Cellular 5'-3' mRNA exonuclease Xrn1 controls double-stranded RNA accumulation and anti-viral responses

Abstract

By accelerating global mRNA decay, many viruses impair host protein synthesis, limiting host defenses and stimulating virus mRNA translation. Vaccinia virus (VacV) encodes two decapping enzymes (D9, D10) that remove protective 5' caps on mRNAs, presumably generating substrates for degradation by the host exonuclease Xrn1. Surprisingly, we find VacV infection of Xrn1-depleted cells inhibits protein synthesis, compromising virus growth. These effects are aggravated by D9 deficiency and dependent upon a virus transcription factor required for intermediate and late mRNA biogenesis. Considerable double-stranded RNA (dsRNA) accumulation in Xrn1-depleted cells is accompanied by activation of host dsRNA-responsive defenses controlled by PKR and 2'-5' oligoadenylate synthetase (OAS), which respectively inactivate the translation initiation factor eIF2 and stimulate RNA cleavage by RNase L. This proceeds despite VacV-encoded PKR and RNase L antagonists being present. Moreover, Xrn1 depletion sensitizes uninfected cells to dsRNA treatment. Thus, Xrn1 is a cellular factor regulating dsRNA accumulation and dsRNA-responsive innate immune effectors.

Graphical abstract

Figure 1

Inhibition of Protein Synthesis and VacV Replication by Xrn1 Depletion (A) NHDFs were transfected with non-silencing (ns) control or one of two Xrn1-specific siRNAs (−1 and −2). After 3 days, total protein was collected and Xrn1 levels analyzed by immunoblotting. Tubulin served as a loading control. (B) NHDFs treated with siRNAs as in (A) were infected with VacV (MOI = 5 × 10⁻⁴). Infectious virus produced after 3 days was quantified by plaque assay. Means of three independent experiments are plotted ± SEM. ^∗∗ indicates p ≤ 0.01 by paired Student’s t test compared to control siRNA-treated samples. (C) NHDFs treated with siRNAs as in (A) were mock-infected or infected with VacV or UV-inactivated VacV (MOI = 5). At 18 hr post-infection (hpi), cells were metabolically pulse-labeled with [³⁵S]Met-Cys for 30 min. Total protein was collected and separated by SDS-PAGE and ³⁵S-labeled proteins visualized by exposing the fixed, dried gel to X-ray film. Molecular mass standards (in kDa) are shown to the right (upper panel). The same lysates were analyzed by immunoblotting (IB) with the indicated antibodies (lower panel). PABP1 served as a loading control. (D) As in (C), except NHDFs were infected with WT VacV or D9 (ΔD9)- or D10 (ΔD10)-deficient VacV viruses (MOI = 3). HSC70 was used as a loading control. See also Figure S1.

Figure 2

Phosphorylated eIF2α Accumulation in Xrn1-Depleted Cells Correlates with Global Protein Synthesis Inhibition Late in the VacV Lifecycle NHDFs transfected with ns control or Xrn1-specific siRNAs were infected with VacV (MOI = 5). At the indicated times (hpi) cells were metabolically pulse-labeled with [³⁵S]Met-Cys for 30 min. Uninfected cells (UI) were harvested in parallel with 18 hpi samples. (A) Total protein was isolated and separated by SDS-PAGE, and the fixed, dried gel exposed to X-ray film. Molecular mass standards (in kDa) are shown to the right. (B) The same lysates were immunoblotted with the indicated antibodies. Tubulin served as a loading control. (C) RNA from NHDFs treated with the indicated siRNAs and infected as in (A) was harvested at 6 hpi and subject to RT-qPCR using primers specific for K3L, E3L, or Xrn1 mRNAs. Each reaction product was normalized to the signal obtained using primers specific for 18S rRNA and expressed as the fold change relative to control siRNA-treated cells. Means of three independent experiments are plotted ± SEM.

Figure 3

Inhibition of Protein Synthesis following Xrn1 Depletion Requires a VacV-Specific Late Gene Transcription Factor (A) NHDFs transfected with ns control or Xrn1-specific siRNAs (−1 and −2) were mock-infected or infected with VacV (MOI = 5) in the presence or absence of PAA. At 18 hpi, cells were metabolically pulse-labeled with [³⁵S]Met-Cys for 30 min. Total protein was collected and separated by SDS-PAGE, and ³⁵S-labeled proteins visualized by exposing the fixed, dried gel to X-ray film. Molecular mass standards (in kDa) are shown to the right. (B) The same lysates were also immunoblotted with the indicated antibodies. Tubulin was used as a loading control. VacV I3 (early expressed) serves as an infection control. (C) As in (A), except NHDFs were infected with WT VacV or an A23-deficient virus (ΔA23). (D) Lysates from (C) were immunoblotted with the indicated antibodies. eIF2α was used as a loading control.

