Affinage

POLDIP3

Polymerase delta-interacting protein 3 · UniProt Q9BY77

Length
421 aa
Mass
46.1 kDa
Annotated
2026-06-10
11 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POLDIP3 (SKAR/PDIP46) is a nuclear protein operating at the interface of mRNA biogenesis, translational control, and DNA replication (PMID:15341740, PMID:26819372). In RNA metabolism, it is deposited at the exon junction complex during pre-mRNA splicing and, upon mTOR activation, recruits S6K1 — which phosphorylates POLDIP3 at S383/S385 — to newly processed mRNPs to enhance the translation efficiency of spliced mRNAs during the pioneer round of translation (PMID:15341740, PMID:18423201). Its own expression is shaped by TDP-43, whose RRM1-dependent RNA binding promotes inclusion of POLDIP3 exon 3, with loss of TDP-43 shifting the balance toward an isoform that augments S6K1 signaling, translational yield, and cell size (PMID:22121224, PMID:22900096). In interferon-α signaling, phosphorylation of POLDIP3 by RSK or S6K1 promotes its interaction with eIF4G and recruitment of activated RSK1 to capped mRNA complexes, an activity required for IFN-α-induced ISG15 and p21 expression (PMID:25049393). In DNA metabolism, POLDIP3 binds PCNA through N-terminal APIM motifs and contacts DNA polymerase δ directly, activating Pol δ and facilitating synthesis through secondary structures (PMID:26819372), and it forms a chromatin-binding complex with the RTEL1 helicase in a shared epistatic pathway that suppresses R-loop accumulation at sites of active replication to limit replication stress and genomic instability (PMID:32561545). POLDIP3 also has antiviral activity that coronaviruses neutralize: nsp5 protease cleaves it at Q176, reducing protein levels and promoting infection (PMID:37801439).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2004 High

    Established POLDIP3/SKAR as a dedicated effector of mTOR/S6K1 signaling by identifying it as a specific S6K1 (not S6K2) substrate with mapped phosphosites and a cell-size phenotype, linking it to growth control.

    Evidence Co-IP, quantitative MS, in vivo phosphorylation mapping (S383/S385), and RNAi with cell-size readout in mammalian cells

    PMID:15341740

    Open questions at the time
    • Did not define the molecular process through which SKAR controls cell size
    • Subcellular site of S6K1 recruitment unresolved
  2. 2006 Medium

    Identified Enhancer of Rudimentary (ER) as a nuclear binding partner mapping to the S6K1-docking/phosphorylation region, situating POLDIP3 in nuclear protein complexes.

    Evidence Yeast two-hybrid, GST pull-down with MS, nuclear co-localization microscopy

    PMID:16984396

    Open questions at the time
    • No functional consequence of the ER interaction demonstrated
    • No rescue or reciprocal in vivo validation
  3. 2008 High

    Resolved how SKAR couples growth signaling to translation by showing it is EJC-deposited during splicing and recruits activated S6K1 to enhance pioneer-round translation of spliced mRNAs.

    Evidence Co-IP with EJC components, spliced vs. nonspliced reporter translation assays, RNAi of SKAR/S6K1, rapamycin/mTOR manipulation in human cells

    PMID:18423201

    Open questions at the time
    • Which spliced transcripts depend on SKAR in vivo not defined
    • Stoichiometry of EJC deposition unresolved
  4. 2011 Medium

    Showed POLDIP3 is itself an alternative-splicing target of TDP-43, with isoform choice tuning S6K1 signaling and cell size, embedding it in a regulatory feedback on growth.

    Evidence Exon arrays, RNAi, minigene splicing reporter, S6K1 signaling and cell-size assays

    PMID:22121224

    Open questions at the time
    • Direct functional difference between isoforms at the protein level not fully characterized
    • Single-lab data
  5. 2012 Medium

    Extended TDP-43 control of POLDIP3 exon 3 inclusion to disease by detecting the variant-2 shift in ALS-affected motor cortex and spinal cord.

    Evidence Exon arrays, TDP-43 siRNA, RT-PCR splice-variant detection, laser capture microdissection of ALS tissue

    PMID:22900096

    Open questions at the time
    • Causal contribution of the POLDIP3 isoform shift to ALS pathology not established
    • Functional consequence in neurons not tested
  6. 2014 Medium

    Defined a role in innate immune translation by showing IFN-α-driven phosphorylation of SKAR drives eIF4G binding and RSK1 recruitment to capped mRNAs, required for ISG15 and p21 induction.

