Suppressor of IKKepsilon forms direct interactions with cytoskeletal proteins, tubulin and α-actinin, linking innate immunity to the cytoskeleton.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29988566", "kind": "science-record", "revision": 6, "content_hash": "sha256:9ee5a88952a7e557bf7862d8fea0794c086bcc74e31911dd58b16d44131f3188", "created_at": "2026-11-01T15:40:35Z", "updated_at": "2026-11-01T21:21:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Suppressor of IKKepsilon forms direct interactions with cytoskeletal proteins, tubulin and α-actinin, linking innate immunity to the cytoskeleton.", "doi": "10.1002/2211-5463.12454", "pmid": "29988566", "authors": ["Halie A Sonnenschein", "Kenneth F Lawrence", "Karli A Wittenberg", "Frank A Slykas", "Emerald L Dohleman", "Jilan B Knoublauch", "Sean M Fahey", "Timothy M Marshall", "James D Marion", "Jessica K Bell"], "journal": "FEBS open bio", "year": 2018, "abstract": "Suppressor of IKKepsilon (SIKE) is associated with the type I interferon response of the innate immune system through TANK-binding kinase 1 (TBK1). Originally characterized as an endogenous inhibitor of TBK1 when overexpressed in viral infection and pathological cardiac hypertrophic models, a mechanistic study revealed that SIKE acts as a high-affinity substrate of TBK1, but its function remains unknown. In this work, we report that scratch assay analysis of parental and SIKE CRISPR/Cas9 knockout HAP1 cells showed an ~ 20% decrease in cell migration. Investigation of the SIKE interaction network through affinity purification/mass spectrometry showed that SIKE formed interactions with cytoskeletal proteins. In immunofluorescence assays, endogenous SIKE localized to cytosolic puncta in both epithelial and myeloid cells and to nuclear puncta in myeloid cells, while in epithelial cells additional staining occurred in stress fiber-like structures and adjacent to the plasma membrane. Using cellular markers, co-occurrence of SIKE fluorescence with actin, α-actinin, and ezrin was detected. Reciprocal immunoprecipitation revealed a SIKE:tubulin interaction sensitive to the phosphorylation state of SIKE, but a SIKE:α-actinin interaction was unchanged by SIKE phosphorylation. In vitro precipitation assays confirmed a direct SIKE interaction with tubulin and α-actinin. These results indicate that SIKE may promote cell migration by directly associating with the cytoskeleton. In this role, SIKE may mediate cytoskeletal rearrangement necessary in innate immunity, but also link a key catalytic hub, TBK1, to the cytoskeleton.\nDATABASE: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD007262.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE 1 partner repository with the dataset identifier PXD007262.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29988566", "locator": "sections[28] \"Criteria for protein identification\" paragraph 3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE 1 partner repository with the dataset identifier PXD007262."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper’s headline result was that SIKE knockout reduced HAP1 cell migration by approximately 20%; differences in scratch closure were assessed by Student’s unpaired two-tailed t-test, and the mass spectrometry proteomics data are available through PRIDE under dataset identifier PXD007262.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29988566", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this work, we report that scratch assay analysis of parental and SIKE CRISPR/Cas9 knockout HAP1 cells showed an ~ 20% decrease in cell migration."}, {"asset": "source:pmid:29988566", "locator": "sections[7] \"SIKE knockout cells show impaired cell migration\" paragraph 3", "quote": "Significantly different values for % closure (95% confidence interval, P ≤ 0.05) were assessed by Student's unpaired t‐test, two‐tailed."}, {"asset": "source:pmid:29988566", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD007262."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper’s headline result was that SIKE knockout reduced HAP1 cell migration by approximately 20%; differences in scratch closure were assessed by Student’s unpaired two-tailed t-test, and the mass spectrometry proteomics data are available through PRIDE under dataset identifier PXD007262.