Aurelie Rakotondrafara

Assistant Professor

Phone: 608-890-1871

793 Russell Labs
1630 Linden Dr
Madison, WI 53706


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

Research Interests

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. Read more at Lab Profile.

Courses Taught

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


J. Zhang, R. Roberts, A. Rakotondrafara (2015). The role of the 5’ untranslated region in Potyviridae. Virus Research 206:74-81

E. Smirnova; A. E. Firth; W. Allen Miller; D. Scheidecker; V. Brault; C. Reinbold; A. M. Rakotondrafara; B. Y.-W. Chung; V. Ziegler-Graff (2015) Discovery of a small non-AUG-initiated ORF in poleroviruses and luteoviruses that is required for long-distance movement of Turnip yellows virus. PLos Pathogens 11(5):e1004868

A.M. Rakotondrafara and M.W. Hentze, MW. (2011). An efficient factor-depleted mammalian in vitro translation system. Nature Protocols. 6(5):563-71

A.V. Pisarev, M.A. Skabkin, V.P. Pisareva, O.V. Skabkina, A.M. Rakotondrafara, M.W. Hentze,C.T. Hellen, T.V. Pestova (2010).The role of ABCE1 in eukaryotic post-termination ribosomal recycling. Molecular Cell. 37:196-210.

A.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.

A.M. Rakotondrafara, Jacquelyn Jackson, Elizabeth Pettit Kneller, W. Allen Miller (2007). Preparation of oat protoplasts for electroporation. Current Protocols of Microbiology. 16D.3.1-16D.3.12. John Wiley & Sons Inc.

A.M. Rakotondrafara, C. Polacek, E. Harris, 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.

R. Shen*, A.M. Rakotondrafara*, W.A. Miller (2006). Trans-regulation of translation by a viral subgenomic RNA. Journal of Virology 80:10045-10054 *co-first authors.

E. Pettit Kneller, A.M. Rakotondrafara W. Allen Miller (2006). Cap-independent translation of plant viral RNAs. Virus Research, 119, 63-75.