Cryphonectria hypovirus 1-Induced Epigenetic Changes in Infected Phytopathogenic Fungus Cryphonectria parasitica

Abstract

Biotic stress caused by virus infections induces epigenetic changes in infected plants and animals, but this is the first report on methylation pattern changes in a fungus after mycovirus infection. As a model pathosystem for mycovirus-host interactions, we used Cryphonectria hypovirus 1 (CHV1) and its host fungus Cryphonectria parasitica, in which deregulation of methylation cycle enzymes upon virus infection was observed previously. Six CHV1 strains of different subtypes were transferred into three different C. parasitica isolates in order to assess the effect of different CHV1 strains and/or subtypes on global cytosine methylation level in infected fungus, using methylation-sensitive amplification polymorphism (MSAP). Infection with CHV1 affected the methylation pattern of the C. parasitica genome; it increased the number and diversity of methylated, hemi-methylated, and total MSAP markers found in infected fungal isolates compared to virus-free controls. The increase in methylation levels correlated well with the CHV1-induced reduction of fungal growth in vitro, indicating that C. parasitica genome methylation upon CHV1 infection, rather than being the defensive mechanism of the fungus, is more likely to be the virulence determinant of the virus. Furthermore, the severity of CHV1 effect on methylation levels of infected C. parasitica isolates depended mostly on individual CHV1 strains and on the combination of host and virus genomes, rather than on the virus subtype. These novel findings broaden our knowledge about CHV1 strains which could potentially be used in human-aided biocontrol of chestnut blight, a disease caused by C. parasitica in chestnut forest ecosystems and orchards.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2

References

  1. 1.

    Cureau N, AlJahdali N, Vo N, Carbonero F (2016) Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives. Epigenomics 8:1259–1273. https://doi.org/10.2217/epi-2016-0057

    CAS  Article  PubMed  Google Scholar 

  2. 2.

    Labra M, Ghiani A, Citterio S, Sgorbati S, Sala F, Vannini C, Ruffini-Castiglione M, Bracale M (2002) Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Biol. 4:694–699. https://doi.org/10.1055/s-2002-37398

    CAS  Article  Google Scholar 

  3. 3.

    Kovalchuk O, Burke P, Arkhipov A, Kuchma N, James SJ, Kovalchuk I, Pogribny I (2003) Genome hypermethylation in Pinus silvestris of Chernobyl—a mechanism for radiation adaptation? Mutat Res-Fundam Mol Mech Mutagen 529:13–20. https://doi.org/10.1016/S0027-5107(03)00103-9

    CAS  Article  Google Scholar 

  4. 4.

    Hua S, Qi B, Fu YP, Li Y (2017) DNA methylation changes in Pleurotus eryngii subsp. tuoliensis (Bailinggu) in response to low temperature stress. Int. J. Agric. Biol. 19:328–334. 10.17957/IJAB/15.0286

    Article  Google Scholar 

  5. 5.

    Jones AL, Thomas CL, Maule AJ (1998) De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus. EMBO J. 17:6385–6393. https://doi.org/10.1093/emboj/17.21.6385

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Zhang C, Wu Z, Li Y, Wu J (2015) Biogenesis, function, and applications of virus-derived small RNAs in plants. Front. Microbiol. 6:1–12. https://doi.org/10.3389/fmicb.2015.01237

    Google Scholar 

  7. 7.

    Kathiria P, Sidler C, Golubov A, Kalischuk M, Kawchuk LM, Kovalchuk I (2010) Tobacco mosaic virus infection results in an increase in recombination frequency and resistance to viral, bacterial, and fungal pathogens in the progeny of infected tobacco plants. Plant Physiol. 153:1859–1870. https://doi.org/10.1104/pp.110.157263

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Raja P, Sanville BC, Buchmann RC, Bisaro DM (2008) Viral genome methylation as an epigenetic defense against geminiviruses. J. Virol. 82:8997–9007. https://doi.org/10.1128/JVI.00719-08

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Paschos K, Allday MJ (2010) Epigenetic reprogramming of host genes in viral and microbial pathogenesis. Trends Microbiol. 18:439–447. https://doi.org/10.1016/j.tim.2010.07.003

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Reyna-López GE, Simpson J, Ruiz-Herrera J (1997) Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol Gen Genet 253:703–710. https://doi.org/10.1007/s004380050374

    Article  PubMed  Google Scholar 

  11. 11.

