Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

PUF proteins bind Pop2p to regulate messenger RNAs

Nature Structural & Molecular Biology volume 13, pages 533–539 (2006)Cite this article

Abstract

PUF proteins, a family of RNA-binding proteins, interact with the 3′ untranslated regions (UTRs) of specific mRNAs to control their translation and stability. PUF protein action is commonly correlated with removal of the poly(A) tail of target mRNAs. Here, we focus on how PUF proteins enhance deadenylation and mRNA decay. We show that a yeast PUF protein physically binds Pop2p, which is a component of the Ccr4p–Pop2p–Not deadenylase complex, and that Pop2p is required for PUF repression activity. By binding Pop2p, the PUF protein simultaneously recruits the Ccr4p deadenylase and two other enzymes involved in mRNA regulation, Dcp1p and Dhh1p. We reconstitute regulated deadenylation in vitro and demonstrate that the PUF-Pop2p interaction is conserved in yeast, worms and humans. We suggest that the PUF-Pop2p interaction underlies regulated deadenylation, mRNA decay and repression by PUF proteins.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mpt5p repression is dependent on POP2.
Figure 2: Mpt5p regulates decay of HO mRNA in vivo.
Figure 3: Mpt5p directly binds Pop2p.
Figure 4: Mpt5p enhances deadenylation in vitro.
Figure 5: Conservation of PUF-Pop2p interaction.
Figure 6: Model of Mpt5p-mediated repression.

Similar content being viewed by others

Accession codes

Accessions

GenBank/EMBL/DDBJ

References

  1. Wickens, M., Goodwin, E.B., Kimble, J., Strickland, S. & Hentze, M.W. Translational control in developemental decisions. in Translational Control (ed. Mathews, M.) 295–370 (Cold Spring Harbor Press, New York, 2000).

    Google Scholar 

  2. Gebauer, F. & Hentze, M.W. Molecular mechanisms of translational control. Nat. Rev. Mol. Cell Biol. 5, 827–835 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Wickens, M., Bernstein, D.S., Kimble, J. & Parker, R.A. PUF family portrait: 3′UTR regulation as a way of life. Trends Genet. 18, 150–157 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Wharton, R.P. & Struhl, G. RNA regulatory elements mediate control of Drosophila body pattern by the posterior morphogen nanos. Cell 67, 955–967 (1991).

    Article  CAS  PubMed  Google Scholar 

  5. Olivas, W. & Parker, R. The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. EMBO J. 19, 6602–6611 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Wreden, C., Verrotti, A.C., Schisa, J.A., Lieberfarb, M.E. & Strickland, S. Nanos and pumilio establish embryonic polarity in Drosophila by promoting posterior deadenylation of hunchback mRNA. Development 124, 3015–3023 (1997).

    CAS  PubMed  Google Scholar 

  7. Crittenden, S.L. et al. A conserved RNA-binding protein controls germline stem cells in Caenorhabditis elegans. Nature 417, 660–663 (2002).

    Article  CAS  PubMed  Google Scholar 

  8. Menon, K.P. et al. The translational repressor Pumilio regulates presynaptic morphology and controls postsynaptic accumulation of translation factor eIF-4E. Neuron 44, 663–676 (2004).

    Article  CAS  PubMed  Google Scholar 

  9. Schweers, B.A., Walters, K.J. & Stern, M. The Drosophila melanogaster translational repressor pumilio regulates neuronal excitability. Genetics 161, 1177–1185 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Bernstein, D., Hook, B., Hajarnavis, A., Opperman, L. & Wickens, M. Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1. RNA 11, 447–458 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Tadauchi, T., Matsumoto, K., Herskowitz, I. & Irie, K. Post-transcriptional regulation through the HO 3′-UTR by Mpt5, a yeast homolog of Pumilio and FBF. EMBO J. 20, 552–561 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Gerber, A.P., Herschlag, D. & Brown, P.O. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2, E79 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Thore, S., Mauxion, F., Seraphin, B. & Suck, D. X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep. 4, 1150–1155 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Denis, C.L. & Chen, J. The CCR4-NOT complex plays diverse roles in mRNA metabolism. Prog. Nucleic Acid Res. Mol. Biol. 73, 221–250 (2003).

