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RNA helicase A is necessary for translation of selected messenger RNAs

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Abstract

RNA helicase A (RHA) is a highly conserved DEAD-box protein that activates transcription, modulates RNA splicing and binds the nuclear pore complex. The life cycle of typical mRNA involves RNA processing and translation after ribosome scanning of a relatively unstructured 5′ untranslated region (UTR). The precursor RNAs of retroviruses and selected cellular genes harbor a complex 5′ UTR and use a yet-to-be-identified host post-transcriptional effector to stimulate efficient translation. Here we show that RHA recognizes a structured 5′-terminal post-transcriptional control element (PCE) of a retrovirus and the JUND growth-control gene. RHA interacts with PCE RNA in the nucleus and cytoplasm, facilitates polyribosome association and is necessary for its efficient translation. Our results reveal a previously unidentified role for RHA in translation and implicate RHA as an integrative effector in the continuum of gene expression from transcription to translation.

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Figure 1: RNA helicase A is a PCE-binding protein.
Figure 2: Selected RNAs coimmunoprecipitate with RHA.
Figure 3: RHA downregulation eliminates PCE activity.
Figure 4: Overexpression of RHA increases PCE activity.
Figure 5: RHA is necessary for efficient translation of PCE-gag RNA.
Figure 6: RHA is necessary for efficient translation of JUND RNA.
Figure 7: RHA immunoprecipitates with JUND and PCE-gag mRNA in the nucleus and cytoplasm.
Figure 8: Model for RHA stimulating translation of PCE RNA.

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  • 14 May 2006

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Notes

  1. * NOTE: In the version of this article initially published online, the label for the x-axis in Figure 5c was incorrect. This error was introduced during the production process for the article. The correct label should read "Time 3H metabolic labeling (min).” The error has been corrected for all versions of the article. We apologize for any inconvenience this may have caused.

References

  1. Merrick, W.C. & Hershey, J.W.B. The pathway and mechanism of eukaryotic protein synthesis. in Translational Control (eds. Hershey, J.W.B., Mathews, D.H. & Sonenberg, N.) 31–69 (Cold Spring Harbor Laboratory Press, Plainview, New York, USA, 1996).

    Google Scholar 

  2. Kozak, M. An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 15, 8125–8148 (1987).

    Article  CAS  Google Scholar 

  3. Ehrenfeld, E. Initiation of translation by picornavirus RNAs. in Translational Control (eds. Hershey, J.W.B., Mathews, M. & Sonenberg, N.) 549–573 (Cold Spring Harbor Laboratory Press, Plainview, New York, USA, 1996).

    Google Scholar 

  4. Wiegand, H.L., Lu, S. & Cullen, B.R. Exon junction complexes mediate the enhancing effect of splicing on mRNA expression. Proc. Natl. Acad. Sci. USA 100, 11327–11332 (2003).

    Article  CAS  Google Scholar 

  5. Nott, A., Le Hir, H. & Moore, M.J. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 18, 210–222 (2004).

    Article  CAS  Google Scholar 

  6. Gudikote, J.P., Imam, J.S., Garcia, R.F. & Wilkinson, M.F. RNA splicing promotes translation and RNA surveillance. Nat. Struct. Mol. Biol. 12, 801–809 (2005).

    Article  CAS  Google Scholar 

  7. Short, J.D. & Pfarr, C.M. Translational regulation of the JunD messenger RNA. J. Biol. Chem. 277, 32697–32705 (2002).

    Article  CAS  Google Scholar 

  8. Yilmaz, A., Bolinger, C. & Boris-Lawrie, K. Retrovirus translation initiation: issues and hypotheses derived from study of HIV-1. Curr. HIV Res. 3, 13 (2006).

    Article  Google Scholar 

  9. Boris-Lawrie, K., Roberts, T.M. & Hull, S. Retroviral RNA elements integrate components of post-transcriptional gene expression. Life Sci. 69, 2697–2709 (2001).

    Article  CAS  Google Scholar 

  10. Hull, S. & Boris-Lawrie, K. RU5 of Mason-Pfizer monkey virus 5′ long terminal repeat enhances cytoplasmic expression of human immunodeficiency virus type 1 gag-pol and nonviral reporter RNA. J. Virol. 76, 10211–10218 (2002).

    Article  CAS  Google Scholar 

  11. Butsch, M., Hull, S., Wang, Y., Roberts, T.M. & Boris-Lawrie, K. The 5′ RNA terminus of spleen necrosis virus contains a novel posttranscriptional control element that facilitates human immunodeficiency virus Rev/RRE-independent Gag production. J. Virol. 73, 4847–4855 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Roberts, T.M. & Boris-Lawrie, K. The 5′ RNA terminus of spleen necrosis virus stimulates translation of nonviral mRNA. J. Virol. 74, 8111–8118 (2000).

