Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing

EMBO Journal

Volumn 30, Issue 12, 2011, Pages 2420-2430

  Van Nues, Robert Willem ^a   Granneman, Sander ^b   Kudla, Grzegorz ^b   Sloan, Katherine Elizabeth ^a   Chicken, Matthew ^a   Tollervey, David ^b   Watkins, Nicholas James ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

methylation; ribosome; rRNA; snoRNA; snoRNP

Indexed keywords

BOX C D SMALL NUCLEOLAR RIBONUCLEOPROTEIN; PROTEIN SUBUNIT; RIBOSOME RNA; SMALL NUCLEOLAR RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CATALYSIS; CATALYST; METHYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN RNA BINDING; RNA METHYLATION; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

BASE PAIRING; BASE SEQUENCE; CATALYSIS; CONSERVED SEQUENCE; DNA METHYLATION; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; RIBONUCLEOPROTEINS, SMALL NUCLEOLAR; RNA PRECURSORS; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 79958849878     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/emboj.2011.148     Document Type: Article

References (35)

1. Bleichert F, Gagnon KT, Brown II BA, Maxwell ES, Leschziner AE, Unger VM, Baserga SJ (2009) A dimeric structure for archaeal box C/D small ribonucleoproteins. Science 325: 1384-1387
2. Cahill NM, Friend K, Speckmann W, Li ZH, Terns RM, Terns MP, Steitz JA (2002) Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J 21: 3816-3828 (Pubitemid 34787054)
3. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190 (Pubitemid 38811555)
4. Decatur WA, Fournier MJ (2002) rRNA modifications and ribosome function. Trends Biochem Sci 27: 344-351 (Pubitemid 34756517)
5. Dennis PP, Omer A (2005) Small non-coding RNAs in Archaea. Curr Opin Microbiol 8: 685-694 (Pubitemid 41643037)
6. Fayet-Lebaron E, Atzorn V, Henry Y, Kiss T (2009) 18S rRNA processing requires base pairings of snR30 H/ACA snoRNA to eukaryote-specific 18S sequences. EMBO J 28: 1260-1270
7. Gagnon KT, Zhang X, Qu G, Biswas S, Suryadi J, Brown II BA, Maxwell ES (2010) Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif. RNA 16: 79-90
8. Ghalei H, Hsiao HH, Urlaub H, Wahl MC, Watkins NJ (2010) A novel Nop5-sRNA interaction that is required for efficient archaeal box C/D sRNP formation. RNA 16: 2341-2348
9. Granneman S, Kudla G, Petfalski E, Tollervey D (2009) Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proc Natl Acad Sci USA 106: 9613-9618
10. Henras AK, Soudet J, Gerus M, Lebaron S, Caizergues-Ferrer M, Mougin A, Henry Y (2008) The post-transcriptional steps of eukaryotic ribosome biogenesis. Cell Mol Life Sci 65: 2334-2359
11. Hughes JM (1996) Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. J Mol Biol 259: 645-654 (Pubitemid 26226005)
12. Janke C, Magiera MM, Rathfelder N, Taxis C, Reber S, Maekawa H, Moreno-Borchart A, Doenges G, Schwob E, Schiebel E, Knop M (2004) A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21 : 947-962 (Pubitemid 39206863)
13. Kiss T (2002) Small nucleolar RNAs: an abundant group of non-coding RNAs with diverse cellular functions. Cell 109: 145-148 (Pubitemid 34518252)
14. Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85: 1077-1088 (Pubitemid 26231174)
15. Kiss-Laszlo Z, Henry Y, Kiss T (1998) Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA. EMBO J 17: 797-807 (Pubitemid 28062058)
16. Kuhn JF, Tran EJ, Maxwell ES (2002) Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res 30: 931-941 (Pubitemid 34679661)
17. Liu B, Fournier MJ (2004) Interference probing of rRNA with snoRNPs: a novel approach for functional mapping of RNA in vivo. RNA 10: 1130-1141 (Pubitemid 38822148)
18. Liu N, Xiao ZD, Yu CH, Shao P, Liang YT, Guan DG, Yang JH, Chen CL, Qu LH, Zhou H (2009) SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics 10: 515
19. Lowe TM, Eddy SR (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283: 1168-1171
20. 0-O-methyl groups in ribosomal RNA. Methods 25: 374-382 (Pubitemid 34183562)
21. Moore T, Zhang Y, Fenley MO, Li H (2004) Molecular basis of box C/ D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure 12: 807-818 (Pubitemid 38595769)
22. Omer AD, Ziesche S, Ebhardt H, Dennis PP (2002) In vitro recon-stitution and activity of a C/D box methylation guide ribonucleo-protein complex. Proc Natl Acad Sci USA 99: 5289-5294 (Pubitemid 34411541)
23. Oruganti S, Zhang Y, Li H (2005) Structural comparison of yeast snoRNP and spliceosomal protein Snu13p with its homologs. Biochem Biophys Res Commun 333: 550-554 (Pubitemid 40848326)
24. Qu G, van Nues RW, Watkins NJ, Maxwell ES (2011) Spatial and functional coupling of Box C/D and C'/D' RNPs are evolutionarily conserved features of the eukaryotic Box C/D snoRNP nucleotide modification complex. Mol Cell Biol 31: 365-374
25. Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y, Caizergues-Ferrer M, Bachellerie JP (1999) Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast. Mol Cell Biol 19: 1144-1158 (Pubitemid 29046857)
26. Reichow SL, Hamma T, Ferre-DAmare AR, Varani G (2007) The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res 35: 1452-1464 (Pubitemid 46592868)
27. Suryadi J, Tran EJ, Maxwell ES, Brown II BA (2005) The crystal structure of the Methanocaldococcus jannaschii multifunctional L7Ae RNA-binding protein reveals an induced-fit interaction with the box C/D RNAs. Biochemistry 44: 9657-9672 (Pubitemid 40994360)
28. Szewczak LB, DeGregorio SJ, Strobel SA, Steitz JA (2002) Exclusive interaction of the 15.5kD protein with the terminal box C/D motif of a methylation guide snoRNP. Chem Biol 9: 1095-1107 (Pubitemid 35240932)
29. Tran EJ, Zhang X, Maxwell ES (2003) Efficient RNA 2'-O-methyla-tion requires juxtaposed and symmetrically assembled archaeal box C/D and C'/D' RNPs. EMBO J 22: 3930-3940 (Pubitemid 36975719)
30. Watkins NJ, Dickmanns A, Luhrmann R (2002) Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. Mol Cell Biol 22: 8342-8352 (Pubitemid 35304065)
31. Watkins NJ, Segault V, Charpentier B, Nottrott S, Fabrizio P, Bachi A, Wilm M, Rosbash M, Branlant C, Luhrmann R (2000) A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell 103: 457-466
32. Xia L, Watkins NJ, Maxwell ES (1997) Identification of specific nucleotide sequences and structural elements required for intro-nic U14 snoRNA processing. RNA 3: 17-26 (Pubitemid 27030246)
33. Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H (2010) Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Mol Cell 39: 939-949
34. Ye K, Jia R, Lin J, Ju M, Peng J, Xu A, Zhang L (2009) Structural organization of box C/D RNA-guided RNA methyltransferase. Proc Natl Acad Sci USA 106: 13808-13813
35. Yu YT, Shu MD, Steitz JA (1997) A new method for detecting sites of 2'-O-methylation in RNA molecules. RNA 3: 324-331