Evolution of a novel subfamily of nuclear receptors with members that each contain two DNA binding domains
© Wu et al; licensee BioMed Central Ltd. 2007
Received: 22 August 2006
Accepted: 23 February 2007
Published: 23 February 2007
Nuclear receptors (NRs) are important transcriptional modulators in metazoans which regulate transcription through binding to the promoter region of their target gene by the DNA binding domain (DBD) and activation or repression of mRNA synthesis through co-regulators bound to the ligand binding domain (LBD). NRs typically have a single DBD with a LBD.
Three nuclear receptors named 2DBD-NRs, were identified from the flatworm Schistosoma mansoni that each possess a novel set of two DBDs in tandem with a LBD. They represent a novel NR modular structure: A/B-DBD-DBD-hinge-LBD. The 2DBD-NRs form a new subfamily of NRs, VII. By database mining, 2DBD-NR genes from other flatworm species (Schmidtea mediterranea and Dugesia japonica), from Mollusks (Lottia gigantean) and from arthropods (Daphnia pulex) were also identified. All 2DBD-NRs possess a P-box sequence of CEACKK in the first DBD, which is unique to 2DBD-NRs, and a P-box sequence of CEGCKG in the second DBD. Phylogenetic analyses of both DBD and ligand binding domain sequences showed that 2DBD-NR genes originate from a common two DBD-containing ancestor gene. A single 2DBD-NR orthologue was found in Arthropoda, Platyhelminths and Mollusca. Subsequent 2DBD-NR gene evolution in Mollusks and Platyhelminths involved gene duplication. Chromosome localization of S. mansoni 2DBD-NR genes by Fluorescent in situ hybridization (FISH) suggests that 2DBD-NR genes duplicated on different chromosomes in the Platyhelminths. Dimerization of Sm2DBDα indicates that 2DBD-NRs may act as homodimers, suggesting either that two repeats of a half-site are necessary for each DBD of 2DBD-NRs to bind to its target gene, or that each 2DBD-NR can recognize multiple sites.
2DBD-NRs share a common ancestor gene which possessed an extra DBD that likely resulted from a recombination event. After the split of the Arthropods, Mollusks and Platyhelminths, 2DBD-NR underwent a recent duplication in a common ancestor of Mollusks, while two rounds of duplication occurred in a common ancestor of the Platyhelminths. This demonstrates that certain NR gene underwent recent duplication in Prostostome lineages after the split of the Prostostomia and Deuterostomia.
Nuclear receptors (NR) regulate homeostasis, differentiation, metamorphosis and reproduction in metazoans. Members of the nuclear receptor superfamily are characterized by a modular structure. Typical NRs contain an N-terminal A/B domain, a C domain (DNA binding domain, DBD), a D domain (hinge) and an E domain (ligand binding domain, LBD). The most conserved region in NRs is the DBD, which contains two zinc finger motifs (CI and CII). There is a conserved sequence element in the DBD, called the P-box, which confers target DNA binding specificity. Another moderately conserved region is the LBD [1–3]. Two highly conserved regions are present within the LBD. The first region is called the signature sequence of LBD (Tau, Tτ), from the C-terminus of helix 3 to the middle of helix 4 [1, 4]. The second conserved region is helix 12 which contains the activation function core motif (AF2-AD) that is required for transcriptional activation and co-regulator recruitment. NRs regulate transcription through binding to the promoter region of their target gene by the DBD and activation or repression of mRNA synthesis through co-regulators bound to the LBD .
Recently, we isolated three partial cDNAs of nuclear receptors which contain two DBDs in the flatworm Schistosoma mansoni . Typical NRs only have a single DBD with a LBD, unusual nuclear receptors are known only to have one DBD without a LBD [7–10] or to posses a LBD without a DBD [11, 12]. To determine the modular structure of these novel nuclear receptors (that is, whether they contain a LBD), cDNAs encoding the entire open reading frame (ORF) of Sm2DBD-NRs were isolated. By data mining, additional 2DBD-NRs were identified in species of Mollusca, Arthropoda and other species of Platyhelminths. The phylogenetic relationship of 2DBD-NRs was constructed, the origin of 2DBD-NRs and their role in understanding metazoan phylogeny is discussed.
Results and Discussion
A novel NR modular structure: A/B-DBD-DBD-hinge-LBD
The LBD is conserved in all three proteins from helix 3 to helix 12. The consensus signature sequence of the LBD (Tτ), ((F, WY)(A, SI)(K, R, E, G)XXX(F, L)XX(L, V, IXXX(D, S)(Q, K)XX(L, V)(L, I, F)) [1, 4], is conserved in each of them (Fig. 1B). A putative AF2 activating domain core (AF2-AD), designated ΦΦXEΦΦ, where Φ represents a hydrophobic amino acid [13–15], is highly conserved in Sm2DBDα and Sm2DBDβ, but not in Sm2DBDγ. In Sm2DBDγ, a glutamine is located in the position which is normally conserved for a glutamic acid (Fig. 1B). Sm2DBDα contains a large F domain. The function of the F domain, which is known to be present in some but not all nuclear receptors, is not well known (eg. [15–22]). The hinge region of each protein is unusually large (Fig. 1A). This trait has been observed in other Schistosoma NRs [15–22]. The role of such a large hinge region is yet to be determined.
