key: cord-0030384-nb0q2st0
authors: Liu, Yuanyuan; Gao, Peng; Zhou, Lei; Ge, Xinna; Zhang, Yongning; Guo, Xin; Han, Jun; Yang, Hanchun
title: Mapping the Key Residues within the Porcine Reproductive and Respiratory Syndrome Virus nsp1α Replicase Protein Required for Degradation of Swine Leukocyte Antigen Class I Molecules
date: 2022-03-26
journal: Viruses
DOI: 10.3390/v14040690
sha: 65a3250da9918e4a14bee9d9093616c8aa675067
doc_id: 30384
cord_uid: nb0q2st0

The nonstructural protein 1α (nsp1α) of the porcine reproductive and respiratory syndrome virus (PRRSV) has been shown to target swine leukocyte antigen class I (SLA-I) for degradation, but the molecular details remain unclear. In this report, we further mapped the critical residues within nsp1α by site-directed mutagenesis. We identified a cluster of residues (i.e., Phe17, Ile81, Phe82, Arg86, Thr88, Gly90, Asn91, Phe94, Arg97, Thr160, and Asn161) necessary for this function. Interestingly, they are all located in a structurally relatively concentrated region. Further analysis by reverse genetics led to the generation of two viable viral mutants, namely, nsp1α-G90A and nsp1α-T160A. Compared to WT, nsp1α-G90A failed to co-localize with either chain of SLA-I within infected cells, whereas nsp1α-T160A exhibited a partial co-localization relationship. Consequently, the mutant nsp1α-G90A exhibited an impaired ability to downregulate SLA-I in infected macrophages as demonstrated by Western blot, indirect immunofluorescence, and flow cytometry analysis. Consistently, the ubiquitination level of SLA-I was significantly reduced in the conditions of both infection and transfection. Together, our results provide further insights into the mechanism underlying PRRSV subversion of host immunity and have important implications in vaccine development.

Porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped, positive-stranded RNA virus in the genus Porartevirus of the family Arteriviridae in the order Nidovirales [1, 2] . This agent mainly causes reproductive failure in sows and severe respiratory distress in piglets with sometimes high morbidity and mortality [3, 4] . Ever since its first emergence in the late 1980s in both North America and Europe, PRRSV has remained a major threat to the worldwide swine industry [5] [6] [7] . The currently available PRRSV modified live-attenuated vaccines (MLVs) are generally effective against the challenge of homologous viruses but fail to induce sterilizing immunity or to provide efficient cross-protection against heterologous strains [3, [8] [9] [10] . The failure of viral clearance from hosts is largely attributed to the intrinsic properties of PRRSV.

Evasion or subversion of host immunity is a prominent feature of PRRSV [11] [12] [13] . This property often leads to dysregulation of innate immunity [14, 15] , delayed and low-level induction of neutralizing antibodies [16, 17] , and inadequate and poor quality of cytotoxic T lymphocyte (CTL) responses [18, 19] . Clinically, PRRSV infection is characterized by to Gln166) using residues Cys76 and His146 as the catalytic dyad; a C-terminal exten region (CTE; Arg167 to Met180) ( Figure 1A ) [30, 31] . We previously showed that an i structure of nsp1α, but not the protease activity, is necessary for SLA-I degradation In this report, we went further to dissect the critical residues of nsp1α in both transfe and infection conditions. Our results revealed the residue Gly90 is a promising targe vaccine development. (A) structure organization of the PRRSV genome and nsp1α; (B-E) screening of nsp1α residues necessary for SLA-I degradation by co-transfection assay. HEK 293T cells were transfected to express FLAG-SLA-I-HC (B-D) or Myc-β2m (E) in combination with HA-nsp1α or its mutants. At 36 h post-transfection, the cells were subject to Western blot analysis with antibodies to FLAG, SLA-I-β2m, nsp1α, or β-actin. Asterisk (*) indicates the mutants that were selected for further analysis. The data are representative of results from three independent experiments. The relative abundance of SLA-I was normalized against β-actin, and the ratio is shown at the bottom of the blots.

Porcine pulmonary alveolar macrophages (PAMs) were prepared as previously described [32] and maintained at 37 • C with 5% CO 2 in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% (v/v) fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA, USA), 50 U/mL penicillin, and 50 mg/mL streptomycin. MARC-145, Vero, and HEK 293T cells were all cultured in Dulbecco's modified Eagle's medium (DMEM) (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% FBS and penicillin (50 U/mL) and streptomycin (50 mg/mL) in a humidified incubator with 5% CO 2 at 37 • C. The HP-PRRSV strain, JXwn06 (GenBank accession no: EF641008), used in this study has been described previously [33] . In infection condition, PAMs or MARC-145 cells were grown at 37 • C with 5% CO 2 in RPMI 1640 medium or DMEM supplemented with 2% FBS and penicillin (50 U/mL) and streptomycin (50 mg/mL).

