A specificity map for the PDZ domain family.

PDZ domains are protein-protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides, we accurately map binding specificity for approximately half of the over 330 PDZ domains in the human and Caenorhabditis elegans proteomes. The domains recognize features of the last seven ligand positions, and we find 16 distinct specificity classes conserved from worm to human, significantly extending the canonical two-class system based on position -2. Thus, most PDZ domains are not promiscuous, but rather are fine-tuned for specific interactions. Specificity profiling of 91 point mutants of a model PDZ domain reveals that the binding site is highly robust, as all mutants were able to recognize C-terminal peptides. However, many mutations altered specificity for ligand positions both close and far from the mutated position, suggesting that binding specificity can evolve rapidly under mutational pressure. Our specificity map enables the prediction and prioritization of natural protein interactions, which can be used to guide PDZ domain cell biology experiments. Using this approach, we predicted and validated several viral ligands for the PDZ domains of the SCRIB polarity protein. These findings indicate that many viruses produce PDZ ligands that disrupt host protein complexes for their own benefit, and that highly pathogenic strains target PDZ domains involved in cell polarity and growth.

Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families.

We present a detailed comparative analysis of the PDZ domains of the human LAP proteins Erbin, Densin-180, and Scribble and the MAGUK ZO-1. Phage-displayed peptide libraries and in vitro affinity assays were used to define ligand binding profiles for each domain. The analysis reveals the importance of interactions with all four C-terminal residues of the ligand, which constitute a core recognition motif, and also the role of interactions with more upstream ligand residues that support and modulate the core binding interaction. In particular, the results highlight the importance of site(-1), which interacts with the penultimate residue of ligand C termini. Site(-1) was found to be monospecific in the Erbin PDZ domain (accepts tryptophan only), bispecific in the first PDZ domain of ZO-1 (accepts tryptophan or tyrosine), and promiscuous in the Scribble PDZ domains. Furthermore, it appears that the level of promiscuity within site(-1) greatly influences the range of potential biological partners and functions that can be associated with each protein. These findings show that subtle changes in binding specificity can significantly alter the range of biological partners for PDZ domains, and the insights enhance our understanding of this diverse family of peptide-binding modules.

Identification of a massive reserve of hematopoietic progenitors in mice.

Previous studies have demonstrated that mice null (-/-) for either CD34 or c-mpl are viable and have greatly decreased numbers of multipotential (CFU-Mix), erythroid (BFU-E), and granulocytemacrophage (CFU-GM) progenitor cells in the bone marrow (BM), spleen (Spl) and peripheral blood (PB), without noticeable decreases in the nucleated cellularity of these organs. To evaluate the significance of these two proteins further, mice null for both CD34 and c-mpl were assessed for hematopoietic progenitor cells (HPC) and nucleated cellularity and compared with these cells in CD34-/- and c-mpl-/- mice. The following progenitors were assessed: CFU-GM, BFU-E, CFU-Mix with an erythroid component, CFU-Mix with erythroid and megakaryocyte components, nonerythroid CFU with a megakaryocyte (Meg) component and pure CFU-Meg. Results demonstrated significant decreases in progenitors in the BM of dual CD34/c-mpl-/- mice compared to decreases from CD34-/- or c-mpl-/- mice; progenitor numbers in CD34/c-mpl-/- mice were decreased by 83-99.3% compared to that in wild-type littermate control mice. Decreases in progenitors in spleens of c-mpl-/- mice (89-96%) were more drastic than those of CD34-/- mice (50-78%) whereas those of dual CD34/c-mpl-/- mice were equal to or lower than that of c-mpl-/- mice (93-98%). Decreases in PB progenitors were seen in the c-mpl-/- and dual CD34/c-mpl-/- mice (75-90%). Whereas progenitor cells in BM, Spl and PB were drastically reduced in dual CD34/c-mpl-/- mice compared to controls, absolute numbers of nucleated cells in these organs were essentially not reduced. These studies demonstrate that CD34 and c-mpl have non-redundant effects on maintenance of steady-state hematopoiesis and highlight how few progenitor cells are required in steady-state conditions to populate and maintain the BM, Spl, and PB with nucleated cells.

