A superfamily of nuclear receptors

Maybe not quite as absent from fungi as was formerly thought. A

combination of sequence profile searching with structural predictions at a genomic scale revealed

heterodimeric transcription factors in yeast that contain ligand-binding domains resembling those of animal receptors.14 Although they share little sequence homology, the resemblance of the ligandbinding structural folds in yeast Oaf1 and Pip2 and the vertebrate PPAR-RXR heterodimers is evident. The ligand-binding domains can bind fatty acids such as oleate, which provoke heterodimer formation (though these may not be the preferred ligands).

classifications have become difficult to sustain. One reason is the promiscuity and rather low affinity of some receptors for their apparent biological ligands. Table 10.1 lists some of the best-characterized receptors and their known binding partners, but it is important to remember that a particular receptor may also bind other ligands. For example, MRs bind not only aldosterone but also cortisol. Another difficulty is that many of them are orphan receptors apparently lacking any physiological ligand.

In evolution, the nuclear receptors first appeared in metazoans (animals and sponges) but are absent from plants, algae, fungi, and protists (but see text box). A retinoic acid receptor, remarkably homologous with the vertebrate retinoid

X receptor (RXR), is present in Cnidarians (animals with mostly radial symmetry, such as jellyfish, hydras, and corals).15 In the worm Caenorhabditis elegans there are 270 nuclear receptors, exceeding by far the 48 in humans.16 However, as with other invertebrates, this species lacks receptors for adrenal steroids (aldosterone and cortisol) and sex steroids (estradiol, progesterone, testosterone).

In vertebrates, these hormones regulate reproduction, differentiation, development, and homeostasis. It is likely that receptors for steroid hormones first arose in a cephalochordate such as Amphioxus17 (see page 3).

Orphan receptors and evolution

The isolation of cDNAs coding the mammalian oestrogen and glucocorticoid receptors was first reported in the 1980s.18–20 About half of the mammalian proteins identified as nuclear receptors are currently designated as ‘orphans’,

having no recognized ligands. In invertebrates, the proportion of orphans is higher still. Indeed, the receptors that have known ligands are only expressed in those subfamilies that evolved comparatively recently,21 suggesting that their ancestral forms were insensitive to ligands.

The most comprehensive classification of nuclear receptors within the superfamily has been obtained by building phylogenetic trees from sequence information. There are six subfamilies.22 In simplified form, this is illustrated in Figure 10.3, where a consensus tree of principally human nuclear receptors is set out. Such analysis shows that receptors for similar ligands are not necessarily confined to particular branches, but are distributed throughout the tree (e.g. RAR and RXR). This lack of correspondence suggests that the acquisition of the capacity to bind particular ligands may have arisen independently and at different times during evolution. Receptors without assigned ligands, such

as the COUP-TF family, the testis receptors TR2 and TR4, and the oestrogenrelated receptors ERR1 and ERR2, are orphans.

Orphan receptors that do not bind ligands may still be able to influence transcription. For example, NURR1 lacks a binding pocket because of the presence of several bulky hydrophobic residues,23 but even so it is a potent transcriptional activator. Furthermore, even if a ligand is identified in the future, it may not play a role in regulation of receptor activity. Other receptors have ligands permanently bound within the cavity and so may be unable to influence activity. In this respect, HNF4 has a constitutively bound fatty acid and the overall molecular conformation corresponds to a transcriptionally active receptor.24

The orphan receptors may represent proteins that never had the ability to be controlled by a ligand, or that once possessed and then subsequently lost

it. A possible mechanism for acquisition would involve primitive receptors existing in an equilibrium between active (able to bind DNA and thus capable of regulating gene function) and inactive conformations. This would be similar to the two-state equilibrium exhibited by cell surface receptors (see page

66). The emergence of the ability to bind ligands that shift the equilibrium towards the DNA-binding conformation would then confer a new tier of control over the expression of specific proteins.

Some orphan receptors (e.g. HNF4) stimulate gene transcription, whereas others (e.g. REV-ERB ) repress it. Although orphan receptors appear

not to be regulated by ligand, they can still be subject to regulation by phosphorylation/dephosphorylation, either of the receptors themselves or of their accessory proteins (see page 290). For example, the ability of HNF4 to bind DNA is prevented by its phosphorylation by PKA.27 Other ways of controlling orphan receptors include restriction of nuclear uptake and, within the nucleus, competitive interactions with other transcription factors for coactivator or corepressor proteins (see page 287).

NURR1 (nuclear receptor related) regulates development in the central nervous system and is essential for the development of dopaminergic neurons in brain.25

It is linked to familial Parkinson’s disease26 and schizophrenia.

HNF4 (hepatocyte nuclear factor 4) is expressed in liver, kidney, gut, and endocrine pancreas. It regulates apolipoprotein expression, glucose metabolism, and insulin

secretion. Mutation of the gene is responsible for a form of diabetes.

REV-ERB is a component of the circadian clock.

Of course, the assignment of a particular receptor to orphan status must

be done with caution. Sometimes activating ligands have become apparent later. Examples of such‘adopted orphans’ are the liver X receptor (LXR) and the farnesoid receptor (FXR). These are now known to have important roles in cholesterol and bile acid metabolism

and they are discussed, together with the xenobiotic receptors CAR and PXR, on page 289.