Restriction enzymes were all purchased from New England Biolabs Inc. (Ipswich, MA, USA). Mouse anti-actin (#A5441) monoclonal antibody (mAb) was from Merck KGaA (Darmstadt, Germany). Mouse anti-FLAG (#M185) mAb was from Medical & Biological Laboratories (MBL, Nagoya, Japan). Rabbit anti-HA (#3724) mAb was from Cell Signaling Technology (CST, Boston, MA, USA). Mouse anti-ubiquitin mAb (#BE4002) was from Bioeasy (Beijing, China). Mouse anti-N protein mAb was kindly provided by Ping Jiang (Nanjing Agriculture University, Nanjing, China). Rabbit anti-nsp1α protein polyclonal Viruses 2022, 14, 690 4 of 17 antibody (pAb) was kindly provided by Changjiang Weng (Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Haerbin, China). Horseradish peroxidase (HRP)-conjugated goat anti-mouse pAb (#ZB-2305) and HRP-conjugated goat anti-rabbit pAb (#ZB-2301) were obtained from ZSGB-BIO (Beijing, China). Both Alexa Fluor 488-conjugated goat anti-mouse IgG(H+L) F(ab )2 fragment (#A-11070) and Alexa Fluor 568-conjugated goat anti-rabbit IgG(H+L) F(ab )2 fragment (#A-11019) were purchased from Thermo Fisher Scientific Inc (Waltham, MA, USA). The mouse anti-SLA-I mAb JM1E3 (#MCA2261GA) and mouse IgG1 antibody (#MCA928) used for flow cytometry were from AbD Serotec (Kidlington, UK). Rabbit anti-SLA-I-HC pAb, rabbit anti-β2m pAb, mouse anti-SLA-I-HC mAb, and mouse anti-β2m mAb were prepared in our laboratory [34] . MG132 (#S2619) was purchased from Selleckchem (Houston, TX, USA).

Plasmids pHA-nsp1α, pFLAG-SLA-I-HC, and pMyc-SLA-I-β2m have been described previously [27] . The plasmid pHA-nsp1α served as the template for the construction of a series of nsp1α mutants using a fast mutagenesis system (TransGen, Beijing, China) to introduce amino acid substitutions. All recombinant plasmids were constructed by standard molecule biology techniques and confirmed by DNA sequencing.

The plasmid pCMV-JXwn06, containing the full-length cDNA clone of PRRSV strain JXwn06, has been described previously [35] . To perform mutagenesis, the fragment A (bases 1-4818) containing the nsp1α-coding region was PCR-amplified from pCMV-JXwn06, using the upstream primer (5 -CAGAGCTGGTTTAGTATTTAAATACCGTCATGACGTATAGGTGT-3 ) containing the Swa I recognition sequence (underlined) and the downstream primer (5 -CCTCCCCCTGAAGGCTTCGAAATTTGCCTGATCTTTAGTCCATT-3 ) containing the Xho I recognition sequence (underlined), and then cloned into the plasmid Pjet1.2/blunt (Thermo Fisher Scientific, Waltham, MA, USA) to construct a shuttle plasmid Pjet1.2-A. Mutagenesis of specific nsp1α nucleotides was then carried out using a fast mutagenesis system (TransGen, Beijing, China). After confirmation by DNA sequencing, fragment A was cut off and inserted back into the PRRSV infectious clone backbone.

For virus recovery, MARC-145 cells seeded on 6-well plates at a confluency of 70-80% were transfected with the infectious clone plasmids by Lipofectamine LTX (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's protocol. The virusinduced cytopathic effect (CPE) was monitored daily. The rescued viruses were passaged 3 times in MARC-145 cells and then examined by indirect immunofluorescence assay (IFA) using the anti-N mAb SDOW17 (Rural Technologies, Brookings, SD, USA). The mutated sites were confirmed by sequencing the genome of the third-passage viruses as described previously [33] .

MARC-145 cells and PAMs were infected with the indicated viruses at the multiplicity of infection (MOI) of 0.1. After incubation for 1 h at 37 • C with 5% CO 2 , MARC-145 cells and PAMs were treated as described previously [35] . The supernatants or the cells were collected at indicated times, and the virus titers were determined using endpoint dilution assays as previously described [36] .

