Control of cap-independent translation by a viral 3' UTR

Summary

Principal Investigator: WYATT ALLEN MILLER
Affiliation: Iowa State University
Country: USA
Abstract: DESCRIPTION (provided by applicant): All viruses must take over the host's protein synthesis (translation) machinery. Cellular mRNAs require a 5'cap and poly(A) tail to recruit the ribosome and initiate translation in a regulated manner. Many viral RNAs avoid this control step, and avoid host defenses, by lacking a 5'cap or poly(A) tail. Instead, many viral mRNAs harbor sequences in the untranslated regions (UTRs) that facilitate highly efficient cap-independent translation. Understanding how viruses do this could lead to development of antiviral agents that specifically target unique viral translation mechanisms. This knowledge could also allow exploitation of viruses as gene therapy vectors in humans, or as expression vectors to produce custom pharmaceutical polypeptides in plants. This proposal focuses on the novel cap-independent translation element (BTE) in the 3'UTR of barley yellow dwarf (BYDV) and other viral RNAs that facilitates translation initiation at the 5'end of the RNA. This process requires long-distance base pairing between the 5'and 3'UTRs. Our goal is to determine how the BTE recruits the translational machinery. In Aim I we will determine the sequence and structural requirements of the BTE at high resolution by high volume mutagenesis, and translation in cell-free wheat germ extracts and in plant protoplasts. In Aim II we will dissect the role and structural requirements of translation initiation factors eIF4G and eIF4E, and possibly other factors that are required for BTE-mediated translation. We will observe binding of mutant factors with the BTE RNA by a variety of RNA-protein interaction assays. The functions of mutant factors will be discerned by reconstituting factor-depleted cell-free extracts, and in cells depleted of factors by virus-induced gene silencing. In Aim III, the mechanism of ribosome entry on the RNA will be investigated by sucrose gradient centrifugation of RNA-ribosome complexes, toeprinting, and other approaches. Throughout the project, the role of the BTE and its interactors in virus replication will be assessed. This research on a model virus and major plant pathogen may contribute to understanding picornaviruses (e.g. polio) that also employ cap-independent translation regulated by interactions between the UTRs, and nidoviruses (e.g. SARS) and flaviviruses (e.g. dengue, West Nile) that regulate gene expression and replication by long-distance RNA base pairing. Finally, the research will provide fundamental insight on eukaryotic translation mechanisms. PUBLIC HEALTH RELEVANCE: All viruses must take over the host's protein synthesis (translation) machinery. Viruses of plants and animals share many common mechanisms for translation. We are using a plant virus as a small, easy-to-use model to investigate the mechanisms by which an RNA virus interacts with the host translational apparatus. This research may contribute to understanding mechanisms by which medically important viruses such as poliovirus, common cold rhinoviruses, the SARS virus, dengue virus, and West Nile viruses regulate gene expression and replication. Finally, the research will provide fundamental insight on translation mechanisms in cells of all higher organisms.
Funding Period: 2009-08-17 - 2011-07-31
more information: NIH RePORT

