{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T16:32:55Z","timestamp":1783960375276,"version":"3.55.0"},"reference-count":118,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T00:00:00Z","timestamp":1751241600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005721","name":"Bielefeld University","doi-asserted-by":"publisher","award":["n.a."],"award-info":[{"award-number":["n.a."]}],"id":[{"id":"10.13039\/501100005721","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Recombinant adeno-associated virus (rAAV) is the leading vector for gene replacement therapy; however, the roles and regulation of host proteins in rAAV production remain incompletely understood. In this comparative proteomic analysis, we focused on proteins in the nucleus, the epicenter of DNA uptake, transcription, capsid assembly, and packaging. HEK-293 cells were analyzed under the following three conditions: (i) untransfected, (ii) mock-transfected with the ITR and an unrelated plasmid, and (iii) triple-transfected with rAAV2 production plasmids. Cells were harvested at 24 and 72 h post-transfection, and nuclear fractions were processed using filter-aided sample preparation (FASP) followed by nano-scale liquid chromatography\u2013tandem mass spectrometry (nLC-Orbitrap MS\/MS). Across all samples, we identified 3384 proteins, revealing significant regulatory changes associated with transfection and rAAV production. Transfection alone accounted for some of the most substantial proteomic shifts, while rAAV production induced diverse regulatory changes linked to cell cycle control, structure, and metabolism. STRING analysis of significantly regulated proteins also identified an enrichment of those associated with the Gene Ontology (GO) term \u2018response to virus\u2019. Additionally, we examined proteins with reported relation to adenoviral components. Our findings help to unravel the complexity of rAAV production, identify interesting targets for further investigation, and may contribute to improving rAAV yield.<\/jats:p>","DOI":"10.3390\/ijms26136315","type":"journal-article","created":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T06:56:54Z","timestamp":1751353014000},"page":"6315","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Nuclear Fraction Proteome Analyses During rAAV Production of AAV2-Plasmid-Transfected HEK-293 Cells"],"prefix":"10.3390","volume":"26","author":[{"given":"Susanne K.","family":"Golm","sequence":"first","affiliation":[{"name":"Department of Biotechnology, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany"},{"name":"Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany"},{"name":"Cell Culture Technology, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0118-0990","authenticated-orcid":false,"given":"Raimund","family":"Hoffrogge","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany"},{"name":"Cell Culture Technology, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany"},{"name":"Center for Biotechnology, Bielefeld University, 33501 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7914-0625","authenticated-orcid":false,"given":"Kristian M.","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany"},{"name":"Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,30]]},"reference":[{"key":"ref_1","unstructured":"(2024, July 08). Glybera. Available online: https:\/\/www.ema.europa.eu\/en\/medicines\/human\/EPAR\/glybera."},{"key":"ref_2","unstructured":"(2024, July 11). Luxturna, Available online: https:\/\/www.fda.gov\/vaccines-blood-biologics\/cellular-gene-therapy-products\/luxturna."},{"key":"ref_3","unstructured":"(2024, July 08). Zolgensma, Available online: https:\/\/www.fda.gov\/vaccines-blood-biologics\/zolgensma."},{"key":"ref_4","unstructured":"(2024, July 09). Hemgenix, Available online: https:\/\/www.fda.gov\/vaccines-blood-biologics\/vaccines\/hemgenix."},{"key":"ref_5","unstructured":"(2025, January 15). Upstaza. Available online: https:\/\/www.ema.europa.eu\/en\/medicines\/human\/EPAR\/upstaza."},{"key":"ref_6","unstructured":"(2024, July 08). Roctavian, Available online: https:\/\/www.fda.gov\/vaccines-blood-biologics\/roctavian."},{"key":"ref_7","unstructured":"(2024, July 09). Elevidys, Available online: https:\/\/www.fda.gov\/vaccines-blood-biologics\/tissue-tissue-products\/elevidys."