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A PtdIns4,5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs

Nature volume 451, pages 1013–1017 (2008)Cite this article

Abstract

Phosphoinositides are a family of lipid signalling molecules that regulate many cellular functions in eukaryotes. Phosphatidylinositol-4,5-bisphosphate (PtdIns4,5P2), the central component in the phosphoinositide signalling circuitry, is generated primarily by type I phosphatidylinositol 4-phosphate 5-kinases (PIPKIα, PIPKIβ and PIPKIγ)1. In addition to functions in the cytosol, phosphoinositides are present in the nucleus2,3, where they modulate several functions4,5,6; however, the mechanism by which they directly regulate nuclear functions remains unknown. PIPKIs regulate cellular functions through interactions with protein partners, often PtdIns4,5P2 effectors, that target PIPKIs to discrete subcellular compartments, resulting in the spatial and temporal generation of PtdIns4,5P2 required for the regulation of specific signalling pathways1,7. Therefore, to determine roles for nuclear PtdIns4,5P2 we set out to identify proteins that interacted with the nuclear PIPK, PIPKIα. Here we show that PIPKIα co-localizes at nuclear speckles and interacts with a newly identified non-canonical poly(A) polymerase, which we have termed Star-PAP (nuclear speckle targeted PIPKIα regulated-poly(A) polymerase) and that the activity of Star-PAP can be specifically regulated by PtdIns4,5P2. Star-PAP and PIPKIα function together in a complex to control the expression of select mRNAs, including the transcript encoding the key cytoprotective enzyme haem oxygenase-1 (refs 8, 9) and other oxidative stress response genes by regulating the 3′-end formation of their mRNAs. Taken together, the data demonstrate a model by which phosphoinositide signalling works in tandem with complement pathways to regulate the activity of Star-PAP and the subsequent biosynthesis of its target mRNA. The results reveal a mechanism for the integration of nuclear phosphoinositide signals and a method for regulating gene expression.

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Figure 1: Identification of a nuclear-localized PIPKIα-interacting protein.
Figure 2: Star-PAP has poly(A) polymerase activity that is stimulated by PtdIns4,5P2.
Figure 3: Star-PAP-interacting proteins and identification of Star-PAP target mRNAs.
Figure 4: Star-PAP and PIPKIα are required for efficient 3′ processing of HO-1 mRNA by a mechanism that assembles a Star-PAP complex.

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Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

The Star-PAP sequence is deposited in the NCBI Library under accession number NP_073741. The microarray data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO series accession number GSE9361.

References

  1. Heck, J. N. et al. A conspicuous connection: structure defines function for the phosphatidylinositol-phosphate kinase family. Crit. Rev. Biochem. Mol. Biol. 42, 15–39 (2007)

    Article  CAS  Google Scholar 

  2. Gonzales, M. L. & Anderson, R. A. Nuclear phosphoinositide kinases and inositol phospholipids. J. Cell. Biochem. 97, 252–260 (2006)

    Article  CAS  Google Scholar 

  3. Boronenkov, I. V., Loijens, J. C., Umeda, M. & Anderson, R. A. Phosphoinositide signaling pathways in nuclei are associated with nuclear speckles containing pre-mRNA processing factors. Mol. Biol. Cell 9, 3547–3560 (1998)

    Article  CAS  Google Scholar 

  4. Zhao, K. et al. Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell 95, 625–636 (1998)

    Article  CAS  Google Scholar 

  5. York, J. D., Odom, A. R., Murphy, R., Ives, E. B. & Wente, S. R. A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science 285, 96–100 (1999)

    Article  CAS  Google Scholar 

  6. Osborne, S. L., Thomas, C. L., Gschmeissner, S. & Schiavo, G. Nuclear PtdIns(4,5)P2 assembles in a mitotically regulated particle involved in pre-mRNA splicing. J. Cell Sci. 114, 2501–2511 (2001)

