{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T13:25:52Z","timestamp":1779888352862,"version":"3.53.1"},"reference-count":64,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2019,10,11]],"date-time":"2019-10-11T00:00:00Z","timestamp":1570752000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["281191-VIRMUT"],"award-info":[{"award-number":["281191-VIRMUT"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","award":["BFU2013-41329"],"award-info":[{"award-number":["BFU2013-41329"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Most DNA viruses exhibit relatively low rates of spontaneous mutation. However, the molecular mechanisms underlying DNA virus genetic stability remain unclear. In principle, mutation rates should not depend solely on polymerase fidelity, but also on factors such as DNA damage and repair efficiency. Most eukaryotic DNA viruses interact with the cellular DNA damage response (DDR), but the role of DDR pathways in preventing mutations in the virus has not been tested empirically. To address this goal, we serially transferred human adenovirus type 5 in cells in which the telangiectasia-mutated PI3K-related protein kinase (ATM), the ATM\/Rad3-related (ATR) kinase, and the DNA-dependent protein kinase (DNA-PK) were chemically inactivated, as well as in control cells displaying normal DDR pathway functioning. High-fidelity deep sequencing of these viral populations revealed mutation frequencies in the order of one-millionth, with no detectable effect of the inactivation of DDR mediators ATM, ATR, and DNA-PK on adenovirus sequence variability. This suggests that these DDR pathways do not play a major role in determining adenovirus genetic diversity.<\/jats:p>","DOI":"10.3390\/v11100938","type":"journal-article","created":{"date-parts":[[2019,10,11]],"date-time":"2019-10-11T10:53:03Z","timestamp":1570791183000},"page":"938","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["High Fidelity Deep Sequencing Reveals No Effect of ATM, ATR, and DNA-PK Cellular DNA Damage Response Pathways on Adenovirus Mutation Rate"],"prefix":"10.3390","volume":"11","author":[{"given":"Jennifer","family":"Risso-Ballester","sequence":"first","affiliation":[{"name":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Val\u00e8ncia-CSIC, Paterna, 46980 Val\u00e8ncia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Sanju\u00e1n","sequence":"additional","affiliation":[{"name":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Val\u00e8ncia-CSIC, Paterna, 46980 Val\u00e8ncia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,10,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"9733","DOI":"10.1128\/JVI.00694-10","article-title":"Viral mutation rates","volume":"84","author":"Nebot","year":"2010","journal-title":"J. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"4433","DOI":"10.1007\/s00018-016-2299-6","article-title":"Mechanisms of viral mutation","volume":"73","year":"2016","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1146\/annurev-virology-101416-041718","article-title":"Mechanisms and concepts in RNA virus population dynamics and evolution","volume":"5","author":"Dolan","year":"2018","journal-title":"Annu. Rev. Virol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1534\/genetics.118.301556","article-title":"Evolutionary virology at 40","volume":"210","author":"Geoghegan","year":"2018","journal-title":"Genetics"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nrg2323","article-title":"Rates of evolutionary change in viruses: Patterns and determinants","volume":"9","author":"Duffy","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Sanju\u00e1n, R. (2012). From Molecular Genetics to phylodynamics: Evolutionary relevance of mutation rates across viruses. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002685"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"a012633","DOI":"10.1101\/cshperspect.a012633","article-title":"Postreplicative mismatch repair","volume":"5","author":"Jiricny","year":"2013","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"vev010","DOI":"10.1093\/ve\/vev010","article-title":"Effect of mismatch repair on the mutation rate of bacteriophage \u03d5X174","volume":"1","year":"2015","journal-title":"Virus Evol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.coviro.2015.08.001","article-title":"Functions of DNA damage machinery in the innate immune response to DNA virus infection","volume":"15","author":"Trigg","year":"2015","journal-title":"Curr. Opin. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.coviro.2018.08.017","article-title":"Ubiquitination at the interface of tumor viruses and DNA damage responses","volume":"32","author":"Dybas","year":"2018","journal-title":"Curr. Opin. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.molcel.2010.09.019","article-title":"The DNA damage response: Making it safe to play with knives","volume":"40","author":"Ciccia","year":"2010","journal-title":"Mol. Cell"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1101\/gad.2021311","article-title":"Dynamics of DNA damage response proteins at DNA breaks: A focus on protein modifications","volume":"25","author":"Polo","year":"2011","journal-title":"Genes Dev."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1038\/nature08467","article-title":"The DNA-damage response in human biology and disease","volume":"461","author":"Jackson","year":"2009","journal-title":"Nature"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1126\/science.1108297","article-title":"ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex","volume":"308","author":"Lee","year":"2005","journal-title":"Science"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/nrm2450","article-title":"ATR: An essential regulator of genome integrity","volume":"9","author":"Cimprich","year":"2008","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1042\/BJ20080413","article-title":"Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining","volume":"417","author":"Mahaney","year":"2009","journal-title":"Biochem. J."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1146\/annurev-virology-031413-085548","article-title":"Viruses and the DNA damage response: Activation and antagonism","volume":"1","author":"Luftig","year":"2014","journal-title":"Annu. Rev. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1099\/vir.0.044412-0","article-title":"DNA viruses and the cellular DNA-damage response","volume":"93","author":"Turnell","year":"2012","journal-title":"J. Gen. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1016\/j.dnarep.2009.04.016","article-title":"Viral manipulation of DNA repair and cell cycle checkpoints","volume":"8","author":"Chaurushiya","year":"2009","journal-title":"DNA Repair"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.tim.2007.01.003","article-title":"Using or abusing: Viruses and the cellular DNA damage response","volume":"15","author":"Lilley","year":"2007","journal-title":"Trends Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5844","DOI":"10.1073\/pnas.0501916102","article-title":"DNA repair proteins affect the lifecycle of herpes simplex virus 1","volume":"102","author":"Lilley","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"4783","DOI":"10.1128\/JVI.78.9.4783-4796.2004","article-title":"Recruitment of cellular recombination and repair proteins to sites of herpes simplex virus type 1 DNA replication is dependent on the composition of viral proteins within prereplicative sites and correlates with the induction of the DNA damage response","volume":"78","author":"Wilkinson","year":"2004","journal-title":"J. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e01884-17","DOI":"10.1128\/JVI.01884-17","article-title":"The ATM and Rad3-related (ATR) protein kinase pathway is activated by Herpes Simplex Virus 1 and required for efficient viral replication","volume":"92","author":"Edwards","year":"2017","journal-title":"J. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"13007","DOI":"10.1128\/JVI.79.20.13007-13017.2005","article-title":"Induction and utilization of an ATM signaling pathway by polyomavirus","volume":"79","author":"Dahl","year":"2005","journal-title":"J. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"40195","DOI":"10.1074\/jbc.C500400200","article-title":"Ataxia-telangiectasia-mutated (ATM) is a T-antigen kinase that controls SV40 viral replication in vivo","volume":"280","author":"Shi","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5316","DOI":"10.1128\/JVI.02677-07","article-title":"Ataxia telangiectasia-mutated damage-signaling kinase- and proteasome-dependent destruction of Mre11-Rad50-Nbs1 subunits in Simian virus 40-infected primate cells","volume":"82","author":"Zhao","year":"2008","journal-title":"J. Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1146\/annurev-virology-092917-043534","article-title":"Virus DNA replication and the host DNA damage response","volume":"5","author":"Weitzman","year":"2018","journal-title":"Annu. Rev. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"14004","DOI":"10.1128\/JVI.79.22.14004-14016.2005","article-title":"Adenovirus exploits the cellular aggresome response to accelerate inactivation of the MRN complex","volume":"79","author":"Liu","year":"2005","journal-title":"J. Virol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"11382","DOI":"10.1128\/JVI.79.17.11382-11391.2005","article-title":"Adenovirus type 5 E4orf3 protein targets the Mre11 complex to cytoplasmic Aggresomes","volume":"79","author":"Araujo","year":"2005","journal-title":"J. Virol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"7034","DOI":"10.1128\/JVI.00029-07","article-title":"Adenovirus E4 34k and E1b 55k oncoproteins target host DNA ligase IV for proteasomal degradation","volume":"81","author":"Baker","year":"2007","journal-title":"J. Virol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1128\/JVI.02134-10","article-title":"The adenovirus E1b55K\/E4orf6 complex induces degradation of the Bloom helicase during infection","volume":"85","author":"Orazio","year":"2011","journal-title":"J. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"12251","DOI":"10.1073\/pnas.0914605107","article-title":"Adenovirus 12 E4orf6 inhibits ATR activation by promoting TOPBP1 degradation","volume":"107","author":"Blackford","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Risso-Ballester, J., Cuevas, J.M., and Sanju\u00e1n, R. (2016). Genome-wide estimation of the spontaneous mutation rate of human adenovirus 5 by high-fidelity deep sequencing. PLoS Pathog., 12.","DOI":"10.1371\/journal.ppat.1006013"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/ng.3489","article-title":"Identification of neutral tumor evolution across cancer types","volume":"48","author":"Williams","year":"2016","journal-title":"Nat. Genet."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1038\/nprot.2014.170","article-title":"Detecting ultralow-frequency mutations by Duplex Sequencing","volume":"9","author":"Kennedy","year":"2014","journal-title":"Nat. Protoc"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3625","DOI":"10.3390\/v7072788","article-title":"Ultra deep sequencing of a baculovirus population reveals widespread genomic variations","volume":"7","author":"Chateigner","year":"2015","journal-title":"Viruses"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"9152","DOI":"10.1158\/0008-5472.CAN-04-2727","article-title":"Identification and characterization of a novel and specific inhibitor of the ataxia-telangiectasia mutated kinase ATM","volume":"64","author":"Hickson","year":"2004","journal-title":"Cancer Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.4161\/cbt.21093","article-title":"The novel ATR inhibitor VE-821 increases sensitivity of pancreatic cancer cells to radiation and chemotherapy","volume":"13","author":"Prevo","year":"2012","journal-title":"Cancer Biol. Ther."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"6083","DOI":"10.1016\/j.bmcl.2004.09.060","article-title":"Identification of a highly potent and selective DNA-dependent protein kinase (DNA-PK) inhibitor (NU7441) by screening of chromenone libraries","volume":"14","author":"Leahy","year":"2004","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_40","first-page":"493","article-title":"Effects of neocarzinostatin on chromatin in HeLa S3 nuclei","volume":"23","author":"Beerman","year":"1983","journal-title":"Mol. Pharmacol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1021\/bi00376a008","article-title":"Mechanism and base specificity of DNA Breakage in intact cells by neocarzinostatin","volume":"26","author":"Kappen","year":"1987","journal-title":"Biochemistry"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1007\/978-1-61779-998-3_40","article-title":"Histone H2AX phosphorylation: A marker for DNA damage","volume":"920","author":"Sharma","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"5858","DOI":"10.1074\/jbc.273.10.5858","article-title":"DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139","volume":"273","author":"Rogakou","year":"1988","journal-title":"J. Biol. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/35043058","article-title":"The many substrates and functions of ATM","volume":"1","author":"Kastan","year":"2000","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nature01368","article-title":"DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation","volume":"421","author":"Bakkenist","year":"2003","journal-title":"Nature"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"9677","DOI":"10.1074\/jbc.C300554200","article-title":"UV-induced ataxia-telangiectasia-mutated and Rad3-related (ATR) activation requires replication stress","volume":"279","author":"Ward","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"47759","DOI":"10.1074\/jbc.C100569200","article-title":"Histone H2AX is phosphorylated in an ATR-dependent manner in response to replicational stress","volume":"276","author":"Ward","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1016\/j.dnarep.2006.01.011","article-title":"DNA-PK phosphorylates histone H2AX during apoptotic DNA fragmentation