A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle

<div><p>Dengue virus (DENV) has emerged as major human pathogen. Despite the serious socio-economic impact of DENV-associated diseases, antiviral therapy is missing. DENV replicates in the cytoplasm of infected cells and induces a membranous replication organelle, formed by invaginations of the endoplasmic reticulum membrane and designated vesicle packets (VPs). Nonstructural protein 1 (NS1) of DENV is a multifunctional protein. It is secreted from cells to counteract antiviral immune responses, but also critically contributes to the severe clinical manifestations of dengue. In addition, NS1 is indispensable for viral RNA replication, but the underlying molecular mechanism remains elusive. In this study, we employed a combination of genetic, biochemical and imaging approaches to dissect the determinants in NS1 contributing to its various functions in the viral replication cycle. Several important observations were made. First, we identified a cluster of amino acid residues in the exposed region of the <i>β-ladder</i> domain of NS1 that are essential for NS1 secretion. Second, we revealed a novel interaction of NS1 with the NS4A-2K-4B cleavage intermediate, but not with mature NS4A or NS4B. This interaction is required for RNA replication, with two residues within the connector region of the NS1 “<i>Wing</i>” domain being crucial for binding of the NS4A-2K-4B precursor. By using a polyprotein expression system allowing the formation of VPs in the absence of viral RNA replication, we show that the NS1 –NS4A-2K-4B interaction is not required for VP formation, arguing that the association between these two proteins plays a more direct role in the RNA amplification process. Third, through analysis of polyproteins containing deletions in NS1, and employing a <i>trans</i>-complementation assay, we show that both <i>cis</i> and <i>trans</i> acting elements within NS1 contribute to VP formation, with the capability of NS1 mutants to form VPs correlating with their capability to support RNA replication. In conclusion, these results reveal a direct role of NS1 in VP formation that is independent from RNA replication, and argue for a critical function of a previously unrecognized NS4A-2K-NS4B precursor specifically interacting with NS1 and promoting viral RNA replication.</p></div

Coordination of Hepatitis C Virus Assembly by Distinct Regulatory Regions in Nonstructural Protein 5A

<div><p>Hepatitis C virus (HCV) nonstructural protein (NS)5A is a RNA-binding protein composed of a N-terminal membrane anchor, a structured domain I (DI) and two intrinsically disordered domains (DII and DIII) interacting with viral and cellular proteins. While DI and DII are essential for RNA replication, DIII is required for assembly. How these processes are orchestrated by NS5A is poorly understood. In this study, we identified a highly conserved basic cluster (BC) at the N-terminus of DIII that is critical for particle assembly. We generated BC mutants and compared them with mutants that are blocked at different stages of the assembly process: a NS5A serine cluster (SC) mutant blocked in NS5A-core interaction and a mutant lacking the envelope glycoproteins (ΔE1E2). We found that BC mutations did not affect core-NS5A interaction, but strongly impaired core–RNA association as well as virus particle envelopment. Moreover, BC mutations impaired RNA-NS5A interaction arguing that the BC might be required for loading of core protein with viral RNA. Interestingly, RNA-core interaction was also reduced with the ΔE1E2 mutant, suggesting that nucleocapsid formation and envelopment are coupled. These findings argue for two NS5A DIII determinants regulating assembly at distinct, but closely linked steps: (i) SC-dependent recruitment of replication complexes to core protein and (ii) BC-dependent RNA genome delivery to core protein, triggering encapsidation that is tightly coupled to particle envelopment. These results provide a striking example how a single viral protein exerts multiple functions to coordinate the steps from RNA replication to the assembly of infectious virus particles.</p></div

Mutations affecting the NS5A basic cluster reduce interaction with HCV RNA.

