Advertisement

Archives of Virology

, Volume 156, Issue 7, pp 1199–1208 | Cite as

Characterization of a novel dsRNA element in the pine endophytic fungus Diplodia scrobiculata

  • Juanita De Wet
  • Wubetu Bihon
  • Oliver Preisig
  • Brenda D. Wingfield
  • Michael J. Wingfield
Original Article

Abstract

Diplodia scrobiculata and Diplodia pinea are endophytic fungi associated with dieback and cankers of mainly Pinus spp. in many parts of the world. These two fungi are closely related and have, in the past, been considered to represent two morphological forms (A and B morphotypes) of D. pinea. dsRNA elements are known to occur in both D. scrobiculata and D. pinea. Two dsRNA elements from D. pinea, SsRV1 and SsRV2, have been characterized previously. The aim of this study was to characterize a third dsRNA element that is most commonly associated with D. scrobiculata and to determine its phylogenetic relationship to other mycoviruses. The 5018-bp genome of this element was sequenced, and it is referred to as D. scrobiculata RNA virus 1, or DsRV1. It has two open reading frames (ORFs), one of which codes for a putative polypeptide with a high degree of similarity to proteins of the vacuolar protein-sorting (VPS) machinery, and the other for an RNA-dependent RNA polymerase (RdRp). Phylogenetic comparisons based on amino acid sequence alignments of the RdRp revealed that DsRV1 is closely related to a dsRNA element isolated from Phlebiopsis gigantea (PgV2), and they grouped separately from virus families in which mycoviruses have previously been described. Although D. pinea and D. scrobiculata are closely related, DsRV1 does not share high sequence identity with SsRV1 or SsRV2, and they probably have different recent evolutionary origins.

Keywords

Endophytic Fungus Fungal Host RdRp Gene Putative Polypeptide dsRNA Element 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We thank the National Research Foundation (NRF), members of the Tree Pathology Co-operative Programme (TPCP) and the THRIP initiative of the Department of Trade and Industry (DTI), South Africa, for financial support.

