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Review
. 2024 Feb 6;12(2):e0256222.
doi: 10.1128/spectrum.02562-22. Epub 2024 Jan 17.

Landscape of protein-protein interactions during hepatitis C virus assembly and release

Affiliations
Review

Landscape of protein-protein interactions during hepatitis C virus assembly and release

Alina Matthaei et al. Microbiol Spectr. .

Abstract

Assembly of infectious hepatitis C virus (HCV) particles requires multiple cellular proteins including for instance apolipoprotein E (ApoE). To describe these protein-protein interactions, we performed an affinity purification mass spectrometry screen of HCV-infected cells. We used functional viral constructs with epitope-tagged envelope protein 2 (E2), protein (p) 7, or nonstructural protein 4B (NS4B) as well as cells expressing a tagged variant of ApoE. We also evaluated assembly stage-dependent remodeling of protein complexes by using viral mutants carrying point mutations abrogating particle production at distinct steps of the HCV particle production cascade. Five ApoE binding proteins, 12 p7 binders, 7 primary E2 interactors, and 24 proteins interacting with NS4B were detected. Cell-derived PREB, STT3B, and SPCS2 as well as viral NS2 interacted with both p7 and E2. Only GTF3C3 interacted with E2 and NS4B, highlighting that HCV assembly and replication complexes exhibit largely distinct interactomes. An HCV core protein mutation, preventing core protein decoration of lipid droplets, profoundly altered the E2 interactome. In cells replicating this mutant, E2 interactions with HSPA5, STT3A/B, RAD23A/B, and ZNF860 were significantly enhanced, suggesting that E2 protein interactions partly depend on core protein functions. Bioinformatic and functional studies including STRING network analyses, RNA interference, and ectopic expression support a role of Rad23A and Rad23B in facilitating HCV infectious virus production. Both Rad23A and Rad23B are involved in the endoplasmic reticulum (ER)-associated protein degradation (ERAD). Collectively, our results provide a map of host proteins interacting with HCV assembly proteins, and they give evidence for the involvement of ER protein folding machineries and the ERAD pathway in the late stages of the HCV replication cycle.IMPORTANCEHepatitis C virus (HCV) establishes chronic infections in the majority of exposed individuals. This capacity likely depends on viral immune evasion strategies. One feature likely contributing to persistence is the formation of so-called lipo-viro particles. These peculiar virions consist of viral structural proteins and cellular lipids and lipoproteins, the latter of which aid in viral attachment and cell entry and likely antibody escape. To learn about how lipo-viro particles are coined, here, we provide a comprehensive overview of protein-protein interactions in virus-producing cells. We identify numerous novel and specific HCV E2, p7, and cellular apolipoprotein E-interacting proteins. Pathway analyses of these interactors show that proteins participating in processes such as endoplasmic reticulum (ER) protein folding, ER-associated protein degradation, and glycosylation are heavily engaged in virus production. Moreover, we find that the proteome of HCV replication sites is distinct from the assembly proteome, suggesting that transport process likely shuttles viral RNA to assembly sites.

