Aurelie Rakotondrafara

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Associate Professor

Phone: 608-890-1871

793 Russell Labs
1630 Linden Dr
Madison, WI 53706

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  • Ph.D. Iowa State University, Ames, Iowa
  • M.S. Iowa State University, Ames, Iowa
  • B.S. Universite d’Antananarivo, Madagascar


To complete translation, replication and movement through cells, a virus relies mostly on the interactions of its genome and encoded-proteins with host factors.  Knockouts of specific factors or even subtle changes in their properties can trigger a lack of compatibility in plant-virus interactions and failure of the virus to infect its host.  Natural recessive resistance against plant viruses often involves mutations within the host translation initiation factors, which are not detrimental to the host.  To understand how these mutations act as resistance genes, it is imperative to know how RNA viruses are translated and what are the key regulatory elements in the viral RNAs.

The broad objective of my research program will be to delve into the mechanistic details of viral translation control, which will be integrated into the larger context of viral replication and plant virus resistance. Of particular interest is the Potyviridaefamily, which encompasses about 30% of the most damaging crop viruses. These RNA viruses pose a curious conundrum on how they are translated.  Unlike cellular mRNAs which utilize a 5’ m7(G)ppp(G) cap structure and a 3’ poly(A) tail, the Potyviridaerather contain an internal ribosome entry site (IRES) elements, which recruit the ribosomes at internal positions at close proximity of the initiation AUG rather than entering or scanning from the 5’ end.   However, to date, little is known on Potyviridae translational strategies.   


Courses Taught

  • Pl Path/Botany 123 Plants, Parasites, and People
  • Pl Path/Botany/Entom 505 Plant-Microbe Interactions: Molecular and Ecological Aspects


  1. Aiuchi D., Moyo D., Ishikura S., Tani M., Kinoshita R., Rakotondrafara A.M., Koike M. (2020) Virulence of Lecanicillium spp. (Hypocreales cordycipitacea) hybrid strains against various biological stages of the greenhouse whitefly, Trialeurodes vaporariorum (Hemiptera: aleyroidae). Biocontrol Science and Technology 30:9, 1006-1017.
  2. Gutierrez Sanchez P.A., Babujee L., Jaramillo-Mesa J., Gannon M, Halterman D., Jahn M., Jiang J., Rakotondrafara A.M. (2020). The overexpression of a resistant eIF4E allele controls Potato virus Y at the transcriptome level. BCM genomics 2(1):18.doi:10.1186/s12864-019-6423-5
  3. Chowdury R., Lasky D., Karki. H., Zhang Z., Goyer A., Haltermann D., and Rakotondrafara A.M. (2020). Suppression of callose deposition contributes to strain-specificity of the Ny mediated resistance against Potato virus Y. Phytopathology 110(1):1640173.
  4. Kraft J., Peterson M., Ki Cho S., Wang Z., Hui A., Rakotondrafara A.M., Miller C., Miller WA. (2019) The 3’ untranslated region of a plant viral RNA directs efficient cap-independent translation in plant and mammalian systems. Pathogens. 8(1). doi: 3390/pathogens8010028.
  5. Jaramillo Mesa , Gannon M., Holshbach E., Zhang J., Roberts R., Buettner M., and Rakotondrafara A.M. (2019). Triticum mosaic virus IRES relies on a picornavirus-like YX-AUG motif to designate the preferred translation initiation site and to likely target the 18S rRNA. Journal of Virology. 93 (5):1-18.
  6. Babujee L., Witherell R. A., Mikami K., Aiuchi D., Charkowski A.O. and Rakotondrafara A.M. (2019). Optimization of an isothermal recombinase polymerase amplification method for real-time detection of Potato virus Y in potato and single aphids. Journal of Virological Methods 267:16-21.
  7. Treder K., Chołuj J, Zacharzewska , Babujee L., Burzyński A., Rakotondrafara A.M. (2018). Magnetic capture reverse transcription loop-mediated amplification assay to detect and differentiate the N and O Potato virus Y serotypes. Archive of Virology 163. 447-458 doi: 10.1007/s00705-017-3635-3.
  8. Rakotondrafara A.M., Byamukama E., Plumb T. Roger (2017). Virus Diseases of Cereals. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0000762.pub3
  9. Roberts, L. K. Mayberry, K. S. Browning, A.M. Rakotondrafara (2017). Triticum mosaic virus IRES preferentially binds eIF4G over eIFiso4G with distinct usage in translation. PLOS one. 12(1):e0169602. doi: 10.1371/journal.pone.0169602.
  10. Roberts, J. Zhang, N. Mihelich, D. Savino, A.M. Rakotondrafara (2017). Manipulation of oat protoplasts for transient expression assays. Methods in Molecular Biology. Ed. Springer. in “Oats: methods and protocols”. Vol. 1536: Oat, 978-1-4939-6680-6, 334999_1_En, (5)
  11. Roberts, Z. Zhang, L. Mayberry,T. Satyanarayana, K. Browning, and A. M. Rakotondrafara. An atypical plant viral translation element found in Triticum mosaic virus (2015) Journal of Virology (89 (24)-12427-12440.).
  12. Zhang, R. Roberts, and A. M. Rakotondrafara. The role of the 5’ untranslated region of Potyviridae in translation (2015) Virus research 206:74-81
  13. Arcibal, K. Morey Gold, S. Flaherty, J. Jiang, M. Jahn, and A. M. Rakotondrafara. (2015) A mutant eIF4E confers resistance to Potato virus Y strains and is inherited in a dominant manner in the potato varieties Atlantic and Russet Norkotah. American journal of Potato Research. 10.1007/s12230-015-9489-x
  14. Smirnova; A.E. Firth; D. Scheidecker; V. Brault; C. Reinbold; A. M. Rakotondrafara; B.Y.-W. Chung; W. A. Miller and V. Ziegler-Graff. (2015) A small non-AUG-initiated ORF in poleroviruses and luteoviruses is required for long-distance movement. PLOS Pathogens 11(5):e1004868
  15. M. Rakotondrafara and M.W. Hentze, MW. (2011). An efficient factor-depleted mammalian in vitro translation system. Nature Protocols. 6(5):563-71.
  16. V. Pisarev, M.A. Skabkin, V.P. Pisareva, O.V. Skabkina, A.M. Rakotondrafara, M.W. Hentze, C.T. Hellen and T.V. Pestova (2010). The role of ABCE1 in eukaryotic post-termination ribosomal recycling. Molecular Cell. 37:196-210.
  17. M. Rakotondrafara and W. Allen Miller (2008). In vitro analysis of translational enhancers. in Methods in Molecular Biology: Plant Virology Protocols Vol: II, Humana Press 451:113-124.
  18. M. Rakotondrafara, Jacquelyn Jackson, Elizabeth Pettit Kneller and W. Allen Miller (2007). Preparation of oat protoplasts for electroporation. Current Protocols of Microbiology. 16D.3.1-16D.3.12. John Wiley & Sons Inc.
  19. M. Rakotondrafara, C. Polacek, E. Harris and W.A. Miller (2006). Oscillating kissing stem-loop interactions mediate 5’ scanning-dependent translation by a viral 3’ cap-independent translation element. RNA, 12:1893-1906.
  20. Shen*, A.M. Rakotondrafara* and W.A. Miller (2006). Trans-regulation of translation by a viral subgenomic RNA. Journal of Virology 80:10045-10054.
  21. E. Pettit Kneller, A.M. Rakotondrafara and W. Allen Miller (2006). Cap-independent translation of plant viral RNAs. Virus Research, 119, 63-75.