    Article  CAS  Google Scholar 

  13. Pelletier, J. & Sonenberg, N. Insertion mutagenesis to increase secondary structure within the 5′ noncoding region of a eukaryotic mRNA reduces translational efficiency. Cell 40, 515–526 (1985).

    Article  CAS  Google Scholar 

  14. Miele, G., Mouland, A., Harrison, G.P., Cohen, E. & Lever, A.M. The human immunodeficiency virus type 1 5′ packaging signal structure affects translation but does not function as an internal ribosome entry site structure. J. Virol. 70, 944–951 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Roberts, T.M. & Boris-Lawrie, K. Primary sequence and secondary structure motifs in spleen necrosis virus RU5 confer translational utilization of unspliced human immunodeficiency virus type 1 reporter RNA. J. Virol. 77, 11973–11984 (2003).

    Article  CAS  Google Scholar 

  16. Dangel, A.W., Hull, S., Roberts, T.M. & Boris-Lawrie, K. Nuclear interactions are necessary for translational enhancement by spleen necrosis virus RU5. J. Virol. 76, 3292–3300 (2002).

    Article  CAS  Google Scholar 

  17. Zhang, S. & Grosse, F. Multiple functions of nuclear DNA helicase II (RNA helicase A) in nucleic acid metabolism. Acta Biochim. Biophys. Sin.(Shanghai) 36, 177–183 (2004).

    Article  CAS  Google Scholar 

  18. Linder, P. Molecular biology. The life of RNA with proteins. Science 304, 694–695 (2004).

    Article  CAS  Google Scholar 

  19. Nakajima, T. et al. RNA helicase A mediates association of CBP with RNA polymerase II. Cell 90, 1107–1112 (1997).

    Article  CAS  Google Scholar 

  20. Anderson, S.F., Schlegel, B.P., Nakajima, T., Wolpin, E.S. & Parvin, J.D. BRCA1 protein is linked to the RNA polymerase II holoenzyme complex via RNA helicase A. Nat. Genet. 19, 254–256 (1998).

    Article  CAS  Google Scholar 

  21. Aratani, S. et al. Dual roles of RNA helicase A in CREB-dependent transcription. Mol. Cell. Biol. 21, 4460–4469 (2001).

    Article  CAS  Google Scholar 

  22. Fujii, R. et al. A role of RNA helicase A in cis-acting transactivation response element-mediated transcriptional regulation of human immunodeficiency virus type 1. J. Biol. Chem. 276, 5445–5451 (2001).

    Article  CAS  Google Scholar 

  23. Kernan, M.J., Kuroda, M.I., Kreber, R., Baker, B.S. & Ganetzky, B. napts, a mutation affecting sodium channel activity in Drosophila, is an allele of mle, a regulator of X chromosome transcription. Cell 66, 949–959 (1991).

    Article  CAS  Google Scholar 

  24. Kuroda, M.I., Kernan, M.J., Kreber, R., Ganetzky, B. & Baker, B.S. The maleless protein associates with the X chromosome to regulate dosage compensation in Drosophila. Cell 66, 935–947 (1991).

    Article  CAS  Google Scholar 

  25. Li, J. et al. A role for RNA helicase A in post-transcriptional regulation of HIV type 1. Proc. Natl. Acad. Sci. USA 96, 709–714 (1999).

    Article  CAS  Google Scholar 

  26. Gatfield, D. et al. The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila. Curr. Biol. 11, 1716–1721 (2001).

    Article  CAS  Google Scholar 

  27. Kedersha, N. et al. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. J. Cell Biol. 169, 871–884 (2005).

    Article  CAS  Google Scholar 

  28. Ryder, K., Lanahan, A., Perez-Albuerne, E. & Nathans, D. jun-D: a third member of the jun gene family. Proc. Natl. Acad. Sci. USA 86, 1500–1503 (1989).

    Article  CAS  Google Scholar 

  29. van Dam, H. & Castellazzi, M. Distinct roles of Jun: Fos and Jun: ATF dimers in oncogenesis. Oncogene 20, 2453–2464 (2001).

    Article  CAS  Google Scholar 

  30. Eferl, R. & Wagner, E.F. AP-1: a double-edged sword in tumorigenesis. Nat. Rev. Cancer 3, 859–868 (2003).

    Article  CAS  Google Scholar 

  31. Ricci, R. et al. Distinct functions of junD in cardiac hypertrophy and heart failure. Genes Dev. 19, 208–213 (2005).

    Article  CAS  Google Scholar 

  32. Braddock, M. et al. Intron-less RNA injected into the nucleus of Xenopus oocytes accesses a regulated translation control pathway. Nucleic Acids Res. 22, 5255–5264 (1994).

