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Structure and conserved RNA binding of the PAZ domain

Nature volume 426, pages 469–474 (2003)Cite this article

An Erratum to this article was published on 15 January 2004

Abstract

The discovery of RNA-mediated gene-silencing pathways, including RNA interference1,2,3, highlights a fundamental role of short RNAs in eukaryotic gene regulation4,5,6,7,8,9,10 and antiviral defence11,12. Members of the Dicer and Argonaute protein families are essential components of these RNA-silencing pathways13,14,15,16,17,18,19. Notably, these two families possess an evolutionarily conserved PAZ (Piwi/Argonaute/Zwille) domain whose biochemical function is unknown. Here we report the nuclear magnetic resonance solution structure of the PAZ domain from Drosophila melanogaster Argonaute 1 (Ago1). The structure consists of a left-handed, six-stranded β-barrel capped at one end by two α-helices and wrapped on one side by a distinctive appendage, which comprises a long β-hairpin and a short α-helix. Using structural and biochemical analyses, we demonstrate that the PAZ domain binds a 5-nucleotide RNA with 1:1 stoichiometry. We map the RNA-binding surface to the open face of the β-barrel, which contains amino acids conserved within the PAZ domain family, and we define the 5′-to-3′ orientation of single-stranded RNA bound within that site. Furthermore, we show that PAZ domains from different human Argonaute proteins also bind RNA, establishing a conserved function for this domain.

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Figure 1: Three-dimensional structure of the D. melanogaster Ago1 PAZ domain.
Figure 2: RNA binding of the D. melanogaster Ago1 PAZ domain.
Figure 3: Mapping the RNA-binding site of the D. melanogaster Ago1 PAZ domain.
Figure 4: Conserved RNA binding of the PAZ domain.

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References

  1. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998)

    Article  ADS  CAS  PubMed  Google Scholar 

  2. Dykxhoorn, D. M., Novina, C. D. & Sharp, P. A. Killing the messenger: short RNAs that silence gene expression. Nature Rev. Mol. Cell Biol. 4, 457–467 (2003)

    Article  CAS  Google Scholar 

  3. Hannon, G. J. RNA interference. Nature 418, 244–251 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001)

    Article  CAS  PubMed  Google Scholar 

  5. Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001)

    Article  CAS  PubMed  Google Scholar 

  6. Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993)

    Article  CAS  PubMed  Google Scholar 

  7. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  8. Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Mochizuki, K., Fine, N. A., Fujisawa, T. & Gorovsky, M. A. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell 110, 689–699 (2002)

    Article  CAS  PubMed  Google Scholar 

  10. Schramke, V. & Allshire, R. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301, 1069–1074 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Ratcliff, F., Harrison, B. D. & Baulcombe, D. C. A similarity between viral defense and gene silencing in plants. Science 276, 1558–1560 (1997)

    Article  CAS  PubMed  Google Scholar 

  12. Waterhouse, P. M., Wang, M. B. & Lough, T. Gene silencing as an adaptive defence against viruses. Nature 411, 834–842 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  13. Zamore, P. D., Tuschl, T., Sharp, P. A. & Bartel, D. P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25–33 (2000)

    Article  CAS  PubMed  Google Scholar 

  14. Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  15. Knight, S. W. & Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269–2271 (2001)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  16. Hammond, S. M., Bernstein, E., Beach, D. & Hannon, G. J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293–296 (2000)

    Article  ADS  CAS  PubMed  Google Scholar 

  17. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150 (2001)

    Article  CAS  PubMed  Google Scholar 

  18. Tabara, H. et al. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132 (1999)

    Article  CAS  PubMed  Google Scholar 

  19. Williams, R. W. & Rubin, G. M. ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proc. Natl Acad. Sci. USA 99, 6889–6894 (2002)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  20. Cerutti, L., Mian, N. & Bateman, A. Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. Trends Biochem. Sci. 25, 481–482 (2000)

    Article  CAS  PubMed  Google Scholar 

  21. Kambach, C. et al. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 96, 375–387 (1999)

    Article  CAS  PubMed  Google Scholar 

  22. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  23. Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906 (2000)

    Article  ADS  CAS  PubMed  Google Scholar 

  24. Nykanen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309–321 (2001)

    Article  CAS  PubMed  Google Scholar 

  25. Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877–6888 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Schwarz, D. S., Hutvagner, G., Haley, B. & Zamore, P. D. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol. Cell 10, 537–548 (2002)

    Article  CAS  PubMed  Google Scholar 

  27. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R. & Tuschl, T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563–574 (2002)

    Article  CAS  PubMed  Google Scholar 

  28. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature advance online publication, 16 November 2003 (doi:10.1038/nature02123)

  29. Dostie, J., Mourelatos, Z., Yang, M., Sharma, A. & Dreyfuss, G. Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9, 180–186 (2003)

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Brunger, A. T. X-PLOR Version 3.1: A System for X-Ray Crystallography and NMR (Yale Univ. Press, New Haven, Connecticut, 1993)

    Google Scholar 

  31. Nilges, M. & O'Donoghue, S. Ambiguous NOEs and automated NOE assignment. Prog. NMR Spectrosc. 32, 107–139 (1998)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank R. W. Williams for providing a D. melanogaster Ago1 expressed sequenced tag clone, T. Tuschl for complementary DNAs encoding human Argonaute proteins, and T. A. Edwards for discussions. K.S.Y. is a recipient of a National Institutes of Health (NIH) predoctoral training grant fellowship. M.-M.Z. is supported by NIH grants, and is a member of the New York Structural Biology Center.

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  1. Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, One Gustave L. Levy Place, New York, 10029-6574, New York, USA

    Kelley S. Yan, Sherry Yan, Amjad Farooq, Arnold Han, Lei Zeng & Ming-Ming Zhou

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Correspondence to Ming-Ming Zhou.

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Yan, K., Yan, S., Farooq, A. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 469–474 (2003). https://doi.org/10.1038/nature02129

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