The human GRK4 gene is composed of 16 exons extending over 75 kilobase pairs of DNA. The two alternatively spliced exons correspond to exons II and XV. The genomic organization of the GRK4 gene is completely distinct from that of the human GRK2 gene, highlighting the evolutionary distance since the divergence of these two genes. Human GRK4 mRNA is expressed highly only in testis, and both alternative exons are abundant in testis mRNA.The four GRK4 proteins have been expressed, and all incorporate [ 3 H]palmitate. GRK4 is capable of augmenting the desensitization of the rat luteinizing hormone/ chorionic gonadotropin receptor upon coexpression in HEK293 cells and of phosphorylating the agonist-occupied, purified ␤ 2 -adrenergic receptor, indicating that GRK4 is a functional protein kinase.

RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug's mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53؉/؊ matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity ϳ4-to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.

The identification and characterization of previously unidentified signal transduction molecules has expanded our understanding of biological systems and facilitated the development of mechanism-based therapeutics. We present a highly validated small interfering RNA (siRNA) screen that functionally annotates the human genome for modulation of the Wnt/beta-catenin signal transduction pathway. Merging these functional data with an extensive Wnt/beta-catenin protein interaction network produces an integrated physical and functional map of the pathway. The power of this approach is illustrated by the positioning of siRNA screen hits into discrete physical complexes of proteins. Similarly, this approach allows one to filter discoveries made through protein-protein interaction screens for functional contribution to the phenotype of interest. Using this methodology, we characterized AGGF1 as a nuclear chromatin-associated protein that participates in beta-catenin-mediated transcription in human colon cancer cells.

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In this study, we used a combination of pharmacological and genetic approaches to determine which endogenous sphingolipid is the likely mediator of growth inhibition. When cells were treated with exogenous phytosphingosine (PHS, 20 M) or structurally similar or metabolically related molecules, including 3-ketodihydrosphingosine, dihydrosphingosine, C 2 -phytoceramide (PHC), and stearylamine, only PHS inhibited growth. Also, PHS was shown to inhibit uptake of uracil, tryptophan, leucine, and histidine. Again this effect was specific to PHS. Because of the dynamic nature of sphingolipid metabolism, however, it was difficult to conclude that growth inhibition was caused by PHS itself. By using mutant yeast strains defective in various steps in sphingolipid metabolism, we further determined the specificity of PHS. The elo2⌬ strain, which is defective in the conversion of PHS to PHC, was shown to have slower biosynthesis of ceramides and to be hypersensitive to PHS (5 M), suggesting that PHS does not need to be converted to PHC. The lcb4⌬ lcb5⌬ strain is defective in the conversion of PHS to PHS 1-phosphate, and it was as sensitive to PHS as the wild-type strain. The syr2⌬ mutant strain was defective in the conversion of DHS to PHS. Interestingly, this strain was resistant to high concentrations of DHS (40 M) that inhibited the growth of an isogenic wild-type strain, demonstrating that DHS needs to be converted to PHS to inhibit growth. Together, these data demonstrate that the active sphingolipid species that inhibits yeast growth is PHS or a closely related and yet unidentified metabolite.Certain sphingolipid metabolites including ceramide, sphingosine, and sphingosine 1-phosphate have pleiotropic effects on cellular growth and proliferation. The yeast Saccharomyces cerevisiae has emerged as an excellent model system for studying sphingolipid-mediated signal transduction. First, compared with over 300 different kinds of sphingolipids found in mammalian cells, there is only a limited number of sphingolipid species in the yeast, which simplifies lipid analysis (2, 3). Moreover, the basic structure, biosynthesis, and metabolism of sphingolipids are well conserved between mammalian and yeast systems. Second, many yeast genes in the sphingolipid biosynthetic and metabolic pathways have been cloned, providing opportunities for studying the effects of endogenous sphingolipids using genetics tools. Finally, although this is not exclusive to sphingolipid studies, yeast genetics provide excellent tools to identify and characterize components in signal transduction pathways (4 -6).Evidence for conservation of the sphingolipid signaling pathway in yeast comes from several studies. These include demonstrating that D-erythro-ceramide inhibited yeast cell growth in liquid culture and activated a protein phosphatase 2A that could be inhibited by okadaic acid (7). Later, Nickels and Broach (8) showed that ceramide inhibited yeast cell growth by arresting cell cycle at G 1 phase and that ceramide-activated protein phosphatase is com...

