The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group

Abstract

BackgroundNuclear receptors are a superfamily of transcription factors important in key biological, developmental and reproductive processes. Several of these receptors are ligand- activated and through their ability to bind endogenous and exogenous ligands, are potentially vulnerable to xenobiotics. Molluscs are key ecological species in defining aquatic and terrestrial habitats and are sensitive to xenobiotic compounds in the environment. However, the understanding of nuclear receptor presence, function and xenobiotic disruption in the phylum Mollusca is limited.ResultsHere, forty-three nuclear receptor sequences were mined from the genome of the Pacific oyster, Crassostrea gigas. They include members of NR0-NR5 subfamilies, notably lacking any NR6 members. Phylogenetic analyses of the oyster nuclear receptors have been conducted showing the presence of a large novel subfamily group not previously reported, which is named NR1P. Homologues to all previous identified nuclear receptors in other mollusc species have also been determined including the putative heterodimer partner retinoid X receptor, estrogen receptor and estrogen related receptor.ConclusionC. gigas contains a highly diverse set of nuclear receptors including a novel NR1 group, which provides important information on presence and evolution of this transcription factor superfamily in invertebrates. The Pacific oyster possesses two members of NR3, the sex steroid hormone receptor analogues, of which there are 9 in humans. This provides increasing evidence that steroid ligand specific expansion of this family is deuterostome specific. This new knowledge on divergence and emergence of nuclear receptors in C. gigas provides essential information for studying regulation of molluscan gene expression and the potential effects of xenobiotics.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-369) contains supplementary material, which is available to authorized users.

Evolution of a novel nuclear receptor subfamily with emphasis on the member from the Pacific oyster Crassostrea gigas

“…3). This phylogenetic relationship between CgNR8A1 and other NR subfamilies was consistent with that observed in a previous study on NR genes in C. gigas (Vogeler et al, 2014). Indeed, NvNR8A1 was an outgroup of NR1/4 and not assigned to a known NR subfamily in a previous study focusing on NR genes in N. vectensis (Reitzel and Tarrant, 2009).…”

“…Interestingly, a recently published study on the NR genes in C. gigas reported that CgNHR42 (named as CgNR8A1 in this study) was an outgroup of NR2/3/5/6 and was described as a pseudogene (Vogeler et al, 2014). To investigate whether CgNR8A1 had any homologs in other animal species, an extensive BLASTp search was conducted against non-redundant protein sequences in NCBI.…”

“…There are 43 NRs in C. gigas, including a novel NR group that belongs to the NR1 subfamily (NR1P) and two outliers that could not be assigned to a receptor subfamily and were previously ignored and designated as pseudogenes (Vogeler et al, 2014). In this study, we cloned one of these two outliers and found homologs of this gene in other metazoans.…”

“…NRs of model species (such as Homo sapiens, Caenorhabditis elegans, and Drosophila melanogaster) were extensively studied in the 1990s, and the nomenclature system was designed on the basis of these NRs (Auwerx et al, 1999). Recently, rapid progress in the genome projects on various other metazoans has provided a new impetus to study the evolution and function of NRs in these species (Wu et al, 2006;Schubert et al, 2008;Reitzel and Tarrant, 2009;Vogeler et al, 2014). For example, a novel NR subfamily containing two tandem DBDs and a single LBD (2DBD-NRs) has been identified and designated as NR7 (Wu et al, 2007a).…”

Oct-GnRH, the first protostomian gonadotropin-releasing hormone-like peptide and a critical mini-review of the presence of vertebrate sex steroids in molluscs

“…There may be differences of inherent coregulators or carryover of non-genomic ER signaling elements of the later. Nuclear receptor (NR) mining from the genome of the Pacific oyster C. gigas has not clearly revealed the presence of NR3 members, which could interact with vertebrate sex steroids (Vogeler et al, 2014). This result provides increasing evidence that the steroid ligand specific expansion of this family is deuterostome specific (Vogeler et al, 2014).…”