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. 2001 Dec;7(12):1855–1866.

PUM2, a novel murine puf protein, and its consensus RNA-binding site.

E K White 1, T Moore-Jarrett 1, H E Ruley 1
PMCID: PMC1370223  PMID: 11780640

Abstract

Members of the Puf family of RNA-binding proteins from Drosophila, Caenorhabditis elegans, and Dictyostelium are known to function as translational repressors. To identify mammalian proteins that might regulate posttranscriptional gene expression, we have characterized a novel murine Puf protein, PUM2. Pum2 transcripts were expressed in all murine tissues examined, suggesting the gene influences processes common to many cell types. Like all Puf family members, PUM2 contains a C-terminal RNA-binding domain related to the Drosophila Pumilio homology domain (PUM-HD). Two features found in the amino-terminus of PUM2, regions rich in serine and glutamine/alanine-rich regions, were also identified in most Puf family members. RNA sequences capable of binding with high affinity (6.5 nM) to a 48-kDa recombinant protein containing the PUM2 PUM-HD were isolated by using an iterative amplification-selection protocol (SELEX). The consensus sequence [UGUANAUARNNNNBBBBSCCS] of the PUM2 binding element (PBE) is related to, but distinct from, the 3' end of the Drosophila Nanos response element. The characterization of PUM2 and potential RNA-binding site will assist efforts to assess the extent and mechanism by which mammalian genes are regulated at a posttranscriptional level.