Vero cells or PAMs seeded on coverslips in 12-well plates were transfected with indicated plasmid or infected with the indicated virus at an MOI of 1.0. At 24 h posttransfection or at 12 h post-infection, the cells were fixed with 3.7% paraformaldehyde for 10 min at room temperature (RT), washed with 1X phosphate-buffered saline (PBS) 3 times, permeabilized with 0.1% Triton X-100/2% bovine serum albumin (BSA) for 10 min, and blocked with 2% BSA/PBS for 30 min (RT). The cells were then incubated with proper primary antibodies for 1 h in a humid chamber (RT) and washed with 1X PBS 3 times. Afterwards, the cells were incubated with appropriate secondary antibodies, including Alexa Fluor 568-conjugated goat anti-rabbit IgG(H+L) F(ab )2 fragment and Alexa Fluor 488-conjugated goat anti-mouse IgG(H+L) F(ab )2 fragment, for another 1 h (RT). Nuclear DNA was stained with 4 ,6-diamidino-2-phenylindole (DAPI) (Thermo Fisher Scientific, Waltham, MA, USA). The images were captured using a Nikon A1 confocal microscope and processed using Image J.

The method for flow cytometry analysis to examine the cell surface expression of SLA-I molecules has been described previously [27] . Briefly, PAMs were seeded into six-well plates at a density of 6 × 10 5 cells/well and gently washed with RPMI 1640 medium to remove the unattached cells. The cells were then mock infected with RPMI 1640 or infected with the indicated virus at an MOI of 1.0. At 12 h post-infection, the cells were dissociated from the plates with 0.1% EDTA and washed twice immediately with ice-cold 1X PBS containing 1% BSA. The cells were then incubated with mouse anti-SLA-I mAb JM1E3 (2 µg/mL) in 1X PBS containing 1% BSA at 4 • C for 30 min, followed by incubation with Alexa Fluor 488-conjugated goat anti-mouse IgG(H+L) F(ab )2 fragment (1:1000) for 30 min at 4 • C. Meanwhile, a mouse IgG antibody was used as the isotype control. A total of 2 × 10 4 cells were analyzed by fluorescence-activated cell sorter (FACS) analysis, and the cell surface expression level of the SLA-I molecules was presented as the mean fluorescence intensity (MFI).

For transfection-based assays, HEK 293T cells seeded in six-well plates were transfected to express SLA-I-HC or β2m and ubiquitin with or without wild-type (WT) nsp1α or nsp1α-G90A. At 18-24 h post-transfection, the cells were treated with 10 µM MG132 for 4 h. In assays using infected cells, PAMs seeded in six-well plates were mock-infected with RPMI 1640 or infected with indicated viruses at an MOI of 1.0. At 4-6 h post infection, MG132 was added at a final concentration of 5 µM and maintained for 8 h. Harvested cells were washed 3 times with ice-cold 1X PBS and then lysed in ice-cold lysis buffer (50 mM Tris-HCl (pH7.4), 1 mM EDTA, 150 mM NaCl, 5 mM MgCl 2 , 10% glycerol, and 1% Triton X-100) supplemented with 1X cocktail (Merck) for 30 min with gentle rotation. Following centrifugation at 12,000 rpm for 30 min at 4 • C, the supernatants were transferred to a fresh tube, precleared with protein A/G magnetic beads (Thermo Fisher Scientific, Waltham, MA, USA, #88802) for 2 h at 4 • C, and then incubated with indicated antibodies for 12 h at 4 • C. The SLA-I complexes were captured with protein A/G magnetic beads for 2 h at RT. The beads were washed with 1X Tris-buffered saline (TBS) containing 0.05% Tween-20 detergent 4 times and purified water once. The immunoprecipitants were separated from the beads by low-pH elution buffer (0.1 M glycine, pH 2.0), neutralized with neutralization buffer (1.0 M Tris-HCl, pH 8.0) and subject to Western blot analysis with proper antibodies.

The extracted total proteins were quantified by a bicinchoninic acid (BCA) protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA). The protein samples were resolved by SDS-PAGE with 12% polyacrylamide gel, transferred onto a 0.2 µm PVDF membrane, blocked with PBST (PBS with 0.05% Tween-20 detergent) containing 5% skim milk powder for 1 h at RT, and then probed with thee appropriate primary antibodies for 2 h at RT. The membranes were washed 3 times with PBST, incubated with the appropriate HRPconjugated secondary antibodies at a dilution of 1-10,000 for 1 h at RT, washed again 3 times with PBST, and then developed using the ECL Western blot system (Thermo Fisher Scientific, Waltham, MA, USA). 

