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. 2014 Oct 8;16(4):462-72.
doi: 10.1016/j.chom.2014.09.009.

Nucleocapsid phosphorylation and RNA helicase DDX1 recruitment enables coronavirus transition from discontinuous to continuous transcription

Chia-Hsin Wu  1 , Pei-Jer Chen  2 , Shiou-Hwei Yeh  3
Affiliations

Nucleocapsid phosphorylation and RNA helicase DDX1 recruitment enables coronavirus transition from discontinuous to continuous transcription

Chia-Hsin Wu et al. Cell Host Microbe. .

Abstract

Coronaviruses contain a positive-sense single-stranded genomic (g) RNA, which encodes nonstructural proteins. Several subgenomic mRNAs (sgmRNAs) encoding structural proteins are generated by template switching from the body transcription regulatory sequence (TRS) to the leader TRS. The process preferentially generates shorter sgmRNA. Appropriate readthrough of body TRSs is required to produce longer sgmRNAs and full-length gRNA. We find that phosphorylation of the viral nucleocapsid (N) by host glycogen synthase kinase-3 (GSK-3) is required for template switching. GSK-3 inhibition selectively reduces the generation of gRNA and longer sgmRNAs, but not shorter sgmRNAs. N phosphorylation allows recruitment of the RNA helicase DDX1 to the phosphorylated-N-containing complex, which facilitates template readthrough and enables longer sgmRNA synthesis. DDX1 knockdown or loss of helicase activity markedly reduces the levels of longer sgmRNAs. Thus, coronaviruses employ a unique strategy for the transition from discontinuous to continuous transcription to ensure balanced sgmRNAs and full-length gRNA synthesis.

