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. 1998 Jun 1;26(11):2638–2643. doi: 10.1093/nar/26.11.2638

Characterization of a DEAD box ATPase/RNA helicase protein of Arabidopsis thaliana.

M Okanami 1, T Meshi 1, M Iwabuchi 1
PMCID: PMC147611  PMID: 9592148

Abstract

We have isolated cDNAs encoding a novel member of the DEAD box RNA helicase family from Arabidopsis. The protein, named AtDRH1, is composed of 619 amino acids and the central portion has high similarity with the helicase core region of a prototypic RNA helicase, the human nuclear protein p68. The N- and C-terminal regions are considerably diverged from the animal and yeast p68 homologs at the amino acid sequence level, but like the p68 subfamily members, an RGG box-like domain is present near the C-terminus. RNA blot analysis showed that the AtDRH1 transcript accumulates at a high level and almost equally in every part of the Arabidopsis plant. The purified, recombinant AtDRH1 was capable of unwinding double-stranded RNA in the presence of ATP or dATP and of hydrolyzing ATP. The ATPase activity was stimulated by some single-stranded RNAs and DNAs, including poly(A) and poly(dT), but not by poly(dA). The ability of the polynucleotides to stimulate the ATPase activity was largely consistent with their affinity for AtDRH1. These results show that AtDRH1 is a novel type of ATP/dATP-dependent RNA helicase and polynucleotide-dependent ATPase.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Barta I., Iggo R. Autoregulation of expression of the yeast Dbp2p 'DEAD-box' protein is mediated by sequences in the conserved DBP2 intron. EMBO J. 1995 Aug 1;14(15):3800–3808. doi: 10.1002/j.1460-2075.1995.tb00049.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Buelt M. K., Glidden B. J., Storm D. R. Regulation of p68 RNA helicase by calmodulin and protein kinase C. J Biol Chem. 1994 Nov 25;269(47):29367–29370. [PubMed] [Google Scholar]
  3. Böddeker N., Stade K., Franceschi F. Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity. Nucleic Acids Res. 1997 Feb 1;25(3):537–545. doi: 10.1093/nar/25.3.537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Dorer D. R., Christensen A. C., Johnson D. H. A novel RNA helicase gene tightly linked to the Triplo-lethal locus of Drosophila. Nucleic Acids Res. 1990 Sep 25;18(18):5489–5494. doi: 10.1093/nar/18.18.5489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fuerst R. A., Soni R., Murray J. A., Lindsey K. Modulation of cyclin transcript levels in cultured cells of Arabidopsis thaliana. Plant Physiol. 1996 Nov;112(3):1023–1033. doi: 10.1104/pp.112.3.1023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fuller-Pace F. V. RNA helicases: modulators of RNA structure. Trends Cell Biol. 1994 Aug;4(8):271–274. doi: 10.1016/0962-8924(94)90210-0. [DOI] [PubMed] [Google Scholar]
  7. Ghisolfi L., Joseph G., Amalric F., Erard M. The glycine-rich domain of nucleolin has an unusual supersecondary structure responsible for its RNA-helix-destabilizing properties. J Biol Chem. 1992 Feb 15;267(5):2955–2959. [PubMed] [Google Scholar]
  8. Gururajan R., Mathews L., Longo F. J., Weeks D. L. An3 mRNA encodes an RNA helicase that colocalizes with nucleoli in Xenopus oocytes in a stage-specific manner. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2056–2060. doi: 10.1073/pnas.91.6.2056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gururajan R., Weeks D. L. An3 protein encoded by a localized maternal mRNA in Xenopus laevis is an ATPase with substrate-specific RNA helicase activity. Biochim Biophys Acta. 1997 Feb 7;1350(2):169–182. doi: 10.1016/s0167-4781(96)00155-8. [DOI] [PubMed] [Google Scholar]
  10. He F., Jacobson A. Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen. Genes Dev. 1995 Feb 15;9(4):437–454. doi: 10.1101/gad.9.4.437. [DOI] [PubMed] [Google Scholar]
  11. Hirling H., Scheffner M., Restle T., Stahl H. RNA helicase activity associated with the human p68 protein. Nature. 1989 Jun 15;339(6225):562–564. doi: 10.1038/339562a0. [DOI] [PubMed] [Google Scholar]
  12. Iggo R. D., Jamieson D. J., MacNeill S. A., Southgate J., McPheat J., Lane D. P. p68 RNA helicase: identification of a nucleolar form and cloning of related genes containing a conserved intron in yeasts. Mol Cell Biol. 1991 Mar;11(3):1326–1333. doi: 10.1128/mcb.11.3.1326. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Iggo R. D., Lane D. P. Nuclear protein p68 is an RNA-dependent ATPase. EMBO J. 1989 Jun;8(6):1827–1831. doi: 10.1002/j.1460-2075.1989.tb03577.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Iost I., Dreyfus M. mRNAs can be stabilized by DEAD-box proteins. Nature. 1994 Nov 10;372(6502):193–196. doi: 10.1038/372193a0. [DOI] [PubMed] [Google Scholar]