},{"key":"ref_8","unstructured":"(2024, July 11). Beqvez, Available online: https:\/\/www.fda.gov\/vaccines-blood-biologics\/cellular-gene-therapy-products\/beqvez."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1099\/0022-1317-36-1-59","article-title":"Characteristics of a Human Cell Line Transformed by DNA from Human Adenovirus Type 5","volume":"36","author":"Russell","year":"1977","journal-title":"J. Gen. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"7673","DOI":"10.1038\/sj.onc.1209040","article-title":"Recent Lessons in Gene Expression, Cell Cycle Control, and Cell Biology from Adenovirus","volume":"24","author":"Berk","year":"2005","journal-title":"Oncogene"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Aponte-Ubillus, J.J., Barajas, D., Sterling, H., Aghajanirefah, A., Bardliving, C., Peltier, J., Shamlou, P., Roy, M., and Gold, D. (2020). Proteome Profiling and Vector Yield Optimization in a Recombinant Adeno-associated Virus-producing Yeast Model. Microbiologyopen, 9.","DOI":"10.1002\/mbo3.1136"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3570","DOI":"10.1016\/j.ymthe.2022.11.001","article-title":"Vector Genome Loss and Epigenetic Modifications Mediate Decline in Transgene Expression of AAV5 Vectors Produced in Mammalian and Insect Cells","volume":"30","author":"Handyside","year":"2022","journal-title":"Mol. Ther."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Merten, O.-W. (2024). Development of Stable Packaging and Producer Cell Lines for the Production of AAV Vectors. Microorganisms, 12.","DOI":"10.3390\/microorganisms12020384"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1002\/bit.28578","article-title":"Recombinant Adeno-associated Virus Production Evaluation in Chinese Hamster Ovary Cells","volume":"121","author":"Cao","year":"2024","journal-title":"Biotechnol. Bioeng."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Le, D.T., Radukic, M.T., and M\u00fcller, K.M. (2019). Adeno-Associated Virus Capsid Protein Expression in Escherichia Coli and Chemically Defined Capsid Assembly. Sci. Rep., 9.","DOI":"10.1038\/s41598-019-54928-y"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3601","DOI":"10.1021\/acssynbio.2c00451","article-title":"Synthesis and Concomitant Assembly of Adeno-Associated Virus-like Particles in Escherichia Coli","volume":"11","author":"Le","year":"2022","journal-title":"ACS Synth. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Strasser, L., Boi, S., Guapo, F., Donohue, N., Barron, N., Rainbow-Fletcher, A., and Bones, J. (2021). Proteomic Landscape of Adeno-Associated Virus (AAV)-Producing HEK293 Cells. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222111499"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.omtm.2023.01.002","article-title":"Production of rAAV by Plasmid Transfection Induces Antiviral and Inflammatory Responses in Suspension HEK293 Cells","volume":"28","author":"Chung","year":"2023","journal-title":"Mol. Ther.\u2014Methods Clin. Dev."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Wang, Y., Fu, Q., Lee, Y.S., Sha, S., and Yoon, S. (2023). Transcriptomic Features Reveal Molecular Signatures Associated with Recombinant Adeno-associated Virus Production in HEK293 Cells. Biotechnol. Prog., 39.","DOI":"10.1002\/btpr.3346"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Lu, M., Lee, Z., and Hu, W. (2024). Multi-omics Kinetic Analysis of Recombinant Adeno-associated Virus Production by Plasmid Transfection of HEK293 Cells. Biotechnol. Prog., 40.","DOI":"10.1002\/btpr.3428"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Lin, Y.-C., Lu, M., Cai, W., and Hu, W.-S. (2024). Comparative Transcriptomic and Proteomic Kinetic Analysis of Adeno-Associated Virus Production Systems. Appl. Microbiol. Biotechnol., 108.","DOI":"10.1007\/s00253-024-13203-5"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"101278","DOI":"10.1016\/j.omtm.2024.101278","article-title":"Temporal Insights into Molecular and Cellular Responses during rAAV Production in HEK293T Cells","volume":"32","author":"Patra","year":"2024","journal-title":"Mol. Ther.\u2014Methods Clin. Dev."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Wang, Y., Fu, Q., Park, S.Y., Lee, Y.S., Park, S.-Y., Lee, D.