Affinage

DDX56

Probable ATP-dependent RNA helicase DDX56 · UniProt Q9NY93

Length
547 aa
Mass
61.6 kDa
Annotated
2026-06-09
15 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/5 claims corpus-supported (80%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

DDX56 (NOH61) is a nucleolar DEAD-box RNA helicase with polynucleotide-stimulated ATPase activity that functions in 60S ribosomal subunit biogenesis, residing in free nucleoplasmic 65S preribosomal particles and showing RNA-dependent nucleolar localization that is lost upon actinomycin D or RNase A treatment (PMID:10749921). This ribosome-assembly role is conserved across stem cell systems: Ddx56 is required for ribosome assembly and viability in mouse embryonic stem cells, where it also binds the Oct4/Sox2 pluripotency complex through Sox2 via its C-terminus to support proliferation independently of its ribosome function (PMID:32703285), and its loss in planarians and human glioblastoma stem cells dysregulates rRNA and disrupts nucleolar integrity prior to stem cell death (PMID:33789112). DDX56 is repeatedly co-opted at the host–virus interface. For West Nile virus it relocalizes from the nucleolus to ER assembly sites, binds the capsid protein in an RNA-independent manner, and uses its helicase activity to support assembly of infectious virions without affecting RNA replication (PMID:21411523, PMID:22925334, PMID:27821284). In innate immunity DDX56 acts as both a proviral suppressor and an antiviral effector depending on context: it inhibits type I interferon signaling for FMDV by cooperating with the 3A protein to block IRF3 phosphorylation (requiring residue D166) (PMID:31445188) and for EMCV by targeting importins KPNA3/KPNA4 to prevent IRF3 nuclear import (PMID:34922148), yet it directly binds a stem-loop in incoming chikungunya virus genomic RNA to destabilize it in an interferon-independent manner (PMID:33109765) and enhances cGAS-STING-IFN-β signaling against pseudorabies virus through direct interaction with cGAS (PMID:36090064). In cancer, DDX56 drives oncogenic transcriptional and post-transcriptional programs, partnering with MECOM to deposit H3K9me1 at the MIST1 promoter and activate PTEN-AKT signaling in HCC (PMID:36168636) and promoting Wnt signaling by facilitating degradation of pri-miR-378a (PMID:34446021).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2000 High

    Established the basic biochemical identity of DDX56 as a nucleolar DEAD-box ATPase and placed it in the ribosome biogenesis pathway, answering what kind of enzyme it is and where it acts.

    Evidence Recombinant ATPase assay, sucrose gradient sedimentation, biochemical fractionation and immunolocalization with actinomycin D/RNase A treatment in cultured cells

    PMID:10749921

    Open questions at the time
    • RNA substrate specificity of helicase activity not defined
    • specific step in 60S maturation not pinpointed
    • no structural model of oligomerization
  2. 2011 High

    Showed DDX56 is hijacked by West Nile virus as a host assembly factor, distinguishing its role from RNA replication and linking it to capsid via direct binding.

    Evidence Yeast two-hybrid, RNA-independent co-immunoprecipitation, siRNA knockdown and viral infectivity assays in infected cells

    PMID:21411523

    Open questions at the time
    • molecular mechanism by which DDX56 packages viral RNA unresolved
    • did not address helicase requirement
  3. 2012 High

    Demonstrated that the helicase enzymatic activity and the capsid-binding interaction are functionally required for WNV virion assembly, moving from correlation to mechanism.

    Evidence Helicase-dead mutant and dominant-negative capsid-binding domain overexpression with infectivity readouts

    PMID:22925334

    Open questions at the time
    • RNA substrate acted upon during assembly unknown
    • stoichiometry of capsid complex undefined
  4. 2016 Medium

    Refined the spatial model of WNV co-option, showing DDX56 and capsid colocalize at ER assembly sites while stable binding occurs in the nucleus, implying a transient cytoplasmic interaction.

    Evidence Super-resolution microscopy and fractionated co-immunoprecipitation

    PMID:27821284

    Open questions at the time
    • transient cytoplasmic interaction not directly captured biochemically
    • trigger for nucleolar-to-ER relocalization unknown
  5. 2020 Medium

    Separated DDX56's ribosome-assembly role from a distinct pluripotency function in stem cells, using a domain mutant to dissociate the two activities.

    Evidence Knockout/RNAi, polysome fractionation, co-IP with Sox2 and C-terminal truncation mutant analysis in mESCs

    PMID:32703285

    Open questions at the time
    • mechanism of Sox2-DDX56 cooperation in proliferation undefined
    • whether helicase activity contributes to pluripotency role unaddressed
  6. 2020 High

    Revealed an intrinsic antiviral activity in which DDX56 directly recognizes and destabilizes viral genomic RNA, contrasting with its proviral roles.

