Slow Binding Inhibition and Mechanism of Resistance of Non-nucleoside Polymerase Inhibitors of Hepatitis C Virus

The binding affinity of four palm and thumb site representative non-nucleoside inhibitors (NNIs) of HCV polymerase NS5B to wild-type and resistant NS5B polymerase proteins was determined, and the influence of RNA binding on NNI binding affinity was investigated. NNIs with high binding affinity potently inhibited HCV RNA polymerase activity and replicon replication. Among the compounds tested, HCV-796 showed slow binding kinetics to NS5B. The binding affinity of HCV-796 to NS5B increased 27-fold over a 3-h incubation period with an equilibrium K_d of 71 ± 2 nm. Slow binding kinetics of HCV-796 was driven by slow dissociation from NS5B with a k_off of 4.9 ± 0.5 × 10⁻⁴ s⁻¹. NS5B bound a long, 378-nucleotide HCV RNA oligonucleotide with high affinity (K_d = 6.9 ± 0.3 nm), whereas the binding affinity was significantly lower for a short, 21-nucleotide RNA (K_d = 155.1 ± 16.2 nm). The formation of the NS5B-HCV RNA complex did not affect the slow binding kinetics profile and only slightly reduced NS5B binding affinity of HCV-796. The magnitude of reduction of NNI binding affinity for the NS5B proteins with various resistance mutations in the palm and thumb binding sites correlated well with resistance -fold shifts in NS5B polymerase activity and replicon assays. Co-crystal structures of NS5B-Con1 and NS5B-BK with HCV-796 revealed a deep hydrophobic binding pocket at the palm region of NS5B. HCV-796 interaction with the induced binding pocket on NS5B is consistent with slow binding kinetics and loss of binding affinity with mutations at amino acid position 316.Hepatitis C virus (HCV)4 constitutes a global health problem. Current therapies are unable to effectively eliminate viral infection in a significant number of patients. The RNA-dependent RNA polymerase (RdRp) of HCV NS5B is an attractive target for the development of orally bioavailable small molecule inhibitors (1, 2). The structure of the NS5B apoenzyme and the NS5B-RNA complex reveals the characteristic right hand architecture of polymerase enzymes, comprising three distinct domains (palm, thumb, and finger) encircling the enzyme active site located in the palm domain (3–6). The structural and biochemical characterization of HCV NS5B polymerase can provide a basis for drug design efforts, and the elucidation of the mechanism of inhibition can guide the optimization of inhibitor efficiency against wild-type and resistant mutants.Among the extensively investigated non-nucleosides documented to inhibit the RdRp activity of HCV NS5B, derivatives of various benzofuran and benzothiadiazine have been reported to bind to allosteric binding sites in the palm domain of NS5B (7, 8). The palm domain, whose geometry is conserved in virtually all DNA and RNA polymerases, contains catalytic aspartic acids responsible for the nucleotidyl transfer reaction. The benzofuran compound HCV-796 has been shown to have significant antiviral effects in patients chronically infected with HCV (9, 10). In addition, two series of compounds based on the thiophene and benzimidazole scaffolds have been reported to inhibit NS5B by binding to two different binding pockets in the thumb domain of NS5B (11, 12). The thumb domain is connected to the palm domain by a β-hairpin