References

  1. 1.
    Adams GC, Wu N-T, Eisenberg BE (2002) Virulence and double-stranded RNA in Sphaeropsis sapinea. For Pathol 32:309–329Google Scholar
  2. 2.
    Bihon W, Slippers B, Burgess T, Wingfield MJ, Wingfield BD (2010a) Diplodia scrobiculata found in the southern hemisphere. For Pathol. doi: 10.1111/j.1439-0329.2010.00649.x
  3. 3.
    Bihon W, Burgess T, Slippers B, Wingfield MJ, Wingfield BD (2010b) Distribution of Diplodia pinea and its genotypic diversity within asymptomatic Pinus patula trees. Australas Plant Pathol (in press)Google Scholar
  4. 4.
    Blodgett JT, Stanosz GR (1997) Sphaeropsis sapinea morphotypes differ in aggressiveness, but both infect nonwounded red and jack pine. Plant Disease 81:143–147CrossRefGoogle Scholar
  5. 5.
    Bruenn JA (1993) A closely related group of RNA-dependent RNA polymerases from double-stranded RNA viruses. Nucleic Acids Res 21:5667–5669PubMedCrossRefGoogle Scholar
  6. 6.
    Buck KW (1986) Fungal virology—an overview. In: Buck KW (ed) Fungal virology. CRC Press, Boca RatonGoogle Scholar
  7. 7.
    Burgess T, Wingfield MJ (2002) Quarantine is important in restricting the spread of exotic seed-borne tree pathogens in the Southern Hemisphere. Int For Rev 4:56–65Google Scholar
  8. 8.
    Burgess TI, Wingfield MJ, Wingfield BD (2004) Global distribution of Diplodia pinea genotypes revealed using simple sequence repeat (SSR) markers. Australas Plant Pathol 33:513–519CrossRefGoogle Scholar
  9. 9.
    Burgess TI, Gordon TR, Wingfield MJ, Wingfield BD (2004) Geographic isolation of Diplodia scrobiculata and its association with native Pinus radiata. Mycol Res 108:1399–1406PubMedCrossRefGoogle Scholar
  10. 10.
    Coutts RHA, Livieratos IC (2003) A rapid method for sequencing the 5’- and 3’termini of double-stranded RNA viral templates using RLM-RACE. J Phytopathol 151:525–527CrossRefGoogle Scholar
  11. 11.
    De Wet J, Wingfield MJ, Coutinho TA, Wingfield BD (2000) Characterization of Sphaeropsis sapinea isolates from South Africa, Mexico and Indonesia. Plant Dis 84:151–156CrossRefGoogle Scholar
  12. 12.
    De Wet J, Wingfield MJ, Preisig O, Wingfield BD (2001) Occurrence of dsRNA elements in isolates of the pine pathogen, Sphaeropsis sapinea from diverse geographical regions. Phytopathology 91:S22Google Scholar
  13. 13.
    De Wet J, Wingfield MJ, Coutinho TA, Wingfield BD (2002) Characterisation of the ‘C’ morphotype of the pine pathogen Sphaeropsis sapinea. For Ecol Manag 161:181–188CrossRefGoogle Scholar
  14. 14.
    De Wet J, Burgess T, Slippers B, Preisig O, Wingfield BD, Wingfield MJ (2003) Multiple gene genealogies and microsatellite markers reflect relationships between morphotypes of Sphaeropsis sapinea and distinguish a new species of Diplodia. Mycol Res 107:557–566PubMedCrossRefGoogle Scholar
  15. 15.
    De Wet J, Preisig O, Wingfield BD, Wingfield MJ (2008) Patterns of multiple virus infections in the conifer pathogenic fungi, Diplodia pinea and Diplodia scrobiculata. J Phytopathol 156:725–731CrossRefGoogle Scholar
  16. 16.
    Domingo E, Baranowski E, Ruiz-Jarabo CM, Martín-Hernández AM, Sáiz JC, Escarmís C (1998) Quasispecies structure and persistence of RNA viruses. Emerg Infect Dis 4:521–527PubMedCrossRefGoogle Scholar
  17. 17.
    Ghabrial SA (1998) Origin, adaptation and evolutionary pathways of fungal viruses. Virus Genes 16:119–131PubMedCrossRefGoogle Scholar
  18. 18.
    Ghabrial SA, Soldevila AI, Havens WM (2002) Molecular genetics of viruses infecting the plant pathogenic fungus Helminthosporium victoriae. In: Tavantzis SM (ed) Molecular biology of double-stranded rna: concepts and applications in agriculture, forestry and medicine, chap 9. CRC Press, Boca Raton, pp 213–236Google Scholar
  19. 19.
    Ghabrial SA, Castón JR (2005) Chrysoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball AL (eds) Virus taxonomy. Eight Report of the International Committee on taxonomy of viruses. Elsevier/Academic Press, LondonGoogle Scholar
  20. 20.
    Gibbs MJ, Pfeiffer P, Fukuhara T (2005) Endornavirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball AL (eds) Virus taxonomy. Eight Report of the International Committee on taxonomy of viruses. Elsevier/Academic Press, LondonGoogle Scholar
  21. 21.
    Hacker CV, Brasier CM, Buck KW (2005) A double-stranded RNA from a Phytophthora species is related to the plant endornaviruses and contains a putative UDP glycosyltransferase gene. J Gen Virol 86:1561–1570PubMedCrossRefGoogle Scholar
  22. 22.
    Harty RN, Brown ME, Wang G, Huibregtse J, Hayes FP (2000) A PPxY motif within the VP40 protein of Ebola virus interacts physically and functionally with a ubiquitin ligase: implications for filovirus budding. Proc Natl Acad Sci USA 97:13871–13876PubMedCrossRefGoogle Scholar
  23. 23.
    Iwaki T, Onishi M, Ikeuchi M, Kita A, Sugiura R, Giga-hama Y, Fukui Y, Takegawa K (2007) Essential roles of class E Vps proteins for sorting into multivesicular bodies in Schizosaccharomyces pombe. Microbiology 153:2753–2764PubMedCrossRefGoogle Scholar
