• BISI - BISI-Molecular & Cellular Biology (MOCB)

We use small plus-strand RNA viruses to study sequences and structures involved in translation and replication and the switch between these two activities, which are incompatible with each other.  We also study the evolution of 3' translational enhancers and the overlp between translation elements and replication elements.

Precise temporal control is needed for RNA viral genomes to translate sufficient replication-required products before clearing ribosomes and initiating replication. We study the switch between translation and replication using small RNA virus model systems that are translated using a cap-independent mechanism:  Turnip crinkle virus (TCV),  Saguaro cactus virus (SCV), and Pea enation mosaic virus (PEMV).  We recently discovered a new paradigm for translation, where a 3’ translational enhancer in TCV overlaps an internal tRNA-like structure that binds to 60S ribosomal subunits.  We investigate the higher order structure in the region and have found that the tRNA-like structure forms a stable scaffold that allows for simultaneous interactions with external sequences through base pairings on both sides of its large internal symmetrical loop. Binding of TCV RNA-dependent RNA polymerase (RdRp) to the region potentiates a widespread conformational shift with substantial rearrangement of the element required for efficient ribosome binding.  The 3’ end of TCV folds into a compact, highly interactive structure allowing RdRp access to multiple elements including the 3’ end, which causes structural changes that potentiate the shift between translation and replication.  Surprisingly, only one other virus in the same genus as TCV contains a tRNA-like structure in the 3’UTR, and thus we investigate SCV to determine if its Y-shaped structure performs similar functions.

Current Research

Precise temporal control is needed for RNA viral genomes to translate sufficient replication-required products before clearing ribosomes and initiating replication. We study the switch between translation and replication using small RNA virus model systems that are translated using a cap-independent mechanism:  Turnip crinkle virus (TCV),  Saguaro cactus virus (SCV), and Pea enation mosaic virus (PEMV).  We recently discovered a new paradigm for translation, where a 3’ translational enhancer in TCV overlaps an internal tRNA-like structure that binds to 60S ribosomal subunits.  We investigate the higher order structure in the region and have found that the tRNA-like structure forms a stable scaffold that allows for simultaneous interactions with external sequences through base pairings on both sides of its large internal symmetrical loop. Binding of TCV RNA-dependent RNA polymerase (RdRp) to the region potentiates a widespread conformational shift with substantial rearrangement of the element required for efficient ribosome binding.  The 3’ end of TCV folds into a compact, highly interactive structure allowing RdRp access to multiple elements including the 3’ end, which causes structural changes that potentiate the shift between translation and replication.  Surprisingly, only one other virus in the same genus as TCV contains a tRNA-like structure in the 3’UTR, and thus we investigate SCV to determine if its Y-shaped structure performs similar functions.

Bayne, C.F., Widawski, M.E., Gao, F., Masab, M.H., Chattopadhyay, M., Murawski, A.M., Sansever, R.M., Lerner, B.D., Castillo, R.J., Griesman, T.M., Fu, J., Hibben, J.K., Perez, A.D., Simon, A.E., and Kushner, D.B.  In vivo SELEX reveals that 5’ domain of Turnip crinkle virus satellite RNA exists in both open and zipped forms.  Manuscript in preparation.

Gao, F., Alekhina, O.M., Vassilenko, K.S., and Simon, A.E.  Non-leaky scanning translation of closely spaced initiation codons for overlapping viral open-reading frames.  Manuscript in preparation.

Johnson, P., Gao, F., and Simon, A.E.  A novel replication element associated with umbravirus Pea Enation Mosaic Virus.  Manuscript submitted.     

Gao, F., and Simon, A.E. 2017.  Differential use of 3’ CITEs by the subgenomic RNA of Pea enation mosaic virus 2.  Virology (in press).

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

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.  DOI: 10.1080/15476286.2017.1325069

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.    Evidence for RNaseIII nucleases as the precursors for eukaryotic antiviral defenses.  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.  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. [SPOTLIGHT selection] 91, e02421.

Kuhlmann, M.M., Chattopadhyay, M., Stupina, V. A., Gao, F., and Simon, A. E.  2016.  An RNA element that facilitates programmed ribosomal readthrough in Turnip crinkle virus adopts multiple conformations.  J. Virol. 90, 8575-8591.

