Fig 1.
Avipoxviruses and related unclassified avipox-related poxviruses encode putative homologs of DUSP11.
(A) Schematic of human DUSP11 (hDUSP11) and select putative viral DUSP11s with predicted domains indicated. The shared colored domain (green) indicates hDUSP11 P-loop with corresponding identical sequences present in putative viral DUSP11 homologs (vDUSP11). Putative vDUSP11 includes shearwaterpox virus 2 vDUSP11 (SWPV2 vDUSP11) and canarypox virus vDUSP11 (CNPV vDUSP11). (B) Key catalytic residues are conserved between hDUSP11 and putative avipox vDUSP11. Multiple sequence comparison (Clustal Omega) of amino acid (AA) sequences for human DUSP11, mouse DUSP11, C. borealis (Shearwater), and putative vDUSP11s from shearwaterpox virus 1 (SWPV1), finchpox virus (FNPV), mudlarkpox virus (MLPV), cheloniidpox virus (ChePV), canarypox virus (CNPV), penguinpox virus 2 (PEPV2), albatrosspox virus (ALPV), magpiepox virus (MPPV), and shearwaterpox virus 2 (SWPV2). A subset of AAs surrounding the hDUSP11 P-loop are shown. Amino acids are colored based on side-chain chemistry. Bar graph indicating relative sequence conservation with consensus amino acid sequence determined from listed sequences. Taller bar height and darker blue color correspond to relative correlation to consensus sequence. The numbering below the consensus sequence corresponds to hDUSP11 amino acid numbering. hDUSP11 residue R192 is indicated by a red arrow. (C) Partial crystal structure of hDUSP11 (PDB:4JMJ, dark blue) with unsolved regions predicted using Alphafold2 (light blue) and Alphafold2 structural prediction shearwaterpox virus 2 vDUSP11 (orange) with structural overlay. Key catalytic residues (P-loop) present in hDUSP11 are indicated in green, and corresponding residues are also indicated on the putative SWPV2 vDUSP11 structural prediction.
Fig 2.
Phylogenetic analysis supports putative vDUSP11 acquisition from host DUSP11 sequence.
An inferred tree built using 160 DUSP amino acid (AA) sequences by maximum-likelihood analysis using PhyML [42]. AA sequences for host atypical DUSPs, poxviral putative vDUSP11s, vaccinia virus DUSP H1L protein phosphatase and avipox homologs, and the large subunit the capping enzyme from poxviruses were aligned using Clustal Omega (S9 Fig) [46]. Clustal alignment was used to run PhyML analysis with LG + R model selected by SMS [53]. Sequences were retrieved from the HGNC sequence database, NCBI sequence database [41] and Uniprot (www.uniprot.org/) (S4 Table). Putative APV/AdjPV vDUSP11s (orange) cluster with host DUSP11s (blue) and not with other host protein DUSPs or other poxviral proteins (pink). Collapsed branches are used to represent proteins with homology that cluster together across numerous species. 100 bootstrap replicates were performed; branch support ≥50% (*) or ≥ 70% (**) are indicated. Nematode DUSP4, a member of the DUSP-family but not an atypical DUSP, was specified as the outgroup.
Fig 3.
vDUSP11 sensitizes HCV 5’ UTR RNA to XRN-mediated degradation.
(A) Confirmation of in vitro translated constructs via immunoblot analysis. Membrane was probed for FLAG-tagged proteins. Plasmid encoding luciferase was used for negative control reactions. (B) In vitro XRN susceptibility assay. In vitro transcribed HCV 5’ UTR RNA was incubated with in vitro translated products from (A) luciferase (Luc), hDUSP11 (D11), hDUSP11 catalytic mutant (D11-CM), shearwaterpox virus 2 vDUSP11 (SWPV) or shearwaterpox virus 2 vDUSP11 catalytic mutant (SWPV-CM)) and RNA was purified. Purified RNA was then subjected to treatment ± recombinant XRN1. Products were separated using urea PAGE and stained with EtBr. Migration of full-length HCV 5’ UTR is indicated, which for unknown reasons migrates as a doublet, the position of the faster-migrating cleavage fragment is indicated. (C) Graphical representation of (B), displaying ratio of band intensity of the ratio of HCV 5’ UTR full-length doublet bands to cleavage fragment band from the XRN-treated to the -XRN1 treatment reactions. Values are represented relative to the negative control Luc treatment. Data are derived from n = 3 independent replicates. In all panels, data are represented as mean ± SEM.