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Figures

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Graphical abstract
Figure 1
Figure 1
GSK-3 Inhibitor Treatment Reduces JHMV Nucleoprotein Phosphorylation at Ser197 and Viral Titer (A) Kinetics of GSK-3-mediated N phosphorylation in cells infected with JHMV at an moi of 1 IU/cell. Proteins were harvested at the indicated time points and probed with N and pS197-N. “V” indicates virions. (B) The total proteins were analyzed for N, pS197-N, and β-actin (loading control) by using western blotting. (C) The viral titers of DMSO and kenpaullone-treated cells were estimated using plaque assay. (D) Northern blotting was used to evaluate the expression levels of viral RNAs, using DIG-labeled N (upper panel) and GAPDH (bottom panel) as probes. Lanes 5 and 6 show hybridization using probes detecting minus-strand RNA. Lanes 3, 4, 7, and 8 represent the shorter exposure results, shown in lanes 1, 2, 5, and 6. (E) The relative abundance of indicated viral RNAs in DMSO and kenpaullone-treated JHMV-infected cells was evaluated by RT-qPCR, with the DMSO control set to a value of 1. “Inf.” indicates infection; “kenp.” indicates kenpaullone.
Figure 2
Figure 2
pS197-N Upregulates The Expression of Longer RNAs, whereas S205A-N Functions as a Dominant-Negative Mutant (A and B) (A) Microscopy and (B) western blotting confirmed the stable expression of GFP proteins or GFP-fused N proteins. Image panels show bright-field images (BF) and green fluorescent (GFP) channels. (C) Viral RNA synthesis was determined by northern blotting, with the N gene (upper) and GAPDH (bottom) as probes. (D) The relative abundance of indicated viral RNAs in stable cells was evaluated by RT-qPCR with GFP control was set to a value of 1. (E) A western blot of the proteins in the infected stable cell lines. The GFP-tagged N and virus-derived N were detected using anti-N antibodies with MW close to 75 kDa and 50 kDa, respectively. (F) The viral titers in the supernatants of stable cells infected with JHMV were determined by plaque assay.
Figure 3
Figure 3
Lighter Fractions Containing the pS197-N-containing Protein Complex Are Involved in the Early Viral Life Cycle (A) Whole-cell extracts prepared from JHMV-infected DBT cells at the indicated time points (cells collected at 6, 8, 10, and 16 hr p.i. were infected at moi = 1; cells collected at 4 hr p.i. were infected at moi = 10) were treated with the vehicle control or kenpaullone and then subjected to sucrose-density sedimentation analysis. The isolated fractions were analyzed using western blotting with anti-pS197-N and anti-N antibodies. (B) JHMV-infected DBT cells (moi = 10) were metabolically labeled for 1 hr with 35S-methionine (upper panel), and then chased for 2 hr (middle panel) or 4 hr (lower panel) in cold media, and then subjected to sucrose gradients analysis and separated into 12 fractions. The immunoprecipitants brought down by anti-N Ab were analyzed by SDS-PAGE and visualized by autoradiography. (C) Northern blots of viral RNA from (A): gradient-purified lysates at 6 hr p.i. (upper panel) and 10 hr p.i. (middle panel), and 6 hr p.i. with kenpaullone treatment (bottom panel), obtained using N as a probe. (D) The localization of N in 8 hr p.i. cells with DMSO (middle panel) or kenpaullone treatment (lower panel) was analyzed using indirect immunofluorescence. “Inf.” indicates infection; “kenp.” indicates kenpaullone.
Figure 4
Figure 4
Confirmation of the Interaction between pS197-N and DDX1 JHMV-infected DBT lysates (moi = 1) with DMSO or kenpaullone treatment were harvested at 6 hr p.i. and subjected to the following analyses. (A) IP-western blot analysis of infected cell lysates with or without RNase A treatment, precipitated with a pS197-N antibody. (B) IP-western blot analysis of infected cells treated with DMSO or kenpaullone, precipitated with an anti-N antibody. (C) The cell lysates subjected to sucrose gradients were fractionated and analyzed using western blotting to characterize the DDX1 sedimentation pattern. (D) Subcellular fractionation was used to confirm the intracellular protein distribution. “N” denotes the nuclear fraction, and “C” indicates the cytosolic fraction. Lamin A/C and tubulin were used as control markers for the nuclear and cytosolic fractions, respectively.
Figure 5
Figure 5
ShRNA-Mediated Knockdown of Ddx1 in DBT Cells Inhibits JHMV Viral RNA Synthesis The shLuc/DBT and shDdx1/DBT cells were (A) mock infected or (B–F) infected by JHMV at a moi of 1 (ending at 8 hr p.i.). (A) Western blotting was used to estimate the efficiency of lentivirus-mediated DDX1 knockdown. (B) Isolated total RNA from the infected cells was analyzed using northern blotting with N- and GAPDH-specific probes. Lanes 4–6 show hybridization using probes detecting minus-strand RNA. (C) The relative abundance of indicated viral RNAs in cells was evaluated by RT-qPCR with shLuc/DBT was set to a value of 1. (D) The infected cell lysates were analyzed for N using western blotting with anti-pS197-N and anti-N antibodies. (E) The viral titers determined by plaque assay are shown in the bar graph. (F) Expression of viral RNAs and proteins of JHMV-infected shLuc/DBT (left panel) and shDdx1/DBT (right panel). Northern hybridization for viral RNA purified from sucrose gradients by an N-specific probe and the western blot analysis for the indicated proteins.
Figure 6
Figure 6
DDX1 Upregulates the Expression of Longer RNAs in an Enzyme Activity-Dependent Manner (A) DBT cells were transfected with the indicated Myc-tagged DDX1 expression construct or an empty vector with (lanes 4–6) or without (lanes 1–3) shDdx1 transduction. The expression of exogenous DDX1 and endogenous DDX1 was confirmed using western blotting. “exo.” indicates exogenous; “endo.” indicates endogenous. (B–E) shDdx1/DBT cells transfected with the indicated plasmid were infected with JHMV (moi = 1), and the samples were harvested 8 hr p.i. for the following analyses. (B) Isolated RNAs were analyzed using northern blotting with N (upper) and GAPDH (bottom) as probes. Lanes 4–6 show hybridization using probes detecting minus-strand RNA. (C) The relative abundance of indicated viral RNAs in cells was evaluated by RT-qPCR with vector transfected DBT was set to a value of 1. (D) The JHMV-infected cells were analyzed using western blotting for the indicated proteins. (E) The plaque assay was applied to determine the supernatant viral titers.
Figure 7
Figure 7
RNA ChIP-qPCR Analysis of the Sequences Associated with pS197-N and DDX1 (A) Schematic representation of the localization of primers. The closed triangle indicates primer sets covering the TRS motif, whereas the open triangle indicates primer sets localized between TRSs. (B) Cells (6 hr p.i.) with DMSO (left panel) or kenpaullone treatment (right panel) were used for RNA ChIP analysis. IP was performed using specific antibodies and amplified by primers as indicated. (C) ChIP-RT-qPCR analysis by using viral RNA from JHMV cells (6 hr p.i.). The results are expressed as percentages of input.
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