Multicomponent 2'-O-Ribose Methylation Machines: Evolving Box C/D RNP Structure and Function

DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution

Volumn , Issue , 2009, Pages 436-449

  Gagnon, Keith T ^a   Qu, Guosheng ^a   Maxwell, E Stuart ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79953726593     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (83)

1. Helm M. Post-transcriptional nucleotide modification and alternative folding of RNA. Nucl Acids Res2006; 34:721-733.
2. Chow C, Lamichhane TN, Mahto SK. Expanding the nucleotide repertoire of the ribosome with posttranscriptional modifications. ACS Chem Biol 2007; 2:610-619.
3. Tollervcy D, Lchtonen H, Jansen R et al Temperature-sensitive mutations demonstrate roles for yeast fibril-larin in pre-rRNA processing, pre-rRNA methylation and ribosome assembly. Cell 1993; 72:443-457.
4. Decatur W, Fournier MJ. rRNA modifications and ribosome function. Trends Biochem Sci 2002; 27:344-351.
5. Liang X, Hury A, Hoze E et al Genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Leishmania major indicates conservation among trypanosomatids in the repertoire and in their rRNA targets. Eukaryot. Cell 2007; 6:361-377.
6. Esguerra J, Warringer J, Blomberg A. Functional importance of individual rRNA 2'-0-ribose mcthylarions revealed by high-resolution phenotyping. RNA 2008; 14:649-656.
7. Darzacq X, Jady BE, Verheggen C et al Cajal body-specific small nuclear RNAs: a novel class of 2’-0-methylation and pseudouridyiation guide RNAs. EMBO J 2002; 21:2746-2756.
8. Beal P, Maydanovych O, Pokharel S. The chemistry and biology of RNA editing by adenosine deaminases. Nucl Acids Symp Ser 2007; 51:83-84.
9. Kishore S, Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 2006; 311:230-232.
10. Bazcley P, Shepelcv V, Talebizadeh Z et al SnoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene 2008; 408:172-179.
11. Dennis PP, Omcr A, Lowe T. A guided tour: small RNA function in Archaca. Mol Microbiol 2001; 40:509-519.
12. I>p nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J Biol Chem2004; 279:47661-47671.
13. Hughes JM, Arcs Jr, M. Depletion of U3 small nucleolar RNA inhibits cleavage in the 5’ external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J1991; 10:4231-4239.
14. Morrissey JP, Tollervey D. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol Cell Biol 1993; 13:2469-2477.
15. Liang WQ, Fournier MJ. U14 base-pairs with 18S rRNA: a novel snoRNA interaction required for rRNA processing. Genes Dev 1995; 9:2433-2443.
16. Peculis B, Steitz J. Disruption of U8 nucleolar snRNA inhibits 5.8S and 28S rRNA processing in the Xenopus oocyte. Cell 1993; 73:1233-1245.
17. Beltramc M, Tollervey D. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J 1995; 14:4350-4356.
18. Schoemakcr RJ, Gultyaev AP. Computer simulation of chaperone effects of archaeal C/D box sRNA binding on rRNA folding. Nuc. Acids Res 2006; 34:2015-2026.
19. Omer AD, Lowe EM, Russell AG et al Homologs of small nucleolar RNAs in Archaca. Science 2000; 288:517-522.
20. Gaspin C, Cavaille J, Erauso G et al Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol 2000; 297:895-906.
21. Huttcnhofer A, Cavaille J, Bachellerie JP. Experimental RNomics: a global approach to identifying small nuclear RNAs and their targets in different model organisms. Methods Mol Biol 2004; 265:409-428.
22. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nuc Acids Res 2005: 33:W686-W689.
23. Tran E, Brown J, Maxwell ES. Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus? Trends Biochem Sci 2004; 29:343-350.
24. Lcstradc L, Weber MJ. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nuc Acids Res 2006; 34:D158-D162.
25. Samarsky DA, Fournier MJ. A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. Nuc Acids Res 1999; 27:161-164.
26. Piekna-Przybylska D, Decatur WA, Fournier MJ. New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 2007; 13:305-312.
27. Cavaille J, Buiting K, Keifinann M et al Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc Natl Acad Sci USA 2000; 97:14311-14316.
28. Nahkuri S, Taft RJ, Korbie DJ et al. Molecular evolution of the HBII-52 snoRNA cluster. J Mol Biol2008; 381:810-815.
29. Brown JW, Echeverria M, Qu LH et al. Plant snoRNA database. Nuc Acids Res 2003; 31:432-435
30. Kiss-Laszlo Z, Henry Y, Kiss T. Sequence and structural elements of méthylation guide snoRNAs essential for site-specific ribose méthylation of pre-rRNA. EMBO J 1998; 17:797-807.
