New insights into the nonconserved noncoding region of the subtype-determinant hemagglutinin and neuraminidase segments of influenza A viruses

Journal of Virology

Volumn 88, Issue 19, 2014, Pages 11493-11503

  Zhao, Lili ^a   Peng, Yousong ^b   Zhou, Kai ^a   Cao, Mengmeng ^a   Wang, Jingfeng ^a   Wang, Xue ^a   Jiang, Taijiao ^b,c   Deng, Tao ^a  

^a INSTITUTE OF PATHOGEN BIOLOGY   (China)

^b HUNAN UNIVERSITY   (China)

^c INSTITUTE OF BIOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS HEMAGGLUTININ; VIRUS SIALIDASE; HEMAGGLUTININ; SIALIDASE; VIRUS PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; INFLUENZA VIRUS A; INFLUENZA VIRUS A H1N1; NONHUMAN; REVERSE GENETICS; VIRUS MUTANT; VIRUS REPLICATION; VIRUS STRAIN; ANIMAL; BIOLOGY; CHEMISTRY; CLASSIFICATION; DOG; GENETIC VARIABILITY; GENETICS; HEK293 CELL LINE; HUMAN; MDCK CELL LINE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEROTYPING; VIRUS DNA CELL DNA INTERACTION;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DOGS; GENETIC VARIATION; HEK293 CELLS; HEMAGGLUTININS; HUMANS; INFLUENZA A VIRUS; MADIN DARBY CANINE KIDNEY CELLS; MOLECULAR SEQUENCE DATA; NEURAMINIDASE; REVERSE GENETICS; SEROTYPING; VIRAL PROTEINS; VIRUS INTEGRATION; VIRUS REPLICATION;

EID: 84906990861     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01337-14     Document Type: Article

References (42)

