Structural Domains Within the 3′ UTR of Turnip Crinkle Virus.
June 28th, 2008 | by admin |Structural Domains Within the 3\’ UTR of Turnip Crinkle Virus.
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 H4, H5, and Pr) and one H-type pseudoknot (Psi3) within the 3\’ terminal 194 nt. In vivo compensatory mutagenesis analyses confirmed the existence of H4a, H4b, Psi3 and a second pseudoknot (Psi2) previously identified in a TCV satellite RNA. In-line structure probing of the 194-nt fragment supported the co-existence of H4, H4a, H4b, Psi3 and a pseudoknot that connects H5 and the 3\’ end (Psi1). 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 Psi3, H4a and H4b or Psi3, H4a, H4b, H5 and Psi2, form functional domains for virus accumulation in vivo. A new 3-D molecular modeling protocol (RNA2D3D) predicted that H4a, H4b, H5, Psi3 and Psi2 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\’ UTR sequences such as translation and replication.
McCormack JC, Yuan X, Yingling YG, Kasprzak W, Zamora RE, Shapiro BA, Simon AE.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA; Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702 USA; Basic Research Program, SAIC-Frederick, Inc., NCI Frederick, Frederick, MD 21702 USA.