Additional file 1: Table S1. of mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway

Proteins involved in nuclear export in the three apicomplexan genomes analyzed. Identification number for proteins involved in nuclear import and export for the apicomplexan genomes, Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium spp. are shown. Gene names for the human homologs are shown, and their corresponding annotation numbers are shown as references. When applicable, the name of the yeast homolog is indicated. Complexes with conserved components are highlighted in color. Statistics (E-value and % identity) are provided for each protein when compared to the human homolog. Conserved proteins are highlighted in bold. (*) indicates that these proteins were previously identified in the respective genomes in another study [77]. The Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium spp. genomes were searched with the following keywords: “nuclear transport receptor”, “nuclear RNA export proteins”, “RNA export”, “importin alpha/beta”, “RNA-binding protein”, “regulator of nonsense transcripts”, “transportin”, “RAs-related nuclear protein/GTP-binding nuclear protein RAN”, “regulator of chromosome condensation”, “major exportin”, “exportins” and “THO complex”. Collected hits were translated into protein sequences, and domains were analyzed using Pfam [91]. To identify human homologs, the collected T. gondii, P. falciparum and Cryptosporidium spp. hits were searched against the Homo sapiens database using the Blastp tool from BLAST, and sequences with the lowest E-value were selected. T. gondii, P. falciparum and Cryptosporidium spp. homologs found were double-checked by searching the T. gondii, P. falciparum and Cryptosporidium spp. genome databases using the human homologs identified in the previous step as queries. Domains identified by Pfam were double-checked using Conserved Domain from BLAST. Using the above strategy, we were able to identify proteins at the protein family level, but the approach was not very accurate for identifying specific homologs. Thus, to identify specific homologs across relevant taxa, we systematically searched mammal, arthropod and apicomplexan databases using the Blastp tool from BLAST. (XLS 52 kb

TgChromo1 expression is cell cycle regulated.

<p><b>A:</b> IFA of TgChromo1-HA (green) and IMC1 (red), a marker of the inner membrane complex, throughout the cell cycle. Parasites representative of interphase (G1) and mitosis are presented. Parasite nuclei are labelled with DAPI. <b>B:</b> Comparison of the intensity of the signal produced by IFA of TgChromo1-HA in interphase (G1) and during budding (Budding, B). IMC1, a marker of the inner membrane complex, is used to identify emerging daughter cells during the budding. Parasites during budding (B) are arrowed. Parasite nuclei are labelled with DAPI. <b>C:</b> TgChromo1 is concentrated in foci of different intensity. IFA was performed using an anti-HA antibody and the IMC1 antibody. Parasites nuclei are labelled with DAPI. Foci of lesser intensity are arrowed.</p

Subtelomeric repeats occupy the same nucleus territory as TgChromo1.

<p>FISH/IFA of TgChromo1-HA (green) and chromosome IX telomeric repeats (red). Parasite nuclei are labelled with DAPI (blue). Colocalising signals from FISH and IFA are arrowed.</p

TgChromo1 binds to peri-centromeric heterochromatin.

<p>ChIP on chip was performed with the TgChromo1 antibody (anti-CHD1, red) or the anti-HA antibody (HA, black) and hybridized on a genome-wide tiling microarray. The regions of enrichment for H3K9me3 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032671#pone.0032671-Brooks1" target="_blank">[12]</a> are represented in blue. A snapshot of the 12 chromosomes where a centromere was identified <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032671#pone.0032671-Brooks1" target="_blank">[12]</a> is presented. ChIP on chip signals are represented as a log2 ratio of the signal given by the immunoprecipitated DNA over the input and plotted according to the genomic position of the oligonucleotide.</p

TgChromo1 participates to the nuclear organisation of the nucleus.

<p>TgChromo1 participates in the functional organisation of the nucleus. The schematic represents the chromosomes in the nucleus with the centromere and telomere clusters occupied by TgChromo1 and their position at the periphery of the nucleus.</p

TgChromo1 is maintained near the centrosome and the centrocone throughout the cell cycle.

<p><b>A:</b> IFA of TgChromo1-HA (green) and centrin1 (red), a marker of the centrosome. Parasite nuclei are labelled with DAPI (blue) at the interphase (G1), mitosis and the beginning of budding. <b>B:</b> IFA of TgChromo1-HA (green) and MORN1 (red), a marker of the centrocone. Parasite nuclei are labelled with DAPI (blue) at the interphase (G1), mitosis and the beginning of budding.</p

Colocalisation of TgChromo1 and peri-centromeric sequences and identification of a missing centromere on chromosome IV.

<p><b>A:</b> Genomic localisation of the FISH probes. Fish probes (red rectangles) approximate locations are plotted against the signal of the TgChromo1-HA ChIP on chip. <b>B:</b> FISH/IFA of TgChromo1-HA (green) and chromosome IX peri-centromeric repeats (red). Parasite nuclei are labelled with DAPI (blue). <b>C:</b> FISH/IFA of TgChromo1-HA (green) and chromosome IV putative peri-centromeric repeats (red). Parasites nuclei are labelled with DAPI (blue). <b>D:</b> Quantification of the overlap coefficient between the signals of FISH and IFA. The coefficient is expressed as a ratio of the number of pixel overlapping in IFA over FISH in a given area.</p