A novel nuclear receptor subfamily enlightens the origin of heterodimerization

Abstract

Background Nuclear receptors are transcription factors of central importance in human biology and associated diseases. Much of the knowledge related to their major functions, such as ligand and DNA binding or dimerization, derives from functional studies undertaken in classical model animals. It has become evident, however, that a deeper understanding of these molecular functions requires uncovering how these characteristics originated and diversified during evolution, by looking at more species. In particular, the comprehension of how dimerization evolved from ancestral homodimers to a more sophisticated state of heterodimers has been missing, due to a too narrow phylogenetic sampling. Here, we experimentally and phylogenetically define the evolutionary trajectory of nuclear receptor dimerization by analyzing a novel NR7 subgroup, present in various metazoan groups, including cnidarians, annelids, mollusks, sea urchins, and amphioxus, but lost in vertebrates, arthropods, and nematodes. Results We focused on NR7 of the cephalochordate amphioxus B. lanceolatum. We present a complementary set of functional, structural, and evolutionary analyses that establish that NR7 lies at a pivotal point in the evolutionary trajectory from homodimerizing to heterodimerizing nuclear receptors. The crystal structure of the NR7 ligand-binding domain suggests that the isolated domain is not capable of dimerizing with the ubiquitous dimerization partner RXR. In contrast, the full-length NR7 dimerizes with RXR in a DNA-dependent manner and acts as a constitutively active receptor. The phylogenetic and sequence analyses position NR7 at a pivotal point, just between the basal class I nuclear receptors that form monomers or homodimers on DNA and the derived class II nuclear receptors that exhibit the classical DNA-independent RXR heterodimers. Conclusions Our data suggest that NR7 represents the “missing link” in the transition between class I and class II nuclear receptors and that the DNA independency of heterodimer formation is a feature that was acquired during evolution. Our studies define a novel paradigm of nuclear receptor dimerization that evolved from DNA-dependent to DNA-independent requirements. This new concept emphasizes the importance of DNA in the dimerization of nuclear receptors, such as the glucocorticoid receptor and other members of this pharmacologically important oxosteroid receptor subfamily. Our studies further underline the importance of studying emerging model organisms for supporting cutting-edge research.

First characterization of the nuclear receptor superfamily in the Mediterranean mussel Mytilus galloprovincialis : developmental expression dynamics and potential susceptibility to environmental chemicals

“…We also identified a representative of the NR6 subfamily in M. galloprovincialis , which was notable because bivalve mollusks were supposed to have lost all members of this subfamily in the course of evolution [10,17]. In addition, the phylogeny of the canonical M. galloprovincialis NRs revealed a representative of the NR7 subfamily [35,36]. Separate phylogenetic analyses further allowed us to define two M. galloprovincialis members of the 2DBD NR subfamily, which have previously been identified, for example, in C. gigas and the trematode worm Schistosoma mansoni , as well as a single M. galloprovincialis member of the NR0 subfamily, as previously documented, for example, in C. gigas (electronic supplementary material, figure S3) [10,17].…”

Updated knowledge and a proposed nomenclature for nuclear receptors with two DNA binding domains (2DBD-NRs)

“…The absence of KR55 in 2DBD-NRs suggests that the first class I salt bridge is absent from 2DBD-NRs. The first salt bridge of class I NRs was missing in Branchiostoma lanceolatum NR7 (of note, NR7 was recently used to describe another group of NRs other than 2DBD-NRs, see next section) [ 52 ]. Experiments showed that 2DBD-NRs could form homodimers in a DNAindependent way [ 14 , 51 ], which suggests that other factors may be involved in regulation of homodimerization of 2DBD-NRs.…”

“…Previously, we suggested placing 2DBD-NRs in a new NR subfamily (NR subfamily 7, NR7) [ 12 , 14 ] and this was accepted by some other studies [ 16 , 54 , 55 ]. However, NR7 was recently used to describe NRs [ 52 ] previously known as NR8 members [ 55 ] and amphioxus NR1Hs [ 33 , 56 ]. To avoid confusion of 2DBD-NRs with other NRs named as NR7, we propose to designate2DBD-NRs as a subfamily instead of using NR7.…”

Updated knowledge and a proposed nomenclature for nuclear receptors with two DNA Binding Domains (2DBD-NRs)

“…Previously, we suggested placing 2DBD-NRs in a new NR subfamily (NR subfamily 7, NR7) when we discovered the 2DBD-NRs [6,8] and this was accepted by some other studies [10,44,45]. However, NR7 was recently used to describe NRs [46] previously known as NR8 members [45] and amphioxus NR1Hs [27,47]. To avoid confusion of 2DBD-NRs with other NRs named as NR7, our proposal keeps 2DBD-NRs as a subfamily instead of using NR7.…”