termed the primer grip motif. The C-terminal region of the thumb protrudes toward the active site (3). The thumb binding inhibitors have been proposed to inhibit the RdRp activity of NS5B, perhaps by interfering with template/primer interaction and conformational dynamics of the protein (13, 14).Despite the elucidation of a number of NNIs that bind to the thumb and palm binding sites, the mechanism by which NNIs cause inhibition of RNA synthesis is unclear. Also, our understanding of the kinetics of NNI interaction with NS5B, the role of NNI binding and kinetics for inhibition, and the inhibitor efficacy on NS5B-resistant mutations remains incomplete. The four representative palm- and thumb-binding NNIs selected in this study have been reported to effectively inhibit replication of subgenomic replicons with low toxicity. Noncompetitive inhibition of NS5B polymerase activity with respect to NTPs has been reported (2, 15, 16). Based on co-crystallization studies with NS5B, it has been proposed that allosteric inhibitors may lock the NS5B protein in an inactive formation by binding tightly to the protein (16, 17). It is important to understand how the binding affinity relates to inhibition potency and resistance to HCV inhibition. Because the intrinsic potency of slowly binding compounds can be underestimated in the short time scale of biochemical studies, insights into slowly binding compounds may help to identify potent inhibitors. Moreover, the effect of the HCV RNA template on binding of NNIs to the enzyme-RNA complex remains to be addressed.Due to the error-prone nature of HCV polymerase in HCV replication, drug resistance can occur in patients who are treated with antiviral therapy directed at HCV-specific enzymes, and this resistance can limit their efficacy (16). Various in vitro studies using an HCV subgenomic replicon system have identified mutations that can confer resistance to inhibition by NNIs (2, 8, 16). Many of the mutations produce cross-resistance to the same family of inhibitors, which will affect the design of optimal combination therapies. Achieving optimal and sustained binding of these antiviral agents to the NS5B polymerase is crucial to ensure a high probability of clinical success.In this work, we have used biochemical and biophysical approaches to investigate binding affinities and binding kinetics of structurally diverse palm- and thumb-binding allosteric NS5B inhibitors. The binding of NNIs to wild-type and NNI-resistant NS5B proteins was studied and compared with inhibition and resistance. First, the NNI binding affinity for the NS5B protein was determined in the presence and absence of HCV RNA template, using a newly developed assay measuring the quenching of NS5B intrinsic fluorescence (FQ) in 96-well plates. The time-dependent NNI binding affinities and NNI binding equilibrium were used to identify slowly binding NNIs. Second, various palm and thumb site-specific mutant proteins were used to determine the mechanism of HCV resistance, and the binding affinities of NNIs were compared with the inhibition potencies determined in the HCV RdRp polymerase assay and HCV replicon assay. Finally, co-crystallization of HCV-796 with NS5B proteins from the Con1 and BK strains was performed to address the role of critical residues involved in HCV-796 resistance and NS5B polymorphism.     

