The Phox Homology (PX) Domain Protein Interaction Network in Yeast

Abstract

Phosphoinositides (PIs)1 act as signaling molecules in a variety of cellular processes including vesicular trafficking and cell motility (1-3). PI signaling is mediated by proteins that contain one or several lipid-binding domains such as PH, FYVE, ENTH, ANTH, FERM, PHD, Tubby, and C2 domains, all of which have been reported to bind PIs. Recently, the PX domain was shown to represent another PI-binding domain (reviewed in Refs. 4 -7).Phox homology (PX) domains were originally identified as a common motif of about 120 amino acids found in the p40 phox and p47 phox subunits of the neutrophil NADPH oxidase (Phox) complex (8). This domain is conserved from yeast to human, and more than 400 examples have been annotated in sequence databases (e.g. SMART (9)). PX domain-containing proteins have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification (reviewed in Refs. 10 and 11).PX domains show relatively little sequence conservation, yet their structure appears to be highly conserved. All published crystal structures exhibit a clearly defined PI-binding pocket (12-15). Although phosphatidylinositol-3-phosphate (PtdIns(3)P) is the primary target of PX domains, binding to phosphatidic acid, phosphatidylinositol-3,4-bisphosphate (PtdIns(3,4)P 2 ), phosphatidylinositol-3,5-bisphosphate (PtdIns-(3,5)P 2 ), phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P 2 ), and phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P 3 ) has been reported as well (16,17).The yeast genome encodes 15 PX domain-containing proteins that are involved in vesicular trafficking, cell signaling, control of bud emergence and cell polarity, or are of largely unknown function (Table I). All yeast PX domains (except the sequence outlier Ypr097p) bind specifically to PtdIns(3)P with different affinities (18).Although most PX domains contain additional domains-or at least additional protein sequences-two yeast proteins, Grd19p and Ypt35p, consist almost exclusively of the PX domain ( Table I). Assuming that signaling proteins are not likely to bind to a membrane for its own sake suggested that these PtdIns(3)P-specific PX domain-only proteins must also be involved in protein-protein interactions in order to transduce a signal from the membrane to some effector. This is further supported by several genetic observations. For example, yeast strains with a deletion of their GRD19 gene mis-sort the TGN membrane proteins A-ALP, Pep12p, and Kex2p to the vacuole (19,20).A direct involvement of the PX domain in protein-protein interactions has been observed in the p47 phox subunit of the neutrophil NADPH oxidase complex. p47 phox is held in an inactive state by an intramolecular interaction between its C-terminal Src homology 3 (SH3) domain and its PX domain. Upon activation by invading microorganisms, p47 phox becomes phosphorylated and the PX-SH3 interaction is disrupted (21, 22). The C-terminal SH3 domain interacts with a proline-rich region of the p47 phox -PX domain (13). Moreove...

The Conserved Foot Domain of RNA Pol II Associates with Proteins Involved in Transcriptional Initiation and/or Early Elongation

“…However, physical interactions have been observed between Mvp1 and three nuclear proteins, Std1, Yra2, and Srb7 (Schmidt et al 1999;Hazbun et al 2003;Vollert and Uetz 2004;Titz et al 2006). Similarly, Spo14 physically interacts with Dcp2 (Fromont-Racine et al 1997) and genetically with the transcription factor Ste12 (Hairfield et al 2001).…”

“…Mvp1, a protein required for sorting proteins to the vacuole (Ekena and Stevens 1995), physically interacts with three Nonet and Young (1989) nuclear proteins, Std1, Yra2, and Srb7 (Schmidt et al 1999;Hazbun et al 2003;Vollert and Uetz 2004;Titz et al 2006). Similarly, Spo14, a phospholipase D involved in Sec14p-independent secretion and required for meiosis and spore formation (Rudge et al 2002;Nakanishi et al 2006), physically interacts with Dcp2, (Fromont-Racine et al 1997) and genetically interacts with the transcription factor Ste12 (Hairfield et al 2001).…”

Phosphoinositides: Tiny Lipids With Giant Impact on Cell Regulation

“…Although the first PX domains were found to bind PtdIns3P (752,1750), and all yeast PX domains bind this lipid (1782), some metazoan PX domains bind PtdIns(4,5)P 2 (327, 810), and the lipid-binding specificity of many mammalian PX domains remains unknown. It is also important to note that PX domains also bind proteins (1540,1643). Recent studies also suggest that class II PI3Ks produce some of the PtdIns3P in higher eukaryotes (370,970,1700), and the molecular cloning of the type II PI4Ks (108, 1058) revealing their presence in endosomes (83, 1060) also suggested the involvement of these latter enzymes in endocytic trafficking in mammalian cells (83, 1060).…”

Inositol-lipid binding motifs: signal integrators through protein-lipid and protein-protein interactions

“…Indeed, the insulin-induced membrane translocation of the p47 phox PX domain has been reported to be only partially dependent on PtdIns(3)P binding (Zhan et al, 2002). In a recent study several PX domains of yeast were found to have protein binding partners in a genome-wide two-hybrid screen (Vollert and Uetz, 2004). Many of the interacting proteins are membrane proteins involved in vesicular trafficking and it will be important to determine whether a common PX-domaininteracting motif can be identified in these proteins.…”