Identification of 2DBD-NR in other organisms
Sequence analysis and phylogenetic tree construction
Alignment of the deduced DBD sequences showed that all 2DBD-NRs possess a P-box sequence, CEACKK, in the first DBD, and the P-box sequence, CEGCKG, in the second DBD (Fig. 2). A blast search against all available databases showed that the P-Box sequence CEACKK is not present in any other NR. This unique P-box present in the first DBD of 2DBD-NRs suggests a novel target DNA specificity may exist for the first DBD. The P-box sequence of second DBD, CEGCKG followed by the amino acid sequence FFRR (CEGCKGFFRR) is identical to that of most members in NR subfamily I (NR I) suggesting that 2DBD-NRs may have a close functional or evolutionary relationship with receptors in NR subfamily I.
NRs can regulate transcription as a homodimer or as a heterodimer with retinoid × receptor (RXR), another nuclear receptor. To determine whether 2DBD-NRs may form dimers and to begin to define the quarternary structure of 2DBD-NRs, the interaction of Sm2DBDα, SmRXR1 and SmRXR2 was evaluated in a yeast two hybrid system.
Nuclear receptors act on target genes by recognizing and binding to specific DNA core motifs in the promoter region of target genes via their P-box motif located in the DBD. The DNA core motif is a typical consensus hexameric sequence AGGTCA called a half-site. When NRs bind to the half-site as a dimer, two P-boxes and a repeat of half-site, with different orientations and spacings between the half sites, are required. 2DBD-NR can interact as a homodimer indicating that four P-boxes may be involved in DNA binding, thus a novel mechanism of DNA binding, which requires two independent pairs of half-site repeats, or four half-site repeats, each with unknown orientations and spacing, are predicted to exist to allow 2DBD-NR to bind to target DNA cis-elements. The protein of the first DBD, second DBD and the first DBD with second DBD were tested for their ability to bind to a direct repeat, an everted repeat and palindromes of the half-site AGGTCA with 1–6 nucleotide spacings by electrphoretic mobility shift assay (EMSAs). No binding compared to controls was observed (data not shown). However, as the flanking sequence of the AGGTCA motif and the spacing between half sites also determines the protein binding to the DNA element, further experiments will be performed using different sets of templates and by determining DNA binding sites using a PCR/EMSA-based approach.
Evolution of 2DBD-NRs
If the traditional phylogenetic scheme is correct, 2DBD-NRs originated in a common ancestor of the Bilateria, because 2DBD-NRs were found in both Acoelomates (flatworms) and Coelomates (mollusks and arthropods) (Fig. 6A). The 2DBD-NR was lost in Pseudocoelomates (nematodes) after the split of Pseudocoelomates and Coelomates (Protostomes and Deuterostomes). As 2DBD-NRs have not been found in Deuterostomes, they were lost in the Deuterostome lineage after the split of Protostomes and Deuterostomes (Fig. 6A).
If the molecular phylogeny hypothesis is correct, there were two possibilities for 2DBD-NR origin. The 2DBD-NR might originate in a common ancestor of Protostomes, since 2DBD-NRs were identified both in Lophotrochozoans (Platyhelminths and Molluscs) and in Ecdysozoans (Crustaceans) (Fig. 6B). The other possibility is that 2DBD-NR might originate in a common ancestor of the Bilateria and was lost in the Deuterostome lineage after the split of Protostomes and Deuterostomes. 2DBD-NR is absent in nematodes suggesting that this gene was lost after the split of the nematodes and arthropods. In arthropods, no 2DBD-NR was found in insects suggesting 2DBD-NR was lost after the split of insects and crustaceans (Fig. 6B).
The phylogeny of the Platyhelminths has itself been under debate (eg. [34–37]). The Platyhelminths have always played a central role in hypotheses concerning metazoan phylogeny and evolution. Recently, many platyhelminth flatworms, previously regarded in the traditional phylogeny as basal bilaterians (Fig. 6A), are now placed within the lophotrochozoan protostomates (Fig. 6B). Furthermore, the Acoelomorpha (Aceola + Nerertoderdermatida) are no longer considered part of the Platyhelminths but are still considered basal bilaterians [34–38]. Certainly, further studies on nuclear receptor evolution in these taxa can contribute to our understanding of the evolution of the Metazoa and Bilateria, especially as nuclear receptors have been identified in sponges , a group that is hypothesized to have given rise to the hypothetical metazoan ancestor .
