Conserved and variable structural elements in the 5' untranslated region of two hypoviruses from the filamentous fungus Cryphonectria parasitica

Virus Research

Volumn 161, Issue 2, 2011, Pages 203-208

  Mu, Rong ^a   Romero, Tammy A ^a,b   Hanley, Kathryn A ^a   Dawe, Angus L ^a  

^a NEW MEXICO STATE UNIVERSITY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Cryphonectria parasitica; Hypovirus; Mfold; Mycovirus; RNA virus; Secondary structure

Indexed keywords

RIBONUCLEASE A; RNA POLYMERASE; SMALL INTERFERING RNA;

5' UNTRANSLATED REGION; ARTICLE; ASCOMYCETES; CRYPHONECTRIA PARASITICA; FUNGAL VIRULENCE; HYPOVIRIDAE; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RNA CLEAVAGE; RNA ISOLATION; RNA REPLICATION; RNA VIRUS; TRANSLATION INITIATION; TRANSLATION REGULATION;

5' UNTRANSLATED REGIONS; ASCOMYCOTA; BASE SEQUENCE; CONSERVED SEQUENCE; INVERTED REPEAT SEQUENCES; NUCLEIC ACID CONFORMATION; RNA VIRUSES; RNA, VIRAL;

CRYPHONECTRIA PARASITICA; FUNGI; HYPOVIRIDAE; HYPOVIRUS; MYCOVIRUS; RNA VIRUSES;

EID: 80053130067     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2011.07.023     Document Type: Article

References (37)