The forkhead transcription factor FOXO4 induces the down-regulation of hypoxia-inducible factor 1 alpha by a von Hippel-Lindau protein-independent mechanism.

Tumors utilize hyperactivation of the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway to cope with deleterious environmental conditions. Activation of the PI3K/AKT pathway has been shown to increase protein expression of the alpha subunit of the hypoxia-inducible factor (HIF) 1, a key regulator of oxygen homeostasis. Elevated levels of HIF-1 alpha induce expression of genes with critical roles in angiogenesis, erythropoiesis, and glucose metabolism, processes that are essential for tumor expansion. Here we examine the involvement of FOXO4 (also known as AFX), a member of the forkhead transcription factor superfamily that is negatively regulated by the PI3K/AKT pathway, in the regulation of HIF-1 alpha protein expression. Nuclear expression of FOXO4 results in the suppression of various responses to hypoxia, including decreased vascular endothelial growth factor, glucose transporter 1, and erythropoietin expression. Interestingly, FOXO4 down-regulates the HIF-1 alpha protein levels, consistent with the lack of hypoxia responsiveness. Previous results have revealed a role for prolyl hydroxylation and resultant von Hippel-Lindau protein (pVHL) interactions in the ubiquitin-proteasome-mediated degradation of HIF-1 alpha. However, neither inhibition of prolyl hydroxylases nor mutation of HIF-1 alpha-hydroxylated prolines involved with pVHL-mediated binding inhibits the observed FOXO4-mediated down-regulation of HIF-1 alpha. These results suggest a novel alternate mechanism for hypoxic regulation that is dependent upon the level of activation of FOXO4-mediated transcription.

Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain.

The LAP (leucine-rich repeat and PDZ-containing) family of proteins play a role in maintaining epithelial and neuronal cell size, and mutation of these proteins can have oncogenic consequences. The LAP protein Erbin has been implicated previously in a number of cellular activities by virtue of its PDZ domain-dependent association with the C termini of both ERB-B2 and the p120-catenins. The present work describes the NMR structure of Erbin PDZ in complex with a high affinity peptide ligand and includes a comprehensive energetic analysis of both the ligand and PDZ domain side chains responsible for binding. C-terminal phage display has been used to identify preferred ligands, whereas binding affinity measurements provide precise details of the energetic importance of each ligand side chain to binding. Alanine and homolog scanning mutagenesis (in a combinatorial phage display format) identifies Erbin side chains that make energetically important contacts with the ligand. The structure of a phage-optimized peptide (Ac-TGW(-4)ETW(-1)V; IC(50) = approximately 0.15 microm) in complex with Erbin PDZ provides a structural context to understand the binding energetics. In particular, the very favorable interactions with Trp(-1) are not Erbin side chain-mediated (and therefore may be generally applicable to many PDZ domains), whereas the beta2-beta3 loop provides a binding site for the Trp(-4) side chain (specific to Erbin because it has an unusually long loop). These results contribute to a growing appreciation for the importance of at least five ligand C-terminal side chains in determining PDZ domain binding energy and highlight the mechanisms of ligand discrimination among the several hundred PDZ domains present in the human genome.

Prostate stem cell antigen as therapy target: tissue expression and in vivo efficacy of an immunoconjugate.

We conducted an expression analysis of prostate stem cell antigen (PSCA)in normal urogenital tissues, benign prostatic hyperplasia (n = 21), prostatic intraepithelial neoplasia (n = 33), and primary (n = 137) and metastatic (n = 42) prostate adenocarcinoma, using isotopic in situ hybridization on tissue microarrays. In normal prostate, we observe PSCA expression in the terminally differentiated, secretory epithelium; strong expression was also seen in normal urothelium. Forty-eight percent of primary and 64% of metastatic prostatic adenocarcinomas expressed PSCA RNA. Our studies did not confirm a positive correlation between level of PSCA RNA expression and high Gleason grade. We characterized monoclonal anti-PSCA antibodies that recognize PSCA expressed on the surface of live cells, are efficiently internalized after antigen recognition, and kill tumor cells in vitro in an antigen-specific fashion upon conjugation with maytansinoid. Unconjugated anti-PSCA antibodies demonstrated efficacy against PSCA-positive tumors by delaying progressive tumor growth in vivo. Maytansinoid-conjugated antibodies caused complete regression of established tumors in a large proportion of animals. Our results strongly suggest that maytansinoid-conjugated anti-PSCA monoclonal antibodies should be evaluated as a therapeutic modality for patients with advanced prostate cancer.