Analysis of the NR superfamily, mainly in Drosophila and vertebrates supports the hypothesis that evolution of nuclear receptors occurred by two serial rounds of duplication [41–45]. The duplication of 2DBD-NRs suggests that certain NR genes have undergone recent duplication in invertebrates after the divergence of various clades within the Bilateria. Our previous study of S. mansoni NRs supports this hypothesis . NRs in insects seem to have undergone extensive gene loss. For example, a recently identified estrogen receptor in the mollusk Aplysia californica  and two thyroid hormone receptors in the Platyhelminth S. mansoni [6, 47] are missing in the insect genera Drosophila and Anopheles. To address the importance of gene duplication in NR evolution, more invertebrates NR complements await to be analyzed.
Developmentally Regulated Expression
Quantitative real-time RT-PCR was performed to evaluate mRNA expression of Sm2DBDα, Sm2DBDβ and Sm2DBDγ. Normalized gene expression (ΔΔCT)  was standardized to the relative quantities of S. mansoni α-tubulin. Sm2DBDα was detected in secondary sporocysts, cercariae, 21-day schistosomules, 28-day schistosomules, female and male worms. Sm2DBDβ was expressed relatively high in eggs, secondary sporocysts, cercariae and male stages. Sm2DBDγ was only detected in cercariae and 28-day worms. The results indicate that the three genes are developmentally regulated and thus have a role in different development stages (Fig. 9). It is of note that Sm2DBDγ, the putative ancestral gene is only expressed in 2 of the developmental stages studied and that both Sm2DBDα and Sm2DBDβ show sex-specific gene expression.
A protein modular structure containing an AB domain, two DNA binding domains in tandem, a hinge region and a ligand binding domain (A/B-DBD-DBD-hinge-LBD) represents a novel NR modular structure, and is named 2DBD-NR. 2DBD-NR s were identified from mollusks, arthropods (crustaceans) and flatworms. 2DBD-NRs may act as homodimers. 2DBD-NR s share a common ancestor gene which possessed an extra DBD that likely resulted from a recombination event. 2DBD-NR s were found in flatworms, mollusks and arthropods whose phylogeny is still under debate [30, 31, 33] (Fig. 6A and 6B). Further studies of 2DBD-NR gene subfamily may contribute to our understanding of gene duplication as an evolutionary force and to the phylogeny of the Metazoa. The conserved zinc finger motifs in each of the two DBDs are the most readily recognized features of 2DBD-NRs. The P-box sequences in the first DBD and the second DBD give members of the 2DBD-NR their unique feature. This feature makes 2DBD-NRs an interesting gene subfamily for studies of metazoan phylogeny.
Isolation of 2DBD-NR cDNAs in the Platyhelminth S. mansoni
cDNAs encoding the entire open reading frame (ORF) of three S. mansoni 2DBD-NRs (Sm2DBDα, Sm2DBDβ and Sm2DBDγ) were isolated by a PCR strategy using a S. mansoni female worm cDNA library (pBluescript SK (+/-) phagemid) pool as template DNA [6, 22]. The PCR primers for one end (either 5' or 3' end) were designed according to a fragment encoding the previously identified DBD region of these genes . The primer for the other end (either 5' or 3' end) was a vector universal primer (M13-Rev and T3, or M13-For and T7 primers). PCR products were separated on 1.2% agarose gels, ligated into pCR2.1 TOPO vector (Invitrogen) and sequenced. After the correct fragments were identified, the cDNA sequence containing the 5' UTR, ORF and 3' UTR were obtained by PCR. The cDNAs were shown to be related to a single mRNA species by sequencing the PCR products obtained from single-stranded cDNA using primers located within the 5'UTR and 3'UTR of each gene.
Whole genomic sequences (WGS) were extracted from the GenBank public ftp site  (up to October 2005) and imported into StarBlast program (DNASTAR) to build a local database which was screened by tblastn using the sequence of the first and second DBD of Sm2DBDα as the query. Any sequence that contained a zinc finger structure of the DBD (Cys-X2-Cys-X13-Cys-X2-Cys or Cys-X5-Cys-X9-Cys-X2-Cys) was retained. Sequence walking was carried out to assemble the contigs. Website databases of GenBank (nr, EST_human, EST_mouse and EST_other databases) , European Bioinformatics Institute  and Swiss-Prot  were also mined by tblasn or blastp using the same query sequence as above.