1. Baird S.D., Turcotte M., Korneluk R.G., Holcik M. Searching for IRES. RNA 2006, 12:1755-1785.
2. Buck K.W. Fungal Virology 1986, CRC Press, Boca Raton, FL, 305.
3. Chen B., Choi G.H., Nuss D.L. Attenuation of fungal virulence by synthetic infectious hypovirus transcripts. Science 1994, 264:1762-1764.
4. Chen B., Nuss D.L. Infectious cDNA clone of hypovirus CHV1-Euro7: a comparative virology approach to investigate virus-mediated hypovirulence of the chestnut blight fungus Cryphonectria parasitica. J. Virol. 1999, 73:985-992.
5. Choi G.H., Nuss D.L. Hypovirulence of chestnut blight fungus conferred by an infectious viral cDNA. Science 1992, 257:800-803.
6. Christiansen J., Egebjerg J., Larsen N., Garrett R.A. Analysis of rRNA structure: experimental and theoretical considerations. Ribosomes and Protein Synthesis: A Practical Approach 1990, 229-252. IRL Press, Oxford, UK. G. Spedding (Ed.).
7. Dawe, A.L., Mu, R., Rivera, G., Salamon, J.A. 2011. Molecular methods for studying the Cryphonectria parasitica hypovirus experimental system. In: Xu, J.-R., Bluhm, B.H. (Eds.), Methods in Molecular Biology, vol. 722 (Fungal Genomics). Humana Press, New York, pp. 225-236.
8. Esteban R., Fujimura T. Launching the yeast 23S RNA Narnavirus shows 5' and 3' cis-acting signals for replication. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:2568-2573.
9. Favaretto P., Bhutkar A., Smith T.F. Constraining ribosomal RNA conformational space. Nucleic Acids Res. 2005, 33:5106-5111.
10. Ghabrial S.A., Suzuki N. Viruses of plant pathogenic fungi. Annu. Rev. Phytopathol. 2009, 47:353-384.
11. Hammond S.M. Dicing and slicing: the core machinery of the RNA interference pathway. FEBS Lett. 2005, 579:5822-5829.
12. Hillman B.I., Suzuki N. Viruses of the chestnut blight fungus, Cryphonectria parasitica. Adv. Virus Res. 2004, 63:423-472.
13. Hillman B.I., Fulbright D.W., Nuss D.L., Van Alfen N.K. Hypoviridae. Sixth Report of the International Committee for the Taxonomy of Viruses 1995, 261-264. Springer-Verlag, New York. F.A. Murphy, C.M. Fauquet, D.H.L. Bishop, S.A. Ghabrial, A.W. Jarvis, G.P. Martelli, M.P. Mayo, M.D. Summers (Eds.).
14. Hollings M. Viruses associated with a die-back disease of cultivated mushroom. Nature 1962, 196(4858):962-965.
15. Jang S.K. Internal initiation: IRES elements of picornaviruses and hepatitis C virus. Virus Res. 2006, 119:2-15.
16. Li W., Manktelow E., von Kirchbach J.C., Gog J.R., Desselberger U., Lever A.M. Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions. Nucleic Acids Res. 2010, 38:7718-7735.
17. Linder-Basso D., Dynek J.N., Hillman B.I. Genome analysis of Cryphonectria hypovirus 4, the most common hypovirus species in North America. Virology 2005, 337:192-203.
18. Lipton H.L., Calenoff M., Bandyopadhyay P., Miller S.D., Dalcanto M.C., Gerety S., Jensen K. The 5' noncoding sequences from a less virulent Theilers virus dramatically attenuate Gdvii neurovirulence. J. Virol. 1991, 65:4370-4377.
19. Mertz J.A., Chadee A.B., Byun H., Russell R., Dudley J.P. Mapping of the functional boundaries and secondary structure of the mouse mammary tumor virus Rem-responsive element. J. Biol. Chem. 2009, 284:25642-25652.
20. Molnar A., Csorba T., Lakatos L., Varallyay E., Lacomme C., Burgyan J. Plant virus-derived small interfering RNAs originate predominantly from highly structured single-stranded viral RNAs. J. Virol. 2005, 79:7812-7818.
21. Nuss D.L. Similarities between hypoviruses of the chestnut blight fungus, plant potyviruses and barley yellow mosaic virus. Proceedings of the Second Symposium of the International Working Group on Plant Viruses with Fungal Vectors 1993.
22. Nuss D.L. Hypovirulence: mycoviruses at the fungal-plant interface. Nat. Rev. Microbiol. 2005, 3:632-642.
23. Pearson M.N., Beever R.E., Boine B., Arthur K. Mycoviruses of filamentous fungi and their relevance to plant pathology. Mol. Plant Pathol. 2009, 10:115-128.
24. Pelletier J., Flynn M.E., Kaplan G., Racaniello V., Sonenberg N. Mutational analysis of upstream AUG codons of poliovirus RNA. J. Virol. 1988, 62:4486-4492.
25. Polacek C., Foley J.E., Harris E. Conformational changes in the solution structure of the dengue virus 5' end in the presence and absence of the 3' untranslated region. J. Virol. 2009, 83:1161-1166.
26. Rae B.P., Hillman B.I., Tartaglia J., Nuss D.L. Characterization of double-stranded RNA genetic elements associated with biological control of chestnut blight: organization of terminal domains and identification of gene products. EMBO J. 1989, 8:657-663.
27. Romero T.A., Tumban E., Jun J., Lott W.B., Hanley K.A. Secondary structure of dengue virus type 4 3' untranslated region: impact of deletion and substitution mutations. J. Gen. Virol. 2006, 87:3291-3296.
28. Shapira R., Choi G.H., Nuss D.L. Virus-like genetic organization and expression strategy for a double-stranded RNA genetic element associated with biological control of chestnut blight. EMBO J. 1991, 10:731-739.
29. Stein S.B., Zhang L., Roos R.P. Influence of Theiler's murine encephalomyelitis virus 5' untranslated region on translation and neurovirulence. J. Virol. 1992, 66:4508-4517.
30. Suzuki N., Chen B.S., Nuss D.L. Mapping of a hypovirus p29 protease symptom determinant domain with sequence similarity to potyvirus HC-Pro protease. J. Virol. 1999, 73:9478-9484.
31. Suzuki N., Geletka L.M., Nuss D.L. Essential and dispensable virus-encoded replication elements revealed by efforts to develop hypoviruses as gene expression vectors. J. Virol. 2000, 74:7568-7577.
32. Truniger V., Nieto C., Gonzalez-Ibeas D., Aranda M. Mechanism of plant eIF4E-mediated resistance against a Carmovirus (Tombusviridae): cap-independent translation of a viral RNA controlled in cis by an (a)virulence determinant. Plant J. 2008, 56:716-727.
33. Tsukiyamakohara K., Iizuka N., Kohara M., Nomoto A. Internal ribosome entry site within hepatitis C virus RNA. J. Virol. 1992, 66:1476-1483.
34. Watts J.M., Dang K.K., Gorelick R.J., Leonard C.W., Bess J.W., Swanstrom R., Burch C.L., Weeks K.M. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 2009, 460:711-716.
35. Yu X., Li B., Fu Y.P., Jiang D.H., Ghabrial S.A., Li G.Q., Peng Y.L., Xie J.T., Cheng J.S., Huang J.B., Yi X.H. A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:8387-8392.
36. Zhang X., Segers G.C., Sun Q., Deng F., Nuss D.L. Characterization of hypovirus-derived small RNAs generated in the chestnut blight fungus by an inducible DCL-2-dependent pathway. J. Virol. 2008, 82:2613-2619.
37. Zuker M., Jacobson A.B. Using reliability information to annotate RNA secondary structures. RNA 1998, 4:669-679.