Statistical analyses were performed using the two-way analysis of variance (ANOVA) test in GraphPad Prism version 5.0 software (San Diego, CA, USA). Differences were considered statistically significant at a p-value < 0.05.

To identify critical residue(s) for nsp1α function, we took the alanine scanning approach by site-directed mutagenesis. We excluded the residues that are important for maintaining the structure of individual domains, such as the six core residues in the N-ZF, PCPα, and CTE domains mentioned above; those (i.e., Cys70, Cys76, His146, and Met180) that tetrahedrally coordinate with C-terminal zinc ions in the nsp1α 3D structure [30] ; those (i.e., Glu69 and Asn143) that can form an elaborate hydrogen bond to stabilize the Cys76-His146 dyad [30] . The mutagenesis blocks ranged from 2 to 6 amino acids (aa) in length. As a result, we constructed a total of 33 nsp1α mutants and tested the mutational effects with a co-transfection assay. The HEK 293T cells were transfected to co-express the mutants together with FLAG-SLA-I-HC, followed by Western blot analysis. The initial screening (Table S1 ) identified 12 mutants, including P12-6A, V18-6A, Q40-5A, F50-5A, L78-5A, P83-5A, T88-5A, N93-5A, G109-5A, V138-4A, T156-5A, and N161-5A, that exhibited reduced activity to degrade SLA-I-HC compared to WT nsp1α. Next, we further shortened the block size to 2-3 amino acids, resulting in 27 additional nsp1α mutants. Ten mutants

, and N161-2A) displaying impaired activity were therefore selected for the third-round analysis (Table S2) . Accordingly, a total of 20 mutants carrying single substitutions were engineered. The results revealed 11 mutants (i.e., F17A, I81A, F82A, R86A, T88A, G90A, N91A, F94A, R97A, T160A, and N161A) with decreased activity ( Figure 1B-D) . The mutational effect of these mutations was also tested on SLA-I-β2m. The results revealed that these mutants showed variable extent of degradation activity on the substrate SLA-I-β2m ( Figure 1E ). As a positive control, nsp1α-F50A retained the ability to induce SLA-I-β2m degradation ( Figure 1E ). Overall, we have identified a cluster of residues that are critical for nsp1α to modulate SLA-I abundance.

We next tested the mutational effect in a dose-dependent manner. HEK 293T cells were transfected to co-express FLAG-SLA-I-HC (1.0 µg) with WT nsp1α or its derivatives at different doses (0, 1.0, 1.5, 2.0, 2.5, and 3.0 µg). Western blot analysis showed that WT nsp1α induced SLA-I-HC degradation in a dose-dependent manner. In contrast, all 11 nsp1α mutants lost the ability to do that even with increased doses (Figures 2A and S1 ). We also looked into the cellular localization of these mutants. In transfected cells ( Figure 2B ), all the mutants exhibited a similar diffusive distribution pattern as to WT nsp1α ( Figure 2B ), suggesting that the decreased activity was less likely due to the alteration of localization. Structurally, all the residues, except I81, were on the surface of the nsp1α molecule, and they were located in a relatively concentrated region ( Figure 2C ), indicating they were maybe involved in some kind of interaction. 

To investigate the mutational effect in the context of PRRSV infection, single-point mutations of the above residues were introduced into the DNA-launched infectious cDNA clone of PRRSV strain JXwn06 [35] . After confirmation by DNA sequencing, both WT and mutant infectious cDNA clones were transfected into MARC-145 cells. For each mutant, we chose 2-3 independent clones for virus recovery. Only two mutant viruses (i.e., G90A and T160A) were successfully recovered, as evidenced by CPE and IFA with antibodies to N protein ( Figure 3A ; Table S3 ). In contrast, the other nine mutants (i.e., F17A, I81A, F82A, R86A, T88A, N91A, F94A, R97A, and N16A) were lethal to the virus. We could not recover the viruses even after 3-4 rounds of blind passages in MARC-145 cells; detection by real-time PCR also gave negative results (data not shown). The two viable mutants of passage 3 (P3) were chosen for growth kinetics analysis in both MARC- 

To investigate the mutational effect in the context of PRRSV infection, single-point mutations of the above residues were introduced into the DNA-launched infectious cDNA clone of PRRSV strain JXwn06 [35] . After confirmation by DNA sequencing, both WT and mutant infectious cDNA clones were transfected into MARC-145 cells. For each mutant, we chose 2-3 independent clones for virus recovery. Only two mutant viruses (i.e., G90A and T160A) were successfully recovered, as evidenced by CPE and IFA with antibodies to N protein ( Figure 3A ; Table S3 ). In contrast, the other nine mutants (i.e., F17A, I81A, 

