High-Throughput Screening of the Yeast Kinome: Identification of Human Serine/Threonine Protein Kinases That Phosphorylate the Hepatitis C Virus NS5A Protein

Department of Microbiology, Washington National Primate Research Center, University of Washington, Seattle, Washington 98195, USA.
Journal of Virology (Impact Factor: 4.44). 05/2004; 78(7):3502-13. DOI: 10.1128/JVI.78.7.3502-3513.2004
Source: PubMed


The hepatitis C virus NS5A protein plays a critical role in virus replication, conferring interferon resistance to the virus through perturbation of multiple intracellular signaling pathways. Since NS5A is a phosphoprotein, it is of considerable interest to understand the role of phosphorylation in NS5A function. In this report, we investigated the phosphorylation of NS5A by taking advantage of 119 glutathione S-transferase-tagged protein kinases purified from Saccharomyces cerevisiae to perform a global screening of yeast kinases capable of phosphorylating NS5A in vitro. A database BLAST search was subsequently performed by using the sequences of the yeast kinases that phosphorylated NS5A in order to identify human kinases with the highest sequence homologies. Subsequent in vitro kinase assays and phosphopeptide mapping studies confirmed that several of the homologous human protein kinases were capable of phosphorylating NS5A. In vivo phosphopeptide mapping revealed phosphopeptides common to those generated in vitro by AKT, p70S6K, MEK1, and MKK6, suggesting that these kinases may phosphorylate NS5A in mammalian cells. Significantly, rapamycin, an inhibitor commonly used to investigate the mTOR/p70S6K pathway, reduced the in vivo phosphorylation of specific NS5A phosphopeptides, strongly suggesting that p70S6 kinase and potentially related members of this group phosphorylate NS5A inside the cell. Curiously, certain of these kinases also play a major role in mRNA translation and antiapoptotic pathways, some of which are already known to be regulated by NS5A. The findings presented here demonstrate the use of high-throughput screening of the yeast kinome to facilitate the major task of identifying human NS5A protein kinases for further characterization of phosphorylation events in vivo. Our results suggest that this novel approach may be generally applicable to the screening of other protein biochemical activities by mechanistic class.

