Ligand binding was acquired during evolution of nuclear receptors

Abstract

The nuclear receptor (NR) superfamily comprises, in addition to ligand-activated transcription factors, members for which no ligand has been identified to date. We demonstrate that orphan receptors are randomly distributed in the evolutionary tree and that there is no relationship between the position of a given liganded receptor in the tree and the chemical nature of its ligand. NRs are specific to metazoans, as revealed by a screen of NR-related sequences in early- and non-metazoan organisms. The analysis of the NR gene duplication pattern during the evolution of metazoans shows that the present NR diversity arose from two waves of gene duplications. Strikingly, our results suggest that the ancestral NR was an orphan receptor that acquired ligand-binding ability during subsequent evolution.

Figure 1

Deduced amino acid sequence alignment of the NR PCR products corresponding to 6 of the 13 studied groups. The sequences are compared with their mammalian or arthropod homologues, which are shaded. Only amino acids different to those in the first sequence are indicated. For each PCR product the number of sequenced clones is indicated. Gaps in the sequence alignment are indicated by stars. Interestingly, in Anemonia and Schistosoma we found several PCR products assigned to a given NR group (e.g., Schistosoma COUP and COUP II). In these cases the Roman number in parentheses is an arbitrary number needed to discriminate different gene versions. This suggests that, at least in these organisms, there is more diversity in NR than previously expected. The precise position of these extra copies was not determined, and it is not known whether these are secondary duplications specific to a given species or rather new receptor genes. In all cases these duplications are independent of the vertebrate gene duplication discussed in Fig. 3. GenBank codes of the sequences are U93406 to U93489.

Figure 2

Phylogenetical tree of 33 selected NRs. The six subfamilies are shown. Subfamilies are defined by clusters supported by high robustness “bootstrap” values above 90 starting from the base of the tree, which was rooted at mid-length of its longest path. Ancestral segments for subfamilies 1 to 5 have their bootstrap value boxed. Subfamily VI defined by only one member is shown by a small box along its branch. Ligands are indicated when applicable. The two boxed sequences correspond to cDNA clones of early metazoan NRs isolated in this study and corresponding to the PCR products of Fig. 1.

Figure 3

Simplified phylogeny of metazoans (A) and chordates (B) showing the organisms where NR genes were found. In A, the subfamilies are indicated for each sequence. For B the number of different sequences found for a given group (e.g., PPAR) is indicated in parentheses. Zoological groups are boxed, previously described receptors from the literature are in bold, and receptors identified in this study are italicized.