PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif

RNA

Volumn 17, Issue 9, 2011, Pages 1737-1746

  Rammelt, Christiane ^a   Bilen, Biter ^b   Zavolan, Mihaela ^b   Keller, Walter ^b  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^b UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Noncanonical poly(A) polymerase; Polyadenylation; RNA surveillance; TRAMP4

Indexed keywords

AMINO ACID; HISTONE; PAPD5 PROTEIN; POLYNUCLEOTIDE ADENYLYLTRANSFERASE; RIBOSOME RNA; UNCLASSIFIED DRUG;

ADENYLATION; ARTICLE; BACTERIUM; CARBOXY TERMINAL SEQUENCE; CATALYSIS; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; IN VITRO STUDY; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CROSS LINKING; PROTEIN EXPRESSION; RNA BINDING; RNA DEGRADATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CATALYTIC DOMAIN; ESCHERICHIA COLI; GENES, FUNGAL; HEK293 CELLS; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; POLYADENYLATION; POLYNUCLEOTIDE ADENYLYLTRANSFERASE; RNA, FUNGAL; RNA, RIBOSOMAL; RNA, TRANSFER; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SUBSTRATE SPECIFICITY;

MAMMALIA;

EID: 84860390193     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2787011     Document Type: Article

References (38)

1. Balwierz P., Carninci P., Daub C., Kawai J., Hayashizaki Y., Van Belle W., Beisel C., Van Nimwegen E. 2009. Methods for analyzing deep sequencing expression data: Constructing the human and mouse promoterome with deepCAGE data. Genome Biol 10: R79. doi: 10.1186/gb-2009-10-7-r79.
2. Betat H., Rammelt C., Martin G., Mörl M. 2004. Exchange of regions between bacterial poly(A) polymerase and CCA adding enzyme generates altered specificities. Mol Cell 15: 389-398. (Pubitemid 39092755)
3. Bühler M., Spies N., Bartel D.P., Moazed D. 2008. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 15: 1015-1023.
4. Callahan K.P., Butler J.S. 2010. TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. J Biol Chem 285: 3540-3547.
5. Carneiro T., Carvalho C., Braga J., Rino J., Milligan L., Tollervey D., Carmo-Fonseca M. 2007. Depletion of the yeast nuclear exosome subunit Rrp6 results in accumulation of polyadenylated RNAs in a discrete domain within the nucleolus. Mol Cell Biol 27: 4157-4165. (Pubitemid 47011011)
6. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., Thompson J.D. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500. (Pubitemid 37442184)
7. Davis C.A., Ares M. Jr. 2006. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci 103: 3262-3267. (Pubitemid 43346458)
8. Dez C., Houseley J., Tollervey D. 2006. Surveillance of nuclearrestricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J 25: 1534-1546.
9. Egecioglu D.E., Henras A.K., Chanfreau G.F. 2006. Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12: 26-32. (Pubitemid 43037450)
10. Griffiths-Jones S., Saini H.K., Van Dongen S., Enright A.J. 2008. miRBase: Tools for microRNA genomics. Nucleic Acids Res 36: D154-D158. (Pubitemid 351149713)
11. Hafner M., Landgraf P., Ludwig J., Rice A., Ojo T., Lin C., Holoch D., Lim C., Tuschl T. 2008. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44: 3-12. (Pubitemid 350297985)
12. Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., Rothballer A., Ascano M. Jr, Jungkamp A-C, Munschauer M., et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
13. Hamill S., Wolin S.L., Reinisch K.M. 2010. Structure and function of the polymerase core of TRAMP, a RNA surveillance complex. Proc Natl Acad Sci 107: 15045-15050.
14. Houseley J., Kotovic K., El Hage A., Tollervey D. 2007. Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J 26: 4996-5006. (Pubitemid 350261284)
15. Kadaba S., Krueger A., Trice T., Krecic A.M., Hinnebusch A.G., Anderson J. 2004. Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev 18: 1227-1240. (Pubitemid 38720591)