    Evidence RNAi screen, CLIP-Seq mapping of a stem-loop binding site, infection assays in human and Drosophila cells

    PMID:33109765

    Open questions at the time
    • mechanism of RNA destabilization (helicase vs recruitment of nucleases) not resolved
    • how DDX56 distinguishes viral from host RNA unknown
  7. 2021 Medium

    Extended DDX56's interferon-suppressive proviral function to EMCV through a specific block on IRF3 nuclear import via importin targeting.

    Evidence Co-IP with KPNA3/KPNA4, IRF3 phosphorylation/translocation assays, IFN-β reporter and knockdown in the MDA5 cascade

    PMID:34922148

    Open questions at the time
    • direct vs indirect KPNA binding not structurally defined
    • relationship to FMDV mechanism not reconciled
  8. 2021 Medium

    Identified DDX56 as a positive host factor for influenza A virus via interaction with NS1, broadening the range of viruses that exploit it.

    Evidence Yeast two-hybrid, mammalian co-IP, colocalization and siRNA knockdown with replication assay

    PMID:33749700

    Open questions at the time
    • functional consequence of NS1 binding mechanistically undefined
    • single-lab interaction without reciprocal mapping
  9. 2021 Medium

    Connected DDX56 to oncogenic Wnt signaling through a post-transcriptional miRNA-processing mechanism, expanding its functional repertoire beyond viral and ribosomal roles.

    Evidence Knockdown/overexpression in vitro, xenograft, miRNA profiling and pri-miR-378a processing qRT-PCR in squamous cell lung carcinoma

    PMID:34446021

    Open questions at the time
    • direct binding of DDX56 to pri-miR-378a not demonstrated
    • helicase requirement for miRNA degradation untested
  10. 2021 Medium

    Established conservation of DDX56's nucleolar/rRNA role in stem cell maintenance across species, tying ribosome biology to stem cell survival.

    Evidence Comparative genomics, planarian RNAi with nucleolar integrity and rRNA assays, human GSC functional assays

    PMID:33789112

    Open questions at the time
    • direct rRNA processing step affected not defined
    • link between nucleolar disruption and cell death mechanistically unmapped
  11. 2022 Medium

    Defined a chromatin-level oncogenic mechanism in which DDX56 partners with MECOM to deposit H3K9me1 and activate the MIST1/PTEN-AKT axis in HCC.

    Evidence Co-IP, ChIP, EMSA, dual-luciferase reporter and xenograft models with knockdown/overexpression

    PMID:36168636

    Open questions at the time
    • how an RNA helicase confers promoter occupancy/methyltransferase recruitment unclear
    • direct vs MECOM-dependent DNA binding not separated
  12. 2022 Medium

    Showed a context-specific antiviral role in which DDX56 directly binds cGAS to enhance IFN-β signaling against PRV, contrasting with its IFN-suppressive activity in other infections.

    Evidence Co-IP, cGAS-knockdown epistasis, IRF3 phosphorylation/translocation and IFN-β assays

    PMID:36090064

    Open questions at the time
    • determinant of pro- vs anti-interferon switching across viruses unknown
    • structural basis of cGAS interaction undefined
  13. 2024 Low

    Proposed an additional oncogenic axis linking DDX56 to EMT and stemness via MELK-FOXM1 signaling in HCC.

    Evidence Knockdown/overexpression in vitro, in vivo metastasis model and EMT/stemness marker analysis

    PMID:38827395

    Open questions at the time
    • no direct DDX56-MELK binding or biochemical mechanism demonstrated
    • pathway-level phenotype only
    • relationship to other oncogenic axes unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • What determines whether DDX56 acts as a proviral interferon suppressor or an antiviral effector, and how its core helicase/ATPase activity is mechanistically deployed across ribosome assembly, viral RNA destabilization, and chromatin/miRNA regulation, remains unresolved.
  • unifying biochemical mechanism linking diverse roles absent
  • no structural data for any partner interaction
  • RNA substrate determinants undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2 GO:0140098 catalytic activity, acting on RNA 2 GO:0140657 ATP-dependent activity 1
Localization
GO:0005730 nucleolus 2 GO:0005829 cytosol 2 GO:0005783 endoplasmic reticulum 1
Pathway
R-HSA-1643685 Disease 4 R-HSA-168256 Immune System 3 R-HSA-8953854 Metabolism of RNA 2
Partners
CGASFMDV 3AKPNA3KPNA4MECOMNS1SOX2WNV CAPSID