It has been shown that nsp1α co-localizes with SLA-I in transfected mammalian cells [27] , but it is not known whether this is true in PRRSV-infected PAMs. In addition, it is not clear about the mutational effect on the nsp1α-SLA-I co-localization relationship. To this end, we infected PAMs with WT or the nsp1α mutant viruses, whereas the mock-infection with RPMI 1640 served as a control. We found that in mock-infected cells, SLA-I-HC exhibited a diffusive distribution pattern in the cytoplasm ( Figure 4A ), whereas in WTinfected cells, it became punctuated and co-localized well with nsp1α ( Figure 4C , the upper panel), indicating an active recruitment to the nsp1α site. A similar result was observed for SLA-I-β2m ( Figure 4B,D, upper panel) . On the other hand, in the cells infected with the nsp1α mutants, nsp1α-G90A co-localized poorly with either SLA-I-HC ( Figure 4C , middle panel) or β2m ( Figure 4D, middle panel) , while nsp1α-T160A showed only partial co-localization with either subunit of SLA-I ( Figure 4C , bottom panel; Figure 4D , bottom panel). Further quantitative analyses revealed that the number of cells without co-localization of nsp1α and SLA-I-HC or β2m in the mutant G90A-infected cells showed a significant increase compared to WT (p < 0.001), while a moderate ratio was observed for the mutant T160A ( Figure 4E ). Consistently, Western blot analysis showed a similar expression level of SLA-I in mutant G90A-infected cells compared to that in mock-infected cells, but lower than that in T160A and WT-infected cells ( Figure 4F) . Thus, it appears that the residue G90 is critical for nsp1α-SLA-I colocalization in infected cells.

We next investigated the decay of SLA-I in a time-course study. The mutant G90A was chosen for further analysis, as the corresponding mutation exhibited a stronger inhibitory effect on nsp1α activity ( Figures 1D,E and 4C,D,F) . PAMs were either mock-infected or infected with WT or the mutant G90A at an MOI of 1.0. At different time points postinfection as indicated, the cells were collected and subjected to Western blot analysis. In WT PRRSV-infected cells, a gradual decline in SLA-I-HC was exhibited as the infection progressed, and this became obvious at 12 h post-infection and pronounced at later time points ( Figure 5A) . A similar trend was observed for SLA-I-β2m ( Figure 5A ). In contrast, in the cells infected with the mutant G90A, the levels of SLA-I were kept steady ( Figure 5A ). Moreover, an increase in the infection doses (MOI = 0.5, 1.0, 1.5, or 2.0) did not change the outcome ( Figure 5B ).

We also examined the cell surface accumulation of SLA-I. In the first assay, PAMs were either mock-infected or infected with WT or mutant viruses and then processed for IFA analysis at 12 h post-infection. Compared to the mock control, WT PRRSV infection led to a clear decrease in SLA-I in the overall fluorescence intensity. In contrast, the infection with the mutant G90A did not have an obvious effect ( Figure 5C ). We also employed FACS analysis to measure the SLA-I cell surface expression. The results were similar to the IFA analysis; the parental virus infection resulted in a significant shift of the mean fluorescence intensity (p < 0.01), whereas the G90A infection exhibited a pattern similar to that of the mock control (p > 0.05) ( Figure 5D ). Together, we concluded that the residue G90 is critical for nsp1α-mediated degradation of SLA-I. localization of nsp1α and SLA-I-HC or β2m in the mutant G90A-infected cells showed a significant increase compared to WT (p < 0.001), while a moderate ratio was observed for the mutant T160A ( Figure 4E ). Consistently, Western blot analysis showed a similar expression level of SLA-I in mutant G90A-infected cells compared to that in mock-infected cells, but lower than that in T160A and WT-infected cells ( Figure 4F ). Thus, it appears that the residue G90 is critical for nsp1α-SLA-I colocalization in infected cells. FACS analysis to measure the SLA-I cell surface expression. The results w the IFA analysis; the parental virus infection resulted in a significant shi fluorescence intensity (p < 0.01), whereas the G90A infection exhibited a pa that of the mock control (p > 0.05) ( Figure 5D ). Together, we concluded th G90 is critical for nsp1α-mediated degradation of SLA-I. 