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Selected References

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  1. Antic D., Keene J. D. Embryonic lethal abnormal visual RNA-binding proteins involved in growth, differentiation, and posttranscriptional gene expression. Am J Hum Genet. 1997 Aug;61(2):273–278. doi: 10.1086/514866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Antic D., Lu N., Keene J. D. ELAV tumor antigen, Hel-N1, increases translation of neurofilament M mRNA and induces formation of neurites in human teratocarcinoma cells. Genes Dev. 1999 Feb 15;13(4):449–461. doi: 10.1101/gad.13.4.449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Asaoka-Taguchi M., Yamada M., Nakamura A., Hanyu K., Kobayashi S. Maternal Pumilio acts together with Nanos in germline development in Drosophila embryos. Nat Cell Biol. 1999 Nov;1(7):431–437. doi: 10.1038/15666. [DOI] [PubMed] [Google Scholar]
  4. Atasoy U., Watson J., Patel D., Keene J. D. ELAV protein HuA (HuR) can redistribute between nucleus and cytoplasm and is upregulated during serum stimulation and T cell activation. J Cell Sci. 1998 Nov;111(Pt 21):3145–3156. doi: 10.1242/jcs.111.21.3145. [DOI] [PubMed] [Google Scholar]
  5. Barker D. D., Wang C., Moore J., Dickinson L. K., Lehmann R. Pumilio is essential for function but not for distribution of the Drosophila abdominal determinant Nanos. Genes Dev. 1992 Dec;6(12A):2312–2326. doi: 10.1101/gad.6.12a.2312. [DOI] [PubMed] [Google Scholar]
  6. Behar L., Marx R., Sadot E., Barg J., Ginzburg I. cis-acting signals and trans-acting proteins are involved in tau mRNA targeting into neurites of differentiating neuronal cells. Int J Dev Neurosci. 1995 Apr;13(2):113–127. doi: 10.1016/0736-5748(95)00001-w. [DOI] [PubMed] [Google Scholar]
  7. Blichenberg A., Schwanke B., Rehbein M., Garner C. C., Richter D., Kindler S. Identification of a cis-acting dendritic targeting element in MAP2 mRNAs. J Neurosci. 1999 Oct 15;19(20):8818–8829. doi: 10.1523/JNEUROSCI.19-20-08818.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bohjanen P. R., Petryniak B., June C. H., Thompson C. B., Lindsten T. An inducible cytoplasmic factor (AU-B) binds selectively to AUUUA multimers in the 3' untranslated region of lymphokine mRNA. Mol Cell Biol. 1991 Jun;11(6):3288–3295. doi: 10.1128/mcb.11.6.3288-3295.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dalby B., Glover D. M. 3' non-translated sequences in Drosophila cyclin B transcripts direct posterior pole accumulation late in oogenesis and peri-nuclear association in syncytial embryos. Development. 1992 Aug;115(4):989–997. doi: 10.1242/dev.115.4.989. [DOI] [PubMed] [Google Scholar]
  10. Edwards T. A., Pyle S. E., Wharton R. P., Aggarwal A. K. Structure of Pumilio reveals similarity between RNA and peptide binding motifs. Cell. 2001 Apr 20;105(2):281–289. doi: 10.1016/s0092-8674(01)00318-x. [DOI] [PubMed] [Google Scholar]
  11. Fitzwater T., Polisky B. A SELEX primer. Methods Enzymol. 1996;267:275–301. doi: 10.1016/s0076-6879(96)67019-0. [DOI] [PubMed] [Google Scholar]
  12. Forbes A., Lehmann R. Nanos and Pumilio have critical roles in the development and function of Drosophila germline stem cells. Development. 1998 Feb;125(4):679–690. doi: 10.1242/dev.125.4.679. [DOI] [PubMed] [Google Scholar]
  13. Gish W., States D. J. Identification of protein coding regions by database similarity search. Nat Genet. 1993 Mar;3(3):266–272. doi: 10.1038/ng0393-266. [DOI] [PubMed] [Google Scholar]
  14. Groisman I., Huang Y. S., Mendez R., Cao Q., Theurkauf W., Richter J. D. CPEB, maskin, and cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. Cell. 2000 Oct 27;103(3):435–447. doi: 10.1016/s0092-8674(00)00135-5. [DOI] [PubMed] [Google Scholar]
  15. Henderson B. R. Iron regulatory proteins 1 and 2. Bioessays. 1996 Sep;18(9):739–746. doi: 10.1002/bies.950180909. [DOI] [PubMed] [Google Scholar]
  16. Hicks G. G., Singh N., Nashabi A., Mai S., Bozek G., Klewes L., Arapovic D., White E. K., Koury M. J., Oltz E. M. Fus deficiency in mice results in defective B-lymphocyte development and activation, high levels of chromosomal instability and perinatal death. Nat Genet. 2000 Feb;24(2):175–179. doi: 10.1038/72842. [DOI] [PubMed] [Google Scholar]
  17. Kern J. A., Warnock L. J., McCafferty J. D. The 3' untranslated region of IL-1beta regulates protein production. J Immunol. 1997 Feb 1;158(3):1187–1193. [PubMed] [Google Scholar]
  18. Kikuno R., Nagase T., Suyama M., Waki M., Hirosawa M., Ohara O. HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project. Nucleic Acids Res. 2000 Jan 1;28(1):331–332. doi: 10.1093/nar/28.1.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Klausner R. D., Rouault T. A., Harford J. B. Regulating the fate of mRNA: the control of cellular iron metabolism. Cell. 1993 Jan 15;72(1):19–28. doi: 10.1016/0092-8674(93)90046-s. [DOI] [PubMed] [Google Scholar]
  20. Kraemer B., Crittenden S., Gallegos M., Moulder G., Barstead R., Kimble J., Wickens M. NANOS-3 and FBF proteins physically interact to control the sperm-oocyte switch in Caenorhabditis elegans. Curr Biol. 1999 Sep 23;9(18):1009–1018. doi: 10.1016/s0960-9822(99)80449-7. [DOI] [PubMed] [Google Scholar]
  21. Lasko P. RNA sorting in Drosophila oocytes and embryos. FASEB J. 1999 Mar;13(3):421–433. doi: 10.1096/fasebj.13.3.421. [DOI] [PubMed] [Google Scholar]
  22. Lin H., Spradling A. C. A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development. 1997 Jun;124(12):2463–2476. doi: 10.1242/dev.124.12.2463. [DOI] [PubMed] [Google Scholar]