Proinsulin and the Genetics of Diabetes Mellitus

Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

The Isomerase Active Site of Cyclophilin A Is Critical for Hepatitis C Virus Replication

Cyclosporine A and nonimmunosuppressive cyclophilin (Cyp) inhibitors such as Debio 025, NIM811, and SCY-635 block hepatitis C virus (HCV) replication in vitro. This effect was recently confirmed in HCV-infected patients where Debio 025 treatment dramatically decreased HCV viral load, suggesting that Cyps inhibitors represent a novel class of anti-HCV agents. However, it remains unclear how these compounds control HCV replication. Recent studies suggest that Cyps are important for HCV replication. However, a profound disagreement currently exists as to the respective roles of Cyp members in HCV replication. In this study, we analyzed the respective contribution of Cyp members to HCV replication by specifically knocking down their expression by both transient and stable small RNA interference. Only the CypA knockdown drastically decreased HCV replication. The re-expression of an exogenous CypA escape protein, which contains escape mutations at the small RNA interference recognition site, restored HCV replication, demonstrating the specificity for the CypA requirement. We then mutated residues that reside in the hydrophobic pocket of CypA where proline-containing peptide substrates and cyclosporine A bind and that are vital for the enzymatic or the hydrophobic pocket binding activity of CypA. Remarkably, these CypA mutants fail to restore HCV replication, suggesting for the first time that HCV exploits either the isomerase or the chaperone activity of CypA to replicate in hepatocytes and that CypA is the principal mediator of the Cyp inhibitor anti-HCV activity. Moreover, we demonstrated that the HCV NS5B polymerase associates with CypA via its enzymatic pocket. The study of the roles of Cyps in HCV replication should lead to the identification of new targets for the development of alternate anti-HCV therapies.Hepatitis C virus (HCV)² is the main contributing agent of acute and chronic liver diseases worldwide (1). Primary infection is often asymptomatic or associated with mild symptoms. However, persistently infected individuals develop high risks for chronic liver diseases such as hepatocellular carcinoma and liver cirrhosis (1). The combination of IFNα and ribavirin that serves as current therapy for chronically HCV-infected patients not only has a low success rate (about 50%) (2) but is often associated with serious side effects (2). There is thus an urgent need for the development of novel anti-HCV treatments (2).The immunosuppressive drug cyclosporine A (CsA) was reported to be clinically effective against HCV (3). Controlled trials showed that a combination of CsA with IFNα is more effective than IFNα alone, especially in patients with a high viral load (4, 5). Moreover, recent in vitro studies provided evidence that CsA prevents both HCV RNA replication and HCV protein production in an IFNα-independent manner (6–10). CsA exerts this anti-HCV activity independently of its immunosuppressive activity because the nonimmunosuppressive Cyp inhibitors such as Debio 025, NIM811, and SCY-635 also block HCV RNA and protein production (9, 11–14). Unlike CsA, these molecules do not display calcineurin affinity and specifically inhibit the peptidyl-prolyl cis-trans-isomerase (PPIase) Cyps. Most importantly, recent clinical data demonstrated that Debio 025 dramatically decreased HCV viral load (3.6 log decrease) in patients coinfected with HCV and HIV (15). This 14-day Debio 025 treatment (1200 mg orally administered twice daily) was effective against the three genotypes (genotypes 1, 3, and 4) represented in the study. More recently, the anti HCV effect of Debio 025 in combination with peginterferon α 2a (peg-IFNα2a) was investigated in treatment-inexperienced patients with chronic hepatitis C. Debio 025 (600 mg administered once daily) in combination with peg-IFNα2a (180 μg/week) for 4 weeks induced a continuous decay in viral load that reached −4.61 ± 1.88 IU/ml in patients with genotypes 1 and 4 and −5.91 ± 1.11 IU/ml in patients with genotypes 2 and 3 at week 4 (16). The Debio 025 findings are critical because they suggest that Cyp inhibitors represent a novel class of anti-HCV agents. However, it remains unclear how these compounds control HCV replication. The fact that several recent studies using small RNA interference knockdown approaches suggest that Cyps are critical for the HCV life cycle (9, 17, 18) strongly implies that there is a direct or indirect link between the CsA- and CsA derivative-mediated inhibitory effect on HCV replication and host Cyps.The discovery 20 years ago of the first cellular protein showing PPIase activity (19) was entirely unrelated to the discovery of CypA as an intracellular protein possessing a high affinity for CsA (20). It is only a few years later that Fischer et al. (21) demonstrated that the 18-kDa protein with PPIase activity and CypA represent a single unique protein. All Cyps contain a common domain of 109 amino acids, called the Cyp-like domain, which is surrounded by domains specific to each Cyp members and which dictates their cellular compartmentalization and function (22). Bacteria, fungi, insects, plants, and mammals contain Cyps, which all have PPIase activity and are structurally conserved (22). To date, 16 Cyp members have been identified, and 7 of them are found in humans: CypA, CypB, CypC, CypD, CypE, Cyp40, and CypNK (22).Although there is a growing body of evidence that Cyps control HCV replication in human hepatocytes, a major disagreement currently exists on the respective roles of Cyp members in HCV replication. One study suggests that CypB, but not CypA, is critical for HCV replication (17), another suggests that CypA, but not CypB and CypC, is critical for HCV replication (18), and a third study suggests that three Cyps, CypA, B, and C, are all required for HCV replication (9). Thus, although it becomes evident that Cyps serve as HCV co-factors, their respective contributions and roles in the HCV life cycle remain to be determined. An understanding of the mechanisms that control the Cyp inhibitor-mediated anti-HCV effect is imperative because it will provide new alternate anti-HCV therapies and shed light on the still poorly understood early and late steps of the HCV life cycle.     