It has been shown that degradation of SLA-I by PRRSV nsp1α depends on the ubiquitin-proteasomal pathway [27] . Thus, we examined the mutational effect of nsp1α on SLA-I ubiquitination in two different assays. In the first assay, HEK 293T cells were transfected to co-express FLAG-SLA-I-HC, Myc-β2m, or HA-ubiquitin with or without WT HA-nsp1α or HA-nsp1α-G90A, and then treated with MG132 at 4 h before collecting for further analysis. The immunoprecipitation (IP) analysis revealed that the level of ubiquitinated SLA-I-HC ( Figure 6A Figure 6C ). Thus, these data suggest that the G90A mutation impairs the ability of nsp1α to mediate SLA-I ubiquitination, providing further evidence for the essential role of Gly90 in the degradation of the SLA-I molecule by nsp1α. and B, lane 4). In contrast, the expression of nsp1α-G90A did not much affect tination of SLA-I-HC ( Figure 6A , lane 6, top panel) or β2m ( Figure 6B , lane 6, Similar results were also obtained in the condition of PRRSV infection of PA 6C). Thus, these data suggest that the G90A mutation impairs the ability of n diate SLA-I ubiquitination, providing further evidence for the essential role the degradation of the SLA-I molecule by nsp1α. 

Swine SLA-I plays a critical role in host antiviral immunity by exposing viral antigens to the innate immune cells and initiating the CTL responses [37] . We have previously shown that PRRSV nsp1α is able to induce the proteasomal degradation of SLA-I [27] , thus providing a novel perspective on how PRRSV might evade CTL responses. As a follow-up study, this report went on further to unveil critical residues for nsp1α function. Our results here revealed two salient messages: (i) the residues critical for nsp1α function in SLA-I degradation were clustered in a structurally relatively concentrated region, and most of them are critical for PRRSV viability; (ii) the PRRSV strain JXwn06 carrying the nsp1α mutation G90A lost the ability to downregulate SLA-I on the PAMs' cell surface. The relevant insights and significance are discussed below. PRRSV nsp1α is a well-known multifunctional replicase protein that participates in multiple aspects of the virus life cycle. During replication, it mediates the co-translational cleavage of itself from the replicase polyprotein pp1a and ppla/b [38, 39] and is important for regulating viral subgenomic (sg) mRNA synthesis [40] . It is also a critical modulator of host immunity, including interferon signaling [39, [41] [42] [43] [44] [45] [46] [47] , inflammation responses [47] [48] [49] , and cellular immunity [27, 50] . Notably, one key mechanism for nsp1α-mediated immune modulation is via the degradation of host cellular factors [27, 44, 46, [51] [52] [53] . A classic target is CREB-binding protein (CBP), a nuclear factor that regulates the activation of many transcriptional factors (e.g., NF-κB and IRF3) as well as the production of some inflammatory cytokines [44, 46, 52] . The most recently identified substrate is SLA-I, a critical mediator of host cellular immunity [27] . In both cases, degradation depends on the ubiquitinproteasomal system and requires an intact nsp1α but not the protease activity [27, 46] . In this report, we mapped the residues critical for this function of nsp1α. This led to the identification of a total of 11 residues that were found to be localized to both the N-ZF and PCPα domains, consistent with the previous result that an intact molecule is necessary for nsp1α degradation activity [27] . Additionally, most of these residues are essential for PRRSV viability and have not been reported to be associated with any known functions of nsp1α, except for the residues Gly90, Asn91, Arg97, and Asn161 that haven been shown to contribute to the dimerization of nsp1α (Asn91 and Asn161) [30] , suppression of IFN signaling (Gly90, Asn91 and Arg97) [45] , and downregulation of TNF-α expression (Gly90 and Arg97) [54] . Notably, all identified key residues, except Phe17, are located within the PCPα domain, and eight of them are located within a continuous double alpha helix (aa. 75-100) ( Figure 2C ), suggesting that this helix might be an important interface for virus-host interactions. Among all the critical residues, the residue Gly90 is quite intriguing, as the mutation of this residue affects all three modulatory functions of nsp1α, including interferon signaling [45] , inflammation response [54] , and SLA-I degradation ( Figures 1C,E and 5A ). This convergent effect puts Gly90 in a unique position and suggests that this residue is either important for nsp1α structure or critical for protein-protein interactions or both. Future studies might be directed to further dissect the mechanisms of how nsp1α mediates the degradation of cellular proteins.

Downregulation of SLA-I accumulation on a cell's surface is a common strategy employed by a variety of viruses to evade a host's cellular immunity. Many viruses encode proteins to target the MHC-I molecule for proteasomal or lysosomal degradation including HIV (Nef protein) [55] , herpesviruses (e.g., ICP47 of herpes simplex virus, US2, US3, US6, and US11 proteins of human cytomegalovirus) [56] [57] [58] , poxvirus (e.g., M153R protein of myxomavirus) [59] , and norovirus (e.g., NS3 and VP2 proteins of MNV) [21, 60] . Moreover, some viruses, such as murine gamma herpesvirus 68, encode ubiquitin E3 ligases to directly conjugate ubiquitin to the substrate's MHC-I molecule [61] . These proteins are important targets for vaccine development. For example, the nef deletion virus induces higher cellular immune responses than WT virus due to the improved antigen presentation and greater T-cell help [62, 63] . The bovine herpesvirus type 1 (BHV-1) mutant lacking the MHC-I downregulation property induces faster onset of cellular immune responses in calves (natural host) [64] . In this study, the G90A mutation disabled the ability of PRRSV to degrade SLA-I in virus-infected PAMs. It will be interesting to investigate whether the same is true in infected pigs and whether the mutant can induce better CTL responses.

Supplementary Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/v14040690/s1, Figure S1 : Dose-dependent effect of HA-nsp1α or its derivatives on the level of Flag-SLA-I-HC in transfected cells; Table S1 : Effect on SLA-I-HC degradation of the nsp1α mutants with 2-6 alanine substitutions; Table S2 : Effect on SLA-I-HC degradation of the nsp1α mutants with 1-3 alanine substitutions; Table S3 : Mutational effect of the nsp1α substitutions on viral viability by reverse genetics. 

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Pathogenesis and control of the Chinese highly pathogenic porcine reproductive and respiratory syndrome virus

Strategies to broaden the cross-protective efficacy of vaccines against porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus: An update on an emerging and re-emerging viral disease of swine

Mystery Swine Disease in the Netherlands-the Isolation of Lelystad Virus

Isolation of the Porcine Reproductive and Respiratory Syndrome Virus in Quebec

Porcine Reproductive and Respiratory Syndrome Modified Live Virus Vaccine: A "Leaky" Vaccine with Debatable Efficacy and Safety

Porcine reproductive and respiratory syndrome virus vaccines: Current status and strategies to a universal vaccine

Improved Vaccine against PRRSV: Current Progress and Future Perspective

Live porcine reproductive and respiratory syndrome virus vaccines: Current status and future direction

Porcine Reproductive and Respiratory Syndrome Virus: Immune Escape and Application of Reverse Genetics in Attenuated Live Vaccine Development

Porcine reproductive and respiratory syndrome virus modifies innate immunity and alters disease outcome in pigs subsequently infected with porcine respiratory coronavirus: Implications for respiratory viral co-infections

Porcine reproductive and respiratory syndrome virus (PRRSV) suppresses interferon-beta production by interfering with the RIG-I signaling pathway

Cytokines transcript levels in lung and lymphoid organs during genotype 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection

Immunological responses of swine to porcine reproductive and respiratory syndrome virus infection

Kinetics of humoral immune response to the major structural proteins of the porcine reproductive and respiratory syndrome virus

Characteristics of the immune response of pigs to wild-type PRRS virus or to commercially available vaccines: An unconventional response

American Association of Swine Practitioners Annual Meeting

Innate and adaptive immunity against Porcine Reproductive and Respiratory Syndrome Virus

The level of virus-specific T-cell and macrophage recruitment in porcine reproductive and respiratory syndrome virus infection in pigs is independent of virus load

Pattern recognition receptors from lepidopteran insects and their biological functions

Mouse Norovirus Infection Reduces the Surface Expression of Major Histocompatibility Complex Class I Proteins and Inhibits CD8(+) T Cell Recognition and Activation

The persistence of CTL memory

HIV type 1 abrogates TAP-mediated transport of antigenic peptides presented by MHC class I. Transporter associated with antigen presentation

Early endosomal rerouting of major histocompatibility class I conformers

Characterization of interaction between porcine reproductive and respiratory syndrome virus and porcine dendritic cells

Porcine reproductive and respiratory syndrome virus productively infects monocyte-derived dendritic cells and compromises their antigen-presenting ability

Targeting Swine Leukocyte Antigen Class I Molecules for Proteasomal Degradation by the nsp1alpha Replicase Protein of the Chinese Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Strain JXwn06

The non-structural protein Nsp2TF of porcine reproductive and respiratory syndrome virus down-regulates the expression of Swine Leukocyte Antigen class I

Nonstructural Protein 4 of Porcine Reproductive and Respiratory Syndrome Virus Modulates Cell Surface Swine Leukocyte Antigen Class I Expression by Downregulating beta2-Microglobulin Transcription

Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus Leader Protease Nsp1 alpha

PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity

Changes in the cellular proteins of pulmonary alveolar macrophage infected with porcine reproductive and respiratory syndrome virus by proteomics analysis

The 30-amino-acid deletion in the Nsp2 of highly pathogenic porcine reproductive and respiratory syndrome virus emerging in China is not related to its virulence

Prokaryotic expression of SLA-I alpha chain and beta chain and antiserum preparation

The nsp2 Hypervariable Region of Porcine Reproductive and Respiratory Syndrome Virus Strain JXwn06 Is Associated with Viral Cellular Tropism to Primary Porcine Alveolar Macrophages

Nsp9 and Nsp10 contribute to the fatal virulence of highly pathogenic porcine reproductive and respiratory syndrome virus emerging in China

Processing and evolution of the N-terminal region of the arterivirus replicase ORF1a protein: Identification of two papainlike cysteine proteases

Identification of two autocleavage products of nonstructural protein 1 (nsp1) in porcine reproductive and respiratory syndrome virus infected cells: Nsp1 function as interferon antagonist

The nsp1alpha and nsp1 papain-like autoproteinases are essential for porcine reproductive and respiratory syndrome virus RNA synthesis

The Zinc-Finger Domain Was Essential for Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein-1 alpha to Inhibit the Production of Interferon-beta

The nonstructural protein 1 papain-like cysteine protease was necessary for porcine reproductive and respiratory syndrome virus nonstructural protein 1 to inhibit interferon-beta induction

Dual Regulation of Host TRAIP Post-translation and Nuclear/Plasma Distribution by Porcine Reproductive and Respiratory Syndrome Virus Non-structural Protein 1alpha Promotes Viral Proliferation

Nuclear export signal of PRRSV NSP1alpha is necessary for type I IFN inhibition

Identification of amino acid residues important for anti-IFN activity of porcine reproductive and respiratory syndrome virus non-structural protein 1

Degradation of CREB-binding protein and modulation of type I interferon induction by the zinc finger motif of the porcine reproductive and respiratory syndrome virus nsp1alpha subunit

Nonstructural protein 1alpha subunit-based inhibition of NF-kappaB activation and suppression of interferon-beta production by porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus non-structural protein 1 suppresses tumor necrosis factor-alpha promoter activation by inhibiting NF-kappaB and Sp1

Transcriptome analysis of pig macrophages expressing porcine reproductive and respiratory syndrome virus non-structural protein 1

Nsp1alpha of Porcine Reproductive and Respiratory Syndrome Virus Strain BB0907 Impairs the Function of Monocyte-Derived Dendritic Cells via the Release of Soluble CD83

Porcine Reproductive and Respiratory Syndrome Virus nsp1alpha Inhibits NF-kappaB Activation by Targeting the Linear Ubiquitin Chain Assembly Complex

Modulation of type I interferon induction by porcine reproductive and respiratory syndrome virus and degradation of CREB-binding protein by non-structural protein 1 in MARC-145 and HeLa cells

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Inhibits RNA-Mediated Gene Silencing by Targeting Ago-2. Viruses

Amino acid residues in the non-structural protein 1 of porcine reproductive and respiratory syndrome virus involved in down-regulation of TNF-alpha expression in vitro and attenuation in vivo

HIV-1 Nef disrupts MHC-I trafficking by recruiting AP-1 to the MHC-I cytoplasmic tail

The C-terminal amino acid of the MHC-I heavy chain is critical for binding to Derlin-1 in human cytomegalovirus US11-induced MHC-I degradation

Herpes simplex virus turns off the TAP to evade host immunity

Bovine Herpesvirus Type 1 (BHV-1) U(L)49.5 Luminal Domain Residues 30 to 32 Are Critical for MHC-I Down-Regulation in Virus-Infected Cells

The PHD/LAP-domain protein M153R of myxomavirus is a ubiquitin ligase that induces the rapid internalization and lysosomal destruction of CD4

Identification of immune and viral correlates of norovirus protective immunity through comparative study of intra-cluster norovirus strains

The viral E3 ubiquitin ligase mK3 uses the Derlin/p97 endoplasmic reticulum-associated degradation pathway to mediate down-regulation of major histocompatibility complex class I proteins

Attenuated nef DNA vaccine construct induces cellular immune response: Role in HIV-1 multiprotein vaccine

Replicating Ad-recombinants encoding non-myristoylated rather than wild-type HIV Nef elicit enhanced cellular immunity

Bovine herpesvirus type 1 (BHV-1) mutant lacking U(L)49.5 luminal domain residues 30-32 and cytoplasmic tail residues 80-96 induces more rapid onset of virus neutralizing antibody and cellular immune responses in calves than the wild-type strain Cooper