Gene regulation of RNA viruses with uncapped and non-polyadenylated genomic RNA

Shen, Ruizhong
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New roles of RNAs as regulators of gene expression have emerged and expanded in recent years. However, gene regulation by viral RNA in trans is less noted and not well understood. Barley yellow dwarf virus (BYDV) is a positive sense RNA virus with a single genomic RNA (gRNA). As it replicates it generates three subgenomic RNAs (sgRNA). Data in this dissertation show that BYDV sgRNA2 serves as a regulatory RNA to control viral gene expression. In vitro and In vivo, BYDV sgRNA2 inhibits translation of gRNA, but has less or little effect on translation of sgRNA1, respectively. These data support and modify a trans-regulation model proposed previously.;I also report that the 3' cap-independent translation element (3'TE) of BYDV functions differently in cis and in trans in plant cells. In cis , the 3'TE confers cap-independent translation and increases translation of capped RNAs as well. In trans, the 3'TE or the 3'TE-containing sgRNA2 serves as a riboregulator to negatively regulate viral replication, most likely via inhibition of translation. Thus a viral subgenomic RNA can perform important regulatory functions instead of acting as a messenger RNA.;RNAs of many important plant and human viruses are translated efficiently in the absence of a 5' cap structure and/or a poly(A) tail. The translation mechanism of the uncapped and non-polyadenylated RNA of Tobacco necrosis virus (TNV) has not been well investigated. Here, I identify a cap-independent translation element (TE) in the 3 ' UTR of TNV strain D (TNV-D) that shares many features with BYDV 3'TE, even though it is in a different family. TNV-D and other members of genus Necrovirus may initiate translation by a BYDV-like TE-mediated cap-independent translation mechanism.;Finally, I show that sequence at the 3' end of TNV-D RNA functionally mimics a poly(A) tail. A phylogenetically conserved double-stem-loop structure is replaceable by, but cannot substitute for a poly(A) tail. The full-length 3' UTR of TNV-D is sufficient to functionally replace a poly(A) tail. Thus, translation of TNV RNA in plant cells requires both cap-mimic and poly(A) mimic elements. This research provides new insight into our understanding of regulation of gene expression.

Plant pathology, Genetics