Top Publications

  1. pmc 3' cap-independent translation enhancers of plant viruses
    Anne E Simon
    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 email
    Annu Rev Microbiol 67:21-42. 2013
  2. pmc Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G
    Jelena J Kraft
    Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 41:3398-413. 2013
  3. pmc Untranslated regions of diverse plant viral RNAs vary greatly in translation enhancement efficiency
    Qiuling Fan
    Department of Plant Pathology and Microbiology, and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA 50011, USA
    BMC Biotechnol 12:22. 2012
  4. pmc The amazing diversity of cap-independent translation elements in the 3'-untranslated regions of plant viral RNAs
    W A Miller
    Plant Pathology Department, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    Biochem Soc Trans 35:1629-33. 2007
  5. pmc The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element
    Zhaohui Wang
    Plant Pathology Department, and Biochemistry, Biophysics, and Molecular Biology Department, Iowa State University, Ames, IA 50011, USA
    Structure 19:868-80. 2011
  6. pmc Crystallization and preliminary X-ray diffraction analysis of the barley yellow dwarf virus cap-independent translation element
    Jelena J Kraft
    Biochemistry, Biophysics and Molecular Biology Department, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:561-4. 2011
  7. pmc Structural plasticity of Barley yellow dwarf virus-like cap-independent translation elements in four genera of plant viral RNAs
    Zhaohui Wang
    Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    Virology 402:177-86. 2010
  8. pmc Structure of a viral cap-independent translation element that functions via high affinity binding to the eIF4E subunit of eIF4F
    Zhaohui Wang
    Department of Plant Pathology and Biochemistry, Iowa State University, Ames, Iowa 50011, USA
    J Biol Chem 284:14189-202. 2009
  9. pmc An overlapping essential gene in the Potyviridae
    Betty Y W Chung
    Biosciences Institute, University College Cork, Cork, Ireland
    Proc Natl Acad Sci U S A 105:5897-902. 2008
  10. pmc Structures required for poly(A) tail-independent translation overlap with, but are distinct from, cap-independent translation and RNA replication signals at the 3' end of Tobacco necrosis virus RNA
    Ruizhong Shen
    Interdepartmental Genetics Program and Department of Plant Pathology, Iowa State University, IA 50011, USA
    Virology 358:448-58. 2007

Scientific Experts

  • WYATT ALLEN MILLER
  • Theo W Dreher
  • Zhaohui Wang
  • Jelena J Kraft
  • Ruizhong Shen
  • Aurelie M Rakotondrafara
  • Krzysztof Treder
  • Anne E Simon
  • Qiuling Fan
  • Betty Y W Chung
  • Elizabeth L Pettit Kneller
  • Mariko S Peterson
  • Marc Parisien
  • Julie A Hoy
  • Kay Scheets
  • Alice Y Hui
  • John F Atkins
  • Andrew E Firth
  • Eva Harris
  • Charlotta Polacek

