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. 2017 Jan 31;91(4):e02049-16.
doi: 10.1128/JVI.02049-16. Print 2017 Feb 15.

The Human Cytomegalovirus IE1 Protein Antagonizes PML Nuclear Body-Mediated Intrinsic Immunity via the Inhibition of PML De Novo SUMOylation

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The Human Cytomegalovirus IE1 Protein Antagonizes PML Nuclear Body-Mediated Intrinsic Immunity via the Inhibition of PML De Novo SUMOylation

Eva-Maria Schilling et al. J Virol. .

Abstract

PML nuclear bodies (NBs) are accumulations of cellular proteins embedded in a scaffold-like structure built by SUMO-modified PML/TRIM19. PML and other NB proteins act as cellular restriction factors against human cytomegalovirus (HCMV); however, this intrinsic defense is counteracted by the immediate early protein 1 (IE1) of HCMV. IE1 directly interacts with the PML coiled-coil domain via its globular core region and disrupts NB foci by inducing a loss of PML SUMOylation. Here, we demonstrate that IE1 acts via abrogating the de novo SUMOylation of PML. In order to overcome reversible SUMOylation dynamics, we made use of a cell-based assay that combines inducible IE1 expression with a SUMO mutant resistant to SUMO proteases. Interestingly, we observed that IE1 expression did not affect preSUMOylated PML; however, it clearly prevented de novo SUMO conjugation. Consistent results were obtained by in vitro SUMOylation assays, demonstrating that IE1 alone is sufficient for this effect. Furthermore, IE1 acts in a selective manner, since K160 was identified as the main target lysine. This is strengthened by the fact that IE1 also prevents As2O3-mediated hyperSUMOylation of K160, thereby blocking PML degradation. Since IE1 did not interfere with coiled-coil-mediated PML dimerization, we propose that IE1 affects PML autoSUMOylation either by directly abrogating PML E3 ligase function or by preventing access to SUMO sites. Thus, our data suggest a novel mechanism for how a viral protein counteracts a cellular restriction factor by selectively preventing the de novo SUMOylation at specific lysine residues without affecting global protein SUMOylation.

Importance: The human cytomegalovirus IE1 protein acts as an important antagonist of a cellular restriction mechanism that is mediated by subnuclear structures termed PML nuclear bodies. This function of IE1 is required for efficient viral replication and thus constitutes a potential target for antiviral strategies. In this paper, we further elucidate the molecular mechanism for how IE1 antagonizes PML NBs. We show that tight binding of IE1 to PML interferes with the de novo SUMOylation of a distinct lysine residue that is also the target of stress-mediated hyperSUMOylation of PML. This is of importance since it represents a novel mechanism used by a viral antagonist of intrinsic immunity. Furthermore, it highlights the possibility of developing small molecules that specifically abrogate this PML-antagonistic activity of IE1 and thus inhibit viral replication.

Keywords: PML nuclear bodies; human cytomegalovirus; immediate early 1; intrinsic immunity; nuclear domain 10; sumoylation.