    Article  CAS  PubMed  Google Scholar 

  15. Collart, M.A. Global control of gene expression in yeast by the Ccr4-Not complex. Gene 313, 1–16 (2003).

    Article  CAS  PubMed  Google Scholar 

  16. Viswanathan, P., Ohn, T., Chiang, Y.C., Chen, J. & Denis, C.L. Mouse CAF1 can function as a processive deadenylase/3′-5′-exonuclease in vitro but in yeast the deadenylase function of CAF1 is not required for mRNA poly(A) removal. J. Biol. Chem. 279, 23988–23995 (2004).

    Article  CAS  PubMed  Google Scholar 

  17. Bianchin, C., Mauxion, F., Sentis, S., Seraphin, B. & Corbo, L. Conservation of the deadenylase activity of proteins of the Caf1 family in human. RNA 11, 487–494 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Daugeron, M.C., Mauxion, F. & Seraphin, B. The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation. Nucleic Acids Res. 29, 2448–2455 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tucker, M. et al. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104, 377–386 (2001).

    CAS  PubMed  Google Scholar 

  20. Duttagupta, R., Vasudevan, S., Wilusz, C.J. & Peltz, S.W. A yeast homologue of Hsp70, Ssa1p, regulates turnover of the MFA2 transcript through its AU-rich 3′ untranslated region. Mol. Cell. Biol. 23, 2623–2632 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Semotok, J.L. et al. Smaug recruits the CCR4/POP2/NOT deadenylase complex to trigger maternal transcript localization in the early Drosophila embryo. Curr. Biol. 15, 284–294 (2005).

    Article  CAS  PubMed  Google Scholar 

  22. Lykke-Andersen, J. & Wagner, E. Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1. Genes Dev. 19, 351–361 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Morris, J.Z., Hong, A., Lilly, M.A. & Lehmann, R. twin, a CCR4 homolog, regulates cyclin poly(A) tail length to permit Drosophila oogenesis. Development 132, 1165–1174 (2005).

    Article  CAS  PubMed  Google Scholar 

  24. Berthet, C. et al. CCR4-associated factor CAF1 is an essential factor for spermatogenesis. Mol. Cell. Biol. 24, 5808–5820 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Nakamura, T. et al. Oligo-astheno-teratozoospermia in mice lacking Cnot7, a regulator of retinoid X receptor beta. Nat. Genet. 36, 528–533 (2004).

    Article  CAS  PubMed  Google Scholar 

  26. Molin, L. & Puisieux, A. C. elegans homologue of the Caf1 gene, which encodes a subunit of the CCR4-NOT complex, is essential for embryonic and larval development and for meiotic progression. Gene 358, 73–81 (2005).

    Article  CAS  PubMed  Google Scholar 

  27. Tucker, M., Staples, R.R., Valencia-Sanchez, M.A., Muhlrad, D. & Parker, R. Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO J. 21, 1427–1436 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Chen, J., Chiang, Y.C. & Denis, C.L. CCR4, a 3′-5′ poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. EMBO J. 21, 1414–1426 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sheth, U. & Parker, R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300, 805–808 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Huh, W.K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003).

    Article  CAS  PubMed  Google Scholar 

  31. Wickens, M. & Goldstrohm, A. Molecular biology. A place to die, a place to sleep. Science 300, 753–755 (2003).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Coller, J.M., Tucker, M., Sheth, U., Valencia-Sanchez, M.A. & Parker, R. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA 7, 1717–1727 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Chagnovich, D. & Lehmann, R. Poly(A)-independent regulation of maternal hunchback translation in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 98, 11359–11364 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank A. Ansari and J. Kimble for helpful comments on the manuscript and all members of the Wickens lab for discussions and suggestions. We also thank T. Tadauchi (Nagoya University) for plasmid YEp195 MPT5 and yeast strain TTC59. We appreciate the work of L. Vanderploeg in preparing figures. This work was supported by the US National Institutes of Health (postdoctoral fellowship to A.C.G. and research grant to M.W.).

Author information

Authors and Affiliations

  1. Department of Biochemistry, 433 Babcock Drive, University of Wisconsin, Madison, 53706, Wisconsin, USA

    Aaron C Goldstrohm, Brad A Hook, Daniel J Seay & Marvin Wickens

Authors
  1. Aaron C Goldstrohm
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brad A Hook
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Daniel J Seay
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marvin Wickens
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marvin Wickens.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Goldstrohm, A., Hook, B., Seay, D. et al. PUF proteins bind Pop2p to regulate messenger RNAs. Nat Struct Mol Biol 13, 533–539 (2006). https://doi.org/10.1038/nsmb1100

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb1100

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing