Abstract
BackgroundNuclear receptors are a superfamily of metazoan transcription factors that regulate diverse developmental and physiological processes. Sequenced genomes from an increasing number of bilaterians have provided a more complete picture of duplication and loss of nuclear receptors in protostomes and deuterostomes but have left open the question of which nuclear receptors were present in the cnidarian-bilaterian ancestor. In addition, nuclear receptor expression and function are largely uncharacterized within cnidarians, preventing determination of conserved and novel nuclear receptor functions in the context of animal evolution.ResultsHere we report the first complete set of nuclear receptors from a cnidarian, the starlet sea anemone Nematostella vectensis. Genomic searches using conserved DNA- and ligand-binding domains revealed seventeen nuclear receptors in N. vectensis. Phylogenetic analyses support N. vectensis orthologs of bilaterian nuclear receptors in four nuclear receptor subfamilies within nuclear receptor family 2 (COUP-TF, TLL, HNF4, TR2/4) and one putative ortholog of GCNF (nuclear receptor family 6). Other N. vectensis genes grouped well with nuclear receptor family 2 but represented lineage-specific duplications somewhere within the cnidarian lineage and were not clear orthologs of bilaterian genes. Three nuclear receptors were not well-supported within any particular nuclear receptor family. The seventeen nuclear receptors exhibited distinct developmental expression patterns, with expression of several nuclear receptors limited to a subset of developmental stages.ConclusionN. vectensis contains a diverse complement of nuclear receptors including orthologs of several bilaterian nuclear receptors. Novel nuclear receptors in N. vectensis may be ancient genes lost from triploblastic lineages or may represent cnidarian-specific radiations. Nuclear receptors exhibited distinct developmental expression patterns, which are consistent with diverse regulatory roles for these genes. Understanding the evolutionary relationships and developmental expression of the N. vectensis nuclear receptor complement provides insight into the evolution of the nuclear receptor superfamily and a foundation for mechanistic characterization of cnidarian nuclear receptor function.
Highlights
Nuclear receptors are a superfamily of metazoan transcription factors that regulate diverse developmental and physiological processes
When DNA-binding domain (DBD) plus ligand-binding domain (LBD) were used for phylogenetic analyses of N. vectensis and bilaterian Nuclear receptors (NRs), the topology of the tree with the highest likelihood was consistent with monophyletic relationships of the recognized NR families
A complementary analysis using neighbor joining with the DBD and LBD resulted in weakly supported nodes for the NR families
Summary
Nuclear receptors are a superfamily of metazoan transcription factors that regulate diverse developmental and physiological processes. Nuclear receptors (NRs) are one of the most abundant classes of transcription factors in metazoans and coordinate diverse processes ranging from developmental patterning to physiological regulation. An analysis by Bertrand et al [5] of NRs from nine bilaterian genomes did much to resolve the evolutionary history of this superfamily They inferred 25 NRs that likely existed in the Urbilaterian with at least one gene from each of the six families. With the increasing availability of sequenced genomes and PCR-based surveys of NR diversity, from non-ecdysozoan protostomes [8-10], it has become apparent that a number of NRs have been lost since the Urbilaterian ancestor, in insects and nematodes
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