ReviewWhat are nuclear receptor ligands?
Introduction
Nuclear receptors (NRs) are proteins that share considerable amino acid sequence similarity in two highly conserved domains – the DNA binding (DBD) and the ligand binding domains (LBD) (Renaud and Moras, 2000). As their names indicate, these domains are responsible for binding specific DNA sequences and small lipophilic ligands, respectively. The DBD in the N-terminal half of the protein is comprised of two zinc-binding motifs that each coordinate a zinc ion through four precisely positioned cysteines. The LBD in the C-terminal half consists of a series of ∼12 alpha helices that create a hydrophobic pocket that can bind a hydrophobic ligand (Fig. 1A). NRs bind specific DNA response elements in the regulatory regions of genes and regulate transcription in response to ligand binding by recruiting co-regulatory molecules that subsequently modify the chromatin and contact the basal transcription machinery (Fig. 1B) (Gronemeyer et al., 2004, Rosenfeld et al., 2006). Examples of classical NRs include estrogen (ER, NR3A), progesterone (PR, NR3C3), androgen (AR, NR3C4), glucocorticoid (NR3C1), Vitamin A (RAR, NR1B), Vitamin D (VDR, NR1I1) and thyroid hormone (TR, NR1A) receptors. While there are an increasing number of examples of NRs playing non-genomic roles at the plasma and other membranes, this review will concentrate on the role and definition of the ligands only in their nuclear capacity; it is in that capacity that we have the greatest understanding of NR action, and yet even that understanding is far from complete.
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Evolutionary origins of NRs
NR genes are present and expressed in some of the simplest animal organisms. They are absent, however, in fungi, plants and choanoflagellates, the closest known relatives of metazoans (King et al., 2008). Therefore, they appear to have arrived on the evolutionary scene ∼635 million years (Myr) ago when animals first appeared in the fossil record (Fig. 2). They have also been associated with the Cambrian explosion – the massive diversification from relatively simple, primarily unicellular
Historical perspective of NR Ligands
Our current concept of what NR ligands are and what they do comes primarily from studies on a relatively few receptor·ligand pairs from man and related mammals. The reason for the anthropocentric bias of NR ligands is an obvious, and practical, one. Most of the first full length NRs cDNAs were cloned from human within a three-year time frame between 1985 and 1987 (GR, PR, ER, VDR, TR, RAR, and mineralcorticoid (MR, NR3C2)); these receptors subsequently defined the steroid and thyroid hormone
Biological perspective of NR ligands
The word “ligand” comes from the Latin ligare which means “to bind.” Whereas in inorganic chemistry a ligand is an atom or molecule that binds a metal, in biochemistry and pharmacology a ligand is defined as a substance that is able to bind to and form a complex with a biomolecule to serve a biological purpose, such as heme binding to myoglobin. This definition is much simpler than the classical notion of a NR ligand as one that induces a conformation change that triggers a cascade of events.
Evolutionary perspective of NR ligands
From an evolutionary perspective, the notion of NR ligands as signaling molecules that help recruit co-regulatory molecules requires that at least some of those co-regulatory molecules (e.g., p300/CBP, GRIP1/SRC, PGC1, SMRT, N-CoR, SWI/SNF, Mediator, etc.) be present in the organisms in which the first ligand-dependent NR arose. This appears to be the case. Whereas several co-regulatory molecules were first identified as interacting with NRs (e.g., GRIP1/SRC, PGC1, SMRT, N-CoR), they are now
Environmental sensors vs. endocrine receptors
The first NRs identified (GR, ER, PR, VDR) were purified based on their ability to bind their respective ligands (Evans, 1988). Most subsequent NRs were cloned or identified via sequence similarity to these first receptors, and hence initially had no ligands associated with them. Indeed, even the retinoic acid receptor RARα (NR1B1) started out as an orphan; although by the end of the original paper describing its cloning retinoic acid had been identified as a ligand (Giguere et al., 1987).
Criteria for NR ligand designation
Having broadened our notion of what constitutes a NR ligand, we must now decide on the precise criteria that should be used to classify a compound as a NR ligand. This will be an increasingly important issue as an increasing number of NRs are identified in newly sequenced genomes of all types of organisms. I propose that we use the simplest, least restrictive definition possible – i.e., that the compound bind the NR. The next criterion would be that the compound bind in the ligand binding
Summary and future directions
While the anthropocentric, pharmacological approach of the past 25 years has without a doubt been instrumental in characterizing in great detail this family of key transcriptional regulators, it is now time to consider NRs and their ligands from an evolutionary perspective. Remarkable advances have been made in our understanding of the evolutionary origins of life on Earth in recent years, in terms of both traditional paleontology and paleobiology (e.g., molecular fossils, genomic evolution).
Acknowledgements
Special thanks to M. Maduro for discussions on organismal development and B. Fang for drawing ligand structures. The Sladek lab is supported by NIH grants R01 DK053892 and R21 MH087397.
References (103)
Trichoplax, the simplest known animal, contains an estrogen-related receptor but no estrogen receptor: implications for estrogen receptor evolution
Biochem. Biophys. Res. Commun.
(2008)- et al.
Digging deep into the pockets of orphan nuclear receptors: insights from structural studies
Trends Cell Biol.
(2004) - et al.
Analysis of protein dimerization and ligand binding of orphan receptor HNF4alpha
J. Mol. Biol.
(2000) - et al.
Anatomical profiling of nuclear receptor expression reveals a hierarchical transcriptional network
Cell
(2006) - et al.
A new deficiency disease produced by rigid exclusion of fat from diet
J. Biol. Chem.
(1929) - et al.
The nature and role of the fatty acids essential in nutrition
J. Biol. Chem.
(1930) Nuclear receptor drug discovery
Curr. Opin. Chem. Biol.
(2008)- et al.
MNAR plays an important role in ERa activation of Src/MAPK and PI3K/Akt signaling pathways
Steroids
(2008) - et al.
Early evolution of metazoan transcription factors
Curr. Opin. Genet. Dev.
(2009) - et al.
Crystal structure of the HNF4 alpha ligand binding domain in complex with endogenous fatty acid ligand
J. Biol. Chem.
(2002)