<p>(A) Schematic representation of the Jc1 genome containing a Flag-tag in NS5A DII. Huh7-Lunet cells were transfected with HCV genomes specified in the bottom and 72 h later cells were lysed and NS5A was enriched by immunoprecipitation (IP) using a Flag-specific monoclonal antibody covalently linked to magnetic beads. Captured NS5A proteins were separated by electrophoresis into an 8% acrylamide gel and analyzed by Western blot using a mono-specific NS5A antibody. The same amounts of input proteins were loaded onto the gel in parallel. The efficiency of the Flag-NS5A IP was determined by quantifying the bands and normalizing to the input signals. The non-tagged HCV genome (WT) served as technical control for specificity of immunoprecipitation. (B) Quantification of HCV RNA co-precipitated with Flag-NS5A. HCV RNA and GAPDH mRNA (specificity control) was determined by RT-qPCR. The percentage of viral RNA copies co-precipitated (co-IP) with NS5A was determined and used to calculate the enrichment of HCV RNA co-precipitated with NS5A. Note that GAPDH mRNA was below the detection limit in the co-precipitated samples and therefore is not displayed. Mean and SEM of six independent experiments is shown. *, <i>p ≤0</i>.<i>05; **</i>, <i>p ≤0</i>.<i>01; not significant (NS)</i>, <i>p ≥0</i>.<i>05</i>.</p

Impact of mutations affecting the basic cluster motif in NS5A DIII on RNA replication and virus production.

<p>(A) Schematic representation of NS5A domains: amphipathic α-helix (AH); domain (D) I, II and III; low complexity sequences (LCS) 1 and 2. The positions of the hemagglutinin (HA) epitope tag inserted within DII and the serine cluster (SC; S452/454/457) in DIII are indicated on the top. An alignment of the amino acid sequence of the NS5A basic cluster motif of several HCV isolates belonging to genotype 1 to 7 is given at the bottom. Numbers refer to amino acid residues 352 to 355 of the JFH1 isolate (corresponding to polyprotein residues 2328 to 2331). *, invariant amino acid residue across the displayed HCV isolates;:, conservation of physicochemical properties of the amino acid. The following HCV genomes were used for the alignment (gene bank accession numbers are given in parenthesis): H77 (AF009606), Con1 (AJ238799), Ad78 (AJ132997), J6 2a (Af177036), 452 (DQ437509), ED43 (Y11604), SA13 (AF064490), 6a33 (AY859526), QC69 (EF108306) and JFH1. (B) Given glutamic acid residue substitutions were inserted into a subgenomic JFH1 Firefly luciferase reporter replicon (sgJFH1-Fluc; top panel) and replication kinetics were determined. The various sgJFH1 constructs were transfected into Huh7-Lunet cells and harvested 4, 12, 18, 24, 48 and 72 h later. Luciferase activity was quantified and values were normalized to the respective 4 h-value. Mean and SEM of three independent experiments are shown. Background was determined with an RdRp-defective mutant (GDD). (C) The same mutations were introduced into the full-length HCV chimera Jc1 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005376#ppat.1005376.ref004" target="_blank">4</a>] shown in the top and 24, 48 and 72 h after transfection into Huh7-Lunet cells virus amounts contained in culture supernatants were quantified by limiting dilution assay. Values were normalized to the wildtype (WT) virus that was set to 100%. Mean and SEM of three independent experiments are shown. Background of the assay was determined with a deletion mutant lacking the envelope glycoprotein coding region (ΔE1E2). (D) NS5A amounts contained in cells 72 h after transfection with the Jc1 variants were determined by Western Blot with NS5A-specific antibodies; ß-actin served as loading control. Numbers in the left refer to apparent molecular weights of marker proteins in kilo Dalton (KDa).</p

Mutations disrupting the NS5A basic cluster increase E2 accumulation in doughnut-like structures without affecting NS5A –core protein colocalization.

<p>Huh7-Lunet cells were transfected with the HCV genomes specified in the left and fixed 48 h later. HCV proteins were detected by immunofluorescence using mono-specific antibodies. (A) Representative images showing E2—core protein subcellular distribution. Images were generated with a spinning disk confocal microscope and deconvolved to generate a 3D reconstruction with deep projection (see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005376#sec010" target="_blank">Materials and Methods</a>). The location of the cropped sections is indicated with white boxes in each overview panel. Scale bars represent 10 μm for overviews and 1 μm for cropped sections. (B) Quantification of core and E2 structures per cell. (C) Amounts of E2, NS5A and core protein were determined by Western blot using mono-specific antibodies; ß-actin served as loading control. (D) Representative images showing core—NS5A co-localization and their proximity to LDs (stained with BODIPY). Scale bars represent 10 μm for overviews and 5 μm for cropped sections. (E) Degree of NS5A - core co-localization as determined by Pearson correlation coefficient. Each dot represents one cell. For each HCV construct, the mean and SD of n = 100 is shown.</p

NS5A basic cluster mutant is impaired in core envelopment.