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 NOH61/DDX56 is a nucleolar DEAD-box protein with demonstrated ATPase activity that is stimulated by polynucleotides; it sediments as homo-oligomeric structures in vitro (~11.5S) but as a monomer (~4S) under high-salt conditions; it is a constituent of free nucleoplasmic 65S preribosomal particles but absent from cytoplasmic ribosomes; its nucleolar localization is disrupted by actinomycin D or RNase A treatment, indicating RNA-dependent nucleolar association. ATPase activity assay with recombinant protein, sucrose gradient sedimentation, immunolocalization, RNase A and actinomycin D treatment of cultured cells, biochemical fractionation Molecular biology of the cell High 10749921
2011 DDX56 interacts with West Nile virus (WNV) capsid protein in infected cells (interaction confirmed by co-immunoprecipitation and shown to be RNA-independent); WNV infection induces relocalization of DDX56 from the nucleolus to a cytoplasmic compartment containing capsid protein; DDX56 is not required for WNV RNA replication but is required for assembly of infectious virions—virions from DDX56-depleted cells contain less viral RNA and are ~100-fold less infectious. Yeast two-hybrid screen, co-immunoprecipitation (RNA-independent), siRNA knockdown, viral infectivity assays, immunofluorescence/localization studies Journal of virology High 21411523
2012 The helicase enzymatic activity of DDX56 is essential for its role in WNV virion assembly; overexpression of the capsid-binding region of DDX56 (acting as a dominant negative) reduces WNV infectivity, indicating that the DDX56–capsid interaction is a functionally important step in the virion assembly pathway. Helicase-dead mutant overexpression, dominant-negative capsid-binding domain overexpression, viral infectivity assays Virology High 22925334
2016 During WNV infection DDX56 relocalizes from nucleoli to virus assembly sites on the endoplasmic reticulum (ER); super-resolution microscopy shows capsid and DDX56 occupy the same ER subcompartment; however, stable interaction between DDX56 and capsid is only detected in the nucleus, suggesting the cytoplasmic interaction is transient during virion morphogenesis. Super-resolution microscopy, co-immunoprecipitation from nuclear and cytoplasmic fractions, immunofluorescence colocalization Virology Medium 27821284
2019 DDX56 interacts with FMDV non-structural protein 3A and cooperates with it to inhibit type I interferon signaling by reducing IRF3 phosphorylation, thereby promoting FMDV replication; the D166 residue of DDX56 is required for both promoting replication and inhibiting IRF3 phosphorylation in cooperation with 3A. Co-immunoprecipitation, siRNA knockdown, overexpression, IRF3 phosphorylation assay, viral replication assays, site-directed mutagenesis (D166) Cellular signalling Medium 31445188
2020 During chikungunya virus (CHIKV) infection, DDX56 relocalizes from the nucleus to the cytoplasm; in the cytoplasm it binds a predicted stem-loop structure on the incoming viral genomic RNA (identified by CLIP-Seq) and destabilizes it, attenuating infection at the earliest step of the replication cycle through an interferon-independent mechanism; this antiviral function is conserved between Drosophila and human cells. RNA interference screen, CLIP-Seq, viral infection assays with DDX56 depletion, immunofluorescence localization, Drosophila genetic knockdown mBio High 33109765
2021 DDX56 interacts with the IAV NS1 protein (confirmed by yeast two-hybrid and co-immunoprecipitation in mammalian cells); DDX56 knockdown significantly reduces influenza A virus replication, indicating DDX56 is a positive host factor for IAV replication. Yeast two-hybrid, co-immunoprecipitation in mammalian cells, colocalization by immunofluorescence, siRNA knockdown with viral replication assay Genetics and molecular biology Medium 33749700
2021 DDX56 promotes EMCV replication by inhibiting IRF3 phosphorylation and nuclear translocation; mechanistically, DDX56 directly targets importin subunits KPNA3 and KPNA4 to block IRF3 nuclear import in the MDA5-triggered signaling cascade, thereby suppressing IFN-β production. Overexpression/knockdown viral replication assays, IRF3 phosphorylation and nuclear translocation assays, co-immunoprecipitation with KPNA3/KPNA4, IFN-β reporter assays Veterinary microbiology Medium 34922148
2020 Ddx56 is required for ribosome assembly in mouse embryonic stem cells (mESCs); knockout or knockdown of Ddx56 causes ribosome dysfunction and cell lethality; separately, Ddx56 interacts with the Oct4/Sox2 pluripotency complex by binding to Sox2 (confirmed by co-IP), and a C-terminal truncation (Ddx56 ΔC-ter) that does not affect ribosome assembly shows reduced Sox2 interaction and decreased mESC proliferation. Knockout/RNAi knockdown, polysome fractionation, co-immunoprecipitation, RNA sequencing, C-terminal truncation mutant analysis Stem cell research & therapy Medium 32703285
2021 DDX56 promotes SqCLC cell growth and migration by post-transcriptionally upregulating Wnt pathway genes (CTNNB1, WNT2B); mechanistically, DDX56 facilitates degradation of primary miR-378a, leading to reduced mature miR-378a-3p and consequent derepression of WNT2B. siRNA knockdown and overexpression in vitro, xenograft in vivo, miRNA profiling, qRT-PCR for pri-miR-378a processing Molecular cancer Medium 34446021
2021 In glioblastoma stem cells, DDX56 localizes to the nucleolus; loss of DDX56 in planarians causes dysregulation of ribosomal RNA expression and loss of nucleolar integrity prior to stem cell death, indicating a conserved role for DDX56 in nucleolar/ribosomal RNA biology in stem cells. Comparative genomics, RNAi knockdown in planarians, nucleolar integrity assays (microscopy), human GSC functional assays Cell reports Medium 33789112
2022 DDX56 interacts with MECOM to promote mono-methylation of H3K9 (H3K9me1) on the MIST1 promoter, leading to enhanced MIST1 transcription and subsequent activation of PTEN/AKT signaling in HCC; ZEB1 transcriptionally activates DDX56 expression; DDX56 occupancy on the MIST1 promoter was confirmed by ChIP and EMSA. Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), dual-luciferase reporter, in vitro/in vivo xenograft models, siRNA knockdown and overexpression Theranostics Medium 36168636
2022 DDX56 directly interacts with cGAS and promotes cGAS expression; this interaction enhances cGAS-STING-IFN-β signaling, including promoting IRF3 phosphorylation and nuclear translocation, thereby inhibiting pseudorabies virus (PRV) replication; knockdown of cGAS abrogates the antiviral and IFN-β-promoting effects of DDX56. Co-immunoprecipitation, overexpression/knockdown, IRF3 phosphorylation/translocation assays, cGAS knockdown epistasis, IFN-β reporter/quantification Frontiers in microbiology Medium 36090064
2024 DDX56 promotes HCC EMT and cancer stemness through the MELK-FOXM1 signaling axis; DDX56 enhances MELK-mediated FOXM1 expression, regulating cancer stemness and malignant traits; knockdown of DDX56 in vivo reduced tumorigenicity and lung metastasis. siRNA knockdown and overexpression in vitro, in vivo tumor-bearing mouse model, EMT and stemness marker assays, MELK-FOXM1 pathway analysis iScience Low 38827395