31. Klein DJ, Schmeing TM, Moore PB et al. The kink-tum: a new RNA secondary structure motif. EMBO J2001; 20:4214-4221.
32. Vidovic I, Nottrot S, Hartmuth K et al. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol Cell 2000; 6:1331-1342.
33. Nolivos S, Carpousis AJ, Clouet-d’Orval B. The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn. Nucl Acids Res 2005; 33:6507-6514.
34. Mao H, White SA, Williamson JR. A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nat Struct Biol 1999; 6:1139-1147.
35. Clery A, Bourguignon-Igel V, Allmang C et al. An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the sclcnocysteine incorporation machinery. Nucl Acids Res 2007; 35:1868-1884.
36. Montange RK, Batey RT. Structure of the S-adenosylmcthioninc riboswitch regulatory mRNA clement. Nature 2006; 441:1172-1175.
37. Kiss-Laszlo Z, Henry Y, Bacheilerie M et al. Site-specific ribose méthylation of prc-ribosomal RNA: a novel function for small nucleolar RNAs. Cell 1996; 85:1077-1088.
38. Tran EJ, Zhang X, Lackey L et al. Conserved spacing between the box C/D and C7D’ RNPs of the archaeal box C/D sRNP complex is required for efficient 2'-0-methylation of target RNAs. RNA 2005; 11:285-293.
39. Starostina NG, Marshbum S, Johnson LS et al Circular box C/D RNAs in Pyrococcus furiosus. Proc Natl Acad Sci 2004; 101:14097-14101.
40. Wu P, Brockenbrough JS, Metcalfe AC et al Nop5p is a small nucleolar ribonudeoprotcin component required for pre-18s rRNA processing in yeast. J Biol Chem 1998; 273:16453-16463.
41. Newman DR, Kuhn JF, Shanab GM et al. Box C/D snoRNA-associated proteins: two pairs of evolu-tionarily ancient proteins and possible links to replication and transcription. RNA 2000; 6:861-879.
42. Watkins NJ, Scgault V, Charpentier B et al. A common core RNP structure shared between the small nucleolar box C/D RNPs and the spliceosomal U4 snRNP. Cell 2000; 103:457-466.
43. Kuhn J, Tran E, Maxwell ES. Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snul3p snoRNP core protein. Nuc Acids Res 2002; 30:931-941.
44. Orner A, Ziesche S, Ebhardt H et al. In vitro reconstitution and activity of a C/D box méthylation guide ribonucleoprotein complex. Proc Natl Acad Sci USA 2002; 99:5289-5294.
45. Tran EJ, Zhang X, Maxwell ES. Efficient RNA 2'-0-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C7D’ RNPs. EMBO J 2003; 22:3930-3940.
46. Hardin JW, Batey RT. The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity. Nud Acids Res 2006; 34:5039-5051.
47. Turner B, Melcher SA, Wilson TJ et al Induced fit of RNA on binding the L7Ae protein to the kink-tum motif. RNA 2005; 11:1192-1200.
48. Gagnon KT, Zhang X, Agris PF et al Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling. J Mol Biol 2006; 362:1025-1042.
49. Cahill NM, Friend K, Speckman W et al. Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J 2002; 21:3816-3828.
50. Szewczak LB, DeGregorio SJ, Strobcl SA et al. Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a méthylation guide snoRNP. Chem Biol 2002; 9:1095-1107.
51. Watkins NJ, Lemm I, Ingelfinger D et al. Assembly and maturation of the U3 snoRNP in the nudeoplasm in a large dynamic multiprotein complex. Mol Cell 2004; 16:789-798.
52. King T, Decatur WA, Bertrand E et al. A well-connected and conserved nudcoplasmic helicasc is required for production of box C/D and H/ACA snoRNAs and localization of snoRNP proteins. Mol Cell Biol 2001; 21:7731-7746.
53. Boulon S, Verheggen C, Jady BE et al. PHAX and CRM1 arc required sequentially to transport U3 snoRNA to nucleoli. Mol Cell 2004; 16:777-787.
54. McKeegan KS, Debieux CM, Boulon S et al A dynamic scaffold of pre-snoRNP factors facilitates human box C/D snoRNP assembly. Mol Cell Biol 2007; 27:6782-6793.
55. Boulon S, Marmicr-Gourrier N, Pradet-Balade B et al The Hsp90 chaperone controls the biogenesis of L7Ae RNPs through conserved machinery. J Cell Biol 2008; 180:579-595.