    Evidence Co-IP with eIF4G/CBP80, phosphorylation assays, RNAi with downstream gene readouts, kinase inhibition

    PMID:25049393

    Open questions at the time
    • Direct mRNA targets selected by SKAR not catalogued
    • Cell-type determinants of RSK vs. S6K1 phosphorylation unclear
  7. 2016 High

    Demonstrated a direct DNA-replication function: POLDIP3 binds PCNA via APIM motifs and contacts Pol δ to stimulate its activity through secondary structures, distinct from its RNA/translation roles.

    Evidence Co-IP, ChIP, chromatin fractionation, in vitro Pol δ activity assays on ssM13 templates, mutagenesis of PCNA/Pol δ binding motifs

    PMID:26819372

    Open questions at the time
    • In vivo replication phenotype of binding-motif mutants not established
    • Relationship between nuclear translation role and Pol δ role unresolved
  8. 2020 High

    Placed POLDIP3 in a defined genome-stability pathway by showing it forms a chromatin complex with RTEL1 and acts epistatically to suppress R-loops at replication sites under stress.

    Evidence MS interaction screen, reciprocal Co-IP, S9.6 R-loop imaging, chromatin fractionation, CRISPR KO, epistasis by double depletion in human cells

    PMID:32561545

    Open questions at the time
    • Biochemical mechanism by which the complex resolves R-loops not defined
    • How POLDIP3 Pol δ activation relates to RTEL1 cooperation unclear
  9. 2023 High

    Identified POLDIP3 as an antiviral factor targeted by coronaviruses, with nsp5 cleaving it at Q176 to abolish its restriction of infection.

    Evidence iTRAQ proteomics, in vitro protease cleavage with Q176 mapping, CRISPR KO and overexpression, in vivo piglet infection model

    PMID:37801439

    Open questions at the time
    • Molecular mechanism of POLDIP3 antiviral activity not defined
    • Which POLDIP3 function (translation vs. DNA replication) underlies restriction unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • How POLDIP3's distinct activities — EJC-coupled translation, Pol δ activation, RTEL1-dependent R-loop suppression, and antiviral restriction — are integrated or partitioned within one protein remains unresolved.
  • No unifying structural or domain map linking the RNA and DNA functions
  • No model for how phosphorylation state switches between roles

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0045182 translation regulator activity 2 GO:0003723 RNA binding 1 GO:0098772 molecular function regulator activity 1
Localization
GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 2
Pathway
R-HSA-168256 Immune System 2 R-HSA-69306 DNA Replication 2 R-HSA-8953854 Metabolism of RNA 2
Partners
EIF4G1ERHPCNAPOLD1RPS6KA1RPS6KB1RTEL1TDP-43
Complex memberships
RTEL1-POLDIP3 complexexon junction complex