<p>(A) Huh7-Lunet cells were transfected with RNA genomes specified in the top: Jc1 wildtype (WT), NS5A R352-355E basic cluster mutant (BCM) and NS5A serine cluster mutant S452/454/457A (SCM). Twelve, 24 and 48 h post transfection cell lysates were prepared and separated by using a 0–30% linear sucrose gradient (left, middle and right panel, respectively). Core protein amounts contained in each fraction were quantified and normalized to total core contained in all fractions. (B) The amounts of E2 (left), NS5A (middle) and ADRP (right) contained in each fraction of cell lysates prepared 48 h post transfection were determined by quantitative Western blot. For each fraction, relative protein amounts are displayed (lower panels). Mean and SEM of two independent experiments are shown. (C) Huh7-Lunet cells were transfected with given HCV genomes and 48 h later cell lysates were prepared and either mock treated or incubated with 15 μg/ml proteinase K (PK) for 40 min on ice. As positive control, samples were treated with 1% Triton X-100 (TX-100) prior to PK digestion. The amount of core protein resistant to PK treatment was determined by Western blot and CMIA (left and right panel, respectively). The graph shows the percentage of PK-resistant core protein. Mean and SEM of three independent experiments is shown. **, <i>p ≤0</i>.<i>01; ***</i>, <i>p ≤0</i>.<i>001</i>.</p

Hypothetical roles of serine- and basic clusters in NS5A domain III for the assembly of infectious HCV particles.

<p>(A) NS5A interacts with core protein to recruit (RNA-containing) replication complexes (RCs) to HCV assembly sites where Core, E1, E2, p7 and NS2 reside. NS5A delivers the viral genome, eventually in conjunction with NS3 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005376#ppat.1005376.ref078" target="_blank">78</a>], from the RCs to core protein to trigger genome encapsidation and nucleocapsid formation. This induces their budding into the ER lumen that might be promoted by the envelope glycoproteins E1 and E2 in conjunction with p7 and NS2 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005376#ppat.1005376.ref011" target="_blank">11</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005376#ppat.1005376.ref019" target="_blank">19</a>]. (B) The NS5A basic cluster (BC) mutant is able to recruit the RCs to the assembly site by interacting with core protein, but is unable to associate with viral RNA for the assembly process. (C) The NS5A serine cluster (SC) mutant does not affect NS5A-HCV RNA association, but fails to interact with core protein and therefore the RCs are not recruited to the assembly site. As a result NS5A and core protein accumulate around distinct cytosolic lipid droplets (cLDs). Overall, both NS5A mutants are unable to load core protein with viral RNA, although for different reasons, and as a consequence envelopment of nucleocapsids is impaired.</p

NS5A basic cluster mutant has a defect in core—HCV RNA association.

<p>(A) No impact of a Flag-tag inserted into core protein of a HCV reporter genome (JcR2a) on viral RNA replication and production of infectious virus particles. A schematic representation of the HCV genome indicating the insertion site in the core coding region (codon 2) is given in the top. Huh7-Lunet cells were transfected with the parental renilla luciferase reporter genome (JcR2a) or the variant containing a Flag-tag in core (JcRa2-Flag-core). Left panel: cells were lysed at given time points after transfection and replication was determined by measuring renilla luciferase activity. Right panel: culture supernatants of transfected cells harvested at given time points were used to infect naïve Huh7.5 cells and renilla luciferase activity was measured 72 h later. (B) Core protein amounts contained in transfected cells or released into culture supernatants 72 h after transfection are shown in the left panel (intra- and extracellular, respectively). Amounts of infectious virus released into culture supernatants and specific infectivity of released virus particles are given in the right panel. Mean and SEM of two independent experiments is shown. (C, D) Effect of mutations in NS5A on association of core protein with HCV RNA. Huh7-Lunet cells were transfected with HCV genomes specified in the bottom, 72 h later cells were lysed and Flag-tagged core was enriched by immunoprecipitation (IP) using a Flag-specific monoclonal antibody covalently linked to magnetic beads. (C) Efficiency of IP was determined by core-specific CMIA and normalized to the input. The non-tagged HCV genome (WT) served as technical control for specificity of immunoprecipitation. (D) HCV RNA and GAPDH mRNA (specificity control) coprecipitated with core protein was quantified by RT-qPCR and HCV RNA copy numbers (Y-axis in the left) or relative GAPDH mRNA values (Y-axis in the right) co-precipitated per pg core protein were calculated. Mean and SEM of ten independent experiments is shown. *, <i>p≤0</i>.<i>05; ***</i>, <i>p≤0</i>.<i>001</i>.</p