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Figures

FIG 1
FIG 1
IE1 induces the loss of polySUMOylated PML. (A and C) HFF cells (A) or PML-kd HFFs stably expressing F-PML I (C) were either mock infected or infected with AD169 at an MOI of 3. At the indicated time points postinfection, cells were harvested and analyzed by Western blotting for IE1, β-actin, and PML (A) or F-PML (C). (B) HFF F-IE1 cells with doxycycline-inducible expression of F-IE1 were either not induced or induced with 0.5 μg/ml doxycycline. Cells were harvested at the indicated time points and analyzed by Western blotting for PML, F-IE1 and β-actin. Asterisks indicate the residual monoSUMOylated PML species. (D) PML-kd HFFs stably overexpressing F-PML I were either mock infected or infected with AD169 at an MOI of 3. At 24 h postinfection the cells were lysed under denaturing conditions in the presence of 20 mM NEM and subjected to immunoprecipitation using anti-FLAG antibody or mouse IgG Fc fragment as a control. Lysates (left panel) and immunoprecipitates (IP) (right panel) were analyzed by Western blotting to detect SUMO2/3 and F-PML I. Lysates were additionally analyzed to detect IE1 as an infection control and β-actin as a loading control.
FIG 2
FIG 2
IE1 specifically affects the SUMOylation of PML K160. (A and B) HEK293T cells were transfected with expression plasmids encoding myc-tagged PML (M-PML) variants (A) or cotransfected with expression plasmids encoding M-PML variants and IE1 (B) as indicated. At 48 h posttransfection, the cells were harvested and analyzed by Western blotting for the detection of M-PML, IE1, and β-actin. Asterisks indicate the residual monoSUMOylated PML species referring to K490 SUMOylation. Circles and diamonds indicate the disappearing SUMOylated PML species referring to K160 and K65/160 SUMOylation, respectively. (C to F) HFFs stably expressing F-PML VI WT (C), F-PML VI K160R (D), F-PML VI K490R (E), or F-PML VI 3KR (F) were either mock infected or infected with AD169 at an MOI of 3. At the indicated time points postinfection, cells were harvested and analyzed by Western blotting for F-PML, IE1, and β-actin.
FIG 3
FIG 3
IE1 prevents arsenic trioxide-mediated PML degradation. (A and B) HFF cells with doxycycline-inducible expression of F-IE1 (A) or F-IE1CORE (B) were either not induced or induced with 0.5 μg/ml doxycycline for 16 h, followed by As2O3 (1 μM) and simultaneous MG132 (10 μM) treatment when indicated. Cells were harvested at the indicated time points and analyzed by Western blotting for PML, F-IE1, and β-actin.
FIG 4
FIG 4
A SUMO mutant resistant to SUMO proteases is stably conjugated to PML. HEK293T cells were cotransfected with expression plasmids encoding M-PML and F-SUMO2 WT or F-SUMO2 Q90P as indicated. At 48 h posttransfection, the cells were lysed by immediately boiling the cell pellet in SDS loading buffer (A) or by incubating the cells with NP-40 buffer without NEM (B) or with 30 mM NEM (C). The lysates were analyzed by Western blotting for the detection of M-PML, β-actin, F-SUMO2 WT, and F-SUMO2 Q90P. Densitometric analysis of the F-SUMO2 signals in panel A, lanes 5 and 6, revealed relative intensities of 100% and 121%, respectively.
FIG 5
FIG 5
IE1 prevents PML de novo SUMOylation in vivo. (A and B) HEK293-IE1 cells were not induced or induced with doxycycline (0.5 μg/ml). (A) At the indicated time points, the cells were harvested and analyzed by Western blotting for IE1 and β-actin. (B) At 24 h post induction, immunodetection of IE1 was conducted by using an anti-IE1 antibody. (C) Timeline for the experiments for panels E and G. (D) Timeline for the experiments for panels F and H. (E to H) HEK293-IE1 cells were cotransfected with expression plasmids encoding M-PML and F-SUMO2 WT or F-SUMO2 Q90P as indicated. IE1 expression was induced with doxycycline (0.5 μg/ml). Cells were harvested after a total time of 72 h and analyzed by Western blotting for the detection of M-PML, IE1, β-actin, F-SUMO2 WT, and F-SUMO2 Q90P. Densitometric analysis of the F-SUMO2-Q90P signals in panel E, lanes 6 and 7, revealed relative intensities of 100% and 31%, while the signal intensities in panel F, lanes 6 and 7, were 100% and 92%, respectively. The signal intensities for F-SUMO2 WT in panel G, lanes 6 and 7, were 100% and 22%, respectively. For panel H, lanes 6 and 7, the signal intensities were 100% and 31%, respectively.
FIG 6
FIG 6
IE1 prevents PML de novo SUMOylation in vitro. (A) GST pulldown analysis of prokaryotically expressed GST, GST-PML, and His-IE1CORE. Bound proteins were eluted by boiling the glutathione-Sepharose beads in SDS loading buffer. Eluted proteins and input were analyzed by Western blotting for the detection of GST fusions and His-IE1CORE. (B to D) Bacterially expressed and purified proteins were incubated together with an in vitro SUMOylation kit containing E1 (SAE1/SAE2), Ubc9, ATP, and SUMO3 for the indicated times (B) or for 4 h (C and D) as described in Materials and Methods. (B and C) The reaction mixes were analyzed by Western blotting using anti-PML antibody (B) or both anti-PML and anti-His antibodies (C). (D) After terminating the reaction by adding 10 mM each EDTA and DTT, the mix was again incubated for 1 h in the presence or absence of bacterially expressed and purified His-IE1CORE. The reaction mixes were analyzed by Western blotting using anti-PML and anti-His antibodies.
FIG 7
FIG 7
IE1 does not act by interfering with PML dimerization. (A) HEK293T cells were cotransfected with expression plasmids encoding F-PML VI and M-PML VI with increasing amounts of M-IE1CORE construct. (B) HEK293T cells were cotransfected with expression plasmids encoding the F-PML coiled-coil domain (CC) and GFP-PML CC with increasing amounts of M-IE1CORE or M-IE1 FL constructs. Upper panels, Western blot detection of M-PML VI (A) or GFP-PML CC (B) after immunoprecipitation with an anti-FLAG antibody (IP). Lower three panels, detection of M-PML VI (A) or GFP-PML CC (B) and F-PML VI (A) or F-PML CC (B) and M-IE1 variants (as indicated) in cell lysates before precipitation (input).

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