We study the structure and function of RNA elements involved in cap-independent translation of plus-strand RNA viruses. The goals of our research are: (1) to understand how translation of genomic and subgenomic RNAs is controlled by 3' elements using carmoviruses and umbraviruses; (2) the process that allows ribosomes to read-through or frameshift at a specific location to synthesize the viral RNA-dependent RNA polymerase; and (3) how virus levels are controlled by nonsense mediated decay.
NEWS FROM THE SIMON LAB
Past and Present
Listen to podcast of Anne Simon discussing women in STEM
Anne Simon elected to the American Academy of Microbiology. Check out an interview with ASM on this link
Congratulations to My-Tra Le, (PhD 2016) now postdoc at Indiana University
Congratulations to Micki Kuhlmann (PhD 2016) now postdoc at the NCI
Congratulations to Maitreyi Chattopadhyay (PhD 2015) now research scientist at the FDA
Congratulations to Megan Young (PhD 2015) now research scientist, industry
Congratulations to Rong Guo (PhD 2011) Now a permanent regulatory officer at the FDA
Congratulations to Xiaoping Sun. (PhD 2006) Professor, Wuhan University
Congratulations to Xuefeng Yuan (Postdoc 2007-2012) Professor, Shandong Agricultural University
Congratulations to Kerong Shi (Postdoc 2008-2010) Associate Professor, Shandong Agricultural University
Congratulations to Jong-Won Oh (PhD 1997) Associate Professor at Yonsei University in Seoul, Korea
Congratulations to Qingzhong Kong (PhD 1997) Associate Professor at Case Western University
Congratulations to Hancheng Guan (PhD 1999) Research Associate Professor, University of Pennsylvania
Congratulations to Jianlong Wang (PhD 1999) Associate Professor, Mount Sinai School of Medicine
Congratulations to Peter Nagy Postdoc (1997-1999) Professor at University of Kentucky
Congratulations to Jiuchun Zhang (PhD 2006) Postdoc at University of Wisconsin
Congratulations to Fengli Zhang (PhD 2007) Senior Microbiologist, Wisconsin State Laboratory of Hygiene
Kwon, S-J, Bodaghi, S, Gadhave, KR, Tzanetakis, IE, Simon, AE, and Vidalakis, G. 2021. Complete nucleotide sequence, genome organization and comparative genomic analyses of citrus yellow-vein associated virus, an umbravirus-like associated virus-like RNA. Front Microbiol, in press.
Liu, J., Carino, E., Bera, S., Gao, F., May, J.P., and Simon, A.E. 2021. Structural analysis and whole genome mapping of a new class of plant virus subviral RNAs: umbravirus-Like associated RNAs. Viruses 13, 646; https://doi.org/10.3390/v13040646.
May, J.P. and Simon, A.E. 2021. Targeting of viral RNAs by Upf1-mediated RNA decay pathways. Curr Opin Virol 47, 1-8.
Ilyas, M, Du, Z. and Simon, A.E. 2021. Opium poppy mosaic virus has an Xrn-resistant, translated subgenomic RNA and a BTE 3’ CITE. J Virol 95 (9): e02109-20 DOI: 10.1128/JVI.02109-20 [SPOTLIGHT selection]
May, J.P., Johnson, P.Z., Ilyas, M., Gao, F., and Simon, A.E. 2020. Disruption of nonsense-mediated decay by the multifunctional long-distance movement protein of Pea enation mosaic virus 2. Mbio 11:e00204-20. https://doi.org/10.1128/mBio
Johnson, P.Z., Kasprzak, W.K., Shapiro, B.A., and Simon, A.E. 2019. RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences. RNA Biol https://doi.org/10.1080/15476286.2019.1659081
May, J.P., Yuan, X-F., Sawicki, E., and Simon, A.E. 2018. RNA virus evasion of nonsense-mediated decay. PLoS Pathog 14(11): e1007459. https://doi.org/10.1371/journal.ppat.1007459
Gao, F., Alekhina, O.M., Vassilenko, K.S., and Simon, A.E. 2018. Unusual dicistronic expression from closely-spaced initiation codons of overlapping open reading frames in Pea enation mosaic virus 2. Nucleic Acids Res 46, 11726–11742 doi: 10.1093/nar/gky871
Gao, F. and Simon, A.E.2017. Differential use of 3’CITEs by the subgenomic RNA of Pea enation mosaic virus 2. Virology 510, 194-204.
Du, Z., Alekhina, O.M., Vassilenko, K.S., and Simon, A.E. 2017. Concerted action of two 3’ cap-independent translation enhancers increases the competitive strength of translated viral genomes. Nucleic Acids Res. doi: 10.1093/nar/gkx643
Aguado, L.C., Schmid, S., May, J., Sabin, L.R., Panis, M., Blanco-Melo, D., Shim, J.V., Sachs, D., Cherry, S., Simon, A.E., Levraud, J.P. and tenOever, B.R. 2017. RNase III nucleases from diverse kingdoms serve as antiviral effectors. Nature 547,114–117
Le, M.-T., Kasprzak, W.K., Kim, T., Gao, F., Young, M.Y.L, Yuan, X., Shapiro, B.A., Seog, J., and Simon, A.E. 2017. Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch. RNA Biology (Solicited Point of View), in press.
Le, M.-T., Kasprzak, W.K., Kim, T., Gao, F., Young, M.Y.L, Yuan, X., Shapiro, B.A., Seog, J., and Simon, A.E. 2017. Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch. eLife 6:e22883. https://t.co/JwfvZSZOmd
May, J., Johnson, P., Saleen, H., and Simon, A.E. 2017. A sequence-independent, unstructured IRES is responsible for internal expression of the coat protein of Turnip crinkle virus. J Virol 91, e02421 [SPOTLIGHT selection].