References
- R. S. Harris and J. P. Dudley, APOBECs and virus restriction, Virology 479–480 (2015) 131–145; https://doi.org/10.1016/j.virol.2015.03.012
- N. Lovšin, B. Gangupam and M. Bergant Marušič, The intricate interplay between APOBEC3 proteins and DNA tumour viruses, Pathogens 13(3) (2024) Article ID 187 (19 pages); https://doi.org/10.3390/pathogens13030187
- P. Simmonds, Rampant C®U hypermutation in the genomes of SARS-CoV-2 and other corona-viruses: Causes and consequences for their short- and long-term evolutionary trajectories, mSphere 5(3) (2020); https://doi.org/10.1128/mSphere.00408-20
- S. M. Wang and C. T. Wang, APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein, Virology 388(1) (2009) 112–120; https://doi.org/10.1016/j.virol.2009.03.010
- Y. H. Zheng, N. Lovsin and B. M. Peterlin, Newly identified host factors modulate HIV replication, Immunol. Lett. 97(2) (2005) 225–234; https://doi.org/10.1016/j.imlet.2004.11.026
- Y. L. Chiu and W. C. Greene, The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements, Annu. Rev. Immunol. 26 (2008) 317–353; https://doi.org/10.1146/annurev.immunol.26.021607.090350
- C. M. Okeoma, N. Lovsin, B. M. Peterlin and S. R. Ross, APOBEC3 inhibits mouse mammary tumour virus replication in vivo, Nature 445(7130) (2007) 927–930; https://doi.org/10.1038/nature05540
- Y. H. Zheng, D. Irwin, T. Kurosu, K. Tokunaga, T. Sata and B. M. Peterlin, Human APOBEC3F is another host factor that blocks human immunodeficiency virus type 1 replication, J. Virol. 78(11) (2004) 6073–6076; https://doi.org/10.1128/JVI.78.11.6073-6076.2004
- B. Mangeat, P. Turelli, G. Caron, M. Friedli, L. Perrin and D. Trono, Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts, Nature 424(6944) (2003) 99–103; https://doi.org/10.1038/nature01709
- J. Ratcliff and P. Simmonds, Potential APOBEC-mediated RNA editing of the genomes of SARS--CoV-2 and other coronaviruses and its impact on their longer term evolution, Virology 556 (2021) 62–72; https://doi.org/10.1016/j.virol.2020.12.018
- N. Lindič, M. Budič, T. Petan, B. A. Knisbacher, E. Y. Levanon and N. Lovšin, Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins, Retrovirology 10 (2013) Article ID 156 (16 pages); https://doi.org/10.1186/1742-4690-10-156
- S. Sharma, S. K. Patnaik, R. T. Taggart, E. D. Kannisto, S. M. Enriquez, P. Gollnick and B. E. Baysal, APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages, Nat. Commun. 6 (2015) Article ID 6881 (15 pages); https://doi.org/10.1038/ncomms7881
- P. Simmonds and M. A. Ansari, Extensive C®U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA, PLoS Pathog. 17(6) e1009596 (25 pages); https://doi.org/10.1371/journal.ppat.1009596
- R. Pecori, S. Di Giorgio, J. Paulo Lorenzo and F. N. Papavasiliou, Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination, Nat. Rev. Genet. 23(8) (2022) 505–518; https://doi.org/10.1038/s41576-022-00459-8
- K. Cervantes-Gracia, A. Gramalla-Schmitz, J. Weischedel and R. Chahwan, APOBECs orchestrate genomic and epigenomic editing across health and disease, Trends Genet. 37(11) (2021) 1028–1043; https://doi.org/10.1016/j.tig.2021.07.003
- P. V. Markov, M. Ghafari, M. Beer, K. Lythgoe, P. Simmonds, N. I. Stilianakis and A. Katzourakis, The evolution of SARS-CoV-2, Nat. Rev. Microbiol. 21(6) (2023) 361–379; https://doi.org/10.1038/s41579-023-00878-2
- K. Kim, P. Calabrese, S. Wang, C. Qin, Y. Rao, P. Feng and X. S. Chen, The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness, Sci Rep. 12(1) (2022) Article ID 14972 (15 pages); https://doi.org/10.1038/s41598-022-19067-x
- N. J. Hardenbrook and P. Zhang, A structural view of the SARS-CoV-2 virus and its assembly, Curr. Opin. Virol. 52 (2022) 123–134; https://doi.org/10.1016/j.coviro.2021.11.011
- S. Khan, M. S. Shafiei, C. Longoria, J. W. Schoggins, R. C. Savani and H. Zaki, SARS-CoV-2 spike protein induces inflammation via TLR2-dependent activation of the NF-κB pathway, Elife 10 (2021) e68563 (26 pages); https://doi.org/10.7554/eLife.68563