1. Palese P, Shaw M. 2013. Orthomyxoviridae, p 1151-1185. In Knipe DM, Howley PM, Cohen JI, Griffin DE, Lamb RA, Martin MA, Racaniello VR, Roizman B (ed), Fields virology, 6th ed. Lippincott Williams and Wilkins, Philadelphia, PA.
2. Neumann G, Noda T, Kawaoka Y. 2009. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 459:931-939. http://dx.doi.org/10.1038/nature08157.
3. Arranz R, Coloma R, Chichon FJ, Conesa JJ, Carrascosa JL, Valpuesta JM, Ortin J, Martin-Benito J. 2012. The structure of native influenza virion ribonucleoproteins. Science 338:1634-1637. http://dx.doi.org/10.1126/science.1228172.
4. Moeller A, Kirchdoerfer RN, Potter CS, Carragher B, Wilson IA. 2012. Organization of the influenza virus replication machinery. Science 338: 1631-1634. http://dx.doi.org/10.1126/science.1227270.
5. Fodor E. 2013. The RNA polymerase of influenza A virus: mechanisms of viral transcription and replication. Acta Virol. 57:113-122. http://dx.doi.org/10.4149/av_2013_02_113.
6. Fodor E, Brownlee GG. 2002. Influenza virus replication, p 1-29. In Potter CW (ed), Influenza. Elsevier Science, New York, NY.
7. Robertson JS. 1979. 5′ and 3′ terminal nucleotide sequences of the RNA genome segments of influenza virus. Nucleic Acids Res. 6:3745-3757. http://dx.doi.org/10.1093/nar/6.12.3745.
8. Poon LL, Pritlove DC, Fodor E, Brownlee GG. 1999. Direct evidence that the poly(A) tail of influenza A virus mRNA is synthesized by reiterative copying of a U track in the virion RNA template. J. Virol. 73:3473- 3476.
9. Desselberger U, Racaniello VR, Zazra JJ, Palese P. 1980. The 3′ and 5′ terminal sequences of influenza A, B and C virus RNA segments are highly conserved and show partial inverted complementarity. Gene 8:315-328. http://dx.doi.org/10.1016/0378-1119(80)90007-4.
10. Bergmann M, Muster T. 1996. Mutations in the nonconserved noncoding sequences of the influenza A virus segments affect viral vRNA formation. Virus Res. 44:23-31. http://dx.doi.org/10.1016/0168-1702(96)01335-4.
11. Zheng H, Palese P, Garcia-Sastre A. 1996. Nonconserved nucleotides at the 3′ and 5′ ends of an influenza A virus RNA play an important role in viral RNA replication. Virology 217:242-251. http://dx.doi.org/10.1006 /viro.1996.0111.
12. Hutchinson EC, von Kirchbach JC, Gog JR, Digard P. 2010. Genome packaging in influenza A virus. J. Gen. Virol. 91:313-328. http://dx.doi.org/10.1099/vir.0.017608-0.
13. Noda T, Kawaoka Y. 2012. Packaging of influenza virus genome: robustness of selection. Proc. Natl. Acad. Sci. U. S. A. 109:8797-8798. http://dx.doi.org/10.1073/pnas.1206736109.
14. Chou YY, Heaton NS, Gao Q, Palese P, Singer RH, Lionnet T. 2013. Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis. PLoS Pathog. 9:e1003358. http://dx.doi.org/10.1371/journal.ppat.1003358.
15. Chou YY, Vafabakhsh R, Doganay S, Gao Q, Ha T, Palese P. 2012. One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis. Proc. Natl. Acad. Sci. U. S. A. 109:9101-9106. http://dx.doi.org/10.1073/pnas.1206069109.
16. Ozawa M, Fujii K, Muramoto Y, Yamada S, Yamayoshi S, Takada A, Goto H, Horimoto T, Kawaoka Y. 2007. Contributions of two nuclear localization signals of influenza A virus nucleoprotein to viral replication. J. Virol. 81:30-41. http://dx.doi.org/10.1128/JVI.01434-06.
17. Dos Santos Afonso E, Escriou N, Leclercq I, van der Werf S, Naffakh N. 2005. The generation of recombinant influenza A viruses expressing a PB2 fusion protein requires the conservation of a packaging signal overlapping the coding and noncoding regions at the 5′ end of the PB2 segment. Virology 341:34-46. http://dx.doi.org/10.1016/j.virol.2005.06.040.
18. Giannecchini S, Wise HM, Digard P, Clausi V, Del Poggetto E, Vesco L, Puzelli S, Donatelli I, Azzi A. 2011. Packaging signals in the 5′-ends of influenza virus PA, PB1, and PB2 genes as potential targets to develop nucleic-acid based antiviral molecules. Antiviral Res. 92:64-72. http://dx.doi.org/10.1016/j.antiviral.2011.06.013.
19. Hutchinson EC, Curran MD, Read EK, Gog JR, Digard P. 2008. Mutational analysis of cis-acting RNA signals in segment 7 of influenza A virus. J. Virol. 82:11869-11879. http://dx.doi.org/10.1128/JVI.01634-08.
20. Liang Y, Hong Y, Parslow TG. 2005. cis-Acting packaging signals in the influenza virus PB1, PB2, and PA genomic RNA segments. J. Virol. 79: 10348-10355. http://dx.doi.org/10.1128/JVI.79.16.10348-10355.2005.
21. Marsh GA, Hatami R, Palese P. 2007. Specific residues of the influenza A virus hemagglutinin viral RNA are important for efficient packaging into budding virions. J. Virol. 81:9727-9736. http://dx.doi.org/10.1128/JVI.01144-07.