Algorithms for Finding Small Attractors in Boolean Networks

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Quantitative Proteomic Analysis of Host-virus Interactions Reveals a Role for Golgi Brefeldin A Resistance Factor 1 (GBF1) in Dengue Infection

Dengue virus is considered to be the most important mosquito-borne virus worldwide and poses formidable economic and health care burdens on many tropical and subtropical countries. Dengue infection induces drastic rearrangement of host endoplasmic reticulum membranes into complex membranous structures housing replication complexes; the contribution(s) of host proteins and pathways to this process is poorly understood but is likely to be mediated by protein-protein interactions. We have developed an approach for obtaining high confidence protein-protein interaction data by employing affinity tags and quantitative proteomics, in the context of viral infection, followed by robust statistical analysis. Using this approach, we identified high confidence interactors of NS5, the viral polymerase, and NS3, the helicase/protease. Quantitative proteomics allowed us to exclude a large number of presumably nonspecific interactors from our data sets and imparted a high level of confidence to our resulting data sets. We identified 53 host proteins reproducibly associated with NS5 and 41 with NS3, with 13 of these candidates present in both data sets. The host factors identified have diverse functions, including retrograde Golgi-to-endoplasmic reticulum transport, biosynthesis of long-chain fatty-acyl-coenzyme As, and in the unfolded protein response. We selected GBF1, a guanine nucleotide exchange factor responsible for ARF activation, from the NS5 data set for follow up and functional validation. We show that GBF1 plays a critical role early in dengue infection that is independent of its role in the maintenance of Golgi structure. Importantly, the approach described here can be applied to virtually any organism/system as a tool for better understanding its molecular interactions.Viruses modify the intracellular environment of infected host cells in a number of important ways, including subverting the antiviral response, reorganizing host membranes, and manipulating host signaling pathways to create an environment more favorable for infection. For example, some viral proteins co-opt host proteins to degrade host interferon signaling components, thus antagonizing the antiviral response (1, 2); other viral proteins recruit metabolic enzymes that are potentially involved in the biogenesis of replication complexes (RCs)¹ (3); and some viral proteins interact with host regulatory proteins to block the cellular stress response (4). These examples illustrate only a few of the ways in which viral-host protein-protein interactions (PPIs) enable the viral life cycle and drive pathogenicity. Because of the limited coding capacity of many viral genomes, in particular RNA virus genomes, viral-host PPIs generally occur between a remarkably small number of viral proteins and a much larger number of host proteins (5). The study of these extensive interactions necessitates comprehensive and quantitative approaches, the development and validation of which will potentially contribute to: 1) our understanding of the mechanisms by which viruses subvert cellular pathways to their own advantage; 2) our understanding of fundamental cell biology; 3) the choice of potential drug targets and the rational design of such drugs; and 4) our understanding of the host response to infection.Dengue virus (DENV) is a positive-sense, single stranded RNA virus in the family Flaviviridae that is transmitted by the bite of an infected Aedes mosquito (6). DENV is an important emerging pathogen that is the causative agent of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome, diseases which cumulatively pose formidable economic and health care burdens in many tropical and subtropical countries worldwide (7). Recent estimates of the global burden of DENV infection have revealed that DENV infection is ∼threefold more prevalent than previously estimated, with ∼400 million annual incidences worldwide (8). Moreover, development of an anti-DENV vaccine has been hindered by the existence of four antigenically distinct DENV serotypes (DENV-1, -2, -3, and -4), each of which is capable of producing the full spectrum of DENV-induced disease (9). DENV is also related to other flaviviruses that cause significant human disease, including yellow fever virus, West Nile virus, and Japanese encephalitis virus (10). Thus, insights into DENV biology may be applicable to other flaviviruses of medical importance.The flavivirus genome encodes only three structural (C, pr/M, and E) and seven nonstructural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5), and is translated as a single polyprotein, which is later cleaved into the mature viral proteins (6). The three structural proteins, capsid (C), membrane (M), and envelope (E) comprise the virion, whereas the NS proteins are mainly responsible for carrying out genome replication in infected cells. Among the seven NS proteins, NS5 and NS3 are the two largest and most highly conserved proteins (11); moreover, each possesses multiple enzymatic activities. NS5 contains an RNA-dependent RNA polymerase domain as well as a nucleoside-2′-O-methyltransferase domain; both of these activities are essential for replication (12, 13). NS3, on the other hand, possesses an N-terminal serine protease domain, which is responsible for cleaving the viral polyprotein at several sites (along with its cofactor, NS2B) (14). The C-terminal domain of NS3 has 5′ RNA triphosphatase, nucleoside triphosphatase, and helicase activities (15–17). NS5 and NS3 have been shown to interact in infected cells (18), most likely in the RC. The precise composition and biogenesis mechanisms of RCs are poorly understood, but likely involve host proteins as well as viral proteins. As with other viruses, DENV-host PPIs have been interrogated by a number of high-throughput yeast two-hybrid assays (19–31) and approaches coupling either affinity purification (AP), immunoprecipitation, or immunoaffinity purification (IP) with MS (32–35). These approaches have yielded a number of putative DENV-host PPIs; however, considering the large repertoire of interactions undertaken by other viruses (36–41), our knowledge of DENV-host PPIs is likely incomplete. One advantage of IP/MS approaches is their potential to comprehensively reveal bona fide time-resolved interactions from the environment of an infected cell; however, the extremely high sensitivity of modern mass spectrometers highlights the need to develop IP/MS workflows capable of reliably discriminating between genuine interactors and nonspecific contaminants (42). Here, we present a workflow incorporating immunoaffinity purification and quantitative proteomics from infected cells, followed by robust statistical analysis to identify high confidence interactors of virtually any protein of interest, and apply this workflow to DENV NS5 and NS3.     

Immunity in Chimpanzees Chronically Infected with Hepatitis C Virus: Role of Minor Quasispecies in Reinfection

We have previously reported that chimpanzees chronically infected with hepatitis C virus (HCV) could be reinfected, even with the original infecting strain. In this study we tested the hypothesis that this might reflect the presence of minor quasispecies to which there was little or no immunity. To evaluate this hypothesis, we sequenced multiple clones taken at intervals after primary infection and rechallenge from four chronically infected chimpanzees. The inoculum used in these studies (HCV-H, genotype 1a) revealed 17 separate variants among 46 clones sequenced. Following challenge, each of the four challenged animals showed marked alterations of their quasispecies distribution. The new variants, which appeared 1 to 6 weeks after challenge, were either identical to or closely resembled variants present in the challenge inoculum. These results, paralleled by an increase in viremia in some of the challenged animals, suggest that quasispecies in the challenge inoculum were responsible for signs of reinfection and that there was little immunity. However, the newly emerged quasispecies completely took over infection in only one animal. In the remaining three chimpanzees the prechallenge quasispecies were able to persist. The natural evolution of infection within chimpanzees resulted in variants able to compete with the inoculum variants. Whether through reexposure or the natural progression of infection, newly emerged quasispecies are likely to play a role in the pathogenesis of chronic HCV infection.Hepatitis C virus (HCV) is estimated to chronically infect about 400 million people worldwide. More than half of these develop chronic active hepatitis, cirrhosis, or hepatocellular carcinoma. The HCV genome consists of a single-stranded RNA molecule approximately 10 kb long which contains a single open reading frame encoding approximately 3,000 amino acids (1, 5). There are at least six genotypes of HCV, and within a given patient the genomes are distributed among quasispecies which show sequence variation, particularly in the variable regions of the genome (4, 9). Hypervariable region 1 (HVR1) is a 27-amino-acid segment in the amino terminus of the second envelope protein which has been identified as the most variable region of the viral genome (11, 20). Sequential changes have been observed during the course of chronic HCV infections in chimpanzees and in humans (4, 11, 12). It has been postulated that these reflect immune system selection of neutralizing epitopes encoded by HVR1 (18, 19) and that persistent infection depends on the ability of the virus to continually evade the effects of neutralizing antibody (7, 10, 15, 17, 20). Due to its variability, HVR1 has been used extensively as an indicator of viral evolution.We have previously reported that chronically infected chimpanzees could seemingly be reinfected, even with the original infecting strain (13). In a recent report a similar phenomenon was observed in patients with posttransfusion hepatitis (6). We postulated that this might reflect the presence of minor quasispecies in the inoculum to which there was little or no immunity (13). Here we test this hypothesis by sequencing multiple clones of HVR1 derived at intervals after initial infection and after rechallenge.     