Phylogenetic tree construction
Phylogenetic trees were constructed from deduced sequences of the DBD and the LBD, respectively. Sequences were aligned with ClustalW . Phylogenetic analysis of the data set was carried out using the Maximum Likelihood method under Jones-Taylor-Thornton (JTT) substitution model  with a gamma distribution of rates between sites (eight categories, parameter alpha, estimated by the program) using PHYML (v2.4.4)) . Support values for the tree were obtained by bootstrapping a 100 replicates. The same data set was also tested by Bayesian inference using MrBAYES v3.1.1 with a mixed amino acid replacement model + invgamma rates (Huelsenbeck and Ronquist, 2001). The trees were started randomly; four simultaneous Markov chains were run for 5 million generations for the DBD data set and 3 million generations for the LBD data set, respectively. The trees were sampled every 100 generations. Bayesian posterior probabilities (PPs) were calculated using a Markov chain Monte Carlo (MCMC) sampling approach implemented in MrBAYES v3.1.1, with a burn-in value setting at 12,500 for DBD data set and 7,500 generations for the LBD data set, respectively.
Yeast two-hybrid Assay: cDNA encoding Sm2DBDα was inserted into the activation domain vector pGAD-T7 to form pGAD-Sm2DBDα. Since Sm2DBDα-AB domain can self-activate as previously determined (data not shown), cDNA encoding Sm2DBDα C-F domain was inserted into pGBK-T7 to form pGBK-Sm2DBDα-C-F. Previously constructed SmRXR1, SmRXR1-C-F and SmRXR2 in activation domain vectors (pACT-SmRXR1 and pACT-SmRXR2), and in DNA binding domain vectors (pAS-SmRXR1-CF and pAS-SmRXR2-AF) were employed [17, 18, 56, 57]. Yeast AH109 were transformed with 1 μg of the following co-transformants: pGBK-Sm2DBDα-C-F/pACT-SmRXR1, pGAD-Sm2DBDα/pAs-SmRXR1-C-F, pGBK-Sm2DBDα-C-F/pACT-SmRXR2, pGAD-Sm2DBDα/pAS-SmRXR2, pGBK-Sm2DBDα-C-F/pGAD-Sm2DBDα, positive control plasmid pSV40/p53 and negative control plasmid pSV40/plamin C. Transformations were performed using the Frozen-EZ transformation II kit (Zymo Research). Transformed yeast were plated on SD/-trp-leu and SD/-trp-his-leu-ade plus 3 mM 3-amino-1,2,4-triazole (3-AT, an inhibitor to prevent the leaky expression of the HIS3 gene).
GST Pull-down: cDNA encoding Sm2DBDα E-F domain was inserted into pGEX-4T-1 and pCITE-4a vectors to form pGEX-Sm2DBDα-E-F and pCITE-Sm2DBDα-E-F, respectively. E. coli AD 494 (DE3) pLys S competent cells (Novagen) were transformed with pGEX-Sm2DBDα-E-F and the GST fusion proteins were purified by passage over a glutathione-Sepharose column according to standard protocols. To produce 35S labeled protein, pCITE-Sm2DBDα-E-F was transcribed and translated using the Single Tube Protein System (Novagen) following the manufacture's protocol. For pull-down experiments, a 50 μl reaction that contained 2 μl of the in vitro translation reaction, Sm2DBDα-E-F GST fusion protein or GST protein (as negative control) affixed to glutathione-Sepharose beads (about 2 μg) and binding buffer (50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10% glycerol, 0.15% Nonidet P40) was used . The reaction was incubated overnight at 4°C, washed three times with binding buffer and the bound proteins were analyzed by 10% SDS-PAGE and autoradiography.
BAC clone screening and localization of 2DBD-NRs on chromosomes of S. mansoni
S. mansoni BAC clones containing Sm2DBD-NRs were identified by screening the S. mansoni CHOR-1 BAC library with methods previously described  or by blast searching databases of S. mansoni BAC end sequences in TIGR  and verified by PCR. Fluorescent in situ hybridization (FISH) was performed on S. mansoni sporocyst metaphase chromosome spreads with BAC DNAs that each contained one of the three S. mansoni 2DBD-NRs (Sm2DBDα, Sm2DBDβ and Sm2DBDγ). FISH was performed using techniques previously described [61, 62].