-Y., and Yoon, S. (2024). Decoding Cellular Mechanism of Recombinant Adeno-Associated Virus (rAAV) and Engineering Host-Cell Factories toward Intensified Viral Vector Manufacturing. Biotechnol. Adv., 71.","DOI":"10.1016\/j.biotechadv.2024.108322"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Gurazada, S.G.R., Kennedy, H.M., Braatz, R.D., Mehrman, S.J., Polson, S.W., and Rombel, I.T. (2025). HEK-Omics: The Promise of Omics to Optimize HEK293 for Recombinant Adeno-Associated Virus (rAAV) Gene Therapy Manufacturing. Biotechnol. Adv., 79.","DOI":"10.1016\/j.biotechadv.2024.108506"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1128\/jvi.71.2.1341-1352.1997","article-title":"Subcellular Compartmentalization of Adeno-Associated Virus Type 2 Assembly","volume":"71","author":"Wistuba","year":"1997","journal-title":"J. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1089\/hum.2020.069","article-title":"Adeno-Associated Virus Genome Interactions Important for Vector Production and Transduction","volume":"31","author":"Maurer","year":"2020","journal-title":"Hum. Gene Ther."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Golm, S.K., H\u00fcbner, W., and M\u00fcller, K.M. (2023). Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses, 15.","DOI":"10.3390\/v15051174"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/s41392-024-01934-w","article-title":"The JAK-STAT Pathway: From Structural Biology to Cytokine Engineering","volume":"9","author":"Lv","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"13316","DOI":"10.1074\/jbc.M609798200","article-title":"Leptin-Induced Growth Stimulation of Breast Cancer Cells Involves Recruitment of Histone Acetyltransferases and Mediator Complex to CYCLIN D1 Promoter via Activation of Stat3","volume":"282","author":"Saxena","year":"2007","journal-title":"J. Biol. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"13505","DOI":"10.1074\/jbc.R000025200","article-title":"CREB-Binding Protein and P300 in Transcriptional Regulation","volume":"276","author":"Vo","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/S1097-2765(04)00094-2","article-title":"Acetylation of the C Terminus of Ku70 by CBP and PCAF Controls Bax-Mediated Apoptosis","volume":"13","author":"Cohen","year":"2004","journal-title":"Mol. Cell"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1111\/imm.13318","article-title":"Cytoplasmic-translocated Ku70 Senses Intracellular DNA and Mediates Interferon-lambda1 Induction","volume":"163","author":"Sui","year":"2021","journal-title":"Immunology"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1128\/JVI.01939-08","article-title":"Identification of Cellular Proteins That Interact with the Adeno-Associated Virus Rep Protein","volume":"83","author":"Nash","year":"2009","journal-title":"J. Virol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1128\/JVI.00318-09","article-title":"Adeno-Associated Virus Replication Induces a DNA Damage Response Coordinated by DNA-Dependent Protein Kinase","volume":"83","author":"Schwartz","year":"2009","journal-title":"J. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.virol.2009.06.005","article-title":"Adeno-Associated Virus and Adenovirus Coinfection Induces a Cellular DNA Damage and Repair Response via Redundant Phosphatidylinositol 3-like Kinase Pathways","volume":"392","author":"Collaco","year":"2009","journal-title":"Virology"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e03528-22","DOI":"10.1128\/mbio.03528-22","article-title":"Adeno-Associated Virus Monoinfection Induces a DNA Damage Response and DNA Repair That Contributes to Viral DNA Replication","volume":"14","author":"Ning","year":"2023","journal-title":"mBio"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Bresch, A.-M., Yerich, N., Wang, R., and Sperry, A.O. (2020). The PP1 Regulator PPP1R2 Coordinately Regulates AURKA and PP1 to Control Centrosome Phosphorylation and Maintain Central Spindle Architecture. BMC Mol. Cell Biol., 21.","DOI":"10.1186\/s12860-020-00327-5"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2589","DOI":"10.1016\/j.cellsig.2015.08.007","article-title":"Protein Phosphatase 1 Is a Key Player in Nuclear Events","volume":"27","author":"Rebelo","year":"2015","journal-title":"Cell. Signal."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13008-018-0040-6","article-title":"The Functional Diversity of Aurora Kinases: A Comprehensive Review","volume":"13","author":"Willems","year":"2018","journal-title":"Cell Div."