Critical Role of Cyclophilin A and Its Prolyl-Peptidyl Isomerase Activity in the Structure and Function of the Hepatitis C Virus Replication Complex

Replication of hepatitis C virus (HCV) RNA occurs on intracellular membranes, and the replication complex (RC) contains viral RNA, nonstructural proteins, and cellular cofactors. We previously demonstrated that cyclophilin A (CyPA) is an essential cofactor for HCV infection and the intracellular target of cyclosporine''s anti-HCV effect. Here we investigate the mechanism by which CyPA facilitates HCV replication. Cyclosporine treatment specifically blocked the incorporation of NS5B into the RC without affecting either the total protein level or the membrane association of the protein. Other nonstructural proteins or viral RNAs in the RC were not affected. NS5B from the cyclosporine-resistant replicon was resistant to this disruption of RC incorporation. We also isolated membrane fractions from both naïve and HCV-positive cells and found that CyPA is recruited into membrane fractions in HCV-replicating cells via an interaction with RC-associated NS5B, which is sensitive to cyclosporine treatment. Finally, we introduced point mutations in the prolyl-peptidyl isomerase (PPIase) motif of CyPA and demonstrated a critical role of this motif in HCV replication in cDNA rescue experiments. We propose a model in which the incorporation of the HCV polymerase into the RC depends on its interaction with a cellular chaperone protein and in which cyclosporine inhibits HCV replication by blocking this critical interaction and the PPIase activity of CyPA. Our results provide a mechanism of action for the cyclosporine-mediated inhibition of HCV and identify a critical role of CyPA''s PPIase activity in the proper assembly and function of the HCV RC.Hepatitis C virus (HCV), of the family Flaviviridae, is an enveloped, positive-stranded RNA virus. Spread mostly by blood-borne transmission, HCV infects more than 170 million people worldwide. The viral genome is composed of a single open reading frame (ORF) plus 5′- and 3′-nontranslated regions. The ORF encodes a large polyprotein that is cleaved by cellular and viral proteases into 10 viral proteins. The structural proteins, including the capsid protein (core), two glycoproteins (E1 and E2), and a small ion channel protein (p7), reside in the N-terminal half of the polyprotein. The rest of the ORF encodes six nonstructural (NS) proteins: NS2, NS3, NS4A, NS4B, NS5A, and NS5B. NS3 through NS5B assemble into a replication complex (RC) and are necessary and sufficient for HCV RNA replication in cell culture (8, 42). NS3 is a multifunctional protein with both a serine protease and an RNA helicase activity. The protease activity is responsible for cleavage at the NS3-NS4A, NS4A-NS4B, NS4B-NS5A, and NS5A-NS5B junctions (5), and the helicase activity is probably required to unwind the double-stranded RNA intermediates formed during replication (38). NS4A serves as an essential cofactor for the NS3 protease and anchors the NS3 protein to intracellular membranes (25, 36, 39). NS4B induces the formation of a “membranous web” that is probably the site of HCV replication (16). It also contains a GTP-binding motif that is required for replication (17). The web is derived from the endoplasmic reticulum (ER) compartment, although proteins of early-endosome origin have also been found to locate to the web (62). NS5A is a phosphoprotein and an integral component of the viral RC. The precise function of NS5A in replication is still unknown but appears to be regulated by phosphorylation and its interaction with several cellular proteins (19, 22, 24, 51, 52, 59, 63, 67). In addition, it may be involved in the transition from replication and particle formation (4, 45, 64). NS5B is the RNA-dependent RNA polymerase that is responsible for copying the RNA genome of the virus during replication. Several cellular cofactors interact with NS5B and modulate its activity in the context of the viral RC (22, 24, 35, 69, 71).Positive-stranded RNA viruses alter the intracellular membranes of host cells to form an RC in which RNA replication occurs. Modifications include the proliferation and reorganization of certain cellular membranes (1). HCV forms an RC associated with altered cellular membranes (16, 23), and crude RCs (CRCs) that maintain the replicase activity in vitro can be isolated by membrane sedimentation or flotation techniques (2, 3, 18, 27, 37).Cyclosporine is a widely used immunosuppressive and anti-inflammatory drug for organ transplant patients. It functions by forming an inhibitory complex with cyclophilins (CyPs) that inhibits the phosphatase activity of calcineurin, which is important for T-cell activation. In recent years, cyclosporine and its derivatives have been shown to be highly effective in suppressing HCV replication in vitro (44, 49, 53, 68) and in vivo (30). The mechanism of this inhibition is independent of its immunosuppressive function and distinct from that of interferon (IFN) (44, 53, 56, 68).We recently showed that HCV infection in vitro is inhibited when CyPA, a major intracellular target of cyclosporine, is downregulated by RNA interference, and mutations in NS5B that confer cyclosporine-resistant binding to CyPA contribute to the cyclosporine resistance of the replicons harboring these mutations (56, 71). Here we report that CyPA is recruited into the HCV RC together with NS5B in HCV replicon or in HCV-infected cells. Cyclosporine disrupts the association between RC-incorporated NS5B and CyPA and results in an exclusion of the polymerase from the viral RC. We also show that the prolyl-peptidyl isomerase (PPIase) motif of CyPA is essential for HCV replication.     

