All viruses depend on the host's translation (protein synthesis) machinery. For this reason, host cells have evolved numerous antiviral mechanisms that shut down or otherwise regulate translation. In the molecular arms race, viruses, in turn, have evolved ways to bypass host translational control. It is this essential step in virus replication that is the focus of this proposal. Host mRNAs contain a 5'"cap" structure and a 3'poly(A) tail that interact with translation initiation factors which recruit the ribosome to the mRNA. In contrast, the RNAs of most RNA viruses are uncapped, so they have evolved RNA structures that recruit the ribosome by noncanonical, cap-independent mechanisms. Many uncapped plant viral RNAs contain a cap-independent translation element (CITE) in the 3'untranslated region that facilitates efficient ribosome entry at the 5'end of the genome. In NIH-funded research the PI's lab showed that this is facilitated by long-distance base pairing between the 3'CITE, which binds a translation initiation factor, and the 5'untranslated region. Unanswered is how the CITE RNA structure causes it to bind a translation initiation factor with high affinity, leading to recruitment of the ribosome. Here, a variety of approaches will be applied to determine the structural requirements of two unrelated 3'CITEs, and the translation factors with which they interact. These include (i) the Barley yellow dwarf virus-like translation element (BTE) which binds and requires initiation factor eIF4G and not eIF4E;and (ii) the Panicum mosaic virus-like translation element (PTE), which binds and requires eIF4E - a protein known previously to bind only to the 5'cap structure. The three aims all can be performed independently, but the knowledge gained from each will feed into the other two aims.
Aim I uses multiple, factor-depletable translation systems of mutant CITEs and mutant cognate translation factors with which they interact. This will reveal the key nucleotides and amino acids required for interaction and translation function.
The second aim uses a variety of methods to measure the interactions of the mutant CITEs with mutant translation factors.
The third aim will determine CITE structure at high resolution by ion-dependent RNA folding and X-ray crystallography methods. This project will provide a new understanding of the way in which viruses take over the cell, which may, in turn, suggest potential targets for antiviral drugs. Although this work focuses on model plant viruses, many growing human viruses such as dengue and hepatitis C viruses use similar mechanisms. Also, this work will shed new light on how the translational machinery works, and the translation system is extremely highly conserved between plants and animals. For example, the PTE functions in mammalian cells and we will use human cells and extracts to study how it uses eIF4E to usurp the ribosomes. Over-active eIF4E causes tumors and restriction of its function inhibits many types of cancers. The tightly binding PTE RNA may provide structural knowledge for design of eIF4E-inhibiting cancer therapeutics.

Public Health Relevance

This research explores mechanisms by which model plant viruses take over the protein synthesis (translation) machinery of the host cell. Because this machinery is highly conserved between plants and animals, this research is relevant to human medicine, including behavior of human viruses and even cancer genes, which also take over the same components of the cellular translation system. Moreover, understanding how plant viruses synthesize proteins so efficiently may allow exploitation of their mechanisms for efficient production of pharmaceutical proteins in plant systems.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM067104-10
Application #
8667461
Study Section
Virology - A Study Section (VIRA)
Program Officer
Bender, Michael T
Project Start
2003-07-01
Project End
2017-02-28
Budget Start
2014-03-01
Budget End
2015-02-28
Support Year
10
Fiscal Year
2014
Total Cost
$275,881
Indirect Cost
$65,741
Name
Iowa State University
Department
Other Basic Sciences
Type
Schools of Earth Sciences/Natur
DUNS #
005309844
City
Ames
State
IA
Country
United States
Zip Code
50011
Miller, W Allen; Shen, Ruizhong; Staplin, William et al. (2016) Noncoding RNAs of Plant Viruses and Viroids: Sponges of Host Translation and RNA Interference Machinery. Mol Plant Microbe Interact 29:156-64
Smirnova, Ekaterina; Firth, Andrew E; Miller, W Allen et al. (2015) Discovery of a Small Non-AUG-Initiated ORF in Poleroviruses and Luteoviruses That Is Required for Long-Distance Movement. PLoS Pathog 11:e1004868
Sharma, Sohani Das; Kraft, Jelena J; Miller, W Allen et al. (2015) Recruitment of the 40S ribosome subunit to the 3'-untranslated region (UTR) of a viral mRNA, via the eIF4 complex, facilitates cap-independent translation. J Biol Chem 290:11268-81
Miller, W Allen; Jackson, Jacquelyn; Feng, Ying (2015) Cis- and trans-regulation of luteovirus gene expression by the 3' end of the viral genome. Virus Res 206:37-45
Miras, Manuel; Sempere, Raquel N; Kraft, Jelena J et al. (2014) Interfamilial recombination between viruses led to acquisition of a novel translation-enhancing RNA element that allows resistance breaking. New Phytol 202:233-46
Simon, Anne E; Miller, W Allen (2013) 3' cap-independent translation enhancers of plant viruses. Annu Rev Microbiol 67:21-42
Kraft, Jelena J; Treder, Krzysztof; Peterson, Mariko S et al. (2013) Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G. Nucleic Acids Res 41:3398-413
Fan, Qiuling; Treder, Krzysztof; Miller, W Allen (2012) Untranslated regions of diverse plant viral RNAs vary greatly in translation enhancement efficiency. BMC Biotechnol 12:22
Wang, Zhaohui; Parisien, Marc; Scheets, Kay et al. (2011) The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element. Structure 19:868-80
Kraft, Jelena J; Hoy, Julie A; Miller, W Allen (2011) Crystallization and preliminary X-ray diffraction analysis of the barley yellow dwarf virus cap-independent translation element. Acta Crystallogr Sect F Struct Biol Cryst Commun 67:561-4

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