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.ceca.2016.03.002","article-title":"Identification of EFHD1 as a Novel Ca2+ Sensor for Mitoflash Activation","volume":"59","author":"Hou","year":"2016","journal-title":"Cell Calcium"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Mun, S.A., Park, J., Park, K.R., Lee, Y., Kang, J.Y., Park, T., Jin, M., Yang, J., Jun, C.-D., and Eom, S.H. (2021). Structural and Biochemical Characterization of EFhd1\/Swiprosin-2, an Actin-Binding Protein in Mitochondria. Front. Cell Dev. Biol., 8.","DOI":"10.3389\/fcell.2020.628222"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1006\/bbrc.2001.5624","article-title":"Characterization of HRG22, a Human Homologue of the Putative Tumor Suppressor Gene HIC1","volume":"287","author":"Deltour","year":"2001","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1980","DOI":"10.1182\/blood.2023023399","article-title":"Let-7 miRNAs Repress HIC2 to Regulate BCL11A Transcription and Hemoglobin Switching","volume":"143","author":"Huang","year":"2024","journal-title":"Blood"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"4536","DOI":"10.1016\/j.asjsur.2023.04.145","article-title":"HIC2 Promotes Cell Cycle Transitions by Upregulating CDK1 Expression in Glioblastoma","volume":"46","author":"Lu","year":"2023","journal-title":"Asian J. Surg."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"4890","DOI":"10.1128\/MCB.22.13.4890-4901.2002","article-title":"The Human Candidate Tumor Suppressor Gene HIC1 Recruits CtBP through a Degenerate GLDLSKK Motif","volume":"22","author":"Deltour","year":"2002","journal-title":"Mol. Cell. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1038\/s41594-021-00693-4","article-title":"Cryo-EM Structures of Human RNA Polymerase I","volume":"28","author":"Misiaszek","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e1782","DOI":"10.1002\/wrna.1782","article-title":"The Pol III Transcriptome: Basic Features, Recurrent Patterns, and Emerging Roles in Cancer","volume":"14","author":"Zhou","year":"2023","journal-title":"WIREs RNA"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1159\/000504174","article-title":"Expression and Clinical Significance of POLR1D in Colorectal Cancer","volume":"98","author":"Tian","year":"2020","journal-title":"Oncology"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s13073-020-0719-6","article-title":"Cell-Free DNA Analysis Reveals POLR1D-Mediated Resistance to Bevacizumab in Colorectal Cancer","volume":"12","author":"Zhou","year":"2020","journal-title":"Genome Med."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Lee, A., Hakuno, F., Northcott, P., Pessin, J.E., and Adcock, M.R. (2013). Nexilin, a Cardiomyopathy-Associated F-Actin Binding Protein, Binds and Regulates IRS1 Signaling in Skeletal Muscle Cells. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0055634"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Shao, Y., Liu, C., Liao, H.-K., Zhang, R., Yuan, B., Yang, H., Li, R., Zhu, S., Fang, X., and Rodriguez Esteban, C. (2024). In Vivo Rescue of Genetic Dilated Cardiomyopathy by Systemic Delivery of Nexilin. Genome Biol., 25.","DOI":"10.1186\/s13059-024-03283-x"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/j.chom.2011.10.014","article-title":"Adeno-Associated Virus 2 Infection Requires Endocytosis through the CLIC\/GEEC Pathway","volume":"10","author":"Nonnenmacher","year":"2011","journal-title":"Cell Host Microbe"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1016\/j.ajhg.2010.10.002","article-title":"Mutations in NEXN, a Z-Disc Gene, Are Associated with Hypertrophic Cardiomyopathy","volume":"87","author":"Wang","year":"2010","journal-title":"Am. J. Hum. Genet."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Kreycy, N., Gotzian, C., Fleming, T., Flechtenmacher, C., Grabe, N., Plinkert, P., Hess, J., and Zaoui, K. (2017). Glyoxalase 1 Expression Is Associated with an Unfavorable Prognosis of Oropharyngeal Squamous Cell Carcinoma. BMC Cancer, 17.","DOI":"10.1186\/s12885-017-3367-5"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Tang, X., Liu, L., Cai, D., Gou, S., Hao, S., Li, Y., Shen, J., Chen, Y., and Zhao, Y. (2024). GLO1 Regulates Hepatocellular Carcinoma Proliferation and Migration through the Cell Cycle Pathway. BMC Cancer, 24.","DOI":"10.1186\/s12885-024-12927-x"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S1570-9639(02)00444-2","article-title":"Structures, Functions and Molecular Evolution of the Penta-EF-Hand Ca2+-Binding Proteins","volume":"1600","author":"Maki","year":"2002","journal-title":"Biochim. Biophys. Acta BBA\u2014Proteins Proteom."