  24. 24.
    Jacob-Wilk D, Turina M, Van Alfen NK (2006) Mycovirus Cryphonectria Hypovirus 1 elements cofractionate with trans-Golgi Network membranes of the fungal host Cryphonectria parasitica. J Virol 80:6588–6596PubMedCrossRefGoogle Scholar
  25. 25.
    Jiang D, Ghabrial SA (2004) Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus. J Gen Virol 85:2111–2121PubMedCrossRefGoogle Scholar
  26. 26.
    Katoh K, Kuma K-I, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl Acids Res 33:511–518PubMedCrossRefGoogle Scholar
  27. 27.
    Khatchikian D, Orlich M, Rott R (1989) Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of a influenza virus. Nature 340:156–157PubMedCrossRefGoogle Scholar
  28. 28.
    Kozak M (1991) Structural features in eukaryotic mRNAs that modulate the initiation of translation. J Biol Chem 266:19867–19870PubMedGoogle Scholar
  29. 29.
    Lai MMC (1998) Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription. Virology 244:1–12PubMedCrossRefGoogle Scholar
  30. 30.
    Liu Y-G, Whittier RF (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25:674–681PubMedCrossRefGoogle Scholar
  31. 31.
    Martin-Serrano J, Yaravoy A, Perez-Caballero D, Bieniasz PD (2003) Divergent retroviral late-budding domains recruit vacuolar protein sorting factors by using alternative adaptor proteins. Proc Natl Acad Sci USA 100:12414–12419PubMedCrossRefGoogle Scholar
  32. 32.
    McGeoch DJ (2001) Molecular evolution of the Y-Herpesvirinae. Philo Trans R Soc Lond Ser B 356:421–435CrossRefGoogle Scholar
  33. 33.
    Meyers G, Rümenapf T, Thiel H-J (1989) Ubiquitin in a togavirus. Nature 341:491PubMedCrossRefGoogle Scholar
  34. 34.
    Nakayama T, Soma M, Rahmutula D, Ozawa Y, Kanmatsuse K (2001) Isolation of the 5’-flanking region of genes by thermal asymmetric interlaced polymerase chain reaction. Med Sci Monit 7:345–349PubMedGoogle Scholar
  35. 35.
    Nuss DL, Hillman BI, Rigling D, Suzuki N (2005) Hypoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball AL (eds) Virus taxonomy. Eight Report of the International Committee on taxonomy of viruses. Elsevier/Academic Press, LondonGoogle Scholar
  36. 36.
    Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar
  37. 37.
    Palmer MA, Stewart EL, Wingfield MJ (1987) Variation among isolates of Sphaeropsis sapinea in the North Central United States. Phytopathology 77:944–948CrossRefGoogle Scholar
  38. 38.
    Preisig O, Wingfield BD, Wingfield MJ (1998) Co-infection of a fungal pathogen by two distinct double-stranded RNA viruses. Virology 252:399–406PubMedCrossRefGoogle Scholar
  39. 39.
    Raeder U, Broda P (1985) Rapid preparation of DNA from filamentous fungi. Lett Appl Microbiol 1:17–20CrossRefGoogle Scholar
  40. 40.
    Reggiori F, Pelham HRB (2001) Sorting of proteins into multivesicular bodies: ubiquitin-dependent and -independent targeting. EMBO J 20:5176–5186PubMedCrossRefGoogle Scholar
  41. 41.
    Soldevila AI, Havens WM, Ghabrial SA (2000) A cellular protein with an RNA-binding activity co-purifies with viral dsRNA from mycovirus-infected Helminthosporium victoriae. Virology 272:183–190PubMedCrossRefGoogle Scholar
  42. 42.
    Soldevila AI, Ghabrial SA (2001) A novel alcohol oxidase/RNA binding protein with affinity for mycovirus double-stranded RNA from the filamentous fungus Helminthosporium (Cochliobolus) victoriae. J Biol Chem 276:4652–4661PubMedCrossRefGoogle Scholar
  43. 43.
    Steenkamp ET, Wingfield BD, Swart WJ, Wingfield MJ (1998) Double-stranded RNA and associated virulence in South African isolates of Sphaeropsis sapinea. Can J Bot 76:1–7Google Scholar
  44. 44.
    Swart WJ, Wingfield MJ (1991) Biology and control of Sphaeropsis sapinea on Pinus species in South Africa. Plant Dis 75:761–766CrossRefGoogle Scholar
  45. 45.
    Wang C-G, Blanchette RA, Jackson WA, Palmer MA (1985) Differences in conidial morphology among isolates of Sphaeropsis sapinea. Plant Dis 69:838–841CrossRefGoogle Scholar
  46. 46.
    White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal rRNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322Google Scholar
  47. 47.
    Wingfield MJ, Knox-Davies PS (1980) Association of Diplodia pinea with a root disease of pines in South Africa. Plant Dis 64:221–223CrossRefGoogle Scholar
  48. 48.
    Wu N-T, Palmer M, Adams G (1989) The relationship of dsRNA to virulence and morphology in type A and type B Sphaeropsis sapinea. Phytopathology 79:1143Google Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Juanita De Wet
    • 1
  • Wubetu Bihon
    • 2
  • Oliver Preisig
    • 1
  • Brenda D. Wingfield
    • 2
  • Michael J. Wingfield
    • 2
  1. 1.Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
  2. 2.Departments of Genetics, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa

Personalised recommendations