XB-IMG-154072
Xenbase Image ID: 154072
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Fig. S1. Phylogenetic relationships of PSC genes. To confirm orthology of X. laevis PSC genes, we performed phylogenetic analysis with 1000 bootstrapping iterations of the neighbor-joining method on protein sequences in ClustalX (Quigley et al., 2010). Genes characterized further in this paper are marked in red and underlined. (A) X. laevis ae1 is an ortholog of human and mouse AE1. Accession numbers: human AE1 (4507021), mouse Ae1 (6755560), zebrafish ae1 (38198629), Xenopus slc4a7 (148225418) and Xenopus ae1 (147900281). A close examination of the curated X. laevis locus suggests a sequencing error that inserted a premature stop codon; we base this inference on strong conservation of downstream sequence. Moreover, our ae1 antibody is directed towards a peptide sequence downstream of this curated stop, suggesting that the sequence to which it binds is translated (Wainwright et al., 1989). Correspondingly, we edited the X. laevis sequence to include this conserved downstream region. (B) X. laevis pendrin and pendrin-like loci are the result of a recent gene duplication. Accession numbers: human Pendrin (4505697), mouse Pendrin (6755022), zebrafish pendrin (125814600), Xenopus pendrin (148236113) and Xenopus pendrin-like (147903861). Our bioinformatic analysis hints that there might be one or more additional uncharacterized X. laevis pendrin orthologs (not shown). (C) X. laevis foxi1 is an ortholog of human and mouse Foxi1. Given the role of X. laevis foxi1 in early ectodermal patterning (Mir et al., 2007) and different roles for foxi1 orthologs in both epidermal and PSC specification in zebrafish (Hsiao et al., 2007; Janicke et al., 2007) we sought to clarify these evolutionary relationships. Zebrafish foxi3a and foxi3b paralogs group with Xenopus, mouse and human Foxi1, suggesting a common role for these genes in PSC differentiation. Accession numbers: human Foxi1 (21618327), mouse Foxi1 (226693365), zebrafish foxi1 (32189364), zebrafish foxi2 (68226724), zebrafish foxi3a (129270185), zebrafish foxi3b (38708001), Xenopus foxi1 (148221999) and Xenopus foxj1 (148233368). (D) X. laevis ubp1 is a derived transcription factor of the grainyhead family. While X. laevis ubp1 most closely resembles lbp1a of other species in sequence similarity, a close syntenic analysis suggests that direct orthologs of ubp1 were not maintained in the human and mouse lineages (not shown). Given that grainyhead proteins heterodimerize for nuclear localization and transcription factor activity (Yoon et al., 1994; Sato et al., 2005; Katsura et al., 2009), we speculate that other grainyhead proteins are performing a function similar to that of Xenopus ubp1 in the kidneys of these mammals. Accession numbers: human LBP1A (189491630), mouse Lbp1a (134032032), zebrafish lbp1a (167621514), human CP2 (21361278), Xenopus cp2 (147903721), human LBP9 (7657299), mouse Tcfcp2l1 (109733355), Xenopus cp2l1 (148237830), Xenopus ubp1 (148886714), Xenopus grainyhead-like 1 (148230919), Xenopus grainyhead-like 2 (58332528) and Xenopus grainyhead-like 3 (147903002).
References
Quigley, I. K., Schmerer, M. W. and Shankland, M. (2010). A member of the six gene family promotes the specification of P cell fates in the O/P equivalence group of the leech Helobdella. Dev. Biol. 344, 319-330.
Wainwright, S. D., Tanner, M. J., Martin, G. E., Yendle, J. E. and Holmes, C. (1989). Monoclonal antibodies to the membrane domain of the human erythrocyte anion transport protein. Localization of the C-terminus of the protein to the cytoplasmic side of the red cell membrane and distribution of the protein in some human tissues. Biochem. J. 258, 211-220. Image published in: Quigley IK et al. (2011) Copyright © 2011. Image reproduced with permission of the publisher and the copyright holder. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. Larger Image Printer Friendly View |