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29988566"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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FLAG‐tagged SIKE was immunoprecipitated from HEK293 lysates, subjected to tryptic digest and resulting peptides analyzed by LC‐MS/MS. Data were analyzed with sequest and x!tandem software", "structure": {"pmcid": "PMC6026704", "section_index": 8, "section_title": "SIKE interaction network identified by co‐immunoprecipitation tandem MS/MS", "row_count": 26, "column_count": 13}, "table": {"label": "Table 1", "caption": "SIKE interactome summary. FLAG‐tagged SIKE was immunoprecipitated from HEK293 lysates, subjected to tryptic digest and resulting peptides analyzed by LC‐MS/MS. Data were analyzed with sequest and x!tandem software", "rows": [["", "", "Protein name", "MW, kDa", "Accession nos UniProt", "WT"], ["Basal", "dsRNA"], ["Run 1", "Run 2", "Run 1", "Run 2"], ["% cov", "SC", "% cov", "SC", "% cov", "SC", "% cov", "SC"], ["BAIT", "", "Suppressor of IKKepsilon", "24", "Q9BRV8", "71", "48", "82", "272", "71", "44", "82", "197"], ["PREY", "Cytoskeleton", "aActin, cytoplasmic 1", "42", "P60709", "", "", "26", "27", "", "", "20", "9"], ["", "aActin, aortic smooth muscle", "42", "P62736", "", "", "18", "15", "", "", "7.2", "5"], ["", "Actin, gamma 1", "40", "P63261", "13", "5", "", "", "9.6", "5", "", ""], ["", "Tubulin alpha‐1C chain", "58", "F5H5D3", "", "", "13", "11", "", "", "6.7", "5"], ["", "bTubulin beta chain", "49", "P07437", "", "", "28", "25", "", "", "14", "6"], ["", "", "bTubulin beta‐4B chain", "50", "P68371", "", "", "21", "17", "", "", "11", "3"], ["", "Chaperone", "cHeat shock 70‐kDa protein 1A/1B", "70", "P0DMV8/P0DMV9", "13", "7", "23", "44", "7.5", "6", "19", "20"], ["", "cHeat shock 70‐kDa protein 6", "71", "P17066", "", "", "9.8", "15", "", "", "8.7", "11"], ["", "Heat shock cognate 71‐kDa protein", "54", "P11142", "13", "5", "", "", "13", "6", "", ""], ["", "Heat shock protein HSP 90‐beta", "83", "P08238", "", "", "5.4", "5", "", "", "1.9", "2"], ["", "Peptidyl‐prolyl cis‐trans isomerase A", "18", "P62937", "33", "5", "", "", "16", "1", "", ""], ["", "DNA/RNA associated", "Nucleophosmin 1, isoform 2", "29", "P06748‐2", "5.3", "2", "18", "12", "9.4", "2", "18", "8"], ["", "Treacle protein", "152", "Q13428", "1.9", "3", "", "", "2.5", "4", "", ""], ["", "Elongation factor 1‐alpha 1", "50", "P68104", "15", "3", "7.6", "3", "4.8", "3", "2.4", "2"], ["", "Activated RNA polymerase II transcriptional coactivator p15", "14", "P53999", "20", "4", "", "", "19", "2", "", ""], ["", "UPF0568 protein C14orf166", "28", "Q9Y224", "18", "2", "", "", "5.7", "2", "", ""], ["", "Heterogeneous nuclear ribonucleoproteins A2/B1", "36", "P22626", "", "", "21", "12", "", "", "13", "7"], ["", "THO complex subunit 4/ALYREF", "27", "Q86V81", "10.9", "3", "", "", "10.9", "4", "", ""], ["", "Enz.", "Lactoylglutathione lyase", "21", "Q04760", "21.2", "2", "", "", "9.2", "2", "", ""], ["", "Alpha‐enolase", "47", "P06733", "17", "3", "13", "8", "17", "6", "6.9", "4"], ["", "Glyceraldehyde‐3‐phosphate dehydrogenase", "32", "P04406", "", "", "16", "7", "", "", "9.9", "4"]], "row_count": 26, "column_count": 13, "numeric_cells": 167, "header_rows": 4, "locator": "section[8]/table-wrap[1]#feb412454-tbl-0001"}}, {"id": "asset:table:pmid:29988566:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9204efd8666549b199cf29b0ceec735238fc85d4f39102956006a2f1868d4219", "bytes": 2683, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[30]/table-wrap[1]#feb412454-tbl-0002", "version": null, "note": "Antibodies used in SIKE interaction assays", "structure": {"pmcid": "PMC6026704", "section_index": 30, "section_title": "Immunoblot", "row_count": 35, "column_count": 3}, "table": {"label": "Table 2", "caption": "Antibodies used in SIKE interaction assays", "rows": [["Cytoskeletal protein immunoprecipitation"], ["Mouse anti‐GFP", "BioLegend, cat. #: MMS‐118P", "7.5 μg"], ["Rabbit anti‐mCherry", "Thermo Fisher Sci, cat. #: PA5‐34974", "7.5 μg"], ["Immunoblots"], ["Rabbit anti‐SIKE", "Sigma‐Aldrich, cat. #: HPA025726", "1 : 300"], ["Mouse anti‐FLAG‐HRP", "Sigma‐Aldrich, cat. #: A8592", "1 : 1000 (IP/IB)"], ["Mouse anti‐FLAG‐HRP", "Sigma‐Aldrich, cat. # 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For dsRNA‐stimulated samples, 21 h after transfection, cells were stimulated with 50 μg·mL−1 polyr", "ium for 3 h. Cells were harvested 24 h after transfection by washing from plate and pelleted by centri"], "order_basis": "paper_text_order:584", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["action network through affinity purification/mass spectrometry showed that SIKE formed interactions with cy", "ub, TBK1, to the cytoskeleton. DATABASE: The mass spectrometry proteomics data have been deposited to the P", "a premature stop codon following residue 78. Mass spectrometry samples Cells were seeded in triplicate on a", "radford method (Bio‐Rad, Hercules, CA, USA). 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