Analysis of C. elegans NR2E nuclear receptors defines three conserved clades and ligand-independent functions

Abstract

BackgroundThe nuclear receptors (NRs) are an important class of transcription factors that are conserved across animal phyla. Canonical NRs consist of a DNA-binding domain (DBD) and ligand-binding domain (LBD). While most animals have 20–40 NRs, nematodes of the genus Caenorhabditis have experienced a spectacular proliferation and divergence of NR genes. The LBDs of evolutionarily-conserved Caenorhabditis NRs have diverged sharply from their Drosophila and vertebrate orthologs, while the DBDs have been strongly conserved. The NR2E family of NRs play critical roles in development, especially in the nervous system. In this study, we explore the phylogenetics and function of the NR2E family of Caenorhabditis elegans, using an in vivo assay to test LBD function.ResultsPhylogenetic analysis reveals that the NR2E family of NRs consists of three broadly-conserved clades of orthologous NRs. In C. elegans, these clades are defined by nhr-67, fax-1 and nhr-239. The vertebrate orthologs of nhr-67 and fax-1 are Tlx and PNR, respectively. While the nhr-239 clade includes orthologs in insects (Hr83), an echinoderm, and a hemichordate, the gene appears to have been lost from vertebrate lineages. The C. elegans and C. briggsae nhr-239 genes have an apparently-truncated and highly-diverged LBD region. An additional C. elegans NR2E gene, nhr-111, appears to be a recently-evolved paralog of fax-1; it is present in C. elegans, but not C. briggsae or other animals with completely-sequenced genomes. Analysis of the relatively unstudied nhr-111 and nhr-239 genes demonstrates that they are both expressed—nhr-111 very broadly and nhr-239 in a small subset of neurons. Analysis of the FAX-1 LBD in an in vivo assay revealed that it is not required for at least some developmental functions.ConclusionsOur analysis supports three conserved clades of NR2E receptors, only two of which are represented in vertebrates, indicating three ancestral NR2E genes in the urbilateria. The lack of a requirement for a FAX-1 LBD suggests that the relatively high level of sequence divergence for Caenorhabditis LBDs reflects relaxed selection on the primary sequence as opposed to divergent positive selection. This observation is consistent with a model in which divergence of some Caenorhabditis LBDs is allowed, at least in part, by the absence of a ligand requirement.

Conserved and Exapted Functions of Nuclear Receptors in Animal Development

“…Still another NR2E gene family member, HR83/nhr-239 , has orthologs in some insects ( HR83), C. elegans (nhr-239) , lophotrochozoans, an echinoderm, and a hemichordate, but has not been identified in vertebrates [184]. There is considerable divergence in the LBD of the nhr-239 clade, and some species-specific orthologs have truncated LBDs.…”

“…By contrast, the LBD is considerably less conserved, especially in C. elegans as compared to other animals [106, 184]. This provides some flexibility in terms of potential ligand control as well as co-activators and co-repressors.…”

Annotation of the Daphnia magna nuclear receptors: Comparison to Daphnia pulex

“…Group B receptors bind to retinoids, are involved in growth, and are key heterodimeric partners with many other receptors (Kliewer et al, 1992; Amoutzias et al, 2007; Wang et al, 2011). There are four NR2E members and several are involved in neural development (Weber et al, 2012). Groups 2C is induced by ecdysone and both 2C and 2F members have been shown to interact with other nuclear receptors and repress transcription (Tran et al, 1992; Fisk and Thummel, 1995; Palanker et al, 2006).…”

“…LBDs are often less conserved than DBDs. For example, the LBDs from the 2E group in C. elegans are poorly conserved in relation to the DBDs when compared to Drosophila or vertebrate 2E members (Weber et al, 2012). It is interesting to speculate as to the purpose and selective advantage of relatively large changes in the amino acid composition of the LBD and how this serves as a selective advantage for D. magna within its natural habitat, especially for receptors often involved in neural and optic development (Miyawaki et al, 2004; Weber et al, 2012).…”

Nuclear receptors in nematode development: Natural experiments made by a phylum

“…Functional analysis of the FAX-1 LBD in an in vivo assay revealed that it is not required for at least some developmental functions since the movement phenotype can be rescued by highly divergent LBDs of C. elegans NHR-111 and NHR-67, LBD of C. briggsae FAX-1 or by a transgene lacking the LBD. This suggests that the relatively high level of sequence divergence for Caenorhabditis elegans LBDs reflects in the case of the NR2E group members the relaxed selection of the primary sequence as opposed to a divergent positive selection [115]. This concept may be more general and may be applicable to NR2E members in other phyla as well as to some HNF4 related genes.…”