{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:01:29Z","timestamp":1760058089379,"version":"build-2065373602"},"reference-count":48,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,3,15]],"date-time":"2025-03-15T00:00:00Z","timestamp":1741996800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wilhelm Sander-Stiftung","award":["2016.115.1","2020.003.1"],"award-info":[{"award-number":["2016.115.1","2020.003.1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Infection of cells with the human cytomegalovirus (HCMV) triggers the expression of interferon-stimulated genes (ISGs). ISGs encode proteins with antiviral functions, such as inhibiting viral replication, promoting cell death of infected cells and enhancing immune responses. HCMV has evolved mechanisms to evade the antiviral effects of ISGs. The viral proteins encoded by the viral genes US7, US8, and US9 have been shown to interfere with interferon induction. US7 to US9 are embedded in a cluster of HCMV genes, termed US2 to US11. The individual members of this gene family interfere on multiple levels with innate and adaptive immune responses to HCMV infection. Using viral mutants with different deletions in US2 to US11, we addressed the question if genes other than US7 to US9 would also influence the IFN responses. Surprisingly, deletion of the complete US2 to US11 gene region led to reduced levels of selected ISGs. Cells infected with viruses in which individual US2 to US11 genes were deleted showed a less pronounced reduction of the selected ISGs. The experiments including RNA-seq analyses indicate that genes of the US2 to US11 gene family have a complex interaction with the IFN-ISG response which is likely regulated on the level of ISG protein stability. As US2\u2013US11 are dispensable for replication in cell culture, the genomic region was frequently used for the insertion of bacterial artificial chromosome vectors in the process of cloning the complete HCMV genome. The results shown here must be considered when viruses derived from BACs with US2\u2013US11 deletions are used and whether appropriate controls must be applied.<\/jats:p>","DOI":"10.3390\/v17030426","type":"journal-article","created":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T07:49:57Z","timestamp":1742197797000},"page":"426","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Deletion of the Human Cytomegalovirus US2 to US11 Gene Family Members Impairs the Type-I Interferon Response"],"prefix":"10.3390","volume":"17","author":[{"given":"Inessa","family":"Penner","sequence":"first","affiliation":[{"name":"Institute for Virology and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadine","family":"Kr\u00e4mer","sequence":"additional","affiliation":[{"name":"Institute for Virology and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia","family":"Hirsch","sequence":"additional","affiliation":[{"name":"Institute for Virology and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"B\u00fcscher","sequence":"additional","affiliation":[{"name":"Institute for Virology and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8915-891X","authenticated-orcid":false,"given":"Hanno","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institute for Virology and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bodo","family":"Plachter","sequence":"additional","affiliation":[{"name":"Institute for Virology and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Deng, Y., Agueda-Pinto, A., and Brune, W. (2024). No Time to Die: How Cytomegaloviruses Suppress Apoptosis, Necroptosis, and Pyroptosis. Viruses, 16.","DOI":"10.3390\/v16081272"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1007\/s00705-024-06080-w","article-title":"Human cytomegalovirus microRNAs: Strategies for immune evasion and viral latency","volume":"169","author":"Sabbaghian","year":"2024","journal-title":"Arch. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Muscolino, E., Luoto, L.M., and Brune, W. (2021). Viral Induced Protein Aggregation: A Mechanism of Immune Evasion. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22179624"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Diggins, N.L., Skalsky, R.L., and Hancock, M.H. (2021). Regulation of Latency and Reactivation by Human Cytomegalovirus miRNAs. Pathogens, 10.","DOI":"10.3390\/pathogens10020200"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Dell\u2019Oste, V., Biolatti, M., Galitska, G., Griffante, G., Gugliesi, F., Pasquero, S., Zingoni, A., Cerboni, C., and De Andrea, M. (2020). Tuning the Orchestra: HCMV vs. Innate Immunity. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00661"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Lim, E.Y., Jackson, S.E., and Wills, M.R. (2020). The CD4+ T Cell Response to Human Cytomegalovirus in Healthy and Immunocompromised People. Front. Cell Infect. Microbiol., 10.","DOI":"10.3389\/fcimb.2020.00202"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/s00018-024-05369-y","article-title":"The battle between host antiviral innate immunity and immune evasion by cytomegalovirus","volume":"81","author":"Li","year":"2024","journal-title":"Cell Mol. Life Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1007\/s12026-012-8304-8","article-title":"Diverse immune evasion strategies by human cytomegalovirus","volume":"54","author":"Noriega","year":"2012","journal-title":"Immunol. Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"4830","DOI":"10.1128\/jvi.69.8.4830-4841.1995","article-title":"Multiple independent loci within the human cytomegalovirus unique short region down-regulate expression of major histocompatibility complex class I heavy chains","volume":"69","author":"Jones","year":"1995","journal-title":"J. Virol."},{"key":"ref_10","first-page":"149","article-title":"Herpesvirus evasion of the immune system","volume":"232","author":"Johnson","year":"1998","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1126\/science.280.5361.248","article-title":"Viral strategies of immune evasion","volume":"280","author":"Ploegh","year":"1998","journal-title":"Science"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1038\/12478","article-title":"Cytomegalovirus US2 destroys two components of the MHC class II pathway, preventing recognition by CD4+ T cells","volume":"5","author":"Tomazin","year":"1999","journal-title":"Nat. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"10929","DOI":"10.1128\/JVI.76.21.10929-10941.2002","article-title":"Inhibition of HLA-DR assembly, transport, and loading by human cytomegalovirus glycoprotein US3: A novel mechanism for evading major histocompatibility complex class II antigen presentation","volume":"76","author":"Hegde","year":"2002","journal-title":"J. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4670","DOI":"10.1038\/s41467-019-12641-4","article-title":"HCMV-encoded US7 and US8 act as antagonists of innate immunity by distinctively targeting TLR-signaling pathways","volume":"10","author":"Park","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/s41467-017-02624-8","article-title":"Human cytomegalovirus-encoded US9 targets MAVS and STING signaling to evade type I interferon immune responses","volume":"9","author":"Choi","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5184","DOI":"10.1128\/jvi.65.10.5184-5189.1991","article-title":"A 15-kilobase-pair region of the human cytomegalovirus genome which includes US1 through US13 is dispensable for growth in cell culture","volume":"65","author":"Bogner","year":"1991","journal-title":"J. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2541","DOI":"10.1128\/jvi.66.4.2541-2546.1992","article-title":"A cluster of dispensable genes within the human cytomegalovirus genome short component: IRS1, US1 through US5, and the US6 family","volume":"66","author":"Jones","year":"1992","journal-title":"J. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"5860","DOI":"10.1128\/jvi.65.11.5860-5872.1991","article-title":"Replacement mutagenesis of the human cytomegalovirus genome: US10 and US11 gene products are nonessential","volume":"65","author":"Jones","year":"1991","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"8320","DOI":"10.1128\/JVI.73.10.8320-8329.1999","article-title":"Cloning of the human cytomegalovirus (HCMV) genome as an infectious bacterial artificial chromosome in Escherichia coli: A new approach for construction of HCMV mutants","volume":"73","author":"Borst","year":"1999","journal-title":"J. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1099\/vir.0.83286-0","article-title":"Cloning and sequencing of a highly productive, endotheliotropic virus strain derived from human cytomegalovirus TB40\/E. J","volume":"89 Pt 2","author":"Sinzger","year":"2008","journal-title":"J. Gen. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1128\/JVI.75.4.1870-1878.2001","article-title":"Human cytomegalovirus with IE-2 (UL122) deleted fails to express early lytic genes","volume":"75","author":"Marchini","year":"2001","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Schilling, E.M., Scherer, M., and Stamminger, T. (2021). Intrinsic Immune Mechanisms Restricting Human Cytomegalovirus Replication. Viruses, 13.","DOI":"10.3390\/v13020179"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Hsu, J.L., van den Boomen, D.J., Tomasec, P., Weekes, M.P., Antrobus, R., Stanton, R.J., Ruckova, E., Sugrue, D., Wilkie, G.S., and Davison, A.J. (2015). Plasma membrane profiling defines an expanded class of cell surface proteins selectively targeted for degradation by HCMV US2 in cooperation with UL141. PLoS Pathog., 11.","DOI":"10.1371\/journal.ppat.1004811"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.virol.2009.06.004","article-title":"Immune evasion proteins gpUS2 and gpUS11 of human cytomegalovirus incompletely protect infected cells from CD8 T cell recognition","volume":"391","author":"Besold","year":"2009","journal-title":"Virology"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2316","DOI":"10.1128\/jvi.76.5.2316-2328.2002","article-title":"Construction of a self-excisable bacterial artificial chromosome containing the human cytomegalovirus genome and mutagenesis of the diploid TRL\/IRL13 gene","volume":"76","author":"Yu","year":"2002","journal-title":"J. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1080\/15548627.2020.1732686","article-title":"Autophagy interferes with human cytomegalovirus genome replication, morphogenesis, and progeny release","volume":"17","author":"Zimmermann","year":"2020","journal-title":"Autophagy"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.molimm.2012.03.024","article-title":"Human cytomegalovirus US3 modulates destruction of MHC class I molecules","volume":"51","author":"Noriega","year":"2012","journal-title":"Mol. Immunol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e36","DOI":"10.1093\/nar\/gni035","article-title":"Simple and highly efficient BAC recombineering using galK selection","volume":"33","author":"Warming","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Penner, I., B\u00fcscher, N., Krauter, S., and Plachter, B. (2023). Subviral Dense Bodies of Human Cytomegalovirus Enhance Interferon-Beta Responses in Infected Cells and Impair Progeny Production. Viruses, 15.","DOI":"10.3390\/v15061333"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/0378-1119(82)90054-3","article-title":"Cloning of the complete human cytomegalovirus genome in cosmids","volume":"18","author":"Fleckenstein","year":"1982","journal-title":"Gene"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Behera, S., Catreux, S., Rossi, M., Truong, S., Huang, Z., Ruehle, M., Visvanath, A., Parnaby, G., Roddey, C., and Onuchic, V. (2024). Comprehensive genome analysis and variant detection at scale using DRAGEN. Nat. Biotechnol., Available online: https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC10802302\/.","DOI":"10.1038\/s41587-024-02382-1"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15.","DOI":"10.1186\/s13059-014-0550-8"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1099\/vir.0.045682-0","article-title":"Suppression of CD8+ T-cell recognition in the immediate-early phase of human cytomegalovirus infection","volume":"94","author":"Hesse","year":"2013","journal-title":"J. Gen. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"13985","DOI":"10.1073\/pnas.94.25.13985","article-title":"Use of differential display analysis to assess the effect of human cytomegalovirus infection on the accumulation of cellular RNAs: Induction of interferon-responsive RNAs","volume":"94","author":"Zhu","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3607","DOI":"10.1128\/MCB.19.5.3607","article-title":"Engagement of the cellular receptor for glycoprotein B of human cytomegalovirus activates the interferon-responsive pathway","volume":"19","author":"Boyle","year":"1999","journal-title":"Mol. Cell Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e02683-20","DOI":"10.1128\/mBio.02683-20","article-title":"The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4\/UL5 Transcripts","volume":"12","author":"Stempel","year":"2021","journal-title":"mBio"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.meegid.2018.06.025","article-title":"Modulation of the innate immune response by human cytomegalovirus","volume":"64","author":"Biolatti","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"001980","DOI":"10.1099\/jgv.0.001980","article-title":"HCMV US2 co-opts TRC8 to degrade the endoplasmic reticulum-resident protein LMAN2L. J","volume":"105","author":"Hunter","year":"2024","journal-title":"Gen. Virol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1084\/jem.185.2.363","article-title":"The HCMV gene products US11 and US2 differ in their ability to attack allelic forms of murine major histocompatibility complex (MHC) class I heavy chains","volume":"185","author":"Machold","year":"1997","journal-title":"J. Exp. Med."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2970","DOI":"10.1128\/jvi.71.4.2970-2979.1997","article-title":"Human cytomegalovirus US2 destabilizes major histocompatibility complex class I heavy chains","volume":"71","author":"Jones","year":"1997","journal-title":"J. Virol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nmeth.4631","article-title":"Improved Ribo-seq enables identification of cryptic translation events","volume":"15","author":"Erhard","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1126\/science.1227919","article-title":"Decoding human cytomegalovirus","volume":"338","author":"Weisburd","year":"2012","journal-title":"Science"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1038\/ni.2097","article-title":"Human cytomegalovirus microRNA miR-US4-1 inhibits CD8(+) T cell responses by targeting the aminopeptidase ERAP1","volume":"12","author":"Kim","year":"2011","journal-title":"Nat. Immunol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.molcel.2021.11.026","article-title":"Life of RISC: Formation, action, and degradation of RNA-induced silencing complex","volume":"82","author":"Iwakawa","year":"2022","journal-title":"Mol. Cell"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"205","DOI":"10.2144\/000114606","article-title":"A TB40\/E-derived human cytomegalovirus genome with an intact US-gene region and a self-excisable BAC cassette for immunological research","volume":"63","author":"Sampaio","year":"2017","journal-title":"Biotechniques"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e49894","DOI":"10.7554\/eLife.49894","article-title":"Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions","volume":"8","author":"Nobre","year":"2019","journal-title":"Elife"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/3\/426\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:54:24Z","timestamp":1760028864000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/3\/426"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,15]]},"references-count":48,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["v17030426"],"URL":"https:\/\/doi.org\/10.3390\/v17030426","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2025,3,15]]}}}