The signaling phospholipid PIP ₃ creates a new interaction surface on the nuclear receptor SF-1

Abstract

The signaling phosphatidylinositol lipids PI(4,5)P 2 (PIP 2 ) and PI (3,4,5)P 3 (PIP 3 ) bind nuclear receptor 5A family (NR5As), but their regulatory mechanisms remain unknown. Here, the crystal structures of human NR5A1 (steroidogenic factor-1, SF-1) ligand binding domain (LBD) bound to PIP 2 and PIP 3 show the lipid hydrophobic tails sequestered in the hormone pocket, as predicted. However, unlike classic nuclear receptor hormones, the phosphoinositide head groups are fully solvent-exposed and complete the LBD fold by organizing the receptor architecture at the hormone pocket entrance. The highest affinity phosphoinositide ligand PIP 3 stabilizes the coactivator binding groove and increases coactivator peptide recruitment. This receptor-ligand topology defines a previously unidentified regulatory protein-lipid surface on SF-1 with the phosphoinositide head group at its nexus and poised to interact with other proteins. This surface on SF-1 coincides with the predicted binding site of the corepressor DAX-1 (dosage-sensitive sex reversal, adrenal hypoplasia critical region on chromosome X), and importantly harbors missense mutations associated with human endocrine disorders. Our data provide the structural basis for this poorly understood cluster of human SF-1 mutations and demonstrates how signaling phosphoinositides function as regulatory ligands for NR5As.T he existence of nuclear, nonmembrane pools of signaling phosphorylated derivatives of phosphatidylinositols or phosphoinositides (PIP n ) was reported over two decades ago (1-3). Consistent with these early reports, lipid-modifying enzymes responsible for phosphoinositide metabolism were also found in the nucleus (4-7); however, the function of PIP n in this cellular compartment remains poorly defined. The nuclear receptors (NRs) steroidogenic factor 1 (SF-1, NR5A1) and liver receptor homolog 1 (LRH-1, NR5A2) bind phosphoinositides as well as other phospholipids in their large hydrophobic pockets (8-13). The ability of NR5As to interact with PIP n is well-conserved with the Caenorhabditis elegans ortholog nhr-25 able to bind both PIP 2 and PIP 3 (14). That phosphoinositides might serve as endogenous NR5A ligands is suggested by the fact that elevating cellular pools of PIP 3 increases SF-1 activity (15) and that impairing PIP 3 uptake decreases SF-1 activity (12). Further, when purified from mammalian cells, the phosphoinositide PIP 2 is found associated with SF-1 and can be modified by the lipid kinase, IPMK, as well as the lipid phosphatase, PTEN (13). Taken together, these data suggest that signaling phosphoinositides are biologically relevant ligands for SF-1.Phosphoinositide ligands diverge chemically from classic NR hormones in that they contain a long, extended hydrophobic moiety and a prominent hydrophilic head group, which is inherently incompatible with the hydrophobic core of the NR5A ligand-binding pocket. Our previous structural analyses of SF-1 bound to phosphatidylcholine suggest that the acyl tails of phosphoinositides should be sequestered...

Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity

“…LRH-1 can bind to several PLs (2,25,40,41), yet only PCs have been shown to drive transactivation (13,20,40,41). It is unclear why LRH-1 responds only to PCs in cells; this may be intrinsic to the receptor or due to uncharacterized PL transporters capable of delivering PC ligands.…”

“…Recent evidence, however, suggests intact PLs are able to directly modulate the activity of transcription factors involved in lipid homeostasis, such as sterol regulatory element-binding protein 1 (SREBP-1), and some members of the nuclear receptor (NR) family of ligand-regulated transcription factors, including peroxisome proliferator-activated receptor ␣ (PPAR␣; NR1C1), steroidogenic factor 1 (NR5A1), and human liver receptor homolog-1 (LRH-1; NR5A2) (1)(2)(3)(4). LRH-1 regulates the expression of genes central to embryonic development, cell cycle progression, steroid synthesis, lipid and glucose homeostasis, and local immune function (5)(6)(7)(8)(9)(10)(11)(12).…”

Phosphatidylinositol-3,4,5-Triphosphate and Cellular Signaling: Implications for Obesity and Diabetes

“…They exert their function either indirectly as the precursor of second messengers, such as inositol-1,4,5-triphosphate (Ins(1,4,5)P3) and diacylglycerol (DAG), or directly by interacting with downstream effector protein molecules and thereby orchestrating the spatio-temporal organization of intracellular signal transduction cascades [3-5]. Recent studies demonstrate the role of PI in a variety of physiological processes, including cell proliferation, survival, cytoskeletal regulation, intracellular vesicle trafficking, and cell metabolism [2, 4].…”

Phosphoinositides in the nucleus and myogenic differentiation: how a nuclear turtle with a PHD builds muscle

“…Some orphan nuclear receptors are able to bind the fatty acid tails of phosphoinositides and present them for further modifications. Binding of phosphoinositide to the orphan nuclear receptors changes both the ability of: (1) phosphoinositide modulating enzymes to use them as substrates and (2) the orphan receptors to act as transcriptional regulators [18,19]. As PtdIns(4,5)P 2 has been found to be localized to many different types of speckle structures we suggest that there are likely to be multiple ways to maintain these different pools of PtdIns(4,5)P 2 .…”