  15. Itadani H., Sugita M., Sugiura M. Structure and expression of a cDNA encoding an RNA helicase-like protein in tobacco. Plant Mol Biol. 1994 Jan;24(1):249–252. doi: 10.1007/BF00040593. [DOI] [PubMed] [Google Scholar]
  16. Jaramillo M., Browning K., Dever T. E., Blum S., Trachsel H., Merrick W. C., Ravel J. M., Sonenberg N. Translation initiation factors that function as RNA helicases from mammals, plants and yeast. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):134–139. doi: 10.1016/0167-4781(90)90154-t. [DOI] [PubMed] [Google Scholar]
  17. Jones P. G., Mitta M., Kim Y., Jiang W., Inouye M. Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):76–80. doi: 10.1073/pnas.93.1.76. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kiledjian M., Dreyfuss G. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J. 1992 Jul;11(7):2655–2664. doi: 10.1002/j.1460-2075.1992.tb05331.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Koonin E. V. Similarities in RNA helicases. Nature. 1991 Jul 25;352(6333):290–290. doi: 10.1038/352290c0. [DOI] [PubMed] [Google Scholar]
  20. Ladomery M., Wade E., Sommerville J. Xp54, the Xenopus homologue of human RNA helicase p54, is an integral component of stored mRNP particles in oocytes. Nucleic Acids Res. 1997 Mar 1;25(5):965–973. doi: 10.1093/nar/25.5.965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lamm G. M., Nicol S. M., Fuller-Pace F. V., Lamond A. I. p72: a human nuclear DEAD box protein highly related to p68. Nucleic Acids Res. 1996 Oct 1;24(19):3739–3747. doi: 10.1093/nar/24.19.3739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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. 1992 Mar 5;267(7):4398–4407. [PubMed] [Google Scholar]
  23. Leeds P., Peltz S. W., Jacobson A., Culbertson M. R. The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 1991 Dec;5(12A):2303–2314. doi: 10.1101/gad.5.12a.2303. [DOI] [PubMed] [Google Scholar]
  24. Lemaire L., Heinlein U. A. High-level expression in male germ cells of murine P68 RNA helicase mRNA. Life Sci. 1993;52(11):917–926. doi: 10.1016/0024-3205(93)90526-9. [DOI] [PubMed] [Google Scholar]
  25. Liang L., Diehl-Jones W., Lasko P. Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities. Development. 1994 May;120(5):1201–1211. doi: 10.1242/dev.120.5.1201. [DOI] [PubMed] [Google Scholar]
  26. Lorković Z. J., Herrmann R. G., Oelmüller R. PRH75, a new nucleus-localized member of the DEAD-box protein family from higher plants. Mol Cell Biol. 1997 Apr;17(4):2257–2265. doi: 10.1128/mcb.17.4.2257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Nakajima T., Uchida C., Anderson S. F., Lee C. G., Hurwitz J., Parvin J. D., Montminy M. RNA helicase A mediates association of CBP with RNA polymerase II. Cell. 1997 Sep 19;90(6):1107–1112. doi: 10.1016/s0092-8674(00)80376-1. [DOI] [PubMed] [Google Scholar]
  28. Okanami M., Meshi T., Tamai H., Iwabuchi M. HALF-1, a bZIP-type protein, interacting with the wheat transcription factor HBP-1a contains a novel transcriptional activation domain. Genes Cells. 1996 Jan;1(1):87–99. doi: 10.1046/j.1365-2443.1996.06006.x. [DOI] [PubMed] [Google Scholar]
  29. Pause A., Méthot N., Sonenberg N. The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis. Mol Cell Biol. 1993 Nov;13(11):6789–6798. doi: 10.1128/mcb.13.11.6789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Pause A., Sonenberg N. Mutational analysis of a DEAD box RNA helicase: the mammalian translation initiation factor eIF-4A. EMBO J. 1992 Jul;11(7):2643–2654. doi: 10.1002/j.1460-2075.1992.tb05330.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Rozen F., Edery I., Meerovitch K., Dever T. E., Merrick W. C., Sonenberg N. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F. Mol Cell Biol. 1990 Mar;10(3):1134–1144. doi: 10.1128/mcb.10.3.1134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Snudden D. K., Hearing J., Smith P. R., Grässer F. A., Griffin B. E. EBNA-1, the major nuclear antigen of Epstein-Barr virus, resembles 'RGG' RNA binding proteins. EMBO J. 1994 Oct 17;13(20):4840–4847. doi: 10.1002/j.1460-2075.1994.tb06810.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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