Ph.D.,
Indiana University, 1982.
Professor
Editor, Virology
Dept.
of Cell Biology and Molecular Genetics
University
of Maryland
College
Park, Maryland 20742
Telephone:
(301) 405-8975
E-mail:
simona@umd.edu
Research
Interest: Virus replication and symptom production
Fax:
(301) 314-7930
Last web page:
http://www.life.umd.edu/CBMG/faculty/asimon
We have developed the turnip crinkle virus (TCV) system as a model to study sequences and structures involved in replication and recombination of RNA templates and the interactions between the virus, host and parasitic subviral RNAs that lead to symptom production or host resistance. TCV (4054 bases) is among the smallest and simplest of the single component RNA viruses and is associated with numerous small, dispensable subviral RNAs (194 to 356 bases). Since subviral RNAs use the virus-encoded RNA-dependent RNA polymerase (RdRp) for replication, it is possible to use these simple, non-protein-coding RNAs as templates in replication and recombination studies. We have developed whole plant (turnip and Arabidopsis), protoplast (single plant cell) and in vitro (cell free) systems with which to study the replication and recombination of viral genomic and subviral RNAs. In addition, subviral RNAs can modulate the symptoms of their helper viruses. Depending on the biological context, TCV subviral RNA satC can intensify or attenuate the symptoms of TCV on host plants.
A major theme of my lab's research is the specific interactions between proteins and RNA that mediate biological processes. For example, we have identified the smallest independent promoters for an RdRp: (i) a 29 base sequence at the 3' end of satC, comprised of a small required hairpin that is sequence non-specific and a required 3' end single-stranded CCUGCCC motif; and (ii) two 11-base sequences, without obvious secondary structure, located near the 3' and 5' ends of satC minus strand that can both function as independent promoters in vitro. The poor processivity of the TCV RdRp leads to the frequent generation of recombinants between the subviral RNAs, and between the subviral RNAs and the TCV genomic RNA. Recombination occurs at sequences that resemble promoter elements and such sequences search as enhancers in vivo. By using in vivo SELEX, where promoter and promoter-like elements are randomized and active sequences selected in the plant, we can determine the precise need for individual bases or motifs.
1. Guan, H and Simon, A. E. (2000) Polymerization of non-template bases prior to transcription initiation by an RNA-dependent RNA polymerase: A novel activity involved in 3'-end repair of viral RNAs. Proc. Natl. Acad. Sci. 97, 12451-12456.
2. Wang, J. and Simon, A. E. (2000) 3'-end stem-loops of the subviral RNAs associated with turnip crinkle virus are involved in symptom modulation and coat protein binding. J. Virol. 74, 6528-6537.
3. Guan, H., Carpenter, C. D., and Simon, A. E. (2000) Requirement of a 5'-proximal linear sequence on minus strands for plus-strand synthesis of a satellite RNA associated with TCV. Virology 268, 355-363.
4. Guan, H., Carpenter, C. D., and Simon, A. E. (2000) Analysis of cis-acting sequences involved in plus-strand synthesis of a TCV-associated satellite RNA identifies a new carmovirus replication element. Virology 268, 345-354.
5. Nagy, P. E., Pogany, J., and Simon, A. E. (1999) RNA elements required for RNA recombination function as replication enhancers in vitro and in vivo in a plus strand RNA virus. EMBO J 18, 5653-5665.
6. Wang, J. and Simon, A. E. (1999) Symptom Attenuation By A Satellite RNA In Vivo Is Dependent On Reduced Levels of Virus Coat Protein. Virology 259, 234-245.
7. Wang, J., Carpenter, C. D., and Simon, A. E. (1999) Minimal sequence and structural requirements of a subgenomic RNA promoter for turnip crinkle virus. Virology 253, 327-336.
8. Nagy, P. D., and Simon, A. E. (1998) In vitro characterization of late steps of RNA recombination in turnip crinkle virus I: role of the motif1-hairpin structure. Virology 249, 379-392.
9. Nagy, P. D., and Simon, A. E. (1998) In vitro characterization of late steps of RNA recombination in turnip crinkle virus II: role of the priming stem and flanking sequences. Virology 249, 393-405.
10. Carpenter, C. D., and Simon, A. E. (1998) Analysis of sequenc es and putative structures required for viral satellite RNA accumulation by in vivo genetic selection. Nucleic Acids Res. 26, 2426-2432.
11. Nagy, P. D., Zhang, C., and Simon, A. E. (1998) Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase. EMBO J. 17, 2392-2403.
12. Guan, H., Song, C., and Simon, A. E. (1997) RNA promoters located on (-)-strands of a subviral RNA associated with turnip crinkle virus. RNA 3, 1401-1412.
13. Stupina, V., and Simon, A. E. (1997) Analysis in vivo of turnip crinkle virus satellite RNA C variants with mutations in the 3' terminal minus strand promoter. Virology 238, 470-477.
14. Kong, Q., Oh, J.-W., Carpenter, C. D. and Simon, A. E. (1997) The coat protein of turnip crinkle virus is involved in subviral RNA-mediated symptom modulation and accumulation. Virology 238, 478-485.
15. Kong, Q., Wang, J., and Simon, A. E. (1997) Satellite RNA-mediated resistance to turnip crinkle virus in Arabidopsis involves a reduction in virus movement. Plant Cell 9, 2051-2063.
16. Wang, J. and Simon, A. E. (1997) Analysis of the two subgenomic RNA promoters for turnip crinkle virus in vivo and in vitro. Virology 232, 174-186.
17. Kreps, J. A, and Simon, A. E. (1997) Environmental and genetic effects on circadian regulated gene expression in Arabidopsis thaliana. Plant Cell 9, 297-304
18. Nagy, P. D., Carpenter, C. D., and Simon, A. E. (1997) A novel 3' end repair mechanism in an RNA virus. Proc. Natl. Acad. Sci. USA. 94, 1113-1118.
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