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Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses
Open accessPublished version of a preprint
Abstract
Proper recognition of viral pathogens is an essential part of the innate immune response. A common viral replicative intermediate and chemical signal that cells use to identify pathogens is the presence of a triphosphorylated 5’ end (5’ppp) RNA, which activates the cytosolic RNA sensor RIG-I and initiates downstream antiviral signaling. While 5’pppRNA generated by viral RNA-dependent RNA polymerases (RdRps) can be a potent activator of the immune response, endogenous RNA polymerase III (RNAPIII) transcripts can retain the 5’ppp generated during transcription and induce a RIG-I-mediated immune response. We have previously shown that host RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) can act on both host and viral RNAs, altering their levels and reducing their ability to induce RIG-I activation. Our previous work explored how experimentally altered DUSP11 activity can impact immune activation, prompting further exploration into natural contexts of altered DUSP11 activity. Here, we have identified viral DUSP11 homologs (vDUSP11s) present in some avipoxviruses. Consistent with the known functions of host DUSP11, we have shown that expression of vDUSP11s: 1) reduces levels of endogenous RNAPIII transcripts, 2) reduces a cell’s sensitivity to 5’pppRNA-mediated immune activation, and 3) restores virus infection defects seen in the absence of DUSP11. Our results identify a context where DUSP11 activity has been co-opted by viruses to alter RNA metabolism and influence the outcome of infection.
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![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.](/paper-figures/904dfb87fab6493baee63aa314fa339d/viral-piracy-of-host-rna-phosphatase-dusp11-by-avipoxviruses-figure-2.jpg)



![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.](/paper-figures/741a290a4cf042f3aa894f27ddcdca72/viral-piracy-of-host-rna-phosphatase-dusp11-by-avipoxviruses-figure-6.jpg)


![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).](/paper-figures/41efa371a0ce4c8ab78debf0cef80238/viral-piracy-of-host-rna-phosphatase-dusp11-by-avipoxviruses-figure-9.jpg)
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Metadata
- Authors
- Szymanik, K. H., Rex, E. A., Pothireddy, V. R., Gammon, D. B., Hancks, D. C., & Sullivan, C. S.
- Affiliations
- The University of Texas at Austin (US)
- The University of Texas Southwestern Medical Center (US)
- Corresponding author
- Hancks, Dustin C.
- Sullivan, Christopher S.
- Venue
- PLOS Pathogens
- Publisher
- Public Library of Science (PLoS)
- Published
- 2025-04-21
- Volume
- 21
- Issue
- 4
- Pages
- e1013101
- ISSN
- 1553-7366 (ISSN-L)
- 1553-7374
- PMC
- PMC12058148
- OpenAlex
- W4409640449
- Cited by
- 0
- References
- 66
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Update notices
- new_version (2025-05-07)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Pathogens (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- NIH (1R35GM142689-04, 1R01AI134980, 1R35GM137978, T32 AI007520)
- Burroughs Wellcome Fund (1011070)
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › interferon and immune responses
- Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
- Life Sciences › Immunology and Microbiology › Immunology › Immune Response and Inflammation
- Keywords
- RIG-I, innate immune evasion, RNA triphosphatase, RNA polymerase III transcripts, viral RNA-dependent RNA polymerase, RNA metabolism
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- Szymanik, K. H., Rex, E. A., Pothireddy, V. R., Gammon, D. B., Hancks, D. C., & Sullivan, C. S. (2025). Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1013101
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