A Novel Immuno-Competitive Capture Mass Spectrometry Strategy for Protein–Protein Interaction Profiling Reveals That LATS Kinases Regulate HCV Replication Through NS5A Phosphorylation*

Mapping protein–protein interactions is essential to fully characterize the biological function of a protein and improve our understanding of diseases. Affinity purification coupled to mass spectrometry (AP-MS) using selective antibodies against a target protein has been commonly applied to study protein complexes. However, one major limitation is a lack of specificity as a substantial part of the proposed binders is due to nonspecific interactions. Here, we describe an innovative immuno-competitive capture mass spectrometry (ICC-MS) method to allow systematic investigation of protein–protein interactions. ICC-MS markedly increases the specificity of classical immunoprecipitation (IP) by introducing a competition step between free and capturing antibody prior to IP. Instead of comparing only one experimental sample with a control, the methodology generates a 12-concentration antibody competition profile. Label-free quantitation followed by a robust statistical analysis of the data is then used to extract the cellular interactome of a protein of interest and to filter out background proteins. We applied this new approach to specifically map the interactome of hepatitis C virus (HCV) nonstructural protein 5A (NS5A) in a cellular HCV replication system and uncovered eight new NS5A-interacting protein candidates along with two previously validated binding partners. Follow-up biological validation experiments revealed that large tumor suppressor homolog 1 and 2 (LATS1 and LATS2, respectively), two closely related human protein kinases, are novel host kinases responsible for NS5A phosphorylation at a highly conserved position required for optimal HCV genome replication. These results are the first illustration of the value of ICC-MS for the analysis of endogenous protein complexes to identify biologically relevant protein–protein interactions with high specificity.The exploration of a protein''s interactome in a given biological system is often critical to understand its function. Since the introduction of yeast two-hybrid experiments, alternative methods to explore protein–protein interactions have emerged (1–3). In particular, the combination of affinity-purification with mass spectrometry (AP-MS)¹ (4) has shown great promise for the identification of protein complexes directly in mammalian cell lines (5). This approach typically involves capturing the protein of interest either through an epitope tag or using a selective antibody. The main challenge with AP-MS is to discern bona fide interactors from highly abundant cellular proteins e.g. cytoskeletal or ribosomal proteins that bind nonspecifically to the affinity matrix (6). This can be partially addressed by including a negative control, such as IP with an antibody of the same isotype against an irrelevant protein or using samples where the target protein is absent (4). More recently, the introduction of quantitative MS (7–9), involving either isotope labeling or label-free strategies (for a review see (9, 10)), have led to a better distinction between true and false-positive interactions. While most of the recent efforts to reduce false positive rates have concentrated on refining data analysis (11), very few attempts have been made to improve the selectivity at the IP step (12). Consequently, classical quantitative side-by-side comparison of a sample with its control (wild type versus knockout cell lysates or capturing antibody versus control isotype) still suffers from the fact that the control sample is not identical to the probed one and both samples can lead to the association of different nonspecific binders.In this study, we present an innovative approach, termed immuno-competitive capture MS (ICC-MS), which involves a competition step between free and bound antibody in the same cellular extract and quantitation using label-free MS. Instead of comparing only one IP with a control, the methodology generates a 12-concentration antibody competition profile. Combined with a robust statistical analysis of the quantified MS signals, the cellular endogenous interactome of a protein of interest can be extracted out of the background of hundreds of proteins. We used this new approach to specifically map the interactome of the HCV NS5A protein, an essential viral regulatory protein for both genome replication and modulation of the host environment (13). Proteins interacting with NS5A have been previously identified using yeast two-hybrid (14) or classical co-expression and co-immunoprecipitation methods (15). In this study, we use a human hepatocyte-derived cellular model of HCV genome replication and uncover eight new NS5A-interacting protein candidates in addition to other well-known partners. In particular, we highlight LATS1 and LATS2, two closely related human serine/threonine protein kinases, and demonstrate that they are new host kinases responsible for NS5A phosphorylation and optimal HCV replication.     