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2004 SKAR (POLDIP3) is a novel and specific binding partner and substrate of S6K1 but not S6K2; serines 383 and 385 of human SKAR are insulin-stimulated, rapamycin-sensitive S6K1 phosphorylation sites, and RNAi-mediated reduction of SKAR decreases cell size. Co-immunoprecipitation, quantitative mass spectrometry, RNAi knockdown with cell size readout, in vivo phosphorylation assays Current biology : CB High 15341740
2008 SKAR is deposited at the exon junction complex (EJC) during pre-mRNA splicing, and upon mTOR activation, recruits activated S6K1 to newly processed mRNPs to enhance the translation efficiency of spliced mRNAs during the pioneer round of translation. Co-immunoprecipitation with EJC components, reporter translation assays comparing spliced vs. nonspliced mRNAs, RNAi knockdown of SKAR and S6K1, mTOR/rapamycin pharmacological manipulation Cell High 18423201
2006 PDIP46/SKAR physically interacts with human Enhancer of Rudimentary (ER) protein; the interaction region maps to residues 274–421 of PDIP46/SKAR, which encompasses the RRM docking site for S6K1 and the S6K1-phosphorylated serines. Both proteins share nuclear co-localization in mammalian cells. Yeast two-hybrid screen, GST-ER pull-down from nuclear extract with MS identification, nuclear co-localization by microscopy The FEBS journal Medium 16984396
2011 TDP-43 regulates alternative splicing of SKAR/POLDIP3 pre-mRNA via its RRM1 domain binding to 5'-GA-3' and 5'-UG-3' repeats; TDP-43 knockdown causes inclusion of an alternatively spliced SKAR isoform that enhances S6K1-dependent signaling, increases translational yield of a splice-dependent reporter, and increases cell size. Affymetrix exon arrays, RNAi knockdown, minigene splicing reporter, S6K1 signaling assays, cell size measurement Nucleic acids research Medium 22121224
2012 TDP-43 RNA binding activity is required for inclusion of POLDIP3 exon 3; loss of TDP-43 leads to increased POLDIP3 variant-2 (lacking exon 3) in cultured cells and in ALS-affected motor cortex and spinal cord tissue. Exon array analysis, TDP-43 siRNA knockdown, RT-PCR splice variant detection, laser capture microdissection from ALS patient tissue PloS one Medium 22900096
2016 PDIP46/POLDIP3 associates with DNA polymerase δ (Pol δ) and PCNA in cell extracts and on chromatin; it contains multiple APIM (AlkB homologue-2 PCNA-Interacting Motif) copies in its N-terminal region that mediate PCNA binding; PDIP46 directly activates Pol δ activity on singly-primed ssM13 DNA templates and facilitates Pol δ synthesis through secondary structures via both PCNA-dependent and PCNA-independent direct Pol δ interaction; mutation of the Pol δ/PCNA binding region abolishes these functions. Co-immunoprecipitation, protein fractionation, ChIP, in vitro DNA polymerase activity assay on ssM13 templates, primer extension and strand displacement assays, mutagenesis of PCNA/Pol δ binding motifs Oncotarget High 26819372
2014 IFN-α induces phosphorylation of SKAR by either RSK or S6K1 in a cell-type-specific manner; this phosphorylation promotes SKAR interaction with eIF4G and recruitment of activated RSK1 to 5' cap mRNA complexes; SKAR is present in CBP80 cap-binding immune complexes via eIF4G; SKAR activity is required for IFN-α-induced expression of ISG15 and p21WAF1/CIP1. Co-immunoprecipitation with eIF4G and CBP80, phosphorylation assays, RNAi knockdown with downstream gene expression readouts, pharmacological kinase inhibition Proceedings of the National Academy of Sciences of the United States of America Medium 25049393
2020 RTEL1 helicase and POLDIP3 form a complex and are mutually dependent for chromatin binding after replication stress; loss of either protein leads to R-loop accumulation confined to sites of active replication, enhanced endogenous replication stress, and genomic instability; the effects of depleting RTEL1 and POLDIP3 are epistatic, placing them in a shared pathway for DNA replication control under stress conditions. Proteomics/MS interaction screen, Co-immunoprecipitation, R-loop detection (S9.6 immunofluorescence), chromatin fractionation, gene editing (CRISPR), epistasis analysis by double depletion Genes & development High 32561545
2023 Coronavirus nsp5 (3C-like protease) cleaves POLDIP3 at glutamine 176 (Q176), reducing POLDIP3 protein levels and abolishing its antiviral activity; POLDIP3 overexpression inhibits PDCoV infection while POLDIP3 knockout promotes it; nsp5 from PEDV, TGEV, and SARS-CoV-2 share this conserved cleavage function on POLDIP3. iTRAQ proteomics, Western blotting, CRISPR-Cas9 knockout, overexpression assays, in vitro protease cleavage assay mapping Q176 site, in vivo piglet infection model PLoS pathogens High 37801439

Source papers

Stage 0 corpus · 11 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2008 SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs. Cell 251 18423201
2004 SKAR is a specific target of S6 kinase 1 in cell growth control. Current biology : CB 156 15341740
2011 TDP-43 regulates global translational yield by splicing of exon junction complex component SKAR. Nucleic acids research 87 22121224
2012 Alteration of POLDIP3 splicing associated with loss of function of TDP-43 in tissues affected with ALS. PloS one 76 22900096
2020 Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution. Genes & development 37 32561545
2006 Human enhancer of rudimentary is a molecular partner of PDIP46/SKAR, a protein interacting with DNA polymerase delta and S6K1 and regulating cell growth. The FEBS journal 37 16984396
2023 Broad antagonism of coronaviruses nsp5 to evade the host antiviral responses by cleaving POLDIP3. PLoS pathogens 21 37801439
2017 An alternative POLDIP3 transcript promotes hepatocellular carcinoma progression. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 20 28236701
2016 PDIP46 (DNA polymerase δ interacting protein 46) is an activating factor for human DNA polymerase δ. Oncotarget 18 26819372
2014 Regulatory effects of SKAR in interferon α signaling and its role in the generation of type I IFN responses. Proceedings of the National Academy of Sciences of the United States of America 11 25049393
2022 POLDIP3: At the Crossroad of RNA and DNA Metabolism. Genes 3 36360158

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