{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T03:29:14Z","timestamp":1792726154800,"version":"4.5.0"},"reference-count":88,"publisher":"American Society for Microbiology","issue":"16","license":[{"start":{"date-parts":[[2009,8,15]],"date-time":"2009-08-15T00:00:00Z","timestamp":1250294400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2009,8,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The positive-strand RNA genome of Japanese encephalitis virus (JEV) terminates in a highly conserved 3\u2032-noncoding region (3\u2032NCR) of six domains (V, X, I, II-1, II-2, and III in the 5\u2032-to-3\u2032 direction). By manipulating the JEV genomic RNA, we have identified important roles for RNA elements present within the 574-nucleotide 3\u2032NCR in viral replication. The two 3\u2032-proximal domains (II-2 and III) were sufficient for RNA replication and virus production, whereas the remaining four (V, X, I, and II-1) were dispensable for RNA replication competence but required for maximal replication efficiency. Surprisingly, a lethal mutant lacking all of the 3\u2032NCR except domain III regained viability through pseudoreversion by duplicating an 83-nucleotide sequence from the 3\u2032-terminal region of the viral open reading frame. Also, two viable mutants displayed severe genetic instability; these two mutants rapidly developed 12 point mutations in domain II-2 in the mutant lacking domains V, X, I, and II-1 and showed the duplication of seven upstream sequences of various sizes at the junction between domains II-1 and II-2 in the mutant lacking domains V, X, and I. In all cases, the introduction of these spontaneous mutations led to an increase in RNA production that paralleled the level of protein accumulation and virus yield. Interestingly, the mutant lacking domains V, X, I, and II-1 was able to replicate in hamster BHK-21 and human neuroblastoma SH-SY5Y cells but not in mosquito C6\/36 cells, indicating a cell type-specific restriction of its viral replication. Thus, our findings provide the basis for a detailed map of the 3\u2032\n            <jats:italic>cis<\/jats:italic>\n            -acting elements in JEV genomic RNA, which play an essential role in viral replication. They also provide experimental evidence for the function of 3\u2032 direct repeat sequences and suggest possible mechanisms for the emergence of these sequences in the 3\u2032NCR of JEV and perhaps in other flaviviruses.\n          <\/jats:p>","DOI":"10.1128\/jvi.02541-08","type":"journal-article","created":{"date-parts":[[2009,6,4]],"date-time":"2009-06-04T00:46:04Z","timestamp":1244076364000},"page":"7909-7930","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":50,"title":["3\u2032\n            <i>cis<\/i>\n            -Acting Elements That Contribute to the Competence and Efficiency of Japanese Encephalitis Virus Genome Replication: Functional Importance of Sequence Duplications, Deletions, and Substitutions"],"prefix":"10.1128","volume":"83","author":[{"given":"Sang-Im","family":"Yun","sequence":"first","affiliation":[{"name":"Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Jeong","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byung-Hak","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young-Min","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M104248200"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2005.06.009"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.11.6631-6643.2005"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2008.01.014"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1006\/smvy.1997.0108"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.69.9.5650-5658.1995"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.71.9.6433-6444.1997"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.18860-0"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(86)90012-7"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(88)90468-0"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3527(03)59001-7"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(92)90575-A"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.mi.44.100190.003245"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.3.2265-2270.2003"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00531-07"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.2002.1407"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2008.07.040"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2004.11.008"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0703348104"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00991-08"},{"key":"e_1_3_2_22_2","first-page":"11","volume":"267","year":"2002","unstructured":"Endy, T. P., and A. Nisalak. 2002. Japanese encephalitis virus: ecology and epidemiology. Curr. Top. Microbiol. Immunol.267:11-48.","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1444206"},{"key":"e_1_3_2_24_2","first-page":"47","year":"2006","unstructured":"Gritsun, T. S., A. Tuplin, and E. A. Gould. 2006. Origin, evolution, and function of flavivirus RNA in untranslated and coding regions: implications for virus transmission, p. 47-99. In M. Kalitzky and P. Borowski (ed.), Molecular biology of the flavivirus. Horizon Scientific Press, Norwich, United Kingdom.","journal-title":"Molecular biology of the flavivirus."},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.81950-0"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2006.03.052"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.82235-0"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2006.09.033"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3527(06)69005-2"},{"key":"e_1_3_2_30_2","first-page":"1153","year":"2007","unstructured":"Gubler, D. J., G. Kuno, and L. Markoff. 2007. Flaviviruses, p. 1153-1252. In D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, and S. E. Straus (ed.), Fields virology, 5th ed. Lippincott Williams & Wilkins Publishers, Philadelphia, PA.","journal-title":"Fields virology"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(87)90455-4"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2008.04.035"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.68.7.4580-4588.1994"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.71.2.1497-1505.1997"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.75.14.6719-6728.2001"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.19.10623-10629.2003"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00789-08"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.80.8.4099-4113.2006"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.56.1.61-79.1992"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.23.11989-12000.2002"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3527(03)59002-9"},{"key":"e_1_3_2_42_2","first-page":"1101","year":"2007","unstructured":"Lindenbach, B. D., H.