MAGI-1: a widely expressed, alternatively spliced tight junction protein.

Tight junctions are apically localized structures that regulate the passage of small molecules and proteins through intercellular regions of epithelial or endothelial cells. These structures are complex multimolecular assemblages that contain both transmembrane and membrane-associated proteins. MAGUKs (Membrane-Associated Guanylate Kinases) are a family of scaffolding proteins that contain multiple protein interaction domains, including PDZ, SH3, WW, and guanylate kinase motifs, and have been grouped into five discrete subfamilies based on homology. Little is known regarding the most recently described subfamily of MAGUKs, termed MAGIs (MAGUKS with Inverted domain structure). Here we show that two of the three known MAGI isoforms, MAGI-1 and MAGI-3, are present in the tight junctions of cultured epithelial cells. A broader examination of MAGI-1 expression in vivo shows that it is present in the tight junctions of all epithelial cell types examined. Human MAGI-1 transcripts are alternatively spliced at three sites, and two forms are expressed only in nonepithelial tissues, predominantly in brain. The major form that is expressed in cultured colon carcinoma epithelial cells, as well as several epithelial-rich tissues, contains an extended carboxy terminus encoding potential nuclear targeting signals. MAGI-1, ZO-1, and ZO-2 all colocalize in nonpolarized epithelial cells, suggesting that they form a preassembled complex that is incorporated into the tight junction upon polarization. Finally, all of the alternatively spliced forms of MAGI-1 show tight junction localization, and this localization occurs in the absence of the guanylate kinase and WW domains as well as the extended carboxy terminus.

The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of delta-catenin and ARVCF.

Erbin is a recently described member of the LAP (leucine-rich repeat and PDZ domain) protein family. We used a C-terminally displayed phage peptide library to identify optimal ligands for the Erbin PDZ domain. Phage-selected peptides were type 1 PDZ ligands that bound with high affinity and specificity to the Erbin PDZ domain in vitro. These peptides most closely resembled the C-terminal PDZ domain-binding motifs of three p120-related catenins: delta-catenin, ARVCF, and p0071 (DSWV-COOH). Analysis of the interactions of the Erbin PDZ domain with synthetic peptides matching the C termini of ARVCF or delta-catenin also demonstrated specific high affinity binding. We characterized the interactions between the Erbin PDZ domain and both ARVCF and delta-catenin in vitro and in vivo. The Erbin PDZ domain co-localized and coprecipitated with ARVCF or delta-catenin complexed with beta-catenin and E/N-cadherin. Mutagenesis and peptide competition experiments showed that the association of Erbin with the cadherin-catenin complex was mediated by the interaction of its PDZ domain with the C-terminal PDZ domain-binding motifs (DSWV-COOH) of ARVCF and delta-catenin. Finally, we showed that endogenous delta-catenin and Erbin co-localized in and co-immunoprecipitated from neurons. These results suggest that delta-catenin and ARVCF may function to mediate the association of Erbin with the junctional cadherin-catenin complex. They also demonstrate that C-terminal phage-display technology can be used to predict physiologically relevant ligands for PDZ domains.

AKT/PKB phosphorylation of p21Cip/WAF1 enhances protein stability of p21Cip/WAF1 and promotes cell survival.

