Phylogenetic analyses of post-synaptic gene families. Statistical values of each essential clade is given in the order of, top left box, Bayesian Inference; top right box, Maximum likelihood; bottom left box, Maximum parsimony; bottom right box, Neighbor joining. Red and yellow colored clades represent gene families that originated before Poriferan-Eumetazoan and Cnidarian-Bilaterian splits, respectively. Green tagged sequences are from Amphimedon queenslandica and blue tagged sequences are from Nematostella vectensis. Abbreviations used in trees are: Sponge, Amphimedon queenslandica; CN, Nematostella vectensis; Human, Homo sapiens; Fly, Drosophila melanogaster; Yeast, Saccharomyces cerevisiae; Dicty, Dictyostelium discoideum; At, Arabidopsis thaliana; Os, Oryza sativa.
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Domain architectures of post-synaptic gene families. Domain architectures of representative members for each gene family are displayed as SMART output. Output was manually edited for legibility for some PFAM domains, otherwise it is presented as SMART prediction. Abbreviations used in displays are: Sponge, Amphimedon queenslandica; CN, Nematostella vectensis; Human, Homo sapiens; Fly, Drosophila melanogaster; Beetle, Tribolium castaneum.
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DLG PDZ-3 sequence alignment through 8 species. Alignment of PDZ3 sequences used for homology modeling. Conserved residues are colored according to the scheme shown. Residues that can interact with CRIPT are noted by a gray line.
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Structural interactions between the C-terminus of the CRIPT peptide and the PDZ3 domain. (A), the C-terminus of the CRIPT peptide and the PDZ3 domain in rat, fish, fly, mosquito, cnidarian, sea urchin, and worm and (B), the C-terminus of the CRIPT peptide and the PDZ-3 domain in sponge. All the distances shown in part A and the “ray” marks indicating hydrophobic contacts are based on the rat (1BE9) crystal structure. Distances to Lys5 are shown to the beta-carbon because this is the last atom whose coordinates were reported in the crystal structure. Hydrophobic contacts from residues G322, A376, and L379 were found to interact in some organisms, but in the rat they were somewhat distant. For each residue, the main label corresponds to the rat sequence, and the smaller (or “residue name”) notes correspond to other organisms (not rat or sponge). Two interactions seen in the worm homology model were not included because they were unlike those seen in other organisms (G330 and P335). In the sponge diagram (part B), interactions that are possible given homology to the rat sequence are indicated, such as the hydrogen-bonds between PDZ3 and peptide. Residue numbering in the sponge structure corresponds to the aligned residue in the rat sequence. Some of the homology models suggested variant hydrogen-bonding patterns in the sponge, especially for residues Gln6 and Asn326. The figure was created using Ligplot and HBPLUS. The identical residues between rat and sponge are: 311, 312, 314, 318, 322*, 323*, 324*, 325*, 326*, 327*, 328*, 329, 330, 331, 335, 336, 337, 338, 339*, 341, 345, 347, 351, 353, 354, 356, 357, 359, 360, 362, 363, 364, 367, 371, 372*, 373, 375, 376, 378, 379, 380*, 382, 383, 385, 386, 387, 392, 393, 394, 396, and 400. Residues that make direct contact with the CRIPT ligand in the rat crystal structure are marked with an asterisk.
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A surface view of an Amphimedon larva showing HOMER is expressed in a limited number of flask cells (arrows) by whole mount in situ hybridization. The large cells are the flask cells interspersed among the more numerous columnar epithelial cells. Transcripts are not detected in the remaining negatively stained flask cells in this field of view.
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Developmental expression of dlg during Amphimedon embryogenesis. All panels are sections of in situ hybridized embryos; posterior pole is to the top. In the blastula, a small number of small cells express dlg. During the gastrulation-like stage, dlg-expressing cells sort to the outer layer; no expression is detected in the inner cell mass. At the later spot and ring stages, prior to hatching, cells expressing dlg are restricted to the outer epithelial-like layer. After hatching (), flask cells in this layer express dlg at a higher level than the surrounding columnar epithelium.
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Protein accession numbers for sequences used in phylogenetic analyses. Each table contains the accession numbers for the sequences used in the corresponding tree from Figure S1
. PDZ and iGluR genes/domains that are shown in table S1.19 and S1.23
in grey letters are not included in phylogenetic analyses. In table S1.23
, PDZ domain amino-acid locations on their corresponding proteins are shown in parenthesis after abbreviation and all gi numbers correspond to their proteins. Abbreviations used are: Sponge, Amphimedon queenslandica
; CN, Nematostella vectensis
; Human, Homo sapiens
; Fly, Drosophila melanogaster
; Yeast, Saccharomyces cerevisiae
; Dicty, Dictyostelium discoideum
; At, Arabidopsis thaliana
; Os, Oryza sativa
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Sponge dlg and Human SAP97 intron/exon structure comparison. Cloned cDNAs of Sponge (Amphimedon) dlg were fully sequenced and mapped to its genomic sequence. Intron/exon structure was compared with its human ortholog SAP97, and about half the exons were found to be almost same size (highlighted in red) and content (in bold). However, human SAP-97 introns were in average 100 times larger than Amphimedon dlg introns (data not shown).
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Presence of post-synaptic gene orthologs in animals, yeast, dicty and plants. Species abbreviations used: Human, Homo sapiens; Fly, Drosophila Melanogaster; Nema, Nematostella vectensis; Sponge, Amphimedon queenslandica; Yeast, Saccharomyces cerevisiae; Dicty, Dictyostelium discoideum; Plants, Arabidopsis thaliana and Oryza sativa.
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