The 3 Untranslated Region of Tobacco Necrosis Virus RNA Contains a Barley Yellow Dwarf Virus-Like Cap-Independent Translation Element

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Shen, Ruizhong
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Miller, W. Allen
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Plant Pathology and Microbiology
The Department of Plant Pathology and Microbiology and the Department of Entomology officially merged as of September 1, 2022. The new department is known as the Department of Plant Pathology, Entomology, and Microbiology (PPEM). The overall mission of the Department is to benefit society through research, teaching, and extension activities that improve pest management and prevent disease. Collectively, the Department consists of about 100 faculty, staff, and students who are engaged in research, teaching, and extension activities that are central to the mission of the College of Agriculture and Life Sciences. The Department possesses state-of-the-art research and teaching facilities in the Advanced Research and Teaching Building and in Science II. In addition, research and extension activities are performed off-campus at the Field Extension Education Laboratory, the Horticulture Station, the Agriculture Engineering/Agronomy Farm, and several Research and Demonstration Farms located around the state. Furthermore, the Department houses the Plant and Insect Diagnostic Clinic, the Iowa Soybean Research Center, the Insect Zoo, and BugGuide. Several USDA-ARS scientists are also affiliated with the Department.
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RNAs of many viruses are translated efficiently in the absence of a 5' cap structure. The tobacco necrosis virus (TNV) genome is an uncapped, nonpolyadenylated RNA whose translation mechanism has not been well investigated. Computational analysis predicted a cap-independent translation element (TE) within the 3' untranslated region (3' UTR) of TNV RNA that resembles the TE of barley yellow dwarf virus (BYDV), a luteovirus. Here we report that such a TE does indeed exist in the 3' UTR of TNV strain D. Like the BYDV TE, the TNV TE (i) functions both in vitro and in vivo, (ii) requires additional sequence for cap-independent translation in vivo, (iii) has a similar secondary structure and the conserved sequence CGGAUCCUGGGAA ACAGG, (iv) is inactivated by a four-base duplication in this conserved sequence, (v) can function in the 5' UTR, and (vi) when located in its natural 3' location, may form long-distance base pairing with the viral 5' UTR that is conserved and probably required. The TNV TE differs from the BYDV TE by having only three helical domains instead of four. Similar structures were found in all members of the Necrovirus genus of the Tombusviridae family, except satellite tobacco necrosis virus, which harbors a different 3' cap-independent translation domain. The presence of the BYDV-like TE in select genera of different families indicates that phylogenetic distribution of TEs does not follow standard viral taxonomic relationships. We propose a new class of cap-independent TE called BYDV-like TE.


This article is from Journal of Virology 78 (2004): 4655, doi: 10.1128/JVI.78.9.4655-4664.2004 . Posted with permission.

Thu Jan 01 00:00:00 UTC 2004