Quantitative real-time RT-PCR
mRNA expression levels of three Sm2DBD-NRs (Sm2DBDα, Sm2DBDβ and Sm2DBDγ) were tested in eggs, daughter sporocysts, cercariae, 21-day, 28-day, adult female and adult male worms. A Puerto-Rican strain of S. mansoni was maintained in snails(Biomphalaria glabrata) and Syrian golden hamsters (Mesocricetus auratus). Cercariae were released from infected snails and harvested on ice. Schistosome worms of different ages (21–45 day-old) were harvested from infected Syrian golden hamsters. Single-sex worms were obtained by separating adult worm pairs. Parasite eggs were obtained from livers of infected hamsters. Total RNA was extracted from the above developmental stages using TRIzol reagent (Invitrogen). All RNA samples were treated with RNase-free DNaseI (RQ1 DNase; Promega) and reverse transcribed using a random hexamer and SuperScript Reverse Transcriptase II (SSRTaseII; Invitrogen) as previously described . Primers specific for Sm2DBDα (forward: 5'-CCGCTGCATCAATCACCTATT-3', reverse: 5'-TGCGCAAAATGTAGCCGAT-3'), Sm2DBDβ (forward: 5'-TGCACTGACTCCCACCACA-3', reverse: 5'-AGCAGTGGATGACGTCGGA-3')and Sm2DBDγ (forward: 5'-GAACATCGTGAATCAATTTTACATTCAG-3', reverse: 5'- ATGTACTGTTTCATTGCATTCATTTG-3') were designed using Primer Express Program (Applied Biosystems™). Primers specific for S. mansoni α-tubulin [GenBank: M80214] were according to . Reverse-transcribed cDNA samples were used as templates for PCR amplification using SYBR Green Master Mix® (Invitrogen) and BIORAD IQ™5 Real-Time PCR Detection System. The efficiency for each primer set is evaluated and recorded during assay development by iQ5 application (cDNA diluted to x1, x10, x100 and x1000 folds). Normalized gene expression (ΔΔCT)  of Sm2DBDα, Sm2DBDβ and Sm2DBDγ were standardized to the relative quantities of S. mansoni tubulin using BioRad IQ™5 Optical System software V1.1 with the Normalized Expression calculations implemented in iQ5. For graphical representation of the expression, the normalized expression was recalculated by dividing the expression level of each stage of the all gene by the highest expression level.
List of abbreviations
nuclear receptor containing two tandem DNA binding domains, BAC: bacterial artificial chromosome, DBD: DNA-binding domain, FISH: Fluorescent in situ hybridization, LBD: ligand binding domain, NR: nuclear receptor, WGS: whole genomic sequence.
This research was supported by NIH grant AI046762 and a grant for Biodiversity Research of the 21st Century COE (A14, Kyoto University). We thank the genome sequencing centers for making their data publicly available.
- Wurtz JM, Bourguet W, Renaud JP, Vivat V, Chambon P, Moras D, Gronemeyer H: A canonical structure for the ligand-binding domain of nuclear receptors. Nat Struct Biol. 1996, 3 (2): 206-10.1038/nsb0296-206.View ArticlePubMedGoogle Scholar
- Renaud JP, Moras D: Structural studies on nuclear receptors. Cell Mol Life Sci. 2000, 57 (12): 1748-1769. 10.1007/PL00000656.View ArticlePubMedGoogle Scholar
- de Groot A, de Rosny E, Juillan-Binard C, Ferrer JL, Laudet V, Pierce RJ, Pebay-Peyroula E, Fontecilla-Camps JC, Borel F: Crystal structure of a novel tetrameric complex of agonist-bound ligand-binding domain of Biomphalaria glabrata retinoid X receptor. J Mol Biol. 2005, 354 (4): 841-853. 10.1016/j.jmb.2005.09.090.View ArticlePubMedGoogle Scholar
- Wang LH, Tsai SY, Cook RG, Beattie WG, Tsai MJ, O'Malley BW: COUP transcription factor is a member of the steroid receptor superfamily. Nature. 1989, 340 (6229): 163-166. 10.1038/340163a0.View ArticlePubMedGoogle Scholar
- Moras D, Gronemeyer H: The nuclear receptor ligand-binding domain: structure and function. Curr Opin Cell Biol. 1998, 10 (3): 384-391. 10.1016/S0955-0674(98)80015-X.View ArticlePubMedGoogle Scholar
- Wu WJ, Niles EG, El-Sayed N, Berriman M, LoVerde PT: Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: Sixteen new members and a novel subfamily. Gene. 2006, 366 (2): 303-315. 10.1016/j.gene.2005.09.013.View ArticlePubMedGoogle Scholar
- Nauber U, Pankratz MJ, Kienlin A, Seifert E, Klemm U, Jackle H: Abdominal segmentation of the Drosophila embryo requires a hormone receptor-like protein encoded by the gap gene knirps. Nature. 1988, 336 (6198): 489-492. 10.1038/336489a0.View ArticlePubMedGoogle Scholar
- Oro AE, Ong ES, Margolis JS, Posakony JW, McKeown M, Evans RM: The Drosophila gene knirps-related is a member of the steroid-receptor gene superfamily. Nature. 1988, 336 (6198): 493-496. 10.1038/336493a0.View ArticlePubMedGoogle Scholar
- Rothe M, Nauber U, Jackle H: Three hormone receptor-like Drosophila genes encode an identical DNA-binding finger. Embo J. 1989, 8 (10): 3087-3094.PubMed CentralPubMedGoogle Scholar
- Sengupta P, Colbert HA, Bargmann CI: The C. elegans gene odr-7 encodes an olfactory-specific member of the nuclear receptor superfamily. Cell. 1994, 79 (6): 971-980. 10.1016/0092-8674(94)90028-0.View ArticlePubMedGoogle Scholar
- Seol W, Choi HS, Moore DD: An orphan nuclear hormone receptor that lacks a DNA binding domain and heterodimerizes with other receptors. Science. 1996, 272 (5266): 1336-1339. 10.1126/science.272.5266.1336.View ArticlePubMedGoogle Scholar
- Zanaria E, Muscatelli F, Bardoni B, Strom TM, Guioli S, Guo W, Lalli E, Moser C, Walker AP, McCabe ER: An unusual member of the nuclear hormone receptor superfamily responsible for X-linked adrenal hypoplasia congenita. Nature. 1994, 372 (6507): 635-641. 10.1038/372635a0.View ArticlePubMedGoogle Scholar
- Nagy L, Kao HY, Love JD, Li C, Banayo E, Gooch JT, Krishna V, Chatterjee K, Evans RM, Schwabe JW: Mechanism of corepressor binding and release from nuclear hormone receptors. Genes Dev. 1999, 13 (24): 3209-3216. 10.1101/gad.13.24.3209.PubMed CentralView ArticlePubMedGoogle Scholar
- Perissi V, Staszewski LM, McInerney EM, Kurokawa R, Krones A, Rose DW, Lambert MH, Milburn MV, Glass CK, Rosenfeld MG: Molecular determinants of nuclear receptor-corepressor interaction. Genes Dev. 1999, 13 (24): 3198-3208. 10.1101/gad.13.24.3198.PubMed CentralView ArticlePubMedGoogle Scholar
- de Mendonca RL, Escriva H, Bouton D, Zelus D, Vanacker JM, Bonnelye E, Cornette J, Pierce RJ, Laudet V: Structural and functional divergence of a nuclear receptor of the RXR family from the trematode parasite Schistosoma mansoni. Eur J Biochem. 2000, 267 (11): 3208-3219. 10.1046/j.1432-1327.2000.01344.x.View ArticlePubMedGoogle Scholar
- de Mendonca RL, Bouton D, Bertin B, Escriva H, Noel C, Vanacker JM, Cornette J, Laudet V, Pierce RJ: A functionally conserved member of the FTZ-F1 nuclear receptor family from Schistosoma mansoni. Eur J Biochem. 2002, 269 (22): 5700-5711. 10.1046/j.1432-1033.2002.03287.x.View ArticlePubMedGoogle Scholar
- Freebern WJ, Niles EG, LoVerde PT: RXR-2, a member of the retinoid x receptor family in Schistosoma mansoni. Gene. 1999, 233 (1-2): 33-38. 10.1016/S0378-1119(99)00161-4.View ArticlePubMedGoogle Scholar
- Freebern WJ, Osman A, Niles EG, Christen L, LoVerde PT: Identification of a cDNA encoding a retinoid X receptor homologue from Schistosoma mansoni. Evidence for a role in female-specific gene expression. J Biol Chem. 1999, 274 (8): 4577-4585. 10.1074/jbc.274.8.4577.View ArticlePubMedGoogle Scholar
- Hu R, Wu W, Niles EG, LoVerde PT: Isolation and characterization of Schistosoma mansoni constitutive androstane receptor. Molecular and Biochemical Parasitology. 2006, 148 (1): 31-43. 10.1016/j.molbiopara.2006.02.017.View ArticlePubMedGoogle Scholar
- Hu R, Wu W, Niles EG, Loverde PT: SmTR2/4, a Schistosoma mansoni homologue of TR2/TR4 orphan nuclear receptor. Int J Parasitol. 2006, 36: 1113-1122. 10.1016/j.ijpara.2006.06.003.View ArticlePubMedGoogle Scholar
- Lu C, Wu W, Niles EG, Loverde PT: Identification and characterization of a novel fushi tarazu factor 1 (FTZ-F1) nuclear receptor in Schistosoma mansoni. Mol Biochem Parasitol. 2006Google Scholar
- Wu W, Niles EG, Hirai H, Loverde PT: Identification and characterization of a nuclear receptor subfamily I member in the Platyhelminth Schistosoma mansoni (SmNR1). Febs J. 2007, 274: 390-405. 10.1111/j.1742-4658.2006.05587.x.View ArticlePubMedGoogle Scholar
