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indirectly as the result of interactions between proteins on the surfaces of neighboring cells and by extracellular hormones and growth factors. In multicellular organisms, these latter signaling molecules are secreted from one cell type and affect the function of cells that may be nearby or at a different location in the organism. One major group of extracellular signals comprises peptides and proteins, which bind to receptors in the plasma membrane. Ligand binding to these receptors triggers intracellular signal-transduction pathways. In Chapters 14 and 15, we describe the major types of cell-surface receptors and intracellular signaling pathways that regulate transcription-factor activity.

In this section, we discuss the second major group of extracellular signals, the small, lipid-soluble hormones— including many different steroid hormones, retinoids, and thyroid hormones—that can diffuse through plasma and nuclear membranes and interact directly with the transcription factors they control (Figure 11-40). As noted earlier, the in-tracellular receptors for most of these lipid-soluble hormones, which constitute the nuclear-receptor superfamily, function as transcription activators when bound to their ligands.

All Nuclear Receptors Share a Common Domain Structure

Cloning and sequencing of the genes encoding various nuclear receptors revealed a remarkable conservation in their amino acid sequences and three functional regions (Figure 11-41). All the nuclear receptors have a unique N-terminal region of variable length (100-500 amino acids). Portions of this variable region function as activation domains in some nuclear receptors. The DNA-binding domain maps near the center of the primary sequence and has a repeat of the C4 zinc-finger motif. The hormone-binding domain, located near the C-terminal end, contains a hormone-dependent activation domain. In some nuclear receptors, the hormone-binding domain functions as a repression domain in the absence of ligand.

Variable region (100-500 aa)

DNA-binding domain (68 aa)

Ligand-binding domain (225-285 aa)

Variable region (100-500 aa)

Amino acid identity: 0

DNA-binding domain (68 aa)

▲ FIGURE 11-41 General design of transcription factors in nuclear-receptor superfamily. The centrally located DNA-binding domain exhibits considerable sequence homology among different receptors and contains two copies of the C4 zinc-finger

Ligand-binding domain (225-285 aa)

motif. The C-terminal hormone-binding domain exhibits somewhat less homology. The N-terminal regions in various receptors vary in length, have unique sequences, and may contain one or more activation domains. [See R. M. Evans, 1988, Science 240:889.]

Nuclear-Receptor Response Elements Contain Inverted or Direct Repeats

The characteristic nucleotide sequences of the DNA sites, called response elements, that bind several nuclear receptors have been determined. The sequences of the consensus response elements for the glucocorticoid and estrogen receptors are 6-bp inverted repeats separated by any three base pairs (Figure 11-42a, b). This finding suggested that the cognate steroid hormone receptors would bind to DNA as symmetrical dimers, as was later shown from the x-ray crystallographic analysis of the homodimeric glucocorticoid receptor's C4 zinc-finger DNA-binding domain (see Figure 11-21b).

Some nuclear-receptor response elements, such as those for the receptors that bind vitamin D3, thyroid hormone, and retinoic acid, are direct repeats of the same sequence recognized by the estrogen receptor, separated by three to five base pairs (Figure 11-42c-e). The specificity for responding to these different hormones by binding distinct receptors is determined by the spacing between the repeats. The receptors that bind to such direct-repeat response elements do so as heterodimers with a common nuclear-receptor monomer called RXR. The vitamin D3 response element, for example, is bound by the RXR-VDR heterodimer,

TGTTCT 3' ACAAGA 5'

TGACCT 3' ACTGGA 5'

AGGTCA 3' TCCAGT 5'

AGGTCA 3' TCCAGT 5'

▲ FIGURE 11-42 Consensus sequences of DNA response elements that bind three nuclear receptors. The response elements for the glucocorticoid receptor (GRE) and estrogen receptor (ERE) contain inverted repeats that bind these homodimeric proteins. The response elements for heterodimeric receptors contain a common direct repeat separated by three to five base pairs, for the vitamin D3 receptor (VDRE), thyroid hormone receptor (TRE), and retinoic acid receptor (RARE). The repeat sequences are indicated by red arrows. [See K. Umesono et al., 1991, Cell 65:1255, and A. M. Naar et al., 1991, Cell 65:1267]

and the retinoic acid response element is bound by RXR-RAR. The monomers composing these heterodimers interact with each other in such a way that the two DNA-binding domains lie in the same rather than inverted orientation, allowing the RXR heterodimers to bind to direct repeats of the binding site for each monomer. In contrast, the monomers in homodimeric nuclear receptors (e.g., GRE and ERE) have an inverted orientation.

Hormone Binding to a Nuclear Receptor Regulates Its Activity as a Transcription Factor

The mechanism whereby hormone binding controls the activity of nuclear receptors differs for heterodimeric and ho-modimeric receptors. Heterodimeric nuclear receptors (e.g., RXR-VDR, RXR-TR, and RXR-RAR) are located exclusively in the nucleus. In the absence of their hormone lig-and, they repress transcription when bound to their cognate sites in DNA. They do so by directing histone deacetylation at nearby nucleosomes by the mechanism described earlier (see Figure 11-32a). As we saw earlier, in the presence of hormone, the ligand-binding domain of the RAR monomer undergoes a dramatic conformational change compared with the ligand-binding domain of a nuclear receptor in the absence of hormone (see Figure 11-25). In the ligand-bound conformation, heterodimeric nuclear receptors containing RXR can direct hyperacetyla-tion of histones in nearby nucleosomes, thereby reversing the repressing effects of the free ligand-binding domain. In the presence of ligand, ligand-binding domains of nuclear receptors also bind mediator, stimulating preinitiation complex assembly.

In contrast to heterodimeric nuclear receptors, homo-dimeric receptors are found in the cytoplasm in the absence of their ligands. Hormone binding to these receptors leads to their translocation to the nucleus. The hormone-dependent translocation of the homodimeric glucocorti-coid receptor (GR) was demonstrated in the transfection experiments shown in Figure 11-43. The GR hormone-binding domain alone mediates this transport. Subsequent studies showed that, in the absence of hormone, GR is anchored in the cytoplasm as a large protein aggregate com-plexed with inhibitor proteins, including Hsp90, a protein related to Hsp70, the major heat-shock chaperone in eu-karyotic cells. As long as the receptor is confined to the cytoplasm, it cannot interact with target genes and hence cannot activate transcription. Hormone binding to a ho-modimeric nuclear receptor releases the inhibitor proteins, allowing the receptor to enter the nucleus, where it can bind to response elements associated with target genes (Figure 11-44). Once the receptor with bound hormone binds to a response element, it activates transcription by interacting with chromatin-remodeling and histone acety-lase complexes and mediator.

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