Sphingolipids are essential eukaryotic membrane lipids that are structurally and metabolically conserved through evolution. Sphingolipids have also been proposed to regulate eukaryotic stress responses as novel second messengers. Here we show that, in Saccharomyces cerevisiae, phytosphingosine, a putative sphingolipid second messenger, mediates heat stress signaling and activates ubiquitin-dependent proteolysis via the endocytosis vacuolar degradation and 26 S proteasome pathways. Inactivation of serine palmitoyltransferase, a key enzyme in generating endogenous phytosphingosine, prevents proteolysis during heat stress. Addition of phytosphingosine bypasses the requirement for serine palmitoyltransferase and restores proteolysis. Phytosphingosine-induced proteolysis requires multiubiquitin chain formation through the stress-responsive lysine 63 residue of ubiquitin. We propose that heat stress increases phytosphingosine and activates ubiquitin-dependent proteolysis.Sphingolipids are complex lipids containing a sphingoid base, which is a long chain amino base. Sphingolipids comprise indispensable structural components of all known eukaryotic plasma membranes and also regulate signal transduction elements including protein kinase C (1). Sphingosine, ceramide, sphingosine 1-phosphate, and other sphingolipid derivatives are also known to play central roles in apoptosis, cellular senescence, cell cycle regulation, inflammation, tumor development, and intracellular calcium mobilization (2)(3)(4).Despite the growing number of cellular functions regulated by sphingolipids and their derivatives, the molecular mechanisms by which these regulatory functions are executed in mammalian cells are poorly understood (5-7). Being ubiquitous and essential components of eukaryotic plasma membranes, sphingolipids are evolutionarily conserved from yeast to humans (8, 9). The yeast Saccharomyces cerevisiae has several advantages as a model system to study sphingolipid-mediated cellular regulation. First, the basic structure and metabolism of sphingolipids are conserved between yeast and mammals, and yet yeast has only three major species of sphingolipids, whereas mammalian cells may contain more than 300 distinct molecular species (10). Second, yeast is a genetically tractable organism whose genome has been completely sequenced (11). Lastly, many yeast genes encoding sphingolipid biosynthetic and metabolic enzymes have been recently identified (12). The controlled expression of these genes can be exploited to modulate intracellular levels of certain sphingolipids and their derivatives.The LCB1 and LCB2 genes encode serine palmitoyltransferase, which catalyzes the first committed step in yeast sphingolipid biosynthesis, the condensation of L-serine and palmitoyl-CoA to produce 3-ketodihydrosphingosine (KDS) 1 (13,14). Recently, heat stress was shown to increase cellular levels of sphingoid bases (dihydrosphingosine (DHS) and phytosphingosine (PHS)) and ceramides with little effect on the levels of complex sphingolipids (15,16). This in...

SUMMARY Recent evolutionary studies reveal that microorganisms including yeasts and fungi are more closely related to mammals than was previously appreciated. Possibly as a consequence, many natural-product toxins that have antimicrobial activity are also toxic to mammalian cells. While this makes it difficult to discover antifungal agents without toxic side effects, it also has enabled detailed studies of drug action in simple genetic model systems. We review here studies on the antifungal actions of antineoplasmic agents. Topics covered include the mechanisms of action of inhibitors of topoisomerases I and II; the immunosuppressants rapamycin, cyclosporin A, and FK506; the phosphatidylinositol 3-kinase inhibitor wortmannin; the angiogenesis inhibitors fumagillin and ovalicin; the HSP90 inhibitor geldanamycin; and agents that inhibit sphingolipid metabolism. In general, these natural products inhibit target proteins conserved from microorganisms to humans. These studies highlight the potential of microorganisms as screening tools to elucidate the mechanisms of action of novel pharmacological agents with unique effects against specific mammalian cell types, including neoplastic cells. In addition, this analysis suggests that antineoplastic agents and derivatives might find novel indications in the treatment of fungal infections, for which few agents are presently available, toxicity remains a serious concern, and drug resistance is emerging.

RNA interference (RNAi) high-throughput screening (HTS) experiments carried out using large (>5000 short interfering [si]RNA) libraries generate a huge amount of data. In order to use these data to identify the most effective siRNAs tested, it is critical to adopt and develop appropriate statistical methods. To address the questions in hit selection of RNAi HTS, we proposed a quartile-based method which is robust to outliers, true hits and nonsymmetrical data. We compared it with the more traditional tests, mean +/- k standard deviation (SD) and median +/- 3 median of absolute deviation (MAD). The results suggested that the quartile-based method selected more hits than mean +/- k SD under the same preset error rate. The number of hits selected by median +/- k MAD was close to that by the quartile-based method. Further analysis suggested that the quartile-based method had the greatest power in detecting true hits, especially weak or moderate true hits. Our investigation also suggested that platewise analysis (determining effective siRNAs on a plate-by-plate basis) can adjust for systematic errors in different plates, while an experimentwise analysis, in which effective siRNAs are identified in an analysis of the entire experiment, cannot. However, experimentwise analysis may detect a cluster of true positive hits placed together in one or several plates, while platewise analysis may not. To display hit selection results, we designed a specific figure called a plate-well series plot. We thus suggest the following strategy for hit selection in RNAi HTS experiments. First, choose the quartile-based method, or median +/- k MAD, for identifying effective siRNAs. Second, perform the chosen method experimentwise on transformed/normalized data, such as percentage inhibition, to check the possibility of hit clusters. If a cluster of selected hits are observed, repeat the analysis based on untransformed data to determine whether the cluster is due to an artifact in the data. If no clusters of hits are observed, select hits by performing platewise analysis on transformed data. Third, adopt the plate-well series plot to visualize both the data and the hit selection results, as well as to check for artifacts.