Archives of Virology

, Volume 153, Issue 9, pp 1765–1770 | Cite as

Genome sequence and characterization of a new virus infecting Mikania micrantha H.B.K.

Brief Report

Abstract

The complete RNA genomic sequence of a new virus infecting Mikania micrantha, designated as Mikania micrantha wilt virus (MMWV), has been determined. The genomic sequence and the predicted gene products of MMWV were similar to those of the other viruses of the genus Fabavirus. The MMWV nucleotide sequence showed 75.6% identity to that of gentian mosaic virus, 56.6 and 57% identity to those of two Broad bean wilt virus1 isolates, and between 55.7 and 58% identity to those of seven Broad bean wilt virus2 isolates. Our results suggested that MMWV represents a distinct isolate of the candidate species Gentian mosaic virus.

Supplementary material

705_2008_180_MOESM1_ESM.doc (164 kb)
Supplemental Figure and Table (DOC 165 kb)

References

  1. 1.
    Argos P (1988) A sequence motif in many polymerases. Nucleic Acids Res 16:9909–9916PubMedCrossRefGoogle Scholar
  2. 2.
    Arnold TE, Yu J, Belasco JG (1998) mRNA stabilization by the ompA 5′ untranslated region: two protective elements hinder distinct pathways for mRNA degradation. RNA 4:319–330PubMedGoogle Scholar
  3. 3.
    Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer ELL (2002) The pfam protein families database. Nucleic Acids Res 30:276–280PubMedCrossRefGoogle Scholar
  4. 4.
    Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500PubMedCrossRefGoogle Scholar
  5. 5.
    Cho HS, Ha NC, Kang LW, Chung KM, Back SH, Jang SK, Oh BH (1998) Crystal structure of RNA helicase from genotype 1b hepatitis C virus a feasible mechanism of unwinding duplex RNA. J Biol Chem 273:15045–15052PubMedCrossRefGoogle Scholar
  6. 6.
    Chomczynski P, Sacchi N (2006) The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat Protocols 1:581–585CrossRefGoogle Scholar
  7. 7.
    Cock MJW, Ellison CA, Evans HC, Ooi PAC (1999) Can failure be turned into success for biological control of mile-a-minute weed (Mikania micrantha). Proceedings of the 10th International Symposium on Biological Control of Weeds, pp 4–14Google Scholar
  8. 8.
    Ding LW, Sun QY, Wang ZY, Sun YB, Xu ZF (2008) Using silica particles to isolate total RNA from plant tissues recalcitrant to extraction in guanidine thiocyanate. Anal Biochem 374:426–428PubMedCrossRefGoogle Scholar
  9. 9.
    Ferrer RM, Guerri J, Luis-Arteaga MS, Moreno P, Rubio L (2005) The complete sequence of a Spanish isolate of Broad bean wilt virus 1 (BBWV-1) reveals a high variability and conserved motifs in the genus Fabavirus. Arch Virol 150:2109–2116PubMedCrossRefGoogle Scholar
  10. 10.
    Ferrer RM, Luis-Arteaga M, Guerri J, Moreno P, Rubio L (2007) Detection and identification of species of the genus Fabavirus by RT–PCR with a single pair of primers. J Virol Methods 144:156–160PubMedCrossRefGoogle Scholar
  11. 11.
    Foster GD, Taylor SC (1998) Plant virology protocols: from virus isolation to transgenic resistance. Humana PressGoogle Scholar
  12. 12.
    Henke W, Herdel K, Jung K, Schnorr D, Loening SA (1997) Betaine improves the PCR amplification of GC-rich DNA sequences. Nucleic Acids Res 25:3957–3958PubMedCrossRefGoogle Scholar
  13. 13.
    Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431PubMedCrossRefGoogle Scholar
  14. 14.
    Hofacker IL, Stadler PF, Stocsits RR (2004) Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics 20:1495–1499PubMedCrossRefGoogle Scholar
  15. 15.
    Hsu YH, Chen HC, Cheng J, Annamali P, Lin BY, Wu CT, Yeh WB, Lin NS (2006) Crucial role of the 5′ conserved structure of Bamboo mosaic virus satellite RNA in downregulation of helper viral RNA replication. J Virol 80:2566–2574PubMedCrossRefGoogle Scholar
  16. 16.
    Ikegami M, Kawashima H, Natsuaki T, Sugimura N (1998) Complete nucleotide sequence of the genome organization of RNA2 of patchouli mild mosaic virus, a new favavirus. Springer, pp 2431–2434Google Scholar
  17. 17.
    Ikegami M, Onobori Y, Sugimura N, Natsuaki T (2001) Complete nucleotide sequence and the genome organization of Patchouli Mild Mosaic Virus RNA1. pp 355–358Google Scholar
  18. 18.
    Ismail BS, Mah LS (1993) Effects of Mikania micrantha H.B.K on germination and growth of weed species. Plant Soil 157:107–113Google Scholar
  19. 19.
    Ismail BS, Kumar A (1996) Effects of aqueous extracts and residues decomposition of Mikania micrantha H.B.K on selected crops. Allelopathy J 3:195–206Google Scholar
  20. 20.
