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A micrococcal nuclease homologue in RNAi effector complexes


RNA interference (RNAi) regulates gene expression by the cleavage of messenger RNA, by mRNA degradation and by preventing protein synthesis. These effects are mediated by a ribonucleoprotein complex known as RISC (RNA-induced silencing complex)1. We have previously identified four Drosophila components (short interfering RNAs1, Argonaute 2 (ref. 2), VIG and FXR3) of a RISC enzyme that degrades specific mRNAs in response to a double-stranded-RNA trigger. Here we show that Tudor-SN (tudor staphylococcal nuclease)—a protein containing five staphylococcal/micrococcal nuclease domains and a tudor domain—is a component of the RISC enzyme in Caenorhabditis elegans, Drosophila and mammals. Although Tudor-SN contains non-canonical active-site sequences, we show that purified Tudor-SN exhibits nuclease activity similar to that of other staphylococcal nucleases. Notably, both purified Tudor-SN and RISC are inhibited by a specific competitive inhibitor of micrococcal nuclease. Tudor-SN is the first RISC subunit to be identified that contains a recognizable nuclease domain, and could therefore contribute to the RNA degradation observed in RNAi.

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Figure 1: Identification and confirmation of Tudor-SN as a component of RISC complexes.
Figure 2: Immunoprecipitations from multiple organisms confirm association between Tudor-SN and components of RISC.
Figure 3: Tudor-SN has nuclease activity.
Figure 4: Staining of animals carrying a transgene expressing LacZ in the seam cells, under the translational control of let-7.


  1. 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  Google Scholar 

  2. 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  Google Scholar 

  3. Caudy, A. A., Myers, M., Hannon, G. J. & Hammond, S. M. Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev. 16, 2491–2496 (2002)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  5. Hamilton, A. J. & Baulcombe, D. C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286, 950–952 (1999)

    Article  CAS  Google Scholar 

  6. 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  Google Scholar 

  7. 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  Google Scholar 

  8. Maurer-Stroh, S. et al. The Tudor domain ‘Royal Family’: Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem. Sci. 28, 69–74 (2003)

    Article  CAS  Google Scholar 

  9. Ponting, C. P. P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease. Protein Sci. 6, 459–463 (1997)

    Article  CAS  Google Scholar 

  10. Callebaut, I. & Mornon, J. P. The human EBNA-2 coactivator p100: Multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. Biochem. J. 321, 125–132 (1997)

    Article  CAS  Google Scholar 

  11. Tong, X., Drapkin, R., Yalamanchili, R., Mosialos, G. & Kieff, E. The Epstein–Barr virus nuclear protein 2 acidic domain forms a complex with a novel cellular coactivator that can interact with TFIIE. Mol. Cell. Biol. 15, 4735–4744 (1995)

    Article  CAS  Google Scholar 

  12. Carmell, M. A., Xuan, Z., Zhang, M. Q. & Hannon, G. J. The Argonaute family: Tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16, 2733–2742 (2002)

    Article  CAS  Google Scholar 

  13. Hutvagner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002)

    Article  ADS  CAS  Google Scholar 

  14. Mourelatos, Z. et al. miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728 (2002)

    Article  CAS  Google Scholar 

  15. 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  Google Scholar 

  16. Keenan, T. W., Winter, S., Rackwitz, H. R. & Heid, H. W. Nuclear coactivator protein p100 is present in endoplasmic reticulum and lipid droplets of milk secreting cells. Biochim. Biophys. Acta 1523, 84–90 (2000)

    Article  CAS  Google Scholar 

  17. Serpersu, E. H., Shortle, D. & Mildvan, A. S. Kinetic and magnetic resonance studies of active-site mutants of staphylococcal nuclease: Factors contributing to catalysis. Biochemistry 26, 1289–1300 (1987)

    Article  CAS  Google Scholar 

  18. Cuatrecasas, P., Fuchs, S. & Anfinsen, C. B. The binding of nucleotides and calcium to the extracellular nuclease of Staphylococcus aureus. Studies by gel filtration. J. Biol. Chem. 242, 3063–3067 (1967)

    CAS  PubMed  Google Scholar 

  19. Slack, F. J. et al. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell 5, 659–669 (2000)

    Article  CAS  Google Scholar 

  20. 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  Google Scholar 

  21. Ketting, R. F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654–2659 (2001)

    Article  CAS  Google Scholar 

  22. 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  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  Google Scholar 

  24. Llave, C., Xie, Z., Kasschau, K. D. & Carrington, J. C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053–2056 (2002)

    Article  ADS  CAS  Google Scholar 

  25. Tang, G., Reinhart, B. J., Bartel, D. P. & Zamore, P. D. A biochemical framework for RNA silencing in plants. Genes Dev. 17, 49–63 (2003)

    Article  CAS  Google Scholar 

  26. Spankuch-Schmitt, B., Bereiter-Hahn, J., Kaufmann, M. & Strebhardt, K. Effect of RNA silencing of polo-like kinase-1 (PLK1) on apoptosis and spindle formation in human cancer cells. J. Natl Cancer Inst. 94, 1863–1877 (2002)

    Article  CAS  Google Scholar 

  27. Capodici, J., Kariko, K. & Weissman, D. Inhibition of HIV-1 infection by small interfering RNA-mediated RNA interference. J. Immunol. 169, 5196–5201 (2002)

    Article  Google Scholar 

  28. Hirayoshi, K. & Lis, J. T. Nuclear run-on assays: assessing transcription by measuring density of engaged RNA polymerases. Methods Enzymol. 304, 351–362 (1999)

    Article  CAS  Google Scholar 

  29. Avalos, R. T., Yu, Z. & Nayak, D. P. Association of influenza virus NP and M1 proteins with cellular cytoskeletal elements in influenza virus-infected cells. J. Virol. 71, 2947–2958 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Spector, D. L. & Smith, H. C. Redistribution of U-snRNPs during mitosis. Exp. Cell Res. 163, 87–94 (1986)

    Article  CAS  Google Scholar 

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We thank A. Mildvan, M. Tijsterman and T. Sijen for discussions. We thank T. Keenan for an anti-p100 antibody, T. Hobman for GERP (EIF2C2/hAgo2) antibody, H. Siomi for a FXR monoclonal antibody, and F. Slack for the lacZlin-41 reporter. A.A.C. is a George A. and Marjorie H. Anderson Fellow of the Watson School of Biological Sciences, and a Howard Hughes Medical Institute Predoctoral Fellow. A.M.D. is a David Koch Fellow of the Watson School of Biological Sciences. J.M.S. is supported by a postdoctoral fellowship from the US Army Prostate Cancer Research programme. G.J.H. is a Rita Allen Foundation Scholar and is supported by an Innovator Award from the US Army Breast Cancer Research programme. This work was also supported by a grant from the National Institutes of Health (G.J.H.) and by a VENI fellowship from the Netherlands Organization for Scientific Research (RFK).

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Correspondence to Gregory J. Hannon or Ronald H. A. Plasterk.

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Caudy, A., Ketting, R., Hammond, S. et al. A micrococcal nuclease homologue in RNAi effector complexes. Nature 425, 411–414 (2003).

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