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"14053","DOI":"10.1074\/jbc.M008649200","article-title":"Peflin and ALG-2, Members of the Penta-EF-Hand Protein Family, Form a Heterodimer That Dissociates in a Ca2+-Dependent Manner","volume":"276","author":"Kitaura","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1006\/bbrc.2002.6600","article-title":"ALG-2 Interacts with the Amino-Terminal Domain of Annexin XI in a Ca2+-Dependent Manner","volume":"291","author":"Satoh","year":"2002","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1111\/j.1600-0854.2004.00210.x","article-title":"Annexin\u2013Actin Interactions","volume":"5","author":"Hayes","year":"2004","journal-title":"Traffic"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1007\/s11427-011-4204-8","article-title":"Structure and Function of ALG-2, a Penta-EF-Hand Calcium-Dependent Adaptor Protein","volume":"54","author":"Maki","year":"2011","journal-title":"Sci. China Life Sci."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"4981","DOI":"10.1074\/jbc.M114.592089","article-title":"A New Role for Annexin A11 in the Early Secretory Pathway via Stabilizing Sec31A Protein at the Endoplasmic Reticulum Exit Sites (ERES)","volume":"290","author":"Shibata","year":"2015","journal-title":"J. Biol. Chem."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Rayl, M., Truitt, M., Held, A., Sargeant, J., Thorsen, K., and Hay, J.C. (2016). Penta-EF-Hand Protein Peflin Is a Negative Regulator of ER-To-Golgi Transport. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0157227"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Perdreau-Dahl, H., Progida, C., Barfeld, S.J., Guldsten, H., Thiede, B., Arntzen, M., Bakke, O., Mills, I.G., Krauss, S., and Morth, J.P. (2020). Sj\u00f6gren Syndrome\/Scleroderma Autoantigen 1 Is a Direct Tankyrase Binding Partner in Cancer Cells. Commun. Biol., 3.","DOI":"10.1038\/s42003-020-0851-2"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"573","DOI":"10.2174\/0929866511320050011","article-title":"Functional and Structural Analysis of the Conserved EFhd2 Protein","volume":"20","author":"Del","year":"2013","journal-title":"Protein Pept. Lett."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"2492","DOI":"10.1038\/s41467-022-30167-0","article-title":"Calcium Bursts Allow Rapid Reorganization of EFhD2\/Swip-1 Cross-Linked Actin Networks in Epithelial Wound Closure","volume":"13","author":"Lehne","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"3266","DOI":"10.1242\/jcs.083907","article-title":"Drosophila Swiprosin-1\/EFHD2 Accumulates at the Prefusion Complex Stage during Drosophila Myoblast Fusion","volume":"124","author":"Griemert","year":"2011","journal-title":"J. Cell Sci."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"jcs260366","DOI":"10.1242\/jcs.260366","article-title":"Swip-1 Promotes Exocytosis of Glue Granules in the Exocrine Drosophila Salivary Gland","volume":"136","author":"Lehne","year":"2023","journal-title":"J. Cell Sci."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1107\/S2052252523001501","article-title":"Structural and Biochemical Insights into Zn2+ -Bound EF-Hand Proteins, EFhd1 and EFhd2","volume":"10","author":"Mun","year":"2023","journal-title":"IUCrJ"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Tworig, J., Grafton, F., H\u00f6rer, M., Reid, C.A., and Mandegar, M.A. (2024). Transcriptomics-Informed Pharmacology Identifies Epigenetic and Cell Cycle Regulators as Enhancers of AAV Production. bioRxiv.","DOI":"10.1101\/2024.06.14.599118"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1002\/cbf.3600","article-title":"Novel Nucleolar Localization of Clusterin and Its Associated Functions in Human Oral Cancers: An in Vitro and in Silico Analysis","volume":"39","author":"Kadam","year":"2021","journal-title":"Cell Biochem. Funct."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"34","DOI":"10.32607\/actanaturae.11041","article-title":"Modification of Nuclear Compartments and the 3D Genome in the Course of a Viral Infection","volume":"12","author":"Razin","year":"2020","journal-title":"Acta Naturae"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1128\/JVI.78.1.389-398.2004","article-title":"Spatial and Temporal Organization of Adeno-Associated Virus DNA Replication in Live Cells","volume":"78","author":"Fraefel","year":"2004","journal-title":"J. Virol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1083\/jcb.131.1.45","article-title":"Targeting of Adenovirus E1A and E4-ORF3 Proteins to Nuclear Matrix-Associated PML Bodies","volume":"131","author":"Carvalho","year":"1995","journal-title":"J. Cell Biol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"5137","DOI":"10.1128\/JVI.73.6.5137-5143.1999","article-title":"Viral Immediate-Early Proteins Abrogate the Modification by SUMO-1 of PML and Sp100 Proteins, Correlating with Nuclear Body Disruption","volume":"73","author":"Dejean","year":"1999","journal-title":"J. Virol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1016\/j.celrep.2019.04.020","article-title":"Conserved Herpesvirus Protein Kinases Target SAMHD1 to Facilitate Virus Replication","volume":"28","author":"Zhang","year":"2019","journal-title":"Cell Rep."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Chamontin, C., Bossis, G., Nisole, S., Arhel, N.J., and Maarifi, G. (2021). Regulation of Viral Restriction by Post-Translational Modifications. Viruses, 13.","DOI":"10.3390\/v13112197"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Valdez, F., Salvador, J., Palermo, P.M., Mohl, J.E., Hanley, K.A., Watts, D., and Llano, M. (2019). Schlafen 11 Restricts Flavivirus Replication. J. Virol., 93.","DOI":"10.1128\/JVI.00104-19"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"e2108173119","DOI":"10.1073\/pnas.2108173119","article-title":"Human Cytomegalovirus Protein RL1 Degrades the Antiviral Factor SLFN11 via Recruitment of the CRL4 E3 Ubiquitin Ligase Complex","volume":"119","author":"Nightingale","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"94","DOI":"10.15252\/embr.201540964","article-title":"SLFN 11 Inhibits Checkpoint Maintenance and Homologous Recombination Repair","volume":"17","author":"Mu","year":"2016","journal-title":"EMBO Rep."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.molcel.2018.01.012","article-title":"SLFN11 Blocks Stressed Replication Forks Independently of ATR","volume":"69","author":"Murai","year":"2018","journal-title":"Mol. Cell"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"4137","DOI":"10.1016\/j.celrep.2020.02.117","article-title":"Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress","volume":"30","author":"Murai","year":"2020","journal-title":"Cell Rep."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/nature11433","article-title":"Codon-Usage-Based Inhibition of HIV Protein Synthesis by Human Schlafen 11","volume":"491","author":"Li","year":"2012","journal-title":"Nature"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1016\/j.cell.2017.06.042","article-title":"Methyltransferase SETD2-Mediated Methylation of STAT1 Is Critical for Interferon Antiviral Activity","volume":"170","author":"Chen","year":"2017","journal-title":"Cell"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.chembiol.2021.10.008","article-title":"An Antibody-Based Proximity Labeling Map Reveals Mechanisms of SARS-CoV-2 Inhibition of Antiviral Immunity","volume":"29","author":"Zhang","year":"2022","journal-title":"Cell Chem. Biol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1038\/nsmb.2123","article-title":"Splicing Enhances Recruitment of Methyltransferase HYPB\/Setd2 and Methylation of Histone H3 Lys36","volume":"18","author":"Grosso","year":"2011","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"7750","DOI":"10.1093\/nar\/gkr470","article-title":"PDE12 Removes Mitochondrial RNA Poly(A) Tails and Controls Translation in Human Mitochondria","volume":"39","author":"Rorbach","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"19681","DOI":"10.1074\/jbc.M115.653113","article-title":"The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors","volume":"290","author":"Wood","year":"2015","journal-title":"J. Biol. Chem."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"e02411-16","DOI":"10.1128\/JVI.02411-16","article-title":"The ATP-Dependent RNA Helicase DDX3X Modulates Herpes Simplex Virus 1 Gene Expression","volume":"91","author":"Khadivjam","year":"2017","journal-title":"J. Virol."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Atkinson, S.C., Heaton, S.M., Audsley, M.D., Kleifeld, O., and Borg, N.A. (2021). TRIM25 and DEAD-Box RNA Helicase DDX3X Cooperate to Regulate RIG-I-Mediated Antiviral Immunity. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22169094"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Niu, Q., Cheng, Y., Wang, H., Yan, Y., and Sun, J. (2018). Chicken DDX3X Activates IFN-b via the chSTING-chIRF7-IFN-b Signaling Axis. Front. Immunol., 10.","DOI":"10.3389\/fimmu.2019.00822"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"5462","DOI":"10.1128\/JVI.03197-14","article-title":"Dynamic Interaction of Stress Granules, DDX3X, and IKK-\u03b1 Mediates Multiple Functions in Hepatitis C Virus Infection","volume":"89","author":"Pene","year":"2015","journal-title":"J Virol"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"5043","DOI":"10.1021\/jm800332m","article-title":"Ring Expanded Nucleoside Analogues Inhibit RNA Helicase and Intracellular Human Immunodeficiency Virus Type 1 Replication","volume":"51","author":"Yedavalli","year":"2008","journal-title":"J. Med. Chem."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/35023595","article-title":"Hsp27 Negatively Regulates Cell Death by Interacting with Cytochrome c","volume":"2","author":"Bruey","year":"2000","journal-title":"Nat. Cell Biol."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"45770","DOI":"10.1074\/jbc.M207485200","article-title":"Modulation of Heat-Shock Protein 27 (Hsp27) Anti-Apoptotic Activity by Methylglyoxal Modification","volume":"277","author":"Sakamoto","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"12305","DOI":"10.1074\/jbc.M801291200","article-title":"Hsp27 Inhibits Bax Activation and Apoptosis via a Phosphatidylinositol 3-Kinase-Dependent Mechanism","volume":"283","author":"Havasi","year":"2008","journal-title":"J. Biol. Chem."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/s40588-020-00150-8","article-title":"TRIM Proteins in Host Defense and Viral Pathogenesis","volume":"7","author":"Giraldo","year":"2020","journal-title":"Curr. Clin. Microbiol. Rep."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"e00833-17","DOI":"10.1128\/JVI.00833-17","article-title":"The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication","volume":"91","author":"Bharaj","year":"2017","journal-title":"J. Virol."},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Van Tol, S., Kalveram, B., Ilinykh, P.A., Ronk, A., Huang, K., Aguilera-Aguirre, L., Bharaj, P., Hage, A., Atkins, C., and Giraldo, M.I. (2022). Ubiquitination of Ebola Virus VP35 at Lysine 309 Regulates Viral Transcription and Assembly. PLoS Pathog., 18.","DOI":"10.1371\/journal.ppat.1010532"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"3349","DOI":"10.1038\/s41467-018-05559-w","article-title":"ZCCHC3 Is a Co-Sensor of cGAS for dsDNA Recognition in Innate Immune Response","volume":"9","author":"Lian","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1016\/j.immuni.2018.08.014","article-title":"The Zinc-Finger Protein ZCCHC3 Binds RNA and Facilitates Viral RNA Sensing and Activation of the RIG-I-like Receptors","volume":"49","author":"Lian","year":"2018","journal-title":"Immunity"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"198876","DOI":"10.1016\/j.virusres.2022.198876","article-title":"Proteomic Analysis Reveals Zinc-Finger CCHC-Type Containing Protein 3 as a Factor Inhibiting Virus Infection by Promoting Innate Signaling","volume":"319","author":"Chen","year":"2022","journal-title":"Virus Res."},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Hoter, A., El-Sabban, M.E., and Naim, H.Y. (2018). The HSP90 Family: Structure, Regulation, Function, and Implications in Health and Disease. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19092560"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"e102666","DOI":"10.7554\/eLife.102666","article-title":"The Known Unknowns of the Hsp90 Chaperone","volume":"13","author":"Silbermann","year":"2024","journal-title":"eLife"},{"key":"ref_104","doi-asserted-by":"crossref","unstructured":"Lubkowska, A., Pluta, W., Stro\u0144ska, A., and Lalko, A. (2021). Role of Heat Shock Proteins (HSP70 and HSP90) in Viral Infection. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22179366"},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Dietmair, S., Hodson, M.P., Quek, L.-E., Timmins, N.E., Gray, P., and Nielsen, L.K. (2012). A Multi-Omics Analysis of Recombinant Protein Production in Hek293 Cells. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0043394"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1007\/s13238-020-00729-3","article-title":"Dephosphorylation of cGAS by PPP6C Impairs Its Substrate Binding Activity and Innate Antiviral Response","volume":"11","author":"Li","year":"2020","journal-title":"Protein Cell"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"e01728-20","DOI":"10.1128\/mBio.01728-20","article-title":"PPP6C Negatively Regulates STING-Dependent Innate Immune Responses","volume":"11","author":"Ni","year":"2020","journal-title":"mBio"},{"key":"ref_108","doi-asserted-by":"crossref","unstructured":"Oshiumi, H. (2020). Recent Advances and Contradictions in the Study of the Individual Roles of Ubiquitin Ligases That Regulate RIG-I-Like Receptor-Mediated Antiviral Innate Immune Responses. Front. Immunol., 11.","DOI":"10.3389\/fimmu.2020.01296"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"8340","DOI":"10.1128\/JVI.00711-09","article-title":"The Adenovirus E4orf4 Protein Induces G2\/M Arrest and Cell Death by Blocking Protein Phosphatase 2A Activity Regulated by the B55 Subunit","volume":"83","author":"Li","year":"2009","journal-title":"J. Virol."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"7556","DOI":"10.1128\/jvi.67.12.7556-7560.1993","article-title":"Adenovirus E4orf4 Protein Binds to Protein Phosphatase 2A, and the Complex Down Regulates ElA-Enhanced junB Transcription","volume":"67","author":"Kleinberger","year":"1993","journal-title":"J. Virol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"9381","DOI":"10.1128\/JVI.00791-08","article-title":"Adenovirus E4orf4 Protein Downregulates MYC Expression through Interaction with the PP2A-B55 Subunit","volume":"82","author":"Sharf","year":"2008","journal-title":"J. Virol."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.virol.2011.05.017","article-title":"The Adenovirus E4 11 k Protein Binds and Relocalizes the Cytoplasmic P-Body Component Ddx6 to Aggresomes","volume":"417","author":"Greer","year":"2011","journal-title":"Virology"},{"key":"ref_113","doi-asserted-by":"crossref","unstructured":"Huang, J.-H., Ku, W.-C., Chen, Y.-C., Chang, Y.-L., and Chu, C.-Y. (2017). Dual Mechanisms Regulate the Nucleocytoplasmic Localization of Human DDX6. Sci. Rep., 7.","DOI":"10.1038\/srep42853"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13008-016-0016-3","article-title":"The Role of Cullin 5-Containing Ubiquitin Ligases","volume":"11","author":"Okumura","year":"2016","journal-title":"Cell Div."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nrm3047","article-title":"The MRE11 Complex: Starting from the Ends","volume":"12","author":"Stracker","year":"2011","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_116","doi-asserted-by":"crossref","unstructured":"Radukic, M.T., Le, D.T., Krassuski, T., Borchert, P., Leach, D.R.F., and M\u00fcller, K.M. (2024). Degradation and Stable Maintenance of AAV Inverted Terminal Repeats in E. coli. bioRxiv.","DOI":"10.1101\/2024.06.03.597121"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/nmeth.1322","article-title":"Universal Sample Preparation Method for Proteome Analysis","volume":"6","author":"Zougman","year":"2009","journal-title":"Nat. Methods"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"D543","DOI":"10.1093\/nar\/gkae1011","article-title":"The PRIDE Database at 20 Years: 2025 Update","volume":"53","author":"Bandla","year":"2025","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/13\/6315\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:01:53Z","timestamp":1760032913000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/13\/6315"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,30]]},"references-count":118,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["ijms26136315"],"URL":"https:\/\/doi.org\/10.3390\/ijms26136315","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,30]]}}}