Fig 4.
vDUSP11 modulates immune activation in response to liposomal 5’-ppp-RNAs.
(A) Schematic diagram of the 5’-triphosphate RNA (5’-ppp-RNA) transfection assay. A549 DUSP11 knockout (KO) reconstituted cells (12-well) were transfected with 5–10 ng of in vitro transcribed 5’-ppp-RNA for 18 hours followed by RT-qPCR to assay induction of ISGs. (B) Immunoblot analysis of A549 DUSP11 knockout (KO) cells transduced with pLenti empty vector (EV), pLenti hDUSP11-3xFLAG (D11), pLenti hDUSP11 catalytic mutant-3xFLAG (D11-CM), pLenti shearwaterpox virus 2 vDUSP11-3xFLAG (SWPV), pLenti shearwaterpox virus 2 vDUSP11 catalytic mutant-3xFLAG (SW-CM/SWPV-CM), pLenti cheloniidpox virus 1 vDUSP11-3xFLAG (ChePV), pLenti 3xFLAG-cheloniidpox virus 1 vDUSP11 catalytic mutant-3xFLAG (Che-CM/ChePV-CM), or negative control pLenti DUSP12-3xFLAG (D12). (C) RT-qPCR analysis of ISG15 and (D) IFNB1 mRNA levels in A549 DUSP11 KO reconstituted cells following transfection with either lipofectamine alone or 5’-ppp-RNA, normalized to GAPDH mRNA levels. Results are represented relative to those of empty vector expressing cells. Data are derived from n = 4 independent replicates and are represented as mean ± SEM. Schematic figures in Fig 4A were created with BioRender.com.
Fig 5.
vDUSP11 catalytic activity promotes VSV virus replication.
(A) Representative GFP images of A549 DUSP11 knockout (KO) cells stably reconstituted with either empty vector (EV) plasmid, hDUSP11 (D11), hDUSP11 catalytic mutant (D11-CM), shearwaterpox virus 2 vDUSP11 (SWPV), shearwaterpox virus 2 vDUSP11 catalytic mutant (SWPV-CM), cheloniidpox virus vDUSP11 (ChePV), cheloniidpox virus vDUSP11 catalytic mutant (ChePV-CM), or protein phosphatase DUSP12 (D12) after infection with GFP-M51R VSV at an MOI of 0.01 PFU/cell at 48 hours post-infection (hpi). (B) VSV viral titer of indicated A549 DUSP11 KO reconstituted cells determined by plaque assay analysis at 48 hpi. (C) Representative images of plaque assay analysis of virus supernatant at 48 hpi. Data are derived from n = 3 independent replicates. Data are presented as mean ± SEM. (*) P < 0.05; (**) P < 0.01 (two-tailed Student’s t-test).
Fig 6.
DUSP11 reduces immune signaling in response to infection by VACV ∆E3L.