Figure 4

PKR-Dependent eIF2α Phosphorylation and RNase L-Mediated rRNA Degradation in Xrn1-Depleted Cells Infected with VacV (A) NHDFs transfected with the indicated siRNAs were mock-infected or infected with VacV (MOI = 5). Total protein was collected at 18 hpi and analyzed by immunoblotting with the indicated antibodies. Tubulin served as a loading control. (B) NHDFs transfected with the indicated siRNAs were mock-infected or infected with VacV (MOI = 5). At 18 hpi, total RNA was isolated and analyzed using a Bioanalyzer Nano LabChip. 28S and 18S rRNA bands are indicated. (C) NHDFs transfected with the indicated siRNAs were infected as in (A). At 18 hpi, cells were metabolically pulse-labeled with [³⁵S]Met-Cys for 30 min. Total protein was collected and separated by SDS-PAGE, and ³⁵S-labeled proteins visualized by exposing the fixed, dried gel to X-ray film. Molecular mass standards (in KDa) are shown to the right (upper panel). The same lysates were also immunoblotted (IB) with the indicated antibodies (lower panel). The RNase L-specific immunoreactive band is indicated by an arrow. Tubulin served as a loading control. (D) Metabolically radiolabelled samples from (C) together with two additional independent replicate experiments were TCA precipitated. ³⁵S incorporation into newly synthesized proteins was quantified by liquid scintillation counting. Means are plotted ± SEM. ^∗ indicates p ≤ 0.05 by paired Student’s t test compared to Xrn1 siRNA-treated cells. See also Figures S2 and S3.

Figure 5

Massive dsRNA Accumulation in Xrn1-Depleted Cells Infected with VacV NHDFs transfected with the indicated siRNAs were mock-infected or infected with VacV (MOI = 5). Cells were fixed at 6, 12, and 18 hpi and stained for immunofluorescence with J2 anti-dsRNA antibody (green). DNA was stained using DAPI (blue). (A) Cells were visualized using fluorescence microscopy with a 20× objective. (B) NHDFs treated with siRNAs and infected as in (A) were harvested and cell-free lysates prepared at 18 hpi. Equal volumes of lysates were dotted onto membrane and dsRNA detected by immunoblotting (upper panel). The dsRNA signal from (B) together with two independent replicates was quantified and the means plotted ± SEM (lower panel). (C) Confocal image of Xrn1 siRNA-treated infected cells from (A), fixed at 18 hpi using 63× objective. (D) Xrn1 siRNA-treated infected cells fixed at 18 hpi were treated with a mixture of single strand-specific RNase A/T1, dsRNA-specific RNase III, or buffer alone prior to immunostaining of dsRNA.

Figure 6

Elevated Viral mRNA Abundance and Their Enrichment in dsRNA Isolated from Xrn1-Depleted, VacV- Infected Cells (A) Cell-free lysates from NHDFs transfected with Xrn1–1 siRNA and infected with VacV (MOI = 5) were prepared at 22 hpi and immunoprecipitated using J2 anti-dsRNA antibody. After treating with RNase A/T1 or RNase III, isolated RNA was analyzed by RT-qPCR using the indicated viral or cellular mRNA primers. mRNA abundances were normalized to actin and calculated relative to input (set to 1). The means of three independent experiments are plotted ± SEM. (B) Equal volumes of buffer, input lysate (IP input), or the unbound fraction (IP unbound) were dotted onto a membrane and dsRNA detected by immunoblotting to demonstrate dsRNA depletion in the unbound fraction. (C and D) NHDFs were treated with the indicated siRNAs and RNA isolated from uninfected cells (C) or 3 hpi with VACV (MOI = 5) (D). RNA was subject to RT-qPCR analysis for the indicated cellular or early viral mRNAs and each reaction product normalized to 18S rRNA and presented as the fold change relative to control siRNA-treated cells. The means of three independent experiments are plotted ± SEM. A significant difference by paired Student’s t test compared to control siRNA-treated cells is indicated by ^∗ (p ≤ 0.05) or ^∗∗ (p ≤ 0.01).

Figure 7

Increased Sensitivity to the dsRNA Analog Poly(I:C) in Response to Xrn1 Depletion in Uninfected Cells (A and B) NHDFs treated with the indicated siRNAs were mock-transfected or transfected with increasing amounts of poly(I:C). After 3 hr, cells were metabolically pulse-labeled with [³⁵S]Met-Cys for 30 min. Total protein was collected and separated by SDS-PAGE, and ³⁵S-labeled proteins directly visualized by exposing the fixed, dried gel to X-ray film. Molecular mass standards (in KDa) are shown to the left (A). The same lysates were also immunoblotted with the indicated antibodies (B). Tubulin served as a loading control. See also Figure S4.