22. Ozawa M, Maeda J, Iwatsuki-Horimoto K, Watanabe S, Goto H, Horimoto T, Kawaoka Y. 2009. Nucleotide sequence requirements at the 5′ end of the influenza A virusMRNA segment for efficient virus replication. J. Virol. 83:3384-3388. http://dx.doi.org/10.1128/JVI.02513-08.
23. Fujii K, Fujii Y, Noda T, Muramoto Y, Watanabe T, Takada A, Goto H, Horimoto T, Kawaoka Y. 2005. Importance of both the coding and the segment-specific noncoding regions of the influenza A virus NS segment for its efficient incorporation into virions. J. Virol. 79:3766-3774. http: //dx.doi.org/10.1128/JVI.79.6.3766-3774.2005.
24. Fujii Y, Goto H, Watanabe T, Yoshida T, Kawaoka Y. 2003. Selective incorporation of influenza virusRNAsegments into virions. Proc. Natl. Acad. Sci. U. S. A. 100:2002-2007. http://dx.doi.org/10.1073/pnas.0437772100.
25. Muramoto Y, Takada A, Fujii K, Noda T, Iwatsuki-Horimoto K, Watanabe S, Horimoto T, Kida H, Kawaoka Y. 2006. Hierarchy among viral RNA(vRNA) segments in their role in vRNA incorporation into influenza A virions. J. Virol. 80:2318-2325. http://dx.doi.org/10.1128/JVI.80.5.2318-2325.2006.
26. Goto H, Muramoto Y, Noda T, Kawaoka Y. 2013. The genomepackaging signal of the influenza A virus genome comprises a genome incorporation signal and a genome-bundling signal. J. Virol. 87:11316- 11322. http://dx.doi.org/10.1128/JVI.01301-13.
27. Wang L, Lee CW. 2009. Sequencing and mutational analysis of the noncoding regions of influenza A virus. Vet. Microbiol. 135:239-247. http: //dx.doi.org/10.1016/j.vetmic.2008.09.067.
28. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D. 2008. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 82:596-601. http://dx.doi.org/10.1128/JVI.02005-07.
29. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. http://dx.doi.org/10.1093/nar/gkh340.
30. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res. 14:1188-1190. http://dx.doi.org /10.1101/gr.849004.
31. Hoffmann E, Krauss S, Perez D, Webby R, Webster RG. 2002. Eight-plasmid system for rapid generation of influenza virus vaccines. Vaccine 20:3165-3170. http://dx.doi.org/10.1016/S0264-410X(02)00268-2.
32. Wang R, Taubenberger JK. 2014. Characterization of the noncoding regions of the 1918 influenza A H1N1 virus. J. Virol. 88:1815-1818. http: //dx.doi.org/10.1128/JVI.03098-13.
33. Wang R, Xiao Y, Taubenberger JK. 2014. Rapid sequencing of influenza A virus vRNA, cRNA and mRNA non-coding regions. J. Virol. Methods 195:26-33. http://dx.doi.org/10.1016/j.jviromet.2013.09.005.
34. Park SJ, Kang BK, Jeoung HY, Moon HJ, Hong M, Na W, Park BK, Poo H, Kim JK, An DJ, Song DS. 2013. Complete genome sequence of a canine-origin H3N2 feline influenza virus isolated from domestic cats in South Korea. Genome Announc. 1:e0025312. http://dx.doi.org/10.1128 /genomeA.00253-12.
35. Park SJ, Park BK, Song DS, Poo H. 2012. Complete genome sequence of a mammalian species-infectious and -pathogenic H6N5 avian influenza virus without evidence of adaptation. J. Virol. 86:12459-12460. http://dx.doi.org/10.1128/JVI.02301-12.
36. Su S, Cao N, Chen J, Zhao F, Li H, Zhao M, Wang Y, Huang Z, Yuan L, Wang H, Zhang G, Li S. 2012. Complete genome sequence of an avian-origin H3N2 canine influenza A virus isolated in farmed dogs in southern China. J. Virol. 86:10238. http://dx.doi.org/10.1128/JVI.01601 -12.
37. Fodor E, Crow M, Mingay LJ, Deng T, Sharps J, Fechter P, Brownlee GG. 2002. A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. J. Virol. 76:8989-9001. http://dx.doi.org/10.1128/JVI.76.18.8989-9001.2002.
38. Hsu MT, Parvin JD, Gupta S, Krystal M, Palese P. 1987. Genomic RNAs of influenza viruses are held in a circular conformation in virions and in infected cells by a terminal panhandle. Proc. Natl. Acad. Sci. U. S. A. 84:8140-8144. http://dx.doi.org/10.1073/pnas.84.22.8140.
39. Liang Y, Huang T, Ly H, Parslow TG, Liang Y. 2008. Mutational analyses of packaging signals in influenza virus PA, PB1, and PB2 genomic RNA segments. J. Virol. 82:229-236. http://dx.doi.org/10.1128/JVI.01541 -07.
40. Fournier E, Moules V, Essere B, Paillart JC, Sirbat JD, Isel C, Cavalier A, Rolland JP, Thomas D, Lina B, Marquet R. 2012. A supramolecular assembly formed by influenza A virus genomic RNA segments. Nucleic Acids Res. 40:2197-2209. http://dx.doi.org/10.1093/nar/gkr985.
41. Marsh GA, Rabadan R, Levine AJ, Palese P. 2008. Highly conserved regions of influenza A virus polymerase gene segments are critical for efficient viralRNApackaging. J. Virol. 82:2295-2304. http://dx.doi.org/10.1128/JVI.02267-07.
42. Fujii K, Ozawa M, Iwatsuki-Horimoto K, Horimoto T, Kawaoka Y. 2009. Incorporation of influenza A virus genome segments does not absolutely require wild-type sequences. J. Gen. Virol. 90:1734-1740. http: //dx.doi.org/10.1099/vir.0.010355-0.