- C. B. Forsyth, L. Zhang, A. Bhushan, B. Swanson, L. Zhang, J. I. Mamede, R. M. Voigt, M. Shaikh, P. A. Engen and A. Keshavarzian, The SARS-CoV-2 S1 spike protein promotes MAPK and NF-kB activation in human lung cells and inflammatory cytokine production in human lung and intestinal epithelial cells, Microorganisms 10(10) (2022) Article ID 1996; https://doi.org/10.3390/microorganisms10101996
- M. G. Frank, M. Fleshner and S. F. Maier, Exploring the immunogenic properties of SARS-CoV-2 structural proteins: PAMP:TLR signaling in the mediation of the neuroinflammatory and neurologic sequelae of COVID-19, Brain Behav. Immun. 111 (2023) 259–269; https://doi.org/10.1016/j.bbi.2023.04.009
- N. Wanner, G. Andrieux, I. M. P. Badia, C. Edler, S. Pfefferle, M. T. Lindenmeyer, C. Schmidt-Lauber, J. Czogalla, M. N. Wong, Y. Okabayashi, F. Braun, M. Lütgehetmann, E. Meister, S. Lu, M. L. M. Noriega, T. Günther, A. Grundhoff, N. Fischer, H. Bräuninger, D. Lindner, D. Westermann, F. Haas, K. Roedl, S. Kluge, M. M. Addo, S. Huber, A. W. Lohse, J. Reiser, B. Ondruschka, J. P. Sperhake, J . Saez-Rodriguez, M. Boerries, S. S. Hayek, M. Aepfelbacher, P. Scaturro, V. G. Puelles and T. B. Huber, Molecular consequences of SARS-CoV-2 liver tropism, Nat. Metab. 4(3) (2022) 310–319; https://doi.org/10.1038/s42255-022-00552-6
- N. Lovšin and J. Marc, Glucocorticoid receptor regulates TNFSF11 Transcription by binding to glucocorticoid responsive element in TNFSF11 proximal promoter region, Int. J. Mol. Sci. 22(3) (2021) Article ID 1054 (14 pages); https://doi.org/10.3390/ijms22031054
- C. K. Yuen, J. Y. Lam, W. M. Wong, L. F. Mak, X Wang, H. Chu, J.-P. Cai, D.-Y. Jin, K. K.-W. To, J. F.-W. Chan, K.-Y. Yuen and K.-H. Kok, SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists, Emerg. Microbes Infect. 9(1) (2020) 1418–1428; https://doi.org/10.1080/22221751.2020.1780953
- C. Huang, Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, L. Zhang, G. Fan, J. Xu, X. Gu, Z. Cheng, T. Yu, J. Xia, Y. Wei, W. Wu, X. Xie, W. Yin, H. Li, M. Liu, Y. Xiao, H. Gao, L. Guo, J. Xie, G. Wang, R. Jiang, Z. Gao, Q. Jin, J. Wang and B. Cao, Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, Lancet 95(10223) (2020) 497–506; https://doi.org/10.1016/s0140-6736(20)30183-5
- C. Qin, L. Zhou, Z. Hu, S. Zhang, S. Yang, Y. Tao, C. Xie, K. Ma, K. Shang, W. Wang and D.-S. Tian, Dysregulation of immune response in patients with coronavirus 2019 (COVID-19) in Wuhan, China, Clin. Infect. Dis. 71(15) (2020) 762–768; https://doi.org/10.1093/cid/ciaa248
- H. Yang and Z. Rao, Structural biology of SARS-CoV-2 and implications for therapeutic development, Nat. Rev. Microbiol. 19(11) (2021) 685–700; https://doi.org/10.1038/s41579-021-00630-8
- Y. Nakata, H. Ode, M. Kubota, T. Kasahara, K. Matsuoka, A. Sugimoto A, M. Imahashi, Y. Yokomaku and Y. Iwatani, Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome, Nucleic Acids Res. 51(2) (2023) 783–795; https://doi.org/10.1093/nar/gkac1238
- P. Jalili, D. Bowen, A. Langenbucher, S. Park, K. Aguirre, R. B. Corcoran, A. G. Fleischman, M. S. Lawrence, L. Zou and R. Buisson, Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots, Nat. Commun. 11(1) (2020) Article ID 2971 (13 pages); https://doi.org/10.1038/s41467-020-16802-8
- E. K. Law, R. Levin-Klein, M. C. Jarvis, H. Kim, P. P. Argyris, M. A. Carpenter, G. J. Starrett, N. A. Temiz, L. K. Larson, C. Durfee, M. B. Burns, R. I. Vogel, S. Stavrou, A. N. Aguilera, S. Wagner, D. A. Largaespada, T. K. Starr, S. R. Ross and R. S. Harris, APOBEC3A catalyzes mutation and drives carcinogenesis in vivo, J. Exp. Med. 217(12) (2020) e20200261 (22 pages); https://doi.org/10.1084/jem.20200261
- M. B. Burns, L. Lackey, M. A. Carpenter, A. Rathore, A. M. Land, B. Leonard, E. W. Refsland, D. Kotandeniya, N. Tretyakova, J. B. Nikas, D. Yee, N. A. Temiz, D. E. Donohue, R. M. McDougle, W. L. Brown, E. K. Law and R. S. Harris, APOBEC3B is an enzymatic source of mutation in breast cancer, Nature 494(7437) (2013) 366–370; https://doi.org/10.1038/nature11881
- J. Liu, Y. Li, Q. Liu, Q. Yao, X. Wang, H. Zhang, R. Chen, L. Ren, J. Min, F. Deng, B. Yan, L. Liu, Z. Hu, M. Wang and Y. Zhou, SARS-CoV-2 cell tropism and multiorgan infection, Cell Discov. 7(1) (2021) Article ID 17 (4 pages); https://doi.org/10.1038/s41421-021-00249-2