16. Kadaba S., Wang X., Anderson J.T. 2006. Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 12: 508-521. (Pubitemid 43290877)
17. LaCava J., Houseley J., Saveanu C., Petfalski E., Thompson E., Jacquier A., Tollervey D. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121: 713-724. (Pubitemid 40797594)
18. Lestrade L., Weber M.J. 2006. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34: D158-D162.
19. Li Z., Pandit S., Deutscher M.P. 1998. Polyadenylation of stable RNA precursors in vivo. Proc Natl Acad Sci 95: 12158-12162. (Pubitemid 28483735)
20. Li Z., Reimers S., Pandit S., Deutscher M.P. 2002. RNA quality control: Degradation of defective transfer RNA. EMBO J 21: 1132-1138. (Pubitemid 34206186)
21. Martin G., Keller W. 2007. RNA-specific ribonucleotidyl transferases. RNA 13: 1834-1849. (Pubitemid 350005209)
22. Martin G., Möglich A., Keller W., Doublié S. 2004. Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase. J Mol Biol 341: 911-925. (Pubitemid 39037353)
23. Mullen T.E., Marzluff W.F. 2008. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 59 to 39 and 39 to 59. Genes Dev 22: 50-65.
24. Nakamura R., Takeuchi R., Takata K., Shimanouchi K., Abe Y., Kanai Y., Ruike T., Ihara A., Sakaguchi K. 2008. TRF4 is involved in polyadenylation of snRNAs in Drosophila melanogaster. Mol Cell Biol 28: 6620-6631.
25. Pruitt K.D., Tatusova T., Maglott D.R. 2005. NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33: D501-D504. (Pubitemid 40207924)
26. San Paolo S., Vanacova S., Schenk L., Scherrer T., Blank D., Keller W., Gerber A.P. 2009. Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. PLoS Genet 5: e1000555. doi: 10.1371/journal.pgen.1000555.
27. Schmidt M-J, Norbury C.J. 2010. Polyadenylation and beyond: Emerging roles for noncanonical poly(A) polymerases. WIREs RNA 1: 142-151.
28. Schmidt M-J, West S., Norbury C.J. 2010. The human cytoplasmic RNA terminal U-transferase ZCCHC11 targets histone mRNAs for degradation. RNA 17: 39-44.
29. Shcherbik N., Wang M., Lapik Y.R., Srivastava L., Pestov D.G. 2010. Polyadenylation and degradation of incomplete RNA polymerase I transcripts in mammalian cells. EMBO Rep 11: 106-111.
30. Slomovic S., Fremder E., Staals R.H.G., Pruijn G.J.M., Schuster G. 2010. Addition of poly(A) and poly(A)-rich tails during RNA degradation in the cytoplasm of human cells. Proc Natl Acad Sci 107: 7407-7412.
31. Smit A.F.A., Hubley R., Green P. 1996-2010. RepeatMasker Open-30. http://www.repeatmasker.org.
32. Ueda H.R., Hayashi S., Matsuyama S., Yomo T., Hashimoto S., Kay S.A., Hogenesch J.B., Iino M. 2004. Universality and flexibility in gene expression from bacteria to human. Proc Natl Acad Sci 101: 3765-3769. (Pubitemid 38381052)
33. Vanacova S., Wolf J., Martin G., Blank D., Dettwiler S., Friedlein A., Langen H., Keith G., Keller W. 2005. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3: e189. doi: 10.1371/journal.pbio. 0030189.
34. Win T.Z., Draper S., Read R.L., Pearce J., Norbury C.J., Wang S-W 2006. Requirement of fission yeast Cid14 in polyadenylation of rRNAs. Mol Cell Biol 26: 1710-1721.
35. Wlotzka W., Kudla G., Granneman S., Tollervey D. 2011. The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J 30: 1790-1803.
36. Wyers F., Rougemaille M., Badis G., Rousselle J-C, Dufour M-E, Boulay J., Régnault B., Devaux F., Namane A., Séraphin B., et al. 2005. Cryptic Pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725-737. (Pubitemid 40797595)
37. Zhang Z.D., Rozowsky J., Snyder M., Chang J., Gerstein M. 2008. Modeling ChIP sequencing in silico with applications. PLoS Comput Biol 4: e1000158. doi: 10.1371/journal.pcbi.1000158.
38. Zhou P., Lugovskoy A.A., Wagner G. 2001. A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins. J Biol NMR 20: 11-14. (Pubitemid 32519649)