in mammalian cells","volume":"5","author":"Mukherjee","year":"2006","journal-title":"DNA Repair"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1016\/j.dnarep.2005.06.005","article-title":"DNA-PK is responsible for enhanced phosphorylation of histone H2AX under hypertonic conditions","volume":"4","author":"Reitsema","year":"2005","journal-title":"DNA Repair"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1002\/jcp.20141","article-title":"Complex H2AX phosphorylation patterns by multiple kinases including ATM and DNA-PK in human cells exposed to ionizing radiation and treated with kinase inhibitors","volume":"202","author":"Wang","year":"2005","journal-title":"J. Cell. Physiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"24617","DOI":"10.1074\/jbc.272.39.24617","article-title":"Dissociation of the protein primer and DNA polymerase after Initiation of adenovirus DNA replication","volume":"272","author":"King","year":"1997","journal-title":"J. Biol. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"8200","DOI":"10.1128\/JVI.76.16.8200-8207.2002","article-title":"Molecular architecture of adenovirus DNA polymerase and location of the protein primer","volume":"76","author":"Brenkman","year":"2002","journal-title":"J. Virol."},{"key":"ref_53","first-page":"131","article-title":"Adenovirus DNA replication","volume":"272","author":"Liu","year":"2003","journal-title":"Curr. Top. Microbiol. Immunol"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"e30","DOI":"10.1093\/nar\/gkq1258","article-title":"Directed adenovirus evolution using engineered mutator viral polymerases","volume":"39","author":"Uil","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.tig.2018.06.004","article-title":"Experimental studies of evolutionary dynamics in microbes","volume":"34","author":"Ba","year":"2018","journal-title":"Trends Genet."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"20160269","DOI":"10.1098\/rstb.2016.0269","article-title":"Take your PIKK: Tumour viruses and DNA damage response pathways","volume":"372","author":"Pancholi","year":"2017","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.jviromet.2013.04.008","article-title":"Virus quantitation by transmission electron microscopy, TCID50, and the role of timing virus harvesting: A case study of three animal viruses","volume":"191","author":"Malenovska","year":"2013","journal-title":"J. Virol Methods"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S0166-0934(02)00263-X","article-title":"Comparison of electron microscopic techniques for enumeration of endogenous retrovirus in mouse and Chinese hamster cell lines used for production of biologics","volume":"108","author":"Reid","year":"2003","journal-title":"J. Virol Methods"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/1743-422X-9-265","article-title":"Evaluation of nanoparticle tracking analysis for total virus particle determination","volume":"9","author":"Kramberger","year":"2012","journal-title":"Virol J."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Nikitin, N., Trifonova, E., Evtushenko, E., Kirpichnikov, M., Atabekov, J., and Karpova, O. (2015). Comparative Study of Non-Enveloped Icosahedral Viruses Size. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0142415"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"7055","DOI":"10.1039\/C4AY03023K","article-title":"Emergence of tunable resistive pulse sensing as a biosensor","volume":"7","author":"Blundell","year":"2015","journal-title":"Anal. Methods"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"William, S.M.W., and Ann, T.E. (2006). Adenovirus Methods and Protocols, Humana Press. [2nd ed.].","DOI":"10.1385\/1597451665"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"421","DOI":"10.2174\/1566523213666131125095046","article-title":"Adenovirus vectors for gene therapy, vaccination and cancer gene therapy","volume":"13","author":"Wold","year":"2013","journal-title":"Curr. Gene Ther."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"307","DOI":"10.2174\/156652311796150372","article-title":"Adenoviral vector immunity: Its implications and circumvention strategies","volume":"11","author":"Ahi","year":"2011","journal-title":"Curr. Gene Ther."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/10\/938\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:25:27Z","timestamp":1760189127000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/10\/938"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,11]]},"references-count":64,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2019,10]]}},"alternative-id":["v11100938"],"URL":"https:\/\/doi.org\/10.3390\/v11100938","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,10,11]]}}}