Genome-wide identification of nuclear receptor (NR) superfamily genes in the copepod Tigriopus japonicus

Abstract

BackgroundNuclear receptors (NRs) are a large superfamily of proteins defined by a DNA-binding domain (DBD) and a ligand-binding domain (LBD). They function as transcriptional regulators to control expression of genes involved in development, homeostasis, and metabolism. The number of NRs differs from species to species, because of gene duplications and/or lineage-specific gene losses during metazoan evolution. Many NRs in arthropods interact with the ecdysteroid hormone and are involved in ecdysone-mediated signaling in arthropods. The nuclear receptor superfamily complement has been reported in several arthropods, including crustaceans, but not in copepods. We identified the entire NR repertoire of the copepod Tigriopus japonicus, which is an important marine model species for ecotoxicology and environmental genomics.ResultsUsing whole genome and transcriptome sequences, we identified a total of 31 nuclear receptors in the genome of T. japonicus. Nomenclature of the nuclear receptors was determined based on the sequence similarities of the DNA-binding domain (DBD) and ligand-binding domain (LBD). The 7 subfamilies of NRs separate into five major clades (subfamilies NR1, NR2, NR3, NR4, and NR5/6). Although the repertoire of NR members in, T. japonicus was similar to that reported for other arthropods, there was an expansion of the NR1 subfamily in Tigriopus japonicus. The twelve unique nuclear receptors identified in T. japonicus are members of NR1L. This expansion may be a unique lineage-specific feature of crustaceans. Interestingly, E78 and HR83, which are present in other arthropods, were absent from the genomes of T. japonicus and two congeneric copepod species (T. japonicus and Tigriopus californicus), suggesting copepod lineage-specific gene loss.ConclusionsWe identified all NR receptors present in the copepod, T. japonicus. Knowledge of the copepod nuclear receptor repertoire will contribute to a better understanding of copepod- and crustacean-specific NR evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-993) contains supplementary material, which is available to authorized users.

Genome description and inventory of immune-related genes of the endangered pen shell Pinna nobilis: a giant bivalve experiencing a mass mortality event

“…The number of NRs found in P. nobilis, namely thirty-two, is in agreement with the number of NRs found in other species, i.e. twenty-one in Drosophila melanogaster [180], thirty-one in the copepod Tigriopus japonicus [181], thirty-three in the owl limpet Lottia gigantea [182], thirty-nine in the gastropod snail Biomphalaria glabrata [182], fortythree in the bivalve C. gigas [183] and forty-eight in humans [184]. Noteworthy, many of the NRs involved in the defensome, such as the ecdysone receptor, PXR, the estrogen receptor (ERR), PPAR and retinoic acid receptors [185,186] were discerned in the P. nobilis genome.…”

Genome streamlining in a minute herbivore that manipulates its host plant

“…However, no homologues of the evolutionary conserved NRs HNF4, HR39, HR78, and HR83 ( Bodofsky et al, 2017 ; Bonneton and Laudet, 2012 ), nor a homologue of the T. urticae Photoreceptor-specific NR (PNR), were detected in the A. lycopersici genome, even though HR78, HNF4, and PNR are present in D. pteronyssinus ( Supplementary file 1 — ‘Table S12.1’ Tab and ‘Table S12.2’ Tab). Further, for six nuclear receptors (E75, DSF, HR4, HR38, HR51, and SVP) that are evolutionary conserved across arthropods and normally have a canonical (DBD+LBD) structure ( Fahrbach et al, 2012 ; Grbić et al, 2011 ; Hwang et al, 2014 ; Litoff et al, 2014 ), an LBD was not predicted for the respective A. lycopersici homologues. LBDs for all of these except HR4 were predicted for both the D. pteronyssinus and T. urticae homologues ( Supplementary file 1 — ‘Table S12.1’ Tab and ‘Table S12.2’ Tab, Figure 4—figure supplements 12 – 17 ).…”

“…pteronyssinus (Supplementary File 1 -"Table S12.1" Tab and "Table S12.2" Tab). Further, for six nuclear receptors (E75, DSF, HR4, HR38, HR51 and SVP) that are evolutionary conserved across arthropods and normally have a canonical (DBD+LBD) structure (Fahrbach et al, 2012;Grbić et al, 2011;Hwang et al, 2014;Litoff et al, 2014), an LBD was not predicted for the respective A. lycopersici homologues. LBDs for all of these except HR4 were predicted for both the D. pteronyssinus and T. urticae homologues (Supplementary File 1 -"Table S12.1" Tab and " Table S12.2" Tab, Figure 4 figure supplements 12-17).…”

Characteristics of Nur77 and its ligands as potential anticancer compounds (Review)

“…In the same year, testicular receptor 3, a human homologue of Nur77, was identified by Chang et al ( 15 ) from a cDNA library of human prostate cancer cells. An increasing number of studies have shown that this transcription factor is present in various species, and it is recognized as a member of NR subfamily 4 group A ( 16 , 17 ).…”