Membrane undulation induced by NS4A of Dengue virus: a molecular dynamics simulation study

<div><p>Nonstructural protein 4A (NS4A) of Dengue virus (DENV) is a membrane protein involved in rearrangements of the endoplasmic reticulum membrane that are required for formation of replication vesicles. NS4A is composed most likely of three membrane domains. The N- and C-terminal domains are supposed to traverse the lipid membrane whereas the central one is thought to reside on the membrane surface, thus forming a <i>u</i>-shaped protein. All three membrane domains are proposed to be helical by secondary structure prediction programs. After performing multi nanosecond molecular dynamics (MD) simulations at various temperatures (300, 310, and 315.15 K) with each of the individual domains, they are used in a docking approach to define putative association motifs of the transmembrane domains (TMDs). Two structures of the <i>u</i>-shaped protein are generated by separating two assembled TMDs linking them with the membrane-attached domain. Lipid undulation is monitored with the structures embedded in a fully hydrated lipid bilayer applying multiple 200 ns MD simulations at 310 K. An intact structure of the protein supports membrane undulation. The strong unwinding of the helices in the domain-linking section of one of the structures lowers its capability to induce membrane curvature. Unwinding of the link region is due to interactions of two tryptophan residues, Trp-96 and 104. These results provide first insights into the membrane-altering properties of DENV NS4A.</p></div

Secretion kinetics and ultrastructural characterization of ΔNS1^TCP-infected helper cell lines.

<p>(<b>A</b>–<b>B</b>) <i>Kinetics of DVR2A</i>^<i>ΔNS1</i><i>TCPs secretion from helper cell lines</i>. (A) Schematic representation of the experimental setting. DVR2A^ΔNS1 TCPs produced in VeroE6_NS1^WT cells (ΔNS1-WT^TCP) were used to infect (MOI = 1) control or helper cell lines expressing different forms of NS1. Culture supernatants were collected 24, 48 and 72 h later, and virus titers were determined by Focus forming unit (FFU) assay on VeroE6_NS1^WT cells, using an E-specific mouse monoclonal antibody. Cell lysates and culture supernatants were analyzed by western blot. (B) FFU titers were determined as specified in panel (A). As reference, naïve VeroE6 cells were infected with DVR2A. The dashed line indicates the limit of detection of the assay. The lower panel shows representative images of foci morphologies of each trans-complemented NS1 variant. (<b>C</b>) <i>Expression levels of intra- and extra-cellular NS1 in DVR2A</i>^<i>ΔNS1</i><i>TCP infected cells</i>. NS1 expression and secretion were evaluated by western-blotting using cell lysates (Intra-) or clarified supernatants (Extra-) from (B) and NS1-, NS5- or GAPDH specific antibodies. (<b>D</b>, <b>E</b>) <i>Ultrastructural characterization of cells infected with DVR2A</i>^<i>ΔNS1</i><i>TCPs</i>. VeroE6_NS1^HA cells were infected with 1 MOI of DVR2A^ΔNS1 TCPs. Forty-eight hours later, cells were fixed, processed and analyzed by transmission electron microscopy as described in materials and methods. Representative images of the perinuclear area (D) or plasma membrane (E) of infected cells are shown. Black arrowheads indicate Vesicle packets (VPs), red arrowheads indicate virion bags. Electron-dense virus particles in proximity to or at the plasma membrane are indicated with black arrows. Boxed areas on the left panels are shown at higher magnification on the right. Black or white scale bars represent 500 or 200 μm, respectively.</p