    Kobayashi YO, Kobayashi A, Nakano M, Hagiwara K, Honda Y, Omura T (2003) Analysis of genetic relations between Broad bean wilt virus 1 and Broad bean wilt virus 2. J Gen Plant Pathol 69:320–326CrossRefGoogle Scholar
  21. 21.
    Kobayashi YO, Kobayashi A, Hagiwara K, Uga H, Mikoshiba Y, Naito T, Honda Y, Omura T (2005) Gentian mosaic virus: a new species in the genus Fabavirus. Phytopathology 95:192–197CrossRefGoogle Scholar
  22. 22.
    Lang AS, Culley AI, Suttle CA (2004) Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo. Virology 320:206–217PubMedCrossRefGoogle Scholar
  23. 23.
    Lanzi G, de Miranda JR, Boniotti MB, Cameron CE, Lavazza A, Capucci L, Camazine SM, Rossi C (2006) Molecular and biological characterization of deformed wing virus of honeybees (Apis mellifera L.). J Virol 80:4998–5009PubMedCrossRefGoogle Scholar
  24. 24.
    Liu P, Li L, Millership JJ, Kang H, Leibowitz JL, Giedroc DP (2007) A U-turn motif-containing stem-loop in the coronavirus 5′ untranslated region plays a functional role in replication. RNA 13:763–780PubMedCrossRefGoogle Scholar
  25. 25.
    Maffei EMD, Marin-Morales MA, Ruas PM, Ruas CF, Matzenbacher NI (1999) Chromosomal polymorphism in 12 populations of Mikania micrantha (Compositae). Genet Mol Biol 22:433–444Google Scholar
  26. 26.
    Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, Chenchik A (1999) Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res 27:1558–1560PubMedCrossRefGoogle Scholar
  27. 27.
    Nevins JR (1983) The pathway of eukaryotic mRNA formation. Annu Rev Biochem 52:441–466PubMedCrossRefGoogle Scholar
  28. 28.
    Ralser M, Querfurth R, Warnatz HJ, Lehrach H, Yaspo ML, Krobitsch S (2006) An efficient and economic enhancer mix for PCR. Biochem Biophys Res Commun 347(3):747–751Google Scholar
  29. 29.
    Ray PS, Das S (2004) Inhibition of hepatitis C virus IRES-mediated translation by small RNAs analogous to stem-loop structures of the 5′-untranslated region. Nucleic Acids Res 32:1678–1687PubMedCrossRefGoogle Scholar
  30. 30.
    Schowalter RM, Wurth MA, Aguilar HC, Lee B, Moncman CL, McCann RO, Dutch RE (2006) Rho GTPase activity modulates paramyxovirus fusion protein-mediated cell-cell fusion. Virology 350:323–334PubMedCrossRefGoogle Scholar
  31. 31.
    Shen H, Ye W, Hong L, Cao H, Wang Z (2005) Influence of the obligate parasite Cuscuta campestris on growth and biomass allocation of its host Mikania micrantha. J Exp Bot 56:1277–1284PubMedCrossRefGoogle Scholar
  32. 32.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  33. 33.
    Valles SM, Strong CA, Dang PM, Hunter WB, Pereira RM, Oi DH, Shapiro AM, Williams DF (2004) A picorna-like virus from the red imported fire ant, Solenopsis invicta: initial discovery, genome sequence, and characterization. Virology 328:151–157PubMedCrossRefGoogle Scholar
  34. 34.
    Valles SM, Strong CA, Hashimoto Y (2007) A new positive-strand RNA virus with unique genome characteristics from the red imported fire ant, Solenopsis invicta. Virology 365:457–463PubMedCrossRefGoogle Scholar
  35. 35.
    Valles SM, Strong CA, Oi DH, Porter SD, Pereira RM, Vander Meer RK, Hashimoto Y, Hooper-Bùi LM, Sánchez-Arroyo H, Davis T, Karpakakunjaram V, Vail KM, “Fudd” Graham LC, Briano JA, Calcaterra LA, Gilbert LE, Ward R, Ward K, Oliver JB, Taniguchi G, Thompson DC (2007) Phenology, distribution, and host specificity of Solenopsis invicta virus-1. J Invertebr Pathol 96:18–27Google Scholar
  36. 36.
    van Munster M, Dullemans AM, Verbeek M, van den Heuvel JFJM, Clerivet A, van der Wilk F (2002) Sequence analysis and genomic organization of Aphid lethal paralysis virus: a new member of the family Dicistroviridae. J Gen Virol 83:3131–3138PubMedGoogle Scholar
  37. 37.
    Weitz M, Baroudy BM, Maloy WL, Ticehurst JR, Purcell RH (1986) Detection of a genome-linked protein (VPg) of hepatitis A virus and its comparison with other picornaviral VPgs. J Virol 60:124–130PubMedGoogle Scholar
  38. 38.
    Zaret KS, Sherman F (1982) DNA sequence required for efficient transcription termination in yeast. Cell 28:563–573PubMedCrossRefGoogle Scholar
  39. 39.
    Zhang LY, Ye WH, Cao HL, Feng HL (2004) Mikania micrantha H.B.K in China-an overview. Weed Res 44:42–49Google Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.State Key Laboratory of Biocontrol, School of Life SciencesSun Yat-Sen UniversityGuangzhouPeople’s Republic of China
  2. 2.State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life SciencesSun Yat-Sen UniversityGuangzhouPeople’s Republic of China

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