Springer Protocols: Abstract: 7. In Vivo Analyses of Viral RNA Translation

7. In Vivo Analyses of Viral RNA Translation

By: William R. Staplin⁶, W. Allen Miller⁶

Abstract

Full Text

Download PDF (261K)

Positive-strand RNA viruses often use noncanonical strategies to usurp the host translational machinery for their own benefit. These strategies have been analyzed using transient expression assays in the absence of replication, with reporter genes replacing viral genes. A sensitive and convenient reporter assay is the dual luciferase system using Renilla (Renilla reniformis) and firefly (Photinus pyralis) reporter genes. Use of recombinant viral constructs containing the reporter luciferase gene allows us to discern whether a particular RNA sequence or secondary structure elicits an effect on initiation of translation or recoding. This chapter describes a standard luciferase protocol that can be molded to fit any viral sequence, in order to detect cis-acting regulatory elements in viral RNA.

Affiliation(s): (6) Molecular Cellular and Developmental Biology, Department of Plant Pathology, Iowa State University, Ames, IA, USA

Book Title: Plant Virology Protocols: From Viral Sequence to Protein Function

Series: Methods in Molecular Biology | Volume: 451 | Pub. Date: Apr-01-2008 | Page Range: 99-112 | DOI: 10.1007/978-1-59745-102-4_7

Subject: Plant Sciences

Key Words: Cap-independent translation - Electroporation - Oat protoplast - Plant cell suspension culture - Recoding - Ribosomal frameshift

References

Download References

1.	1. Kneller, E.R, Rakotondrafara, A.M., Miller, W.A., Cap-independent translation of plant vial RNAs. Virus Res, 2005. 119: 63–75.

2.	Matsuda, D., Dreher, T., In Vivo Translation Studies of Plant Viral RNAs Using Reporter Genes. Current Protocols in Microbiology. 2005. 16K.2.1–16K.2.11.

3.	Gallie, D.R., The cap and poly (A) tail function synergistically to regulate mRNA translational efficiency. Cold Spring Harbor Laboratory, 1991: p. 2108–2116.

4.	4. Gallie, D.R., Kobayashi, M., The role of the 3′ Untranslated region of nonpolyadenylated plant mRNAs in regulating translational efficiency. Gene, 1994. 142: 159–165.

5.	5. Brasier, A.R.a.F, J.J., Nonisotopic assays for reporter gene activity. In: Current Protocols in Molecular Biology, R. Brent. F.M. Ausubel, R.E. Kingston, D.D. Moore, J.G Seidman, J.A. Smith, K. Struhl (eds.). 1995, Hoboken, N.J.: John Wiley & Sons. 9.7.12–9.7–21.

6.	6. Matsuda, D., Bauer, L., Tinnesand, K., Dreher, T.W., Expression of the two nested overlapping reading frames of TYMV RNA is enhanced by a 5′ cap and by 5′ and 3′ viral sequences. J Virol, 2004. 78: 9325–9335.

7.	7. Yamaji, Y., Kobayashi, T., Hamada, K., Sakurai, K, Yoshii, A, Suzuki, M., Namba, S., Hibi, T. et al., In vivo interaction between Tobacco mosaic virus RNA-dependent RNA polymerase and host translation elongation factor 1A. Virology, 2006. 347, 100–108.

8.	8. Brierley, I., Dos Ramos, F.J., Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV. Virus Res, 2006. 119(1): 29–42.

9.	9. Baril, M., Brakier-Gingras, L., Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a + 1 reading frame relative to the polyprotein. Nucleic Acids Res, 2005. 33(5): 1474–1486.

10.	10. Plant, E.R, Perez-Alvarado, G.C., Jacobs, J.L., Mukhopadhyay, B., Hennig, M., Dinman, J.D. A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PLoS Biol, 2005. 3(6): el72.

11.	11. Dreher, T.W., Miller, W.A., Translational control in positive strand RNA plant viruses. Virology, 2006. 344(1): 185–197.

12.	12. McInerney, P., T. Mizutani, T. Shiba, Inorganic polyphosphate interacts with ribosomes and promotes translation fidelity in vitro and in vivo. Mol Microbiol, 2006. 60(2): 438–447.

13.	Rakotondrafara, A.M., Jackson, J.R., Pettit Kneller, E., Miller, WA. Preparation and electroporation of oat protoplasts from cell suspension culture. Curr. Protocols Micro., 2007. 16D.3.1–16D.3.12.

14.	14. Kozak, M., New ways of initiating translation in eukaryotes? Mol Cell Biol, 2001. 21: 1899–1907.

15.	15. Thoma, C, et al., Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly (A) tail is independent of intact eIF4G and PABP. Mol Cell, 2004. 15(6): 925–935.

16.	16. Sanchez, M., et al., Iron Regulation and the Cell Cycle: Identification of an iron-responsive element in the 3′ -untranslated region of human cell division cycle 14A mRNA by a refined micro array-based screening strategy J Biol Chem, 2006. 281(32): 22865–22874.

17.	17. Meulewaeter, F., Van Montagu, M., Cornelissen, M., Features of the autonomous function of the translational enhancer domain of satellite tobacco necrosis virus. RNA, 1998. 4(11): 1347–1356.

18.	18. Qin, X., Sarnow, P., Preferential translation of internal ribosome entry site-containing mRNAs during the mitotic cycle in mammalian cells. J Biol Chem, 2004. 279: 13721–13728.

19.	19. Barry, J.K., Miller, W.A., A-l ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA. Proc Natl Acad Sci U S A, 2002. 99(17): 11133–11138.

20.	20. Rakotondrafara, A.M., et al., Oscillating kissing stem-loop interactions mediate 5′ scanning-dependent translation by a viral 3′-cap-independent translation element. RNA, 2006. 12: 1893–1906.

Comments (Loading...)

Post comment/View all comments