56. Zhao R, Kakihara Y, Gribun A et al. Molecular chaperone Hsp90 stabilizes Pihl/Nopl7 to maintain R2TP complex activity that regulates snoRNA accumulation. J Cell Biol 2008; 180:563-578.
57. Bachellerie JP, Cavaille J. Huttenhofer A. The expanding snoRNA world. Biochimie 2002; 84:775-790.
58. Hirosc T, Shu MD, Stein JA. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell 2003; 12:113-123.
59. Kiss T, Fayet E, Jady BE et al. Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harb Symp Quant Biol 2006; 71:407-417.
60. Liu S, Li P, Dybkov O et al Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP. Science 2007; 316:115-120.
61. Charron C, Manival X, Clery A et al. The archaeal sRNA binding protein L7Ae has a 3D structure very similar to that of its eukaryal counterpart while having a broader RNA-binding specificity. J Mol Biol2004; 342:757-773.
62. Koonin EV, Bork P, Sander C. A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme? Nucl Acids Res 1994; 22:2166-2167.
63. Moore T, Zhang Y, Fenlcy MO et al Molecular basis of box C/D RNA-protein interactions: cocrystal structure of archaeal L7Ac and a box C/D RNA. Structure 2004; 12:807-818.
64. Welting TJM, van Vcnrooij WJ, Pruijn GJM. Mutual interactions between subunits of the human RNase MRP ribonucleoprotcin complex. Nucl Acids Res 2004; 32:2138-2146.
65. Allmang C, Carbon P, Krol A. The SBP2 and 15.5 kD/Snul3p proteins share the same RNA-bind-ing domain: identification of SBP2 amino acids important to SECIS RNA binding. RNA 2002; 8:1308-1318.
66. Wang C, Meier UT. Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonuclcoproteins. EMBO J 2004; 23:1857-1867.
67. Aittaleb M, Rashid R, Chen Q et al. Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol 2003; 10:256-263.
68. Gautier T, Berges T, Tollervey D et al Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Noplp and are required for ribosome biogenesis. Mol Cell Biol 1997; 17:7088-7098.
69. Oruganti S, Zhang Y, Li H et al. Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs. J Mol Biol 2007; 371:1141-1150.
70. Aittaleb M, Visone T, Fenley MO et al. Structural and thermodynamic evidence for a stabilizing role of Nop5p in S-adenosyl-L-methionine binding to fibrillarin. J Biol Chem 2004; 279:41822-41829.
71. Liu S, Rauhut R, Vomlocher H-P et al. The network of protein—protein interactions within the human U4/U6.U5 tri-snRNP. RNA 2006; 12:1418-1430.
72. Fatica A, Galardi S, Altieri F et al Fibrillarin binds directly and specifically to U16 box C/D snoRNA. RNA 2000; 6:88-95.
73. Lafontaine DL, Tollervey D. Synthesis and assembly of the box C+D small nucleolar RNPs. Mol Cell Biol 2000; 20:2650-2659.
74. Niewmierzycka A, Clarke S. S-Adenosylmethioninc-dependent méthylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransfcrasc. J Biol Chem 1999; 274:814-824.
75. Deng L, Starostina NG, Liu ZJ et al. Structure determination of fibrillarin from the hyperthermophilic archaeon Pyrococcus furiosus. Biochem Biophys Res Comm 2004; 315:726-732.
76. Wang H, Boisvert D, Kim K et al. Crystal structure of a fibrillarin homologue from Mcthanococcus jannaschii, a hypcrthermophile, at 1.6À resolution. EMBO J 2000; 19:317-323.
77. Snaar S, Wiesmcijcr K, Jochemsen AG et al Mutational analysis of fibrillarin and its mobility in living human cells. J Cell Biol 2000; 151:653-662.
78. Amiri KA. Fibrillarin-like proteins occur in the domain Archaea. J Bactcriol 1994; 176:2124-2127.
79. Feder M, Pas J, Wÿrwicz LS et al Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribosc 2'-0-methyltransferases. Gene 2003; 302:129-138.
80. Hager J, Stakcr BL, Bugl H et al Active site in RrmJ, a heat shock-induced methyltransferase. J Biol Chem 2002; 277:41978-41986.
81. Klimasauskas S, Kumar S, Roberts RJ et al Hhal methyltransferase flips its target base out of the DNA helix. Cell 1994; 76:357-369.
82. Jones KW, Gorzynski K, Hales CM et al. Direct interaction of the spinal muscular atrophy disease protein SMN with the small nucleolar RNA-associated protein fibrillarin. J Biol Chem 2001; 276:38645-38651.
83. Watkins NJ, Dickmanns A, Luhrmann R. 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 2002; 22:8342-8352.