    Article  CAS  Google Scholar 

  33. Matsumoto, K., Wassarman, K.M. & Wolffe, A.P. Nuclear history of a pre-mRNA determines the translational activity of cytoplasmic mRNA. EMBO J. 17, 2107–2121 (1998).

    Article  CAS  Google Scholar 

  34. Kim, V.N., Kataoka, N. & Dreyfuss, G. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293, 1832–1836 (2001).

    Article  CAS  Google Scholar 

  35. Nott, A., Meislin, S.H. & Moore, M.J. A quantitative analysis of intron effects on mammalian gene expression. RNA 9, 607–617 (2003).

    Article  CAS  Google Scholar 

  36. Lu, S. & Cullen, B.R. Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells. RNA 9, 618–630 (2003).

    Article  CAS  Google Scholar 

  37. Mangus, D.A., Evans, M.C. & Jacobson, A. Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol. 4, 223 (2003).

    Article  Google Scholar 

  38. Isken, O. et al. Members of the NF90/NFAR protein group are involved in the life cycle of a positive-strand RNA virus. EMBO J. 22, 5655–5665 (2003).

    Article  CAS  Google Scholar 

  39. Svitkin, Y.V. et al. The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure. RNA 7, 382–394 (2001).

    Article  CAS  Google Scholar 

  40. Lee, C.G. & Hurwitz, J. A new RNA helicase isolated from HeLa cells that catalytically translocates in the 3′ to 5′ direction. J. Biol. Chem. 267, 4398–4407 (1992).

    CAS  PubMed  Google Scholar 

  41. Moore, M.J. From birth to death: the complex lives of eukaryotic mRNAs. Science 309, 1514–1518 (2005).

    Article  CAS  Google Scholar 

  42. Tseng, S.S. et al. Dbp5p, a cytosolic RNA helicase, is required for poly(A)+ RNA export. EMBO J. 17, 2651–2662 (1998).

    Article  CAS  Google Scholar 

  43. Snay-Hodge, C.A., Colot, H.V., Goldstein, A.L. & Cole, C.N. Dbp5p/Rat8p is a yeast nuclear pore-associated DEAD-box protein essential for RNA export. EMBO J. 17, 2663–2676 (1998).

    Article  CAS  Google Scholar 

  44. Chan, C.C. et al. eIF4A3 is a novel component of the exon junction complex. RNA 10, 200–209 (2004).

    Article  CAS  Google Scholar 

  45. Ferraiuolo, M.A. et al. A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc. Natl. Acad. Sci. USA 101, 4118–4123 (2004).

    Article  CAS  Google Scholar 

  46. Chuang, R.Y., Weaver, P.L., Liu, Z. & Chang, T.H. Requirement of the DEAD-Box protein ded1p for messenger RNA translation. Science 275, 1468–1471 (1997).

    Article  CAS  Google Scholar 

  47. Yedavalli, V.S., Neuveut, C., Chi, Y.H., Kleiman, L. & Jeang, K.T. Requirement of DDX3 DEAD box RNA helicase for HIV-1 Rev-RRE export function. Cell 119, 381–392 (2004).

    Article  CAS  Google Scholar 

  48. Coller, J. & Parker, R. General translational repression by activators of mRNA decapping. Cell 122, 875–886 (2005).

    Article  CAS  Google Scholar 

  49. Butsch, M. & Boris-Lawrie, K. Translation is not required to generate virion precursor RNA in human immunodeficiency virus type 1-infected T cells. J. Virol. 74, 11531–11537 (2000).

    Article  CAS  Google Scholar 

  50. Hull, S. & Boris-Lawrie, K. Analysis of synergy between divergent simple retrovirus posttranscriptional control elements. Virology 317, 146–154 (2003).

    Article  CAS  Google Scholar 

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Acknowledgements

We are grateful to K. Green-Church and the Ohio State University CCIC proteomics core for mass spectrophotometry, W.C. Merrick for valuable discussion, K. Hayes, I. Younis and members of the K.B.-L. laboratory for comments on the manuscript and T. Vojt for figure preparation. This work was supported by grants from the US National Institutes of Health (P01CA16058 and P30CA100730).

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Correspondence to Kathleen Boris-Lawrie.

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Hartman, T., Qian, S., Bolinger, C. et al. RNA helicase A is necessary for translation of selected messenger RNAs. Nat Struct Mol Biol 13, 509–516 (2006). https://doi.org/10.1038/nsmb1092

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