Keywords: ERAD; HSPA5; Rad23B; affinity purification; endoplasmic reticulum; hepatitis C virus; host-pathogen interactions; lipoproteins; proteomics; viral assembly and release; virus-host interactions.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig 1
Fig 1
Properties of viral constructs used for analysis of the HCV assembly proteome. (A) Schematic overview of the HCV genome. HA- or double HA-tag insertion sites are depicted above the viral polyprotein. Mutations introduced in specific constructs are indicated below. (B) Influence of HA-tag insertion on infectious virus production. We quantified infectious virus production using a limiting dilution assay. Mean values of three independent biological replicates and the standard deviation are given. We transfected given HCV constructs into Huh-7.5 cells and monitored transfection efficiency by a core-specific enzyme-linked immunosorbent assay (ELISA) (n = 1; at 48 hours, right panels in B and C). (C) Influence of given point mutations on infectious virus production of the HA-E2 virus construct. Experimental setup as in panel B. (B and C) Mean ± SD.
Fig 2
Fig 2
Mass spectrometry workflow and quality control. (A) Scheme of the workflow of our lLiquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) proteomics approach. (B) We controlled the transfection efficiency of Huh-7.5 cells 24 hours post transfection (hpt) with viral RNA generated via in vitro transcription (IVT), by using indirect immunofluorescence staining with an anti-NS5A antibody. The percentage of NS5A-positive cells is given for each biological replicate. The horizontal line represents the mean value (n = 3). (C) Huh-7.5 cells transfected with the indicated constructs were lysed 48 hpt. We confirmed the presence of the given prey proteins in the total lysate, the eluate, and on the beads after elution by immunoblotting. (D) We determined the abundance of proteins by mass spectrometry using the MaxQuant software to calculate intensity-based absolute quantification (IBAQ) values as a measure of protein abundance [IBAQ (log2)] (42, 43). Total protein amounts of HA-E2 (red), HAHA-p7 (dark blue), HA-NS4B Q31A (light blue), and HA-ApoE (beige) are given for all IPs. Mean enrichment factors of these proteins were calculated by comparing protein abundance in immune precipitations from epitope-tagged samples to untagged control samples (n = 3).
Fig 3
Fig 3
Profile plot of quantified HCV proteins in co-IPs performed with anti-HA antibody-tagged beads. Total protein abundance is depicted for each viral protein (legend) for all performed co-IPs. In the table below, the fold change of protein abundance between the respective bait proteins and the corresponding untagged Jc1 control is shown. Boxes containing values of controls for viral proteins are highlighted in light gray. Red boxes indicate the enrichment of NS2 with E2 and blue with p7 (n = 3).
Fig 4
Fig 4
Interactomes of cellular ApoE and viral E2, p7, and NS4B proteins in liver cells producing infectious HCV. Volcano plots of interacting proteins of HA-tagged bait proteins ApoE (A), E2 (B), p7 (C), and NS4B Q31R (D), which were compared to untagged Jc1 for analyses (B–D) or Huh-7.5 cells with an endogenous ApoE expression (A). (A–D) We applied a two-sided t-test for statistical analysis. Significant interactors (Welch’s t-test; FDR ≤0.1, S0 = 1, results from three independent biological replicates). (E) Venn diagram of host factors interacting with bait proteins E2 (red), p7 (dark blue), NS4B (light blue), and ApoE (beige). Factors specific for one interactor or interacting with more than one bait protein are depicted.
Fig 5
Fig 5
The HCV E2 primary interactome and changes to E2 protein interactions caused by assembly disrupting mutations. (A) Volcano plot of HA-E2 wt versus Jc1 wt virus. (B) Venn diagram comparing the HA-E2 interactomes from the first and second analyses. We defined those factors significantly binding in both screens as the primary E2 interactome and the ones we found in at least one of the screens as accessory interactors. (C–E) Volcano plots of mutant virus E2 interactomes. We identified E2 binding proteins of the indicated HA-E2 tagged virus mutants and used the cognate untagged viruses as control. (A and C–E) A two-sided t-test was applied. (FDR ≤0.05; S0 = 1; three valid values in the first group, n = 3–4). (C–E) Novel HA-E2 binders are underlined.
Fig 6
Fig 6
STRING and KEGG pathway analyses of the HCV assembly proteome. (A) STRING interaction network of host factors binding to HA-E2 (only primary HA-E2 interactors were considered), HAHA-p7, and HA-ApoE (confidence of 0.4 and no more than 50 interactors). Nodes are color coded based on the interaction partners co-precipitating the respective host protein: E2 (red), p7 (blue), and ApoE (yellow). Markov cluster algorithm clustering was performed (inflation parameter = 3). Lines indicate defined clusters, which were then subjected to pathway analysis. Dotted lines indicate connection between the different clusters. (B) KEGG annotated pathways, which are enriched for the factors occurring in this STRING network, including all depicted nodes (B I) for upper left cluster I, (B II) for the upper right cluster, (B III) for the middle right cluster III, (B IV) for the bottom right cluster IV, (B V) for the bottom middle cluster V, and (B VI) for the middle left cluster VI.
Fig 7
Fig 7
HCV core and E1 mutations modulate the HA-E2 protein interactome. Heat map showing alterations of the E2 interactome between the mutant viruses. All primary and accessory HA-E2 binders and RAD23A and B were plotted. For statistical testing, we used multi-parametric two-way analysis of variance (ANOVA) (FDR ≤0.05; S0 = 0; second ANOVA P-value ≤0.05). Significant interactomic changes are highlighted with asterisks. Boxplots on the right show IBAQ values of those proteins whose HA-E2 interaction significantly changed between the viral mutants. Values were normalized to wt E2 (bait) (n = 3–4, mean ± SD).
Fig 8
Fig 8
RNA interference screening of host factors of the HCV assembly proteome. Host factors identified as HA-E2 primary and accessory interaction partners (Fig. 5B), HAHA-p7, and HA-ApoE binders (Fig. 4) were silenced by RNA interference with a pool of three siRNAs per target. Moreover, SLC4A7, OS9, SDF2L1, and C5orf42, de novo HA-E2 interactors identified with at least one of the mutants, as well as Rad23A and RAD23B were included as interactors of NGLY1, an HA-E2 interactor. Subsequently, these cells were infected with the reporter virus JcR2a, and RNA replication was measured 48 hours later. The z-score of a knock-down was calculated by subtracting the median of the negative controls on the same plate and dividing by the standard deviations of the controls. Mean z-scores were calculated by averaging over knock-downs targeting the same gene. Values x < 0 indicate a reduction, and x > 0, an increase of HCV replication or assembly and release compared to the mean of controls. On the y-axis, the log10 of the P-values of the scores are plotted. (A) Infectious progeny produced at this time point were passed on to naïve cells, and infection efficiency reflecting assembly of new viral progeny in the silenced cells was quantified 48 hours post second round infection. (B) PI4KA and ApoE (green dots) were silenced as controls for host factors influencing RNA replication and assembly, respectively. Hit calling was based on mean score ≥2 and P-value ≥0.05; t-test was applied following the RNAither pipeline (50), n = 4–6. Host factors meeting these inclusion criteria are highlighted as red circles.
Fig 9
Fig 9
Modulation of RAD23A and B expression influences HCV infectious virus production. (A) We transfected Huh-7.5/FLuc cells with one of three different siRNAs per factor or a pool of these siRNAs. Forty-eight hours post transfection (hpt), we infected these cells with the reporter virus JcR2a. We passed the culture fluid of these cells to naïve Huh-7.5/Fluc cells and quantified infection 48 hours later. The heat map shows infection data normalized for cell viability and RNA replication quantified in the dual luciferase assay (n = 3). (B) In uninfected Huh-7.5 cells, we quantified the abundance of RAD23A and RAD23B mRNA by qRT-PCR and (C) Rad23A and Rad23B protein levels by Western blot at 48 hours post siRNA transfection. Western blot from one representative experiment is shown. (D) Huh-7.5/FLuc cells were transduced with an empty lentiviral vector or vectors encoding RAD23A or RAD23B. Forty-eight hpt, we infected the cells with JcR2a, and 48 hours later, we measured cell viability as well as cell entry/RNA replication. Culture supernatant was transferred to naïve Huh-7.5/FLuc cells to measure infectious virus production 48 hours post second round infection. Samples were normalized to infected cells treated with an empty control vector (n = 7). (E) Protein expression was analyzed 48 hpt (representative experiment). (F and G) Focus-forming unit (FFU) assay using the untagged HCV Jc1 strain in Huh7.5 cells. Cells were transfected with siRNA, and after 24 hours, cells were infected with a multiplicity of infection of 0.1 TCID50/cell . (G) Forty-eight hours post infection, cells were lysed, and Western blot was performed (representative experiment). (F) Supernatant of infected cells was titrated on naϊve Huh7.5 cells, and infections were stopped 48 hours later. Virus was fluorescently stained with an anti-NS5A antibody, FFUs were counted manually, and data were normalized to the scr control (n = 4) (mean ± SD, Kruskal-Wallis test, only significant differences are highlighted by an asterisk, *P < 0.05, **P < 0.005).

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