- Bourguet W, Vivat V, Wurtz JM, Chambon P, Gronemeyer H, Moras D: Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. Mol Cell. 2000, 5 (2): 289-298. 10.1016/S1097-2765(00)80424-4.View ArticlePubMedGoogle Scholar
- Gampe RT, Montana VG, Lambert MH, Miller AB, Bledsoe RK, Milburn MV, Kliewer SA, Willson TM, Xu HE: Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors. Mol Cell. 2000, 5 (3): 545-555. 10.1016/S1097-2765(00)80448-7.View ArticlePubMedGoogle Scholar
- Blair JE, Ikeo K, Gojobori T, Hedges SB: The evolutionary position of nematodes. BMC evolutionary biology. 2002, 2: 7-10.1186/1471-2148-2-7.PubMed CentralView ArticlePubMedGoogle Scholar
- Copley RR, Aloy P, Russell RB, Telford MJ: Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans. Evolution & development. 2004, 6 (3): 164-169. 10.1111/j.1525-142X.2004.04021.x.View ArticleGoogle Scholar
- Dopazo H, Santoyo J, Dopazo J: Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. Bioinformatics (Oxford, England). 2004, 20 Suppl 1: I116-I121. 10.1093/bioinformatics/bth902.View ArticleGoogle Scholar
- Philippe H, Lartillot N, Brinkmann H: Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol. 2005, 22 (5): 1246-1253. 10.1093/molbev/msi111.View ArticlePubMedGoogle Scholar
- Wolf YI, Rogozin IB, Koonin EV: Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 2004, 14 (1): 29-36. 10.1101/gr.1347404.PubMed CentralView ArticlePubMedGoogle Scholar
- Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA: Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 1997, 387 (6632): 489-493. 10.1038/387489a0.View ArticlePubMedGoogle Scholar
- Halanych KM, Bacheller JD, Aguinaldo AM, Liva SM, Hillis DM, Lake JA: Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science. 1995, 267 (5204): 1641-1643. 10.1126/science.7886451.View ArticlePubMedGoogle Scholar
- Halanych KM: The new view of animal phylogeny. Annu Rev Ecol Evol Syst. 2004, 35: 229-256. 10.1146/annurev.ecolsys.35.112202.130124.View ArticleGoogle Scholar
- Winnepenninckx B, Backeljau T, Mackey LY, Brooks JM, De Wachter R, Kumar S, Garey JR: 18S rRNA data indicate that Aschelminthes are polyphyletic in origin and consist of at least three distinct clades. Mol Biol Evol. 1995, 12 (6): 1132-1137.PubMedGoogle Scholar
- Baguna J, Riutort M: The dawn of bilaterian animals: the case of acoelomorph flatworms. Bioessays. 2004, 26 (10): 1046-1057. 10.1002/bies.20113.View ArticlePubMedGoogle Scholar
- Baguna J, Riutort M: Molecular phylogeny of the Platyhelminthes. Can J Zool. 2004, 82: 168-193. 10.1139/z03-214.View ArticleGoogle Scholar
- Jondelius U, Ruiz-Trillo I, Baguna J, Riutort M: The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. Zoologica Scripta. 2002, 31 (2): 201-215. 10.1046/j.1463-6409.2002.00090.x.View ArticleGoogle Scholar
- Telford MJ, Lockyer AE, Cartwright-Finch C, Littlewood DT: Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms. Proceedings. 2003, 270 (1519): 1077-1083.Google Scholar
- Ruiz-Trillo I, Paps J, Loukota M, Ribera C, Jondelius U, Baguna J, Riutort M: A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. Proc Natl Acad Sci U S A. 2002, 99 (17): 11246-11251. 10.1073/pnas.172390199.PubMed CentralView ArticlePubMedGoogle Scholar
- Wiens M, Batel R, Korzhev M, Muller WE: Retinoid X receptor and retinoic acid response in the marine sponge Suberites domuncula. J Exp Biol. 2003, 206 (Pt 18): 3261-3271. 10.1242/jeb.00541.View ArticlePubMedGoogle Scholar
- Muller WE, Schroder HC, Skorokhod A, Bunz C, Muller IM, Grebenjuk VA: Contribution of sponge genes to unravel the genome of the hypothetical ancestor of Metazoa (Urmetazoa). Gene. 2001, 276 (1-2): 161-173. 10.1016/S0378-1119(01)00669-2.View ArticlePubMedGoogle Scholar
- Bertrand S, Brunet FG, Escriva H, Parmentier G, Laudet V, Robinson-Rechavi M: Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems. Mol Biol Evol. 2004, 21 (10): 1923-1937. 10.1093/molbev/msh200.View ArticlePubMedGoogle Scholar
- Escriva H, Bertrand S, Laudet V: The evolution of the nuclear receptor superfamily. Essays Biochem. 2004, 40: 11-26.View ArticlePubMedGoogle Scholar