  23. Lüscher B., Stauber C., Schindler R., Schümperli D. Faithful cell-cycle regulation of a recombinant mouse histone H4 gene is controlled by sequences in the 3'-terminal part of the gene. Proc Natl Acad Sci U S A. 1985 Jul;82(13):4389–4393. doi: 10.1073/pnas.82.13.4389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Macdonald P. M. The Drosophila pumilio gene: an unusually long transcription unit and an unusual protein. Development. 1992 Jan;114(1):221–232. doi: 10.1242/dev.114.1.221. [DOI] [PubMed] [Google Scholar]
  25. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Murata Y., Wharton R. P. Binding of pumilio to maternal hunchback mRNA is required for posterior patterning in Drosophila embryos. Cell. 1995 Mar 10;80(5):747–756. doi: 10.1016/0092-8674(95)90353-4. [DOI] [PubMed] [Google Scholar]
  27. Nagase T., Miyajima N., Tanaka A., Sazuka T., Seki N., Sato S., Tabata S., Ishikawa K., Kawarabayasi Y., Kotani H. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1. DNA Res. 1995;2(1):37–43. doi: 10.1093/dnares/2.1.37. [DOI] [PubMed] [Google Scholar]
  28. Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. DNA Res. 1996 Oct 31;3(5):321-9, 341-54. doi: 10.1093/dnares/3.5.321. [DOI] [PubMed] [Google Scholar]
  29. Nakahata S., Katsu Y., Mita K., Inoue K., Nagahama Y., Yamashita M. Biochemical identification of Xenopus Pumilio as a sequence-specific cyclin B1 mRNA-binding protein that physically interacts with a Nanos homolog, Xcat-2, and a cytoplasmic polyadenylation element-binding protein. J Biol Chem. 2001 Mar 29;276(24):20945–20953. doi: 10.1074/jbc.M010528200. [DOI] [PubMed] [Google Scholar]
  30. Nickells J., Res J., Mitchell I. A. Re-wiring an arterial line. A novel technique. Anaesth Intensive Care. 2000 Jun;28(3):331–332. doi: 10.1177/0310057X0002800317. [DOI] [PubMed] [Google Scholar]
  31. Olivas W., Parker R. The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. EMBO J. 2000 Dec 1;19(23):6602–6611. doi: 10.1093/emboj/19.23.6602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Parisi M., Lin H. The Drosophila pumilio gene encodes two functional protein isoforms that play multiple roles in germline development, gonadogenesis, oogenesis and embryogenesis. Genetics. 1999 Sep;153(1):235–250. doi: 10.1093/genetics/153.1.235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Parisi M., Lin H. Translational repression: a duet of Nanos and Pumilio. Curr Biol. 2000 Jan 27;10(2):R81–R83. doi: 10.1016/s0960-9822(00)00283-9. [DOI] [PubMed] [Google Scholar]
  34. Pérez I., Lin C. H., McAfee J. G., Patton J. G. Mutation of PTB binding sites causes misregulation of alternative 3' splice site selection in vivo. RNA. 1997 Jul;3(7):764–778. [PMC free article] [PubMed] [Google Scholar]
  35. Shaw G., Kamen R. A conserved AU sequence from the 3' untranslated region of GM-CSF mRNA mediates selective mRNA degradation. Cell. 1986 Aug 29;46(5):659–667. doi: 10.1016/0092-8674(86)90341-7. [DOI] [PubMed] [Google Scholar]
  36. Sonoda J., Wharton R. P. Drosophila Brain Tumor is a translational repressor. Genes Dev. 2001 Mar 15;15(6):762–773. doi: 10.1101/gad.870801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sonoda J., Wharton R. P. Recruitment of Nanos to hunchback mRNA by Pumilio. Genes Dev. 1999 Oct 15;13(20):2704–2712. doi: 10.1101/gad.13.20.2704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Souza G. M., da Silva A. M., Kuspa A. Starvation promotes Dictyostelium development by relieving PufA inhibition of PKA translation through the YakA kinase pathway. Development. 1999 Jun;126(14):3263–3274. doi: 10.1242/dev.126.14.3263. [DOI] [PubMed] [Google Scholar]
  39. 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. 2001 Feb 1;20(3):552–561. doi: 10.1093/emboj/20.3.552. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990 Aug 3;249(4968):505–510. doi: 10.1126/science.2200121. [DOI] [PubMed] [Google Scholar]
  42. Wang W., Caldwell M. C., Lin S., Furneaux H., Gorospe M. HuR regulates cyclin A and cyclin B1 mRNA stability during cell proliferation. EMBO J. 2000 May 15;19(10):2340–2350. doi: 10.1093/emboj/19.10.2340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Wang X., Zamore P. D., Hall T. M. Crystal structure of a Pumilio homology domain. Mol Cell. 2001 Apr;7(4):855–865. doi: 10.1016/s1097-2765(01)00229-5. [DOI] [PubMed] [Google Scholar]
  44. Wang Z. F., Whitfield M. L., Ingledue T. C., 3rd, Dominski Z., Marzluff W. F. The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. Genes Dev. 1996 Dec 1;10(23):3028–3040. doi: 10.1101/gad.10.23.3028. [DOI] [PubMed] [Google Scholar]
  45. Wharton R. P., Sonoda J., Lee T., Patterson M., Murata Y. The Pumilio RNA-binding domain is also a translational regulator. Mol Cell. 1998 May;1(6):863–872. doi: 10.1016/s1097-2765(00)80085-4. [DOI] [PubMed] [Google Scholar]
  46. Wharton R. P., Struhl G. RNA regulatory elements mediate control of Drosophila body pattern by the posterior morphogen nanos. Cell. 1991 Nov 29;67(5):955–967. doi: 10.1016/0092-8674(91)90368-9. [DOI] [PubMed] [Google Scholar]
  47. Zamore P. D., Bartel D. P., Lehmann R., Williamson J. R. The PUMILIO-RNA interaction: a single RNA-binding domain monomer recognizes a bipartite target sequence. Biochemistry. 1999 Jan 12;38(2):596–604. doi: 10.1021/bi982264s. [DOI] [PubMed] [Google Scholar]
  48. Zamore P. D., Williamson J. R., Lehmann R. The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. RNA. 1997 Dec;3(12):1421–1433. [PMC free article] [PubMed] [Google Scholar]
  49. Zhang B., Gallegos M., Puoti A., Durkin E., Fields S., Kimble J., Wickens M. P. A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Nature. 1997 Dec 4;390(6659):477–484. doi: 10.1038/37297. [DOI] [PubMed] [Google Scholar]
  50. de Moor C. H., Richter J. D. Cytoplasmic polyadenylation elements mediate masking and unmasking of cyclin B1 mRNA. EMBO J. 1999 Apr 15;18(8):2294–2303. doi: 10.1093/emboj/18.8.2294. [DOI] [PMC free article] [PubMed] [Google Scholar]

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