The nuclear hormone receptor (NHR) superfamily represents one of the largest families of transcription factors in eukaryotes. These transcription factors typically bind to small lipophilic hormones and regulate key processes such as development, reproduction, homeostasis, and differentiation. The NHR family members include the receptors for thyroid hormone, retinoids, fatty acids, vitamin D, bile acids, steroids, and xenobiotics. In addition, there are many members of the family, denoted orphan receptors, for which the biologically relevant ligand continues to remain unclear. Members of this family generally bind to specific DNA sequences, called hormone response elements (HRE), either as homodimers or as heterodimers with other NHRs, and occasionally as monomers, and regulate transcription of target genes through recruitment of larger protein complexes.
Members of the NHR superfamily are thought to have evolved from a common receptor ancestor and share a common modular domain structure that includes DNA binding and ligand binding domains. Based on additional properties, such as the nature of the ligand or dimer partner, investigators have attempted to categorize the many members. One frequently used classification divides the family into three subgroups: Type I receptors include the steroid receptors such as the estrogen receptor (ER), androgen receptor (AR), glucocorticoid receptor (GR), and progesterone receptor (PR); Type II receptors include the thyroid hormone receptor (TR), vitamin D3 receptor (VDR), retinoic acid receptor (RAR), and retinoid-X receptor (RXR); and the third group are the orphan receptors, for which the naturally occurring ligands have yet to be characterized, and includes the COUP-TF and Rev-Erb receptors. Over time, many of the orphan receptors have been shown to bind various fatty acid metabolites and xenobiotics and have thus been labeled “adopted” orphan receptors.
Examples include the peroxisome proliferator-activated receptor (PPAR) (fatty acids), liver-X receptor (LXR) (oxysterols), and farnesoid X-activated receptor (FXR) (bile acids). With the discovery of additional NHRs and the adoption of several known members, the classification of nuclear receptors has become quite cumbersome, leading some to suggest a unifying classification scheme based on a phylogenetic tree that is organized by comparing the sequences of the well-conserved DNA binding and ligand binding domains.
The members of the NHR superfamily perform diverse roles in cells and organisms as a whole. The steroid hormone-binding Type I receptors, such as the ER, PR, and AR play key roles in sexual development and differentiation processes including breast development, menstrual cycle regulation, and spermatogenesis. Another Type I receptor, the GR, is involved in metabolism and inflammation. Type II receptors, such as the TR, RAR, and VDR, play critical roles in metabolism, development, immunity, and bone metabolism. For example, TRs are crucial for the regulation of metabolism, homeostasis, brain development, and amphibian metamorphosis; whereas, RARs are involved in the embryonic development of the anteriorposterior axis, central nervous system, and facial structures. Furthermore, VDRs have an important function in calcium homeostasis, bone metabolism, and the immune system. Orphan and adopted orphan receptors, including PPARs, LXR, and FXR, play key roles in lipid metabolism and processing of xenobiotics.
As mentioned above, each nuclear hormone receptor shares a common, modular structure. The primary structure of most NHRs can be divided into six domains, A through F. The A/B domain is highly variable in both length and sequence between receptors, the C domain comprises the DNA binding domain (DBD), and the D, E, and F domains (often referred to as the D/E/F domain) form the ligand binding domain (LBD). The next several sections will introduce the various domains and their general role in NHR physiology.
The A/B domain is a highly variable domain amongst NHRs and can contain sequences, referred to as the activation function 1 (AF-1) domain, that play a role in the ligand-independent transcriptional activation of target genes for some of the NHRs although the functions of the domain on the whole remain incompletely understood. This domain is frequently different in sequence and/or length between various NHRs. For example, the A/B domain of TRβ-1 and its alternatively spliced isoform TRβ-2, vary by the length of the A/B domain; whereas the A/B domain of TRα-1 and v-erbA, an oncogenic TR found in the avian erythroblastosis virus (AEV), differs both in length and sequence as a result of mutations sustained over the course of the virus’ evolution. In addition to its AF-1 function, the A/B domain has been reported to affect DNA binding specificity; furthermore, the TRβ-2 A/B domain may play a role in transcriptional activation on specific promoter sequences by interfering with the formation of a coregulator complex.
The C domain is highly conserved between the members of the NHR superfamily and, as noted before, plays a significant role in determining classification of the receptors. This domain represents the DBD of the receptor and contains two zinc finger motifs with alpha helical segments and coordinated zinc ions. This zinc finger region contains the “P box” alpha helix which mediates specific binding of the NHRs to their respective HREs and the “D box” amino acids which are involved in receptor dimerization and polarity as well as HRE spacing recognition. In addition, the zinc finger-containing C domain also contains additional receptor dimerization interfaces at the tip of the first zinc finger as well as C-terminal to the second zinc finger, the latter an alpha helical region denoted the “T box”. Finally, immediately C-terminal to the T box is another stretch of alpha helix referred to as the “A box” and which plays additional roles in DNA binding specificity. To summarize, the C domain contains two zinc fingers with associated alpha helical segments that principally mediate the DNA binding and dimerization properties of the receptor.