Detail Information

Publications15

  1. pmc 3' cap-independent translation enhancers of plant viruses
    Anne E Simon
    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 email
    Annu Rev Microbiol 67:21-42. 2013
    ..Several of these 3' CITEs are interchangeable and there is evidence that natural recombination allows exchange of modular CITE units, which may overcome genetic resistance or extend the virus's host range. ..
  2. pmc Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G
    Jelena J Kraft
    Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 41:3398-413. 2013
    ..The data support the model in which the eIF4F complex binds directly to the BTE which base pairs simultaneously to the 5'-UTR, allowing eIF4F to recruit the 40S ribosomal subunit to the 5'-end...
  3. pmc Untranslated regions of diverse plant viral RNAs vary greatly in translation enhancement efficiency
    Qiuling Fan
    Department of Plant Pathology and Microbiology, and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA 50011, USA
    BMC Biotechnol 12:22. 2012
    ..Here, we compare the effects of untranslated regions (UTRs) containing translation elements from six plant viruses on translation in wheat germ extract and in monocotyledenous and dicotyledenous plant cells...
  4. pmc The amazing diversity of cap-independent translation elements in the 3'-untranslated regions of plant viral RNAs
    W A Miller
    Plant Pathology Department, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    Biochem Soc Trans 35:1629-33. 2007
    ..These results greatly expand our understanding of ways in which mRNAs can recruit ribosomes, and they provide insight into the regulation of virus gene expression...
  5. pmc The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element
    Zhaohui Wang
    Plant Pathology Department, and Biochemistry, Biophysics, and Molecular Biology Department, Iowa State University, Ames, IA 50011, USA
    Structure 19:868-80. 2011
    ..We propose that the cap-binding pocket of eIF4E clamps around a pseudoknot, placing a highly SHAPE-reactive guanosine in the pocket in place of the normal m⁷GpppN cap. This reveals a new mechanism of mRNA recognition by eIF4E...
  6. pmc Crystallization and preliminary X-ray diffraction analysis of the barley yellow dwarf virus cap-independent translation element
    Jelena J Kraft
    Biochemistry, Biophysics and Molecular Biology Department, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:561-4. 2011
    ..9 Å resolution. This crystal form indexes with an R(merge) of 0.094 in the monoclinic space group C2, with unit-cell parameters a = 316.6, b = 54.2, c = 114.5 Å, α = γ = 90, β = 105.1°...
  7. pmc Structural plasticity of Barley yellow dwarf virus-like cap-independent translation elements in four genera of plant viral RNAs
    Zhaohui Wang
    Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    Virology 402:177-86. 2010
    ..We conclude that BTEs tolerate striking evolutionary plasticity in structure, while retaining the ability to stimulate cap-independent translation...
  8. pmc Structure of a viral cap-independent translation element that functions via high affinity binding to the eIF4E subunit of eIF4F
    Zhaohui Wang
    Department of Plant Pathology and Biochemistry, Iowa State University, Ames, Iowa 50011, USA
    J Biol Chem 284:14189-202. 2009
    ..We conclude that the PTE recruits eIF4F by binding eIF4E. The PTE represents a different class of translation enhancer element, as defined by its structure and ability to bind eIF4E in the absence of an m(7)G cap...
  9. pmc An overlapping essential gene in the Potyviridae
    Betty Y W Chung
    Biosciences Institute, University College Cork, Cork, Ireland
    Proc Natl Acad Sci U S A 105:5897-902. 2008
    ....
  10. pmc Structures required for poly(A) tail-independent translation overlap with, but are distinct from, cap-independent translation and RNA replication signals at the 3' end of Tobacco necrosis virus RNA
    Ruizhong Shen
    Interdepartmental Genetics Program and Department of Plant Pathology, Iowa State University, IA 50011, USA
    Virology 358:448-58. 2007
    ..This work shows that a viral genome can harbor distinct cap- and poly(A) tail-mimic sequences in the 3' UTR...
  11. pmc trans regulation of cap-independent translation by a viral subgenomic RNA
    Ruizhong Shen
    Plant Pathology Department, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    J Virol 80:10045-54. 2006
    ..These results reveal (i) a new level of control of subgenomic-RNA gene expression, (ii) a new role for a viral subgenomic RNA, and (iii) a new mechanism for RNA-mediated regulation of translation...
  12. pmc Oscillating kissing stem-loop interactions mediate 5' scanning-dependent translation by a viral 3'-cap-independent translation element
    Aurelie M Rakotondrafara
    Molecular, Cellular, and Developmental Biology Program and Plant Pathology Department, Iowa State University, Ames, Iowa 50011, USA
    RNA 12:1893-906. 2006
    ..We propose that the kissing interaction is repeatedly disrupted by the scanning ribosome and re-formed in an oscillating process that regulates ribosome entry on the RNA...
  13. pmc Long-distance RNA-RNA interactions in plant virus gene expression and replication
    W Allen Miller
    Plant Pathology Department, Iowa State University, Ames, Iowa 50011, USA
    Annu Rev Phytopathol 44:447-67. 2006
    ..We emphasize viruses in the Tombusviridae and Luteoviridae families in which long-distance interactions are best characterized, but similar phenomena in other viruses are also discussed. Many more examples likely remain undiscovered...
  14. pmc Translational control in positive strand RNA plant viruses
    Theo W Dreher
    Department of Microbiology and Center for Gene Research and Biotechnology, 220 Nash Hall, Oregon State University, Corvallis, OR 97331, USA
    Virology 344:185-97. 2006
    ..Finally, future directions for research on the translation of plant positive strand viruses are discussed...
  15. pmc Cap-independent translation of plant viral RNAs
    Elizabeth L Pettit Kneller
    Interdepartmental Plant Physiology Program, Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    Virus Res 119:63-75. 2006
    ..Much remains to be learned about how these elements enable plant viruses to usurp the host translational machinery...