p21(Cip1/WAF1) (p21), a p53-inducible protein, is a critical regulator of cell cycle and cell survival. p21 binds to and inhibits both the DNA synthesis regulator proliferating cell nuclear antigen and cyclin A/E-CDK2 complexes. Recently, p21 has also been shown to be a positive regulator of cell cycle progression as p21 is necessary for the assembly and activation of cyclin D1-CDK4/6 complexes. Furthermore, elevated p21 protein levels have been observed in various aggressive tumors as well as linked to chemoresistance. Here we demonstrate that p21 is directly phosphorylated by AKT/PKB, a survival kinase that is hyperactivated in many late stage tumors. Two sites (Thr(145) and Ser(146)) in the carboxyl terminus of p21 are phosphorylated by AKT/PKB in vitro and in vivo. Phosphorylation of Thr(145) inhibits PCNA binding, whereas phosphorylation of Ser(146) significantly increases p21 protein stability. Glioblastoma cell lines with activated AKT/PKB show enhanced p21 stability, and they are more resistant to taxol-mediated toxicity. Finally, AKT/PKB controls the assembly of cyclin D1-CDK4 complexes through modulation of p21 and cyclin D1 levels. These data imply that enhanced levels of p21 in tumors are due, in part, to phosphorylation by activated AKT/PKB. Furthermore, they suggest that one mechanism of AKT/PKB regulation of tumor cell survival and/or proliferation is to stabilize p21 protein.

The forkhead transcription factor AFX activates apoptosis by induction of the BCL-6 transcriptional repressor.

The activation of the AKT/protein kinase B kinases by mutation of the PTEN lipid phosphatase results in enhanced survival of a diversity of tumors. This resistance to apoptosis is partly accomplished by the inhibition of genetic programs induced by a subfamily of forkhead transcription factors including AFX. Here we describe an AFX-regulated pathway that appears to account for at least part of this apoptotic regulatory system. Cells induced to synthesize an active form of AFX die by activating the apoptotic death pathway. An analysis of genes regulated by AFX demonstrated that BCL-6, a transcriptional repressor, is up-regulated approximately 4-7-fold. An examination of the BCL-6 promoter demonstrated that AFX bound to specific target sites that could activate transcription. BCL-X(L), an anti-apoptotic protein, contains potential BCL-6 target sites in its promoter. An analysis of endogenous BCL-X(L) levels in AFX-expressing cells revealed enhanced down-regulation of the transcript ( approximately 1.3-1.7-fold) and protein, and BCL-6 directly binds to and suppresses the BCL-X(L) promoter. Finally, macrophages isolated from BCL-6-/- mice show enhanced survival in vitro. These results suggest that AFX regulates apoptosis in part by suppressing the levels of anti-apoptotic BCL-XL through the transcriptional repressor BCL-6.

PSTPIP is a substrate of PTP-PEST and serves as a scaffold guiding PTP-PEST toward a specific dephosphorylation of WASP.

PSTPIP is a tyrosine-phosphorylated protein involved in the organization of the cytoskeleton. Its ectopic expression induces filipodial-like membrane extensions in NIH 3T3 cells. We previously observed a defect in cytokinesis and an increase in the tyrosine phosphorylation of PSTPIP in PTP-PEST-deficient fibroblasts. In this article, we demonstrate that PTP-PEST and PSTPIP are found in the same complexes in vivo and that they interact directly through the CTH domain of PTP-PEST and the coiled-coil domain of PSTPIP. We tested pathways that could regulate the tyrosine phosphorylation of PSTPIP. We found that the activation of the epidermal growth factor and platelet-derived growth factor receptors can induce PSTPIP phosphorylation. With the use of the PP2 inhibitor, we demonstrate that Src kinases are not involved in the epidermal growth factor-mediated phosphorylation of PSTPIP. Together with previous results, this suggests that c-Abl is the critical tyrosine kinase downstream of growth factor receptors responsible for PSTPIP phosphorylation. We also demonstrate that PTP-PEST dephosphorylates PSTPIP at tyrosine 344. Importantly, we identified tyrosine 344 as the main phosphorylation site of PSTPIP by performing tryptic phosphopeptide maps. This is an important finding since tyrosine 367 of PSTPIP was also proposed as a candidate phosphorylation site involved in the negative regulation of the association between PSTPIP and WASP. In this respect, we observed that the PSTPIP.WASP complex is stable in vivo and is not affected by the phosphorylation of PSTPIP. Furthermore, we demonstrate that PSTPIP serves as a scaffold protein between PTP-PEST and WASP and allows PTP-PEST to dephosphorylate WASP. This finding suggests a possible mechanism for PTP-PEST to directly modulate actin remodeling through the PSTPIP-WASP interaction.