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    • "Also, it will be useful to identify the corresponding kinases that recognize these motifs due to its potential as drug targets [9]. However, previous studies do not consider the corresponding substrate site specificities of catalytic kinases [10]. "
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    ABSTRACT: Background The phosphorylation of virus proteins by host kinases is linked to viral replication. This leads to an inhibition of normal host-cell functions. Further elucidation of phosphorylation in virus proteins is required in order to aid in drug design and treatment. However, only a few studies have investigated substrate motifs in identifying virus phosphorylation sites. Additionally, existing bioinformatics tool do not consider potential host kinases that may initiate the phosphorylation of a virus protein. Results 329 experimentally verified phosphorylation fragments on 111 virus proteins were collected from virPTM. These were clustered into subgroups of significantly conserved motifs using a recursively statistical method. Two-layered Support Vector Machines (SVMs) were then applied to train a predictive model for the identified substrate motifs. The SVM models were evaluated using a five-fold cross validation which yields an average accuracy of 0.86 for serine, and 0.81 for threonine. Furthermore, the proposed method is shown to perform at par with three other phosphorylation site prediction tools: PPSP, KinasePhos 2.0 and GPS 2.1. Conclusion In this study, we propose a computational method, ViralPhos, which aims to investigate virus substrate site motifs and identify potential phosphorylation sites on virus proteins. We identified informative substrate motifs that matched with several well-studied kinase groups as potential catalytic kinases for virus protein substrates. The identified substrate motifs were further exploited to identify potential virus phosphorylation sites. The proposed method is shown to be capable of predicting virus phosphorylation sites and has been implemented as a web server
    BMC Bioinformatics 10/2013; 14(16). DOI:10.1186/1471-2105-14-S16-S10 · 2.58 Impact Factor
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    • "MAP kinases can also phosphorylate hepatitis B virus large envelope protein (Rothmann et al., 1998). The PI3K/Akt pathway induced phosphorylation of a nonstructural protein, NS5A, of Hepatitis C virus (HCV), which is associated with HCV replication (Coito et al., 2004; Mannova & Beretta, 2005). These findings lead us to postulate that the PI3K/Akt pathway may regulate influenza vRNA synthesis by direct or indirect phosphorylation of viral products. "
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    ABSTRACT: The phosphatidylinositol 3-kinase (PI3K)/Akt signalling pathway has attracted much recent interest due to its central role in modulating diverse downstream signalling pathways associated with cell survival, proliferation, differentiation, morphology and apoptosis. An increasing amount of information has demonstrated that many viruses activate the PI3K/Akt pathway to augment their efficient replication. In this study, the effect of the PI3K/Akt signalling pathway on influenza virus propagation was investigated. It was found that Akt phosphorylation was elevated in the late phase of influenza A/PR/8/34 infection in human lung carcinoma cells (A549). The PI3K-specific inhibitor LY294002 could suppress Akt phosphorylation, suggesting that influenza A virus-induced Akt phosphorylation is PI3K-dependent. UV-irradiated influenza virus failed to induce Akt phosphorylation, indicating that viral attachment and entry were not sufficient to trigger PI3K/Akt pathway activation. Blockage of PI3K/Akt activation by LY294002 and overexpression of the general receptor for phosphoinositides-1 PH domain (Grp1-PH) led to a reduction in virus yield. Moreover, in the presence of LY294002, viral RNA synthesis and viral protein expression were suppressed and, possibly as a consequence of low NP and M1 protein level, viral RNP nuclear export was also suppressed. These data suggest that the PI3K/Akt signalling pathway plays a role in influenza virus propagation.
    Journal of General Virology 04/2007; 88(Pt 3):942-50. DOI:10.1099/vir.0.82483-0 · 3.18 Impact Factor
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    • "Protein kinases A and CK2 were identified as candidate kinases several years ago, based on in vitro results showing NS5A phosphorylation by recombinant enzymes (Ide et al., 1997; Kim et al., 1999). Very recently, Katze and co-workers identified several NS5A kinases from the Saccharomyces cerevisiae kinome and could further demonstrate in vitro NS5A phosphorylation by related mammalian protein kinases such as CK1δ, AKT1, p70S6K, MEK1 and MKK6 (Coito et al., 2004). "
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    ABSTRACT: The development of novel antiviral drugs against hepatitis C is a challenging and competitive area of research. Progress of this research has been hampered due to the quasispecies nature of the hepatitis C virus, the absence of cellular infection models and the lack of easily accessible and highly representative animal models. The current combination therapy consisting of interferon-alpha and ribavirin mainly acts by supporting host cell defence. These therapeutics are the prototypic representatives of indirect antiviral agents as they act on cellular targets. However, the therapy is not a cure, when considered from the long-term perspective, for almost half of the chronically infected patients. This draws attention to the urgent need for more efficient treatments. Novel anti-hepatitis C treatments under study are directed against a number of so-called direct antiviral targets such as polymerases and proteases, which are encoded by the virus. Although such direct antiviral approaches have proven to be successful in several viral indications, there is a risk of resistant viruses developing. In order to avoid resistance, the development of indirect antiviral compounds has to be intensified. These act on host cell targets either by boosting the immune response or by blocking the virus host cell interaction. A particularly interesting approach is the development of inhibitors that interfere with signal transduction, such as protein kinase inhibitors. The purpose of this review is to stress the importance of developing indirect antiviral agents that act on host cell targets. In doing so, a large source of potential targets and mechanisms can be exploited, thus increasing the likelihood of success. Ultimately, combination therapies consisting of drugs against direct and indirect viral targets will most probably provide the solution to fighting and eradicating hepatitis C virus in patients.
    Antiviral chemistry & chemotherapy 02/2005; 16(2):69-90. DOI:10.1177/095632020501600201
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