Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of Caenorhabditis elegans is partially mediated via a subclass-specific P-box residue

<p>Abstract</p> <p>Background</p> <p>The nuclear receptors of the NR2E class play important roles in pattern formation and nervous system development. Based on a phylogenetic analysis of DNA-binding domains, we define two conserved groups of orthologous NR2E genes: the NR2E1 subclass, which includes <it>C. elegans nhr-67, Drosophila tailless </it>and <it>dissatisfaction</it>, and vertebrate Tlx (NR2E2, NR2E4, NR2E1), and the NR2E3 subclass, which includes <it>C. elegans fax-1 </it>and vertebrate PNR (NR2E5, NR2E3). PNR and Tll nuclear receptors have been shown to bind the hexamer half-site AAGTCA, instead of the hexamer AGGTCA recognized by most other nuclear receptors, suggesting unique DNA-binding properties for NR2E class members.</p> <p>Results</p> <p>We show that NR2E3 subclass member FAX-1, unlike NHR-67 and other NR2E1 subclass members, binds to hexamer half-sites with relaxed specificity: it will bind hexamers with the sequence ANGTCA, although it prefers a purine to a pyrimidine at the second position. We use site-directed mutagenesis to demonstrate that the difference between FAX-1 and NHR-67 binding preference is partially mediated by a conserved subclass-specific asparagine or aspartate residue at position 19 of the DNA-binding domain. This amino acid position is part of the "P box" that plays a critical role in defining binding site specificity and has been shown to make hydrogen-bond contacts to the second position of the hexamer in co-crystal structures for other nuclear receptors. The relaxed specificity allows FAX-1 to bind a much larger repertoire of half-sites than NHR-67. While NR2E1 class proteins bind both monomeric and dimeric sites, the NR2E3 class proteins bind only dimeric sites. The presence of a single strong site adjacent to a very weak site allows dimeric FAX-1 binding, further increasing the number of dimeric binding sites to which FAX-1 may bind <it>in vivo</it>.</p> <p>Conclusion</p> <p>These findings identify subclass-specific DNA-binding specificities and dimerization properties for the NR2E1 and NR2E3 subclasses. For the NR2E1 protein NHR-67, Asp-19 permits binding to AAGTCA half-sites, while Asn-19 permits binding to AGGTCA half-sites. The apparent conservation of DNA-binding properties between vertebrate and nematode NR2E receptors allows for the possibility of evolutionarily-conserved regulatory patterns.</p

Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue-0

<p><b>Copyright information:</b></p><p>Taken from "Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue"</p><p>http://www.biomedcentral.com/1471-2199/9/2</p><p>BMC Molecular Biology 2008;9():2-2.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2225407.</p><p></p>-1 antiserum [31]. B. EMSA of FAX-1 protein binding to DR1A sequences (AAGTCA DR1) and failing to bind to DRNC sequences (AATTCA repeats). Binding could be competed with 10-fold and 100-fold molar excess of unlabeled competitor DR1G and DR1A DNA, but not DRNC DNA (wedges). Similar results (not shown) were obtained using radioactively-labeled DR1G DNA (AGGTCA DR1). C. and D. EMSA of FAX-1 protein binding to DR1T sequences (ATGTCA DR1) and DR1C sequences (ACGTCA DR1), respectively

Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue-2

<p><b>Copyright information:</b></p><p>Taken from "Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue"</p><p>http://www.biomedcentral.com/1471-2199/9/2</p><p>BMC Molecular Biology 2008;9():2-2.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2225407.</p><p></p>irs, respectively). Competition experiments with DR2A, DR3A, and DR1A are shown at 10-fold and 100-fold molar excess (wedges) or 10-fold molar excess only (DR3A). We observed additional shifted species in this experiment, however these bands could not be competed with equivalent unlabeled oligonucleotides

Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue-1

<p><b>Copyright information:</b></p><p>Taken from "Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue"</p><p>http://www.biomedcentral.com/1471-2199/9/2</p><p>BMC Molecular Biology 2008;9():2-2.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2225407.</p><p></p>MON1 and DR1A DNA sequences did not reduce non-specific background bands. Similar results (not shown) were obtained with MON2 sequences (single AAGTCA site in different position). B. EMSA of FAX-1 protein binding to HRSW sequences (AAGTCA strong binding site followed by AATTCA weak binding site). Binding could be competed with 10-fold and 100-fold molar excess of unlabeled competitor HRSW DNA, but not DRNC DNA (wedges). Although we obtained strong shifted bands, the proportion of labeled DNA shifted was considerably less than that observed with DR1A sequences (Table 1). We obtained similar results (not shown) with HRWS DNA (AATTCA weak site followed by AAGTCA strong site)

Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue-3

<p><b>Copyright information:</b></p><p>Taken from "Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of is partially mediated via a subclass-specific P-box residue"</p><p>http://www.biomedcentral.com/1471-2199/9/2</p><p>BMC Molecular Biology 2008;9():2-2.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2225407.</p><p></p>smid derived from pLacZi that contained a single DR1A binding site upstream of the gene. Each strain included either no activator or a fusion construct containing a nematode nuclear receptor DBD fused to the yeast GAL4 activation domain. B. β-galactosidase activity for yeast containing DR1G binding sites. Error bars show standard deviations. Asterisks indicate results that are significantly different than no activator control by student's t-test (p < 0.05). The difference between the FAX-1 and FAX-1 N19D mutant activators on DR1A sites is also statistically significant. We performed equivalent experiments using strains containing negative control DRNC sites and activator constructs. These strains did not show β-gal activity relative to controls that had no activator (data not shown). We performed equivalent experiments using strains containing MON1 sites and HRWS sites (both AAGTCA monomers) and a FAX-1 DBD activator, which also did not show β-gal activity relative to controls (data not shown)