0.5.3), the extensive color coding is explained at the lower right. Except Arp1, all other actin related proteins contain additional amino acid stretches that disrupt the conventional actin domain profile. This is especially obvious in Arp4, Arp5, Arp6, Arp8 and Arp11.</p

Expression of actin genes.

<p>(A) The expression of individual actin genes in vegetative and developing <i>D. discoideum</i> NC4 cells was analyzed 1985 by Firtel and coworkers with gene-specific probes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002654#pone.0002654-Romans3" target="_blank">[26]</a>. The nomenclature of the actin genes was now updated and the tabular values of actins from the Act8 group were taken for the graph in the upper panel. Act8 mRNA is present throughout development and at high concentration. Act4 and Act11 mRNAs have been analyzed together and followed a distinct developmental pattern. Among the lower concentrated mRNAs only Act6, Act9, Act13 and Act14 mRNAs reach levels above 5% of total actin RNA. The graph shows that essentially all genes from the Act8 group are transcribed. (B) Also the number of identified ESTs reflects mRNA concentrations from specific genes. The actinome ESTs listed in dictyBase were counted and grouped according to their numbers. The genes from the Act8 group are shown in bold and all of them have a large or very large number of ESTs.</p