Previously characterized A549NT (non-targeted) and A549 RIG-I knock out cells (∆RIG-I) [34] were either mock infected (Mock), infected with wild-type recombinant vaccinia virus (VACV) (WT-R), or infected with an E3L deficient VACV (∆E3L/VACV ∆E3L). (A). RT-qPCR analysis of ISG15 and (B) IFNB1 mRNA normalized to GAPDH mRNA levels. Results are represented relative to those of non-targeted cells. (C) RT-qPCR analysis of ISG15 and (D) IFNB1 mRNA normalized to GAPDH mRNA of A549 DUSP11 KO cells expressing either empty vector (EV), hDUSP11 (D11), shearwaterpox virus vDUSP11 (SWPV), or cheloniidpox virus vDUSP11 (ChePV) at 16 hpi following either mock infection or infection with VACV ∆E3L. Results are represented relative to mock infected A549 DUSP11 KO cells reconstituted with EV. For panels A and B, non-targeted cells infected with either WT-R or VACV ∆E3L at 8 hpi, data are derived from n = 3 independent replicates. For all other time points, data are derived from n = 4 independent replicates. All data are represented as mean ± SEM. (*) P < 0.05; (**) P < 0.01; (***) P < 0.001; (****); P < 0.0001. Statistical analysis for panels A and B included two-tailed students t-tests; C and D included one-way ANOVAs followed by Dunnett’s multiple comparison test.
Fig 7.
vDUSP11 modulates steady-state RNA levels of endogenous RNAP III transcripts.
(A) Schematic diagram of vtRNA northern blot. RNA was collected from resting A549 DUSP11 KO cells stably reconstituted with empty vector (EV) plasmid, hDUSP11 (D11), hDUSP11 catalytic mutant (D11-CM), shearwaterpox virus 2 vDUSP11 (SWPV), shearwaterpox virus 2 vDUSP11 catalytic mutant (SWPV-CM), cheloniidpox virus vDUSP11 (ChePV), cheloniidpox virus vDUSP11 catalytic mutant (ChePV-CM), or negative control protein phosphatase DUSP12 (D12). Purified RNA was then subjected to northern blot analysis. (B) Northern blot analysis of vtRNA1–1 and vtRNA2–1 using RNA from A549 DUSP11 KO reconstituted cells. (C) Graphical representation of relative band intensity of vtRNA1–1 and (D) vtRNA2–1 normalized to the relative band intensity of the 5’ monophosphate control cysteine-tRNA. Values are represented relative to the A549 DUSP11 KO + EV cell line. Data are derived from n = 3 independent replicates. In all panels, data are represented as mean ± SEM. (*) P < 0.05; (**) P < 0.01 (two-tailed Student’s t-test). Schematic figures in Fig 7A were created with BioRender.com.
Fig 8.
vDUSP11s differ in subcellular localization compared to hDUSP11.
Representative confocal images of A549 DUSP11 KO cells stably expressing either an empty vector (EV) plasmid or individual 3xFLAG tagged proteins including hDUSP11 (D11), hDUSP11 catalytic mutant (D11-CM), SWPV2 vDUSP11 (SWPV), SWPV2-CM (SWPV-CM), ChePV1 vDUSP11 (ChePV), ChePV1 vDUSP11-CM (ChePV-CM), or negative control protein phosphatase DUSP12 (D12). Prolong Gold Antifade Mountant (Thermo Fisher Scientific) was used in slide preparation to visualize nuclei.
Fig 9.
A single acquisition event for vDUSP11 is indicated by synteny analysis.
(A) Graphical representation of avipoxvirus genome using published information from the canarypox virus genome as a model [62]. Inverted terminal repeats (ITRs) are indicated in light blue, relative genome position of vDUSP11 indicated in black. (B) Analysis of upstream and downstream flanking genes indicated vDUSP11s (black) reside at similar genomic locations across poxvirus genomes. Protein homologs were determined using reciprocal BLAST hits for the 5 genes upstream (left of vDUSP11) and 5 genes downstream (right of vDUSP11) of vDUSP11. Homologous genes are indicated by shared color. Genes oriented to the right indicate ORFs on the top strand while genes oriented to the left indicate genes on the bottom strand. Cladogram indicating virus relatedness from published data [63] to the right of each gene diagram. (C) Corresponding functional annotation for genes indicated in (B). Predicted functional annotations were determined using NCBI database genome annotations [41]. For genes lacking descriptive annotations, more detailed annotations based on identified homologous genes were used (S5 Table).