Source papers

Stage 0 corpus · 15 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2011 The capsid-binding nucleolar helicase DDX56 is important for infectivity of West Nile virus. Journal of virology 74 21411523
2000 A novel helicase-type protein in the nucleolus: protein NOH61. Molecular biology of the cell 58 10749921
2012 The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles. Virology 49 22925334
2016 The nucleolar helicase DDX56 redistributes to West Nile virus assembly sites. Virology 33 27821284
2019 DDX56 cooperates with FMDV 3A to enhance FMDV replication by inhibiting the phosphorylation of IRF3. Cellular signalling 26 31445188
2021 DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma. Molecular cancer 25 34446021
2020 DDX56 Binds to Chikungunya Virus RNA To Control Infection. mBio 24 33109765
2022 DDX56 transcriptionally activates MIST1 to facilitate tumorigenesis of HCC through PTEN-AKT signaling. Theranostics 23 36168636
2021 The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells. Cell reports 17 33789112
2024 DDX56 promotes EMT and cancer stemness via MELK-FOXM1 axis in hepatocellular carcinoma. iScience 13 38827395
2021 Human DDX56 protein interacts with influenza A virus NS1 protein and stimulates the virus replication. Genetics and molecular biology 12 33749700
2021 DDX56 antagonizes IFN-β production to enhance EMCV replication by inhibiting IRF3 nuclear translocation. Veterinary microbiology 11 34922148
2020 Ddx56 maintains proliferation of mouse embryonic stem cells via ribosome assembly and interaction with the Oct4/Sox2 complex. Stem cell research & therapy 11 32703285
2022 DDX56 inhibits PRV replication through regulation of IFN-β signaling pathway by targeting cGAS. Frontiers in microbiology 7 36090064
2025 Identifying the crucial oncogenic mechanisms of DDX56 based on a machine learning-based integration model of RNA-binding proteins. NPJ precision oncology 0 40670701

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