Approximately 3,500 mammalian genes are predicted to be secreted or single-pass transmembrane proteins. The function of the majority of these genes is still unknown, and a number of the encoded proteins might find use as new therapeutic agents themselves or as targets for small molecule or antibody drug development. To analyze the physiological activities of the extracellular proteome, we developed a large-scale, high-throughput protein expression, purification, and screening platform. For this study, the complete human extracellular proteome was analyzed and prioritized based on genomewide disease association studies to select 529 initial target genes. These genes were cloned into three expression vectors as native sequences and as N-terminal and C-terminal Fc fusions to create an initial collection of 806 purified secreted proteins. To determine its utility, this library was screened in an OCT4-based cellular assay to identify regulators of human embryonic stem-cell self-renewal. We found that the pigment epithelium-derived factor can promote longterm pluripotent growth of human embryonic stem cells without bFGF or TGFβ/Activin/Nodal ligand supplementation. Our results further indicate that activation of the pigment epithelium-derived factor receptor-Erk1/2 signaling pathway by the pigment epitheliumderived factor is sufficient to maintain the self-renewal of pluripotent human embryonic stem cells. These experiments illustrate the potential for discovering novel biological functions by directly screening protein diversity in cell-based phenotypic or reporter assays.secreted proteins | human embryonic stem cells | pigment epitheliumderived factor | automated protein expression | high throughput M any physiological processes are regulated by secreted proteins, making the extracellular proteome a rich source of molecules for understanding basic pathways involved in normal physiological function, development, and human disease. Although many examples of bioactive secreted proteins have been identified, recent technologic advances allow us to directly screen this proteomic diversity for new factors influencing important biological pathways. Efforts to survey the extracellular proteome using conditioned media from transiently transfected cell lines have shown that novel factors can be identified in a prospective screening approach. Lin et al. (1) evaluated ∼3,400 genes encompassing predicted secreted proteins or extracellular domains of single-pass transmembrane proteins. Each gene of interest was expressed by transient transfection using liposomal reagents in 293 T cells, and relative quantitation was determined by ELISA using an affinity tag. Conditioned media from this set was used to screen for biological activity in various assays. However, such screens are complicated by secondary metabolites, the release of cytoplasmic proteins by cell lysis, and variable and undefined levels of extracellular proteins. To overcome these challenges, we have created a collection of purified and physically characterized extracel...

Galactosylsphingosine, glucosylsphingosine and sphingosine all inhibited cytochrome c oxidase activity in mitochondria from rat liver; more than 50% inhibition was caused by 5 microM lipid (0.1 mumol/mg mitochondrial protein). However, these lysosphingolipids did not suppress the activity of purified cytochrome c oxidase. When the enzyme was "reconstituted" with phosphatidylcholine, the lysosphingolipids clearly inhibited the activity. On the other hand, galactosylsphingosine, glucosylsphingosine and sphingosine all hemolyzed erythrocytes, indicating that lysosphingolipids can disrupt the membrane. Thus, it appears that the inhibition of cytochrome c oxidase, a membrane-bound enzyme in mitochondria, is due to perturbation of the environment of the enzyme and that the primary attacking site of the lysosphingolipids is the membrane. Because the potency to inhibit cytochrome c oxidase and to hemolyze erythrocytes did not differ among these lysosphingolipids and because galactosylceramide caused neither inhibition of cytochrome c oxidase nor hemolysis, the free amino group in the lysosphingolipids seems to be essential to give the effects. In addition, both inhibition of cytochrome c oxidase and hemolysis caused by lysosphingolipids were completely abolished by albumin, suggesting that toxic effects of lysosphingolipids may not be apparent in blood.

One common and characteristic feature of the extension peptides of mitochondrial enzyme precursors is the presence of repeating short stretches of uncharged amino acids linked by basic amino acids. We synthesized several model peptides having this particular feature of the extension peptides. The peptides contained arginine or lysine as a basic amino acid residue linking sequences of two to four residues of leucine and alanine. We examined the effects of the peptides on the import of the precursors of two mitochondrial enzymes, cytochrome P-450(SCC) and adrenodoxin, and found that the peptides were generally inhibitory to the import of the precursors into mitochondria. The effective concentrations of some of the inhibitory peptides were as low as a few microM. The peptides containing lysine instead of arginine had an essentially similar inhibitory effect on the import. The peptides did not inhibit the binding of pre-P450(SCC) to the surface of mitochondria. The synthetic model peptides uncoupled oxidative phosphorylation of mitochondria prepared from either rat liver or bovine adrenal cortex, and induced leakage of enzymes from the inner compartments of mitochondria. However, the synthetic model peptides did not solubilize membrane-bound enzymes from mitochondria, suggesting that their effect on the membranes is different from that of detergents. The synthetic model peptides seem to bind to the membranes causing significant perturbation in the membrane structure, which is possibly related to the functions of the particular common sequence found in the extension peptides of mitochondrial enzyme precursors.