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Journal of Virology, September 2008, p. 8706-8720, Vol. 82, No. 17
0022-538X/08/$08.00+0     doi:10.1128/JVI.00416-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Structural Domains within the 3' Untranslated Region of Turnip Crinkle Virus{triangledown}

John C. McCormack,1 Xuefeng Yuan,1 Yaroslava G. Yingling,2 Wojciech Kasprzak,3 Rodolfo E. Zamora,1 Bruce A. Shapiro,2 and Anne E. Simon1*

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742,1 Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702,2 Basic Research Program, SAIC-Frederick, Inc., NCI Frederick, Frederick, Maryland 217023

Received 26 February 2008/ Accepted 16 June 2008

The genomes of positive-strand RNA viruses undergo conformational shifts that complicate efforts to equate structures with function. We have initiated a detailed analysis of secondary and tertiary elements within the 3' end of Turnip crinkle virus (TCV) that are required for viral accumulation in vivo. MPGAfold, a massively parallel genetic algorithm, suggested the presence of five hairpins (H4a, H4b, and previously identified hairpins H4, H5, and Pr) and one H-type pseudoknot ({Psi}3) within the 3'-terminal 194 nucleotides (nt). In vivo compensatory mutagenesis analyses confirmed the existence of H4a, H4b, {Psi}3 and a second pseudoknot ({Psi}2) previously identified in a TCV satellite RNA. In-line structure probing of the 194-nt fragment supported the coexistence of H4, H4a, H4b, {Psi}3 and a pseudoknot that connects H5 and the 3' end ({Psi}1). Stepwise replacements of TCV elements with the comparable elements from Cardamine chlorotic fleck virus indicated that the complete 142-nt 3' end, and subsets containing {Psi}3, H4a, and H4b or {Psi}3, H4a, H4b, H5, and {Psi}2, form functional domains for virus accumulation in vivo. A new 3-D molecular modeling protocol (RNA2D3D) predicted that H4a, H4b, H5, {Psi}3, and {Psi}2 are capable of simultaneous existence and bears some resemblance to a tRNA. The related Japanese iris necrotic ring virus does not have comparable domains. These results provide a framework for determining how interconnected elements participate in processes that require 3' untranslated region sequences such as translation and replication.

* Corresponding author. Mailing address: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742. Phone: (301) 405-8975. Fax: (301) 805-1318. E-mail: simona{at}umd.edu

{triangledown} Published ahead of print on 25 June 2008.

Journal of Virology, September 2008, p. 8706-8720, Vol. 82, No. 17
0022-538X/08/$08.00+0     doi:10.1128/JVI.00416-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Yuan, X., Shi, K., Meskauskas, A., Simon, A. E. (2009). The 3' end of Turnip crinkle virus contains a highly interactive structure including a translational enhancer that is disrupted by binding to the RNA-dependent RNA polymerase. RNA 15: 1849-1864 [Abstract] [Full Text]  
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  • Guo, R., Lin, W., Zhang, J., Simon, A. E., Kushner, D. B. (2009). Structural Plasticity and Rapid Evolution in a Viral RNA Revealed by In Vivo Genetic Selection. J. Virol. 83: 927-939 [Abstract] [Full Text]  
  • Stupina, V. A., Meskauskas, A., McCormack, J. C., Yingling, Y. G., Shapiro, B. A., Dinman, J. D., Simon, A. E. (2008). The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits. RNA 14: 2379-2393 [Abstract] [Full Text]  


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