    CAS  PubMed  Google Scholar 

  7. Doughman, R. L., Firestone, A. J. & Anderson, R. A. Phosphatidylinositol phosphate kinases put PI4,5P2 in its place. J. Membr. Biol. 194, 77–89 (2003)

    Article  CAS  Google Scholar 

  8. Keum, Y. S. et al. Induction of heme oxygenase-1 (HO-1) and NAD[P]H: quinone oxidoreductase 1 (NQO1) by a phenolic antioxidant, butylated hydroxyanisole (BHA) and its metabolite, tert-butylhydroquinone (tBHQ) in primary-cultured human and rat hepatocytes. Pharm. Res. 23, 2586–2594 (2006)

    Article  CAS  Google Scholar 

  9. Duckers, H. J. et al. Heme oxygenase-1 protects against vascular constriction and proliferation. Nature Med. 7, 693–698 (2001)

    Article  CAS  Google Scholar 

  10. Raabe, T., Bollum, F. J. & Manley, J. L. Primary structure and expression of bovine poly(A) polymerase. Nature 353, 229–234 (1991)

    Article  ADS  CAS  Google Scholar 

  11. Rouhana, L. et al. Vertebrate GLD2 poly(A) polymerases in the germline and the brain. RNA 11, 1117–1130 (2005)

    Article  CAS  Google Scholar 

  12. Cocco, L., Manzoli, L., Barnabei, O. & Martelli, A. M. Significance of subnuclear localization of key players of inositol lipid cycle. Adv. Enzyme Regul. 44, 51–60 (2004)

    Article  CAS  Google Scholar 

  13. Kyriakopoulou, C. B., Nordvarg, H. & Virtanen, A. A novel nuclear human poly(A) polymerase (PAP), PAPγ. J. Biol. Chem. 276, 33504–33511 (2001)

    Article  CAS  Google Scholar 

  14. Martin, G. & Keller, W. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases. EMBO J. 15, 2593–2603 (1996)

    Article  CAS  Google Scholar 

  15. Trippe, R. et al. Identification, cloning, and functional analysis of the human U6 snRNA-specific terminal uridylyl transferase. RNA 12, 1494–1504 (2006)

    Article  CAS  Google Scholar 

  16. Rissland, O. S., Mikulasova, A. & Norbury, C. J. Efficient RNA polyuridylation by noncanonical poly(A) polymerases. Mol. Cell. Biol. 27, 3612–3624 (2007)

    Article  CAS  Google Scholar 

  17. LaCava, J. et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121, 713–724 (2005)

    Article  CAS  Google Scholar 

  18. Colgan, D. F. & Manley, J. L. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11, 2755–2766 (1997)

    Article  CAS  Google Scholar 

  19. Wang, L., Eckmann, C. R., Kadyk, L. C., Wickens, M. & Kimble, J. A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans. Nature 419, 312–316 (2002)

    Article  ADS  CAS  Google Scholar 

  20. Takagaki, Y. & Manley, J. L. Complex protein interactions within the human polyadenylation machinery identify a novel component. Mol. Cell. Biol. 20, 1515–1525 (2000)

    Article  CAS  Google Scholar 

  21. Hirose, Y. & Manley, J. L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000)

    CAS  PubMed  Google Scholar 

  22. Mandel, C. R. et al. Polyadenylation factor CPSF-73 is the pre-mRNA 3′-end-processing endonuclease. Nature 444, 953–956 (2006)

    Article  ADS  CAS  Google Scholar 

  23. Shatkin, A. J. & Manley, J. L. The ends of the affair: capping and polyadenylation. Nature Struct. Biol. 7, 838–842 (2000)

    Article  CAS  Google Scholar 

  24. Nagaoka, K., Suzuki, T., Kawano, T., Imakawa, K. & Sakai, S. Stability of casein mRNA is ensured by structural interactions between the 3′-untranslated region and poly(A) tail via the HuR and poly(A)-binding protein complex. Biochim. Biophys. Acta 1759, 132–140 (2006)

    Article  CAS  Google Scholar 

  25. Gilbert, C., Kristjuhan, A., Winkler, G. S. & Svejstrup, J. Q. Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation. Mol. Cell 14, 457–464 (2004)

    Article  CAS  Google Scholar 

  26. Christofori, G. & Keller, W. 3′ cleavage and polyadenylation of mRNA precursors in vitro requires a poly(A) polymerase, a cleavage factor, and a snRNP. Cell 54, 875–889 (1988)

    Article  CAS  Google Scholar 

  27. Zhao, J., Hyman, L. & Moore, C. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63, 405–445 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Stevenson, A. L. & Norbury, C. J. The Cid1 family of non-canonical poly(A) polymerases. Yeast 23, 991–1000 (2006)

    Article  CAS  Google Scholar 

  29. Kwak, J. E. & Wickens, M. A family of poly(U) polymerases. RNA 13, 860–867 (2007)

    Article  CAS  Google Scholar 

  30. Ding, J. et al. Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev. 13, 1102–1115 (1999)

    Article  CAS  Google Scholar 

  31. Ling, K., Doughman, R. L., Firestone, A. J., Bunce, M. W. & Anderson, R. A. Type Iγ phosphatidylinositol phosphate kinase targets and regulates focal adhesions. Nature 420, 89–93 (2002)

    Article  ADS  CAS  Google Scholar 

  32. Kendziorski, C. M., Newton, M. A., Lan, H. & Gould, M. N. On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat. Med. 22, 3899–3914 (2003)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank J. L. Manley for the gift of antibodies against CPSF-73, CstF-64 and PAPα; M. Wickens for the generous gift of the PAPα construct and for advice and discussion; D. Brow, S. Miyamoto, D. Wassarman and R. Tibbetts for reading the manuscript and for comments; and C. Song for technical assistance in the early parts of the project. R.A.A. is supported by grants from the National Institutes of Health (NIH). M.L.G., D.L.M. and C.S. were supported by the American Heart Association. C.A.B. is supported by the National Research Service Award. D.L.M. and M.L.G. received Research Training Grant support from the NIH.

Author Contributions D.L.M. contributed to Figs 1a, d, f, 2, 3a, b, 4g–k and Supplementary Figs 1, 2, 4–7. M.L.G. contributed to Figs 1a, 3c, f, 4a–f and Supplementary Fig. 1. C.A.B. contributed to Fig. 3d, e, Supplementary Fig. 1 and Supplementary Tables 1 and 2. C.S. contributed to Fig. 1a, c, e and Supplementary Figs 3 and 6. P.W. and C.K. analysed the microarray data. R.A.A. directed the experimental approach and project. D.L.M., M.L.G., C.A.B. and R.A.A. analysed and interpreted the experiments, and conceptualized and wrote the paper.

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Author notes

  1. David L. Mellman, Michael L. Gonzales, Chunhua Song and Christy A. Barlow: These authors contributed equally to this work.

Authors and Affiliations

  1. Program in Molecular and Cellular Pharmacology,,

    David L. Mellman, Michael L. Gonzales & Richard A. Anderson

  2. Department of Pharmacology, and,

    Chunhua Song, Christy A. Barlow & Richard A. Anderson

  3. Department of Biostatistics and Medical Informatics, University of Wisconsin Medical School, University of Wisconsin-Madison, 1300 University Avenue, Madison, Wisconsin 53706, USA,

    Ping Wang & Christina Kendziorski

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  1. David L. Mellman
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Correspondence to Richard A. Anderson.

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The file contains Supplementary Methods, Supplementary Figures 1-7 with Legends and Supplementary Tables 1-2. (PDF 11680 kb)

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Mellman, D., Gonzales, M., Song, C. et al. A PtdIns4,5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs. Nature 451, 1013–1017 (2008). https://doi.org/10.1038/nature06666

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