    Allen TD, Dawe AL, Nuss DL (2003) Use of cDNA microarrays to monitor transcriptional responses of the chestnut blight fungus Cryphonectria parasitica to infection by virulence-attenuating hypoviruses. Eucaryotic cell 2:1253–1265. https://doi.org/10.1128/EC.2.6.1253

    CAS  Article  Google Scholar 

  12. 12.

    Allen TD, Nuss DL (2004) Specific and common alterations in host gene transcript accumulation following infection of the chestnut blight fungus by mild and severe hypoviruses. J. Virol. 78:4145–4155. https://doi.org/10.1128/jvi.78.8.4145-4155.2004

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Liao S, Li R, Shi L, Wang J, Shang J, Zhu P, Chen B (2012) Functional analysis of an S-adenosylhomocysteine hydrolase homolog of chestnut blight fungus. FEMS Microbiol. Lett. 336:64–72. https://doi.org/10.1111/j.1574-6968.2012.02657.x

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Milgroom MG, Cortesi P (2004) Biological control of chestnut blight with hypovirulence: a critical analysis. Annu. Rev. Phytopathol. 42:311–338. https://doi.org/10.1146/annurev.phyto.42.040803.140325

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Allemann C, Hoegger PJ, Heiniger U, Rigling D (1999) Genetic variation of Cryphonectria hypoviruses (CHV1) in Europe, assessed using restriction fragment length polymorphism (RFLP) markers. Mol. Ecol. 8:843–854. https://doi.org/10.1046/j.1365-294X.1999.00639.x

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    Van Alfen NK, Jaynes RA, Anagnostakis SL, Day PR (1975) Chestnut blight: biological control by transmissible hypovirulence in Endothia parasitica. Science 189:890–891. https://doi.org/10.1126/science.189.4206.890

    Article  PubMed  Google Scholar 

  17. 17.

    Grente J, Berthelay-Sauret S (1978) Biological control of chestnut blight in France. In: MacDonald W (ed) American chestnut symposium proceedings. West Wirginia University Agricultural Experiment Station and United States Department of Agriculture, Morgantown, pp 30–34

  18. 18.

    Elliston JE (1985) Characteristics of dsRNA-free and dsRNA-containing strains of Endothia parasitica in relation to hypovirulence. Phytopathology 75:151–158. https://doi.org/10.1094/Phyto-75-151

    Article  Google Scholar 

  19. 19.

    Peever TL, Liu YC, Cortesi P, Milgroom MG (2000) Variation in tolerance and virulence in the chestnut blight fungus-hypovirus interaction. Appl. Environ. Microbiol. 66:4863–4869. https://doi.org/10.1128/AEM.66.11.4863-4869.2000

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Hillman BI, Suzuki N (2004) Viruses of the chestnut blight fungus, Cryphonectria parasitica. Adv. Virus Res. 63:423–472. https://doi.org/10.1016/S0065-3527(04)63007-7

    CAS  Article  PubMed  Google Scholar 

  21. 21.

    Gobbin D, Hoegger PJ, Heiniger U, Rigling D (2003) Sequence variation and evolution of Cryphonectria hypovirus 1 (CHV-1) in Europe. Virus Res. 97:39–46. https://doi.org/10.1016/S0168-1702(03)00220-X

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Sotirovski K, Milgroom MG, Rigling D, Heiniger U (2006) Occurrence of Cryphonectria hypovirus 1 in the chestnut blight fungus in Macedonia. For. Pathol. 36:136–143. https://doi.org/10.1111/j.1439-0329.2006.00443.x

    Article  Google Scholar 

  23. 23.

    Krstin L, Novak-Agbaba S, Rigling D, Krajačić M, Ćurković-Perica M (2008) Chestnut blight fungus in Croatia: diversity of vegetative compatibility types, mating types and genetic variability of associated Cryphonectria hypovirus 1. Plant Pathol. 57:1086–1096. https://doi.org/10.1111/j.1365-3059.2008.01905.x

    Article  Google Scholar 

  24. 24.

    Robin C, Lanz S, Soutrenon A, Rigling D (2010) Dominance of natural over released biological control agents of the chestnut blight fungus Cryphonectria parasitica in south-eastern France is associated with fitness-related traits. Biol. Control 53:55–61. https://doi.org/10.1016/j.biocontrol.2009.10.013

    Article  Google Scholar 

  25. 25.