Heterogeneous Ribonucleoprotein K (hnRNP K) Binds miR-122, a Mature Liver-Specific MicroRNA Required for Hepatitis C Virus Replication

Heterogeneous ribonucleoprotein K (hnRNP K) binds to the 5′ untranslated region of the hepatitis C virus (HCV) and is required for HCV RNA replication. The hnRNP K binding site on HCV RNA overlaps with the sequence recognized by the liver-specific microRNA, miR-122. A proteome chip containing ∼17,000 unique human proteins probed with miR-122 identified hnRNP K as one of the strong binding proteins. In vitro kinetic study showed hnRNP K binds miR-122 with a nanomolar dissociation constant, in which the short pyrimidine-rich residues in the central and 3′ portion of the miR-122 were required for hnRNP K binding. In liver hepatocytes, miR-122 formed a coprecipitable complex with hnRNP K. High throughput Illumina DNA sequencing of the RNAs precipitated with hnRNP K was enriched for mature miR-122. SiRNA knockdown of hnRNP K in human hepatocytes reduced the levels of miR-122. These results show that hnRNP K is a cellular protein that binds and affects the accumulation of miR-122. Its ability to also bind HCV RNA near the miR-122 binding site suggests a role for miR-122 recognition of HCV RNA.MicroRNAs (miRNAs) are a class of noncoding RNA of ∼22-nucleotides in length that can regulate gene expression by either targeting RNA for degradation or suppressing their translation through base pairing to the RNAs (1). Since their discovery in 1993 in Caenorhabditis elegans, miRNAs have been found in many species and are involved in the regulation of proliferation, differentiation, apoptosis, and development (1, 2). Moreover, miRNAs are also critical factors in the development of cancers, neurodegenerative diseases, and infectious diseases (3).MiR-122 is a highly abundant RNA in hepatocytes that regulates lipid metabolism, regeneration, and neoplastic transformation (4–6). In addition, miR-122 is required for the replication of the hepatitis C virus (HCV), a positive-strand RNA virus that infects over 170 million people worldwide (7–9). MiR-122 binds to a conserved sequence in the 5′ untranslated region (UTR) of the HCV RNA to increase the stability of the HCV RNA (10). Silencing of miR-122 can abolish HCV RNA accumulation in non-human primates (11). The expression of human miR-122 in non-hepatic cells can confer the ability to replicate HCV RNA (12). MiR-122 is one of the most critical host factors for HCV replication.We previously reported that the HCV RNA sequence that anneals to miR-122 is recognized by the heterogeneous ribonucleoprotein K (hnRNP K), a multifunctional RNA-binding protein known to be involved in RNA processing, translation, and the replication of several RNA viruses (13–15). In an unbiased screen for proteins from human proteome chips containing over 17,000 proteins, we identified 40 proteins that bind mature miR-122, including hnRNP K. Recombinant hnRNP K recognizes short pyrimidine sequences in miR-122 in vitro and a similar sequence in the HCV 5′ UTR. In hepatocytes endogenous hnRNP K can form a coprecipitable complex with miR-122, whether or not the cells contain replicating HCV. HnRNP K is thus a protein that binds a mature microRNA.     

The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]