-J. Thiel, and C. M. Rice. 2007. Flaviviridae: the viruses and their replication, p. 1101-1152. In D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, and S. E. Straus (ed.), Fields virology, 5th ed. Lippincott Williams & Wilkins Publishers, Philadelphia, PA.","journal-title":"Fields virology"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.18.10004-10014.2003"},{"key":"e_1_3_2_44_2","first-page":"49","volume":"267","year":"2002","unstructured":"Mackenzie, J. S., C. A. Johansen, S. A. Ritchie, A. F. Van Den Hurk, and R. A. Hall. 2002. Japanese encephalitis as an emerging virus: the emergence and spread of Japanese encephalitis virus in Australasia. Curr. Top. Microbiol. Immunol.267:49-73.","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm1144"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.1993.1247"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.72.3.2132-2140.1998"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3527(03)59006-6"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2700"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.70.6.3930-3937.1996"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(91)90433-C"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M310839200"},{"key":"e_1_3_2_53_2","first-page":"1370","volume":"7","year":"2001","unstructured":"Olsthoorn, R. C., and J. F. Bol. 2001. Sequence comparison and secondary structure analysis of the 3\u2032 noncoding region of flavivirus genomes reveals multiple pseudoknots. RNA7:1370-1377.","journal-title":"RNA"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M705755200"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.2001.0846"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.6.1194"},{"key":"e_1_3_2_57_2","first-page":"779","volume":"3","year":"1997","unstructured":"Rauscher, S., C. Flamm, C. W. Mandl, F. X. Heinz, and P. F. Stadler. 1997. Secondary structure of the 3\u2032-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities. RNA3:779-791.","journal-title":"RNA"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.4023707"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.82182-0"},{"key":"e_1_3_2_60_2","unstructured":"Molecular cloning: a laboratory manual 1989"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1006\/abio.2000.4753"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi952398v"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.82811-0"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1080\/13550280390194037"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.1261\/rna.993608"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.1006\/smvy.1997.0115"},{"key":"e_1_3_2_67_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.11.5108-5115.2000"},{"key":"e_1_3_2_68_2","first-page":"981","year":"2005","unstructured":"Thiel, H.-J., M. S. Collett, E. A. Gould, F. X. Heinz, M. Houghton, G. Meyers, R. H. Purcell, and C. M. Rice. 2005. Family Flaviviridae, p. 981-998. In C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger, and L. A. Ball (ed.), Virus taxonomy: eighth report of the international committee on taxonomy of viruses. Elsevier Academic Press, San Diego, CA.","journal-title":"Virus taxonomy: eighth report of the international committee on taxonomy of viruses."},{"key":"e_1_3_2_69_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.19462-0"},{"key":"e_1_3_2_70_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.15.8159-8171.2004"},{"key":"e_1_3_2_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2004.07.022"},{"key":"e_1_3_2_72_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1006"},{"key":"e_1_3_2_73_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(81)90182-3"},{"key":"e_1_3_2_74_2","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-67-6-1183"},{"key":"e_1_3_2_75_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3527(03)59004-2"},{"key":"e_1_3_2_76_2","doi-asserted-by":"publisher","DOI":"10.1006\/abio.1999.4085"},{"key":"e_1_3_2_77_2","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-80-10-2535"},{"key":"e_1_3_2_78_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2006.07.042"},{"key":"e_1_3_2_79_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01796-07"},{"key":"e_1_3_2_80_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.274.47.33714"},{"key":"e_1_3_2_81_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M010923200"},{"key":"e_1_3_2_82_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.3.1352-1366.2004"},{"key":"e_1_3_2_83_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.4.2309-2324.2005"},{"key":"e_1_3_2_84_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.11.6450-6465.2003"},{"key":"e_1_3_2_85_2","first-page":"225","year":"2006","unstructured":"Yun, S.-I., and Y.-M. Lee. 2006. Japanese encephalitis virus: molecular biology and vaccine development, p. 225-271. In M. Kalitzky and P. Borowski (ed.), Molecular biology of the flavivirus. Horizon Scientific Press, Norwich, United Kingdom.","journal-title":"Molecular biology of the flavivirus."},{"key":"e_1_3_2_86_2","doi-asserted-by":"publisher","DOI":"10.1080\/13550280701684651"},{"key":"e_1_3_2_87_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.72.9.7510-7522.1998"},{"key":"e_1_3_2_88_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2008.01.016"},{"key":"e_1_3_2_89_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg595"}],"container-title":["Journal of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.02541-08","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.02541-08","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T12:32:06Z","timestamp":1646483526000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JVI.02541-08"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,8,15]]},"references-count":88,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2009,8,15]]}},"alternative-id":["10.1128\/JVI.02541-08"],"URL":"https:\/\/doi.org\/10.1128\/jvi.02541-08","relation":{},"ISSN":["0022-538X","1098-5514"],"issn-type":[{"value":"0022-538X","type":"print"},{"value":"1098-5514","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,8,15]]},"assertion":[{"value":"2008-12-10","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2009-05-26","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2009-08-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}