Gao, F., and Simon, A. E.  2016.  Multiple cis-acting elements modulate programmed-1 ribosomal frameshifting in Pea enation mosaic virus.   Nucleic Acids Res. 44, 878-895.

Le, M.-T., Brown, R. E., Longhini, A. P., Simon, A. E., and Dayie, T. K.  2015. In vivo, site-specific labeling of homogeneous, recombinant RNA in wild type and mutant E. coli for NMR structural studies.  Methods Enzymol. 265, 495-535.

Chattopadhyay, M., Stupina, V.A., Gao, F., Szarko, C.R., Kuhlmann, M.M., Yuan, X., Shi, K., and Simon, A.E.  2015.  Requirement for host RNA silencing components and the virus silencing suppressor when second-site mutations compensate for structural defects in the 3’UTR.  J Virol. 89, 11603-11618.

Murawski, A.M.,  Nieves, J.L., Chattopadhyay, M., Young, M.Y.,  Szarko, C.,  Tajalli, H.F.,  Azad, T.,  Jean-Jacques, N.B.,  Simon, A.E.,  and Kushner, D.B.  2015.  Rapid evolution of in vivo-selected sequences and structures replacing 20% of a subviral RNA.  Virology 483, 149-162.   

Simon, A.E.  2015.  3’UTR of carmoviruses.  Virus Res.  206, 27-36.

Dashtia, A., Schwandera, P., Langloisb, R., Funga, R., Lib, W., Hosseinizadeha, A., Liaob, H.Y., Pallensenc, J., Sharmab, G., Stupina, V.A., Simon, A.E., Dinman, J. D., Frank, J., and Ourmazd, A.  2014.  Trajectories of the ribosome as a Brownian nanomachine.  Proc. Natl. Acad. Sci. USA. 111, 17492–17497

Babaie, G., Habibi, M.K., Massah, A., Dizadji, A., Izadinejad, L., and Simon, A. E.  2014.  Complete genome sequence and genome analysis of Eggplant mottled dwarf virus-Iranian isolate.  J. Phytopathol. 163, 331-341. 

Gao, F., Kasprzak, W, Szarko, C, Shapiro, BA, and Simon, AE.  2014.  The 3' untranslated region of Pea enation mosaic virus contains two T-shaped, ribosome-binding, cap-independent translation enhancers.  J. Virol .88, 11696-11712.  PMCID: PMC4178710

Chattopadhyay, M., Kuhlmann, M., Kumar, K., and Simon, A.E.  2014.  Position of the kissing-loop interaction associated with PTE-type 3’CITEs can affect enhancement of cap-independent translation.  Virology, 458-459, 43-52.  PMCID: PMC4101382

Gao, F., Reddy, S., Kasprzak, W., Shapiro, B.A., Dinman, J.D., and Simon, A.E.  2013. The kissing-loop T-shaped structure translational enhancer of Pea enation mosaic virus can bind simultaneously to ribosomes and a 5′ proximal hairpin.  J. Virol. 87, 11987-2002. PMCID: PMC3807929

Simon, A. E., and Miller, W. A.  2013.   3’ Cap-independent translation enhancers of plant viruses.  Annu. Rev. Microbiol. 67: 21–42. PMCID: PMC4034384

Stupina, V.A. and Simon, A.E.  2013.   Preparation of biologically active Arabidopsis ribosomes and comparison with yeast ribosomes for binding to a tRNA-mimic that enhances translation of plant plus-strand RNA viruses. Front. Plant Sci. 4, 271. doi: 10.3389/fpls.2013.  PMCID: PMC3718319

Gao, F., Kasprzak, W., Stupina, V.A., Shapiro, B.A. and Simon, A.E.  2012.  A ribosome-binding, 3’ translational enhancer has a T-shaped structure and engages in a long distance RNA:RNA interaction.  J. Virol. 86, 9828-9842.  PMCID: PMC3446580

Yuan, X., Shi, K., and Simon, A.E.  2012.  An interactive network of RNA elements supports translation and replication in Turnip crinkle virus.  J. Virol. 86, 4065-4081.  PMCID: PMC3318645

Guo, R., Meskauskas, A., Dinman, J.D., and Simon, A.E.  2011.  Evolution of a helper virus-derived ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus.  Virology 419, 10-16.  PMCID: PMC3176665

B.A., University of California San Diego

Ph.D., Indiana University, 1982

Postdocs, Indiana University, University of California San Diego