- Escriva H, Langlois MC, Mendonca RL, Pierce R, Laudet V: Evolution and diversification of the nuclear receptor superfamily. Ann N Y Acad Sci. 1998, 839: 143-146. 10.1111/j.1749-6632.1998.tb10747.x.View ArticlePubMedGoogle Scholar
- Laudet V, Hanni C, Coll J, Catzeflis F, Stehelin D: Evolution of the nuclear receptor gene superfamily. Embo J. 1992, 11 (3): 1003-1013.PubMed CentralPubMedGoogle Scholar
- Thornton JW: Nonmammalian nuclear recptors: Evolution and endocrine disruption. Pure Appl Chem. 2003, 75: 1827-1839.View ArticleGoogle Scholar
- Thornton JW, Need E, Crews D: Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science. 2003, 301 (5640): 1714-1717. 10.1126/science.1086185.View ArticlePubMedGoogle Scholar
- Verjovski-Almeida S, DeMarco R, Martins EA, Guimaraes PE, Ojopi EP, Paquola AC, Piazza JP, Nishiyama MY, Kitajima JP, Adamson RE, Ashton PD, Bonaldo MF, Coulson PS, Dillon GP, Farias LP, Gregorio SP, Ho PL, Leite RA, Malaquias LC, Marques RC, Miyasato PA, Nascimento AL, Ohlweiler FP, Reis EM, Ribeiro MA, Sa RG, Stukart GC, Soares MB, Gargioni C, Kawano T, Rodrigues V, Madeira AM, Wilson RA, Menck CF, Setubal JC, Leite LC, Dias-Neto E: Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nat Genet. 2003, 35 (2): 148-157. 10.1038/ng1237.View ArticlePubMedGoogle Scholar
- Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25 (4): 402-408. 10.1006/meth.2001.1262.View ArticlePubMedGoogle Scholar
- GenBank public ftp site. [ftp://ftp.ncbi.nlm.nih.gov/pub/TraceDB/]
- GenBank. [http://www.ncbi.nlm.nih.gov/BLAST/]
- European Bioinformatics Institute. [http://www.ebi.ac.uk/blast2]
- Swiss-Prot. [http://www.expasy.ch/sprot/]
- ClustalW. [http://www.cf.ac.uk/biosi/research/biosoft/Downloads/clustalw.html]
- Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992, 8 (3): 275-282.PubMedGoogle Scholar
- Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52 (5): 696-704. 10.1080/10635150390235520.View ArticlePubMedGoogle Scholar
- Fantappie MR, Freebern WJ, Osman A, LaDuca J, Niles EG, LoVerde PT: Evaluation of Schistosoma mansoni retinoid X receptor (SmRXR1 and SmRXR2) activity and tissue distribution. Mol Biochem Parasitol. 2001, 115 (1): 87-99. 10.1016/S0166-6851(01)00274-2.View ArticlePubMedGoogle Scholar
- Fantappie MR, Osman A, Ericsson C, Niles EG, LoVerde PT: Cloning of Schistosoma mansoni Seven in Absentia (SmSINA)(+) homologue cDNA, a gene involved in ubiquitination of SmRXR1 and SmRXR2. Mol Biochem Parasitol. 2003, 131 (1): 45-54. 10.1016/S0166-6851(03)00188-9.View ArticlePubMedGoogle Scholar
- Osman A, Niles EG, LoVerde PT: Identification and characterization of a Smad2 homologue from Schistosoma mansoni, a transforming growth factor-beta signal transducer. J Biol Chem. 2001, 276 (13): 10072-10082. 10.1074/jbc.M005933200.View ArticlePubMedGoogle Scholar
- Le Paslier MC, Pierce RJ, Merlin F, Hirai H, Wu W, Williams DL, Johnston D, LoVerde PT, Le Paslier D: Construction and characterization of a Schistosoma mansoni bacterial artificial chromosome library. Genomics. 2000, 65 (2): 87-94. 10.1006/geno.2000.6147.View ArticlePubMedGoogle Scholar
- TIGR. [http://tigrblast.tigr.org/er-blast/index.cgi?project=sma1]
- Hirai H, LoVerde PT: FISH techniques for constructing physical maps on schistosome chromosomes. Parasitol Today. 1995, 11 (8): 310-314. 10.1016/0169-4758(95)80048-4.View ArticlePubMedGoogle Scholar
- Hirai H, Hirai Y: FISH mapping for helminth genome. Methods Mol Biol. 2004, 270: 379-394.PubMedGoogle Scholar
- Oger F, Bertin B, Caby S, Dalia-Cornette J, Adams M, Vicogne J, Capron M, Pierce RJ: Molecular cloning and characterization of Schistosoma mansoni Ftz-F1 interacting protein-1 (SmFIP-1), a novel corepressor of the nuclear receptor SmFtz-F1. Mol Biochem Parasitol. 2006, 148 (1): 10-23. 10.1016/j.molbiopara.2006.02.016.View ArticlePubMedGoogle Scholar
- Renaud JP, Rochel N, Ruff M, Vivat V, Chambon P, Gronemeyer H, Moras D: Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid. Nature. 1995, 378 (6558): 681-689. 10.1038/378681a0.View ArticlePubMedGoogle Scholar
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