    Krstin L, Novak-Agbaba S, Rigling D, Ćurković-Perica M (2011) Diversity of vegetative compatibility types and mating types of Cryphonectria parasitica in Slovenia and occurrence of associated Cryphonectria hypovirus 1. Plant Pathol. 60:752–761. https://doi.org/10.1111/j.1365-3059.2011.02438.x

    Article  Google Scholar 

  26. 26.

    Montenegro D, Aguín O, Sainz MJ, Hermida M, Mansilla JP (2008) Diversity of vegetative compatibility types, distribution of mating types and occurrence of hypovirulence of Cryphonectria parasitica in chestnut stands in NW Spain. For. Ecol. Manag. 256:973–980. https://doi.org/10.1016/j.foreco.2008.05.056

    Article  Google Scholar 

  27. 27.

    Zamora P, Martín AB, Rigling D, Diez JJ (2012) Diversity of Cryphonectria parasitica in western Spain and identification of hypovirus-infected isolates. For. Pathol. 42:412–419. https://doi.org/10.1111/j.1439-0329.2012.00775.x

    Article  Google Scholar 

  28. 28.

    Akilli S, Ulubaş Serçe Ç, Katircioǧlu YZ, Maden S, Rigling D (2013) Characterization of hypovirulent isolates of the chestnut blight fungus, Cryphonectria parasitica from the Marmara and Black Sea regions of Turkey. Eur. J. Plant Pathol. 135:323–334. https://doi.org/10.1007/s10658-012-0089-z

    CAS  Article  Google Scholar 

  29. 29.

    Chen B, Nuss DL (1999) 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. 73:985–992

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Bryner SF, Rigling D (2011) Temperature-dependent genotype-by-genotype interaction between a pathogenic fungus and its hyperparasitic virus. Am. Nat. 177:65–74. https://doi.org/10.1086/657620

    Article  PubMed  Google Scholar 

  31. 31.

    Krstin L, Katanić Z, Ježić M, Poljak I, Nuskern L, Matković I, Idžojtić M, Ćurković-Perica M (2017) Biological control of chestnut blight in Croatia: an interaction between host sweet chestnut, its pathogen Cryphonectria parasitica and the biocontrol agent Cryphonectria hypovirus 1. Pest Manag. Sci. 73:582–589. https://doi.org/10.1002/ps.4335

    CAS  Article  PubMed  Google Scholar 

  32. 32.

    Nuskern L, Tkalec M, Ježić M, Katanić Z, Krstin L, Ćurković-Perica M (2017) Cryphonectria hypovirus 1-induced changes of stress enzyme activity in transfected phytopathogenic fungus Cryphonectria parasitica. Microb. Ecol. 74:302–311. https://doi.org/10.1007/s00248-017-0945-7

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Bauman JM (2015) A comparison of the growth and asexual reproduction by Cryphonectria parasitica isolates infected with hypoviruses CHV3-County Line, CHV1-Euro7, and CHV1-Ep713. Am. J. Plant Sci. 6:73–83

    Article  Google Scholar 

  34. 34.

    Ježić M, Krstin L, Poljak I, Liber Z, Idžojtić M, Jelić M, Meštrović J, Zebec M, Ćurković-Perica M (2014) Castanea sativa: genotype-dependent recovery from chestnut blight. Tree Genet. Genomes 10:101–110. https://doi.org/10.1007/s11295-013-0667-z

    Article  Google Scholar 

  35. 35.

    Cortesi P, Milgroom MG (1998) Genetics of vegetative incompatibility in Cryphonectria parasitica. Appl. Environ. Microbiol. 64:2988–2994

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Schulz B, Eckstein RL, Durka W (2014) Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb. Mol. Ecol. 23:3523–3537. https://doi.org/10.1111/mec.12835

    Article  PubMed  Google Scholar 

  37. 37.

    Herrmann D, Poncet BN, Manel S, Rioux D, Gielly L, Tabarlet P, Gugerli F (2010) Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Genome / Natl Res Counc Canada 53:302–310. https://doi.org/10.1139/G10-006

    CAS  Article  Google Scholar 

  38. 38.

    Schulz B, Eckstein RL, Durka W (2013) Scoring and analysis of methylation-sensitive amplification polymorphisms for epigenetic population studies. Mol. Ecol. Resour. 13:642–653. https://doi.org/10.1111/1755-0998.12100

    CAS  Article  PubMed  Google Scholar 

  39. 39.

    Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Paleontol Electron 4:1–9

    Google Scholar 

  40. 40.

    Howitt RLJ, Beever RE, Pearson MN, Forster RLS (2001) Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus resembling plant “potex-like” viruses. J Gen Virol 82:67–78. https://doi.org/10.1007/s00705-005-0621-y

    CAS  Article  PubMed  Google Scholar 

  41. 41.

    Howitt RLJ, Beever RE, Pearson MN, Forster RLS (2006) Genome characterization of a flexuous rod-shaped mycovirus, Botrytis virus X, reveals high amino acid identity to genes from plant “potex-like” viruses. Arch. Virol. 151:563–579. https://doi.org/10.1007/s00705-005-0621-y

    CAS  Article  PubMed  Google Scholar 

  42. 42.

    Xie J, Wei D, Jiang D, Fu Y, Li G, Ghabrial S, Peng Y (2006) Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotina sclerotorium. J Gen Virol 87:241–249. https://doi.org/10.1099/vir.0.81522-0

    CAS  Article  PubMed  Google Scholar 

  43. 43.

    Shapira R, Choi GH, Nuss DL (1991) Virus-like genetic organization and expression strategy for a double-stranded RNA genetic element associated with biological control of chestnut blight. EMBO J. 10:731–739

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Deng F, Allen TD, Hillman BI, Nuss DL (2007) Comparative analysis of alterations in host phenotype and transcript accumulation following hypovirus and mycoreovirus infections of the chestnut blight fungus Cryphonectria parasitica. Eukaryot. Cell 6:1286–1298. https://doi.org/10.1128/EC.00166-07

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  45. 45.

    Lee KM, Cho WK, Yu J, Son M, Choi H, Min K, Lee YW, Kim KH (2014) A comparison of transcriptional patterns and mycological phenotypes following infection of Fusarium graminearum by four mycoviruses. PLoS One 9:e100989. https://doi.org/10.1371/journal.pone.0100989

    Article  PubMed  PubMed Central  Google Scholar 

  46. 46.

    Li H, Fu Y, Jiang D, Li G, Ghabrial SA, Yi X (2008) Down-regulation of Sclerotinia sclerotiorum gene expression in response to infection with Sclerotinia sclerotiorum debilitation-associated RNA virus. Virus Res. 135:95–106. https://doi.org/10.1016/j.virusres.2008.02.011

    CAS  Article  PubMed  Google Scholar 

  47. 47.

    Wang H, Hao L, Shung CY, Sunter G, Bisaro DM (2003) Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. Plant Cell 15:3020–3032. https://doi.org/10.1105/tpc.015180.Beet

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Yang X, Xie Y, Raja P, Li S, Wolf JN, Shen Q, Bisaro DM, Zhou X (2011) Suppression of methylation-mediated transcriptional gene silencing by βc1-SAHH protein interaction during geminivirus-betasatellite infection. PLoS Pathog. 7:e1002329. https://doi.org/10.1371/journal.ppat.1002329

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Birdwell CE, Queen KJ, Kilgore P, Rollyson P, Trutschl M, Cvek U, Scott RS (2014) Genome-wide DNA methylation as an epigenetic consequence of Epstein-Barr virus infection of immortalized keratinocytes. J. Virol. 88:11442–11458. https://doi.org/10.1128/JVI.00972-14

    Article  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Sotirovski K, Rigling D, Heiniger U, Milgroom MG (2011) Variation in virulence of Cryphonectria hypovirus 1 in Macedonia. For. Pathol. 41:59–65. https://doi.org/10.1111/j.1439-0329.2009.00637.x

    Article  Google Scholar 

Download references

Acknowledgements

This research was funded by Croatian Science Foundation (project no. 5381) and SNSF (SCOPES project no. IZ73Z0_152525/1). We thank Dr. Daniel Rigling for providing the virus strains EP713 and SHE30 and Dr. Zlatko Šatović for the useful suggestions on data analysis.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Mirna Ćurković-Perica.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Nuskern, L., Ježić, M., Liber, Z. et al. Cryphonectria hypovirus 1-Induced Epigenetic Changes in Infected Phytopathogenic Fungus Cryphonectria parasitica . Microb Ecol 75, 790–798 (2018). https://doi.org/10.1007/s00248-017-1064-1

Download citation

Keywords

  • Fungus-mycovirus interaction
  • Biotic stress
  • MSAP epigenotyping
  • Biocontrol
  • Chestnut blight