The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn

Nucleic Acids Research

Volumn 33, Issue 20, 2005, Pages 6507-6514

  Nolivos, Sophie ^a   Carpousis, Agamemnon J ^a   Clouet d'Orval, Béatrice ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; METHYLTRANSFERASE; PROTEIN L7AE; RIBONUCLEOPROTEIN; RIBOSOME RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; GENE SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN STRUCTURE; PYROCOCCUS; RNA METHYLATION; RNA STRUCTURE; STRUCTURE ANALYSIS;

ARCHAEAL PROTEINS; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PYROCOCCUS; RIBONUCLEOPROTEINS; RNA, ARCHAEAL; RNA, GUIDE;

ARCHAEA; BACTERIA (MICROORGANISMS); PYROCOCCUS;

EID: 29144449192     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki962     Document Type: Article

References (44)

1. Omer,A.D., Ziesche,S., Decatur,W.A., Fournier,M.J. and Dennis,P.P. (2003) RNA-modifying machines in archaea. Mol. Microbiol., 48, 617-629.
2. Kiss,T. (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell, 109, 145-148.
3. Tang,T.H., Bachellerie,J.P., Rozhdestvensky,T., Bortolin,M.L., Huber,H., Drungowski,M., Elge,T., Brosius,J. and Huttenhofer,A. (2002) Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc. Natl Acad. Sci. USA, 99, 7536-7541.
4. Decatur,W.A. and Fournier,M.J. (2003) RNA-guided nucleotide modification of ribosomal and other RNAs. J. Biol. Chem., 278, 695-698.
5. Fatica,A. and Tollervey,D. (2003) Insights into the structure and function of a guide RNP. Nature Struct. Biol., 10, 237-239.
6. Clouet d'Orval,B., Bortolin,M.L., Gaspin,C. and Bachellerie,J.P. (2001) Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res., 29, 4518-4529.
7. Dennis,P.P., Omer,A. and Lowe,T. (2001) A guided tour: small RNA function in Archaea. Mol. Microbiol., 40, 509-519.
8. Caffarelli,E., Fatica,A., Prislei,S., De Gregorio,E., Fragapane,P. and Bozzoni,I. (1996) Processing of the intron-encoded U16 and U18 snoRNAs: the conserved C and D boxes control both the processing reaction and the stability of the mature snoRNA. EMBO J., 15, 1121-1131.
9. Watkins,N.J., Segault,V., Charpentier,B., Nottrott,S., Fabrizio,P., Bachi,A., Wilm,M., Rosbash,M., Branlant,C. and 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.
10. Kiss-Laszlo,Z., Henry,Y., Bachellerie,J.P., Caizergues-Ferrer,M. and Kiss,T. (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell, 85, 1077-1088.
11. Kuhn,J.F., Tran,E.J. and Maxwell,E.S. (2002) Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res., 30, 931-941.
12. Szewczak,L.B., DeGregorio,S.J., Strobel,S.A. and Steitz,J.A. (2002) Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a methylation guide snoRNP. Chem. Biol., 9, 1095-1107.
13. Watkins,N.J., Dickmanns,A. and 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.
14. Tran,E.J., Zhang,X. and Maxwell,E.S. (2003) Efficient RNA 2′-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C′/D′ RNPs. EMBO J., 22, 3930-3940.
15. Bortolin,M.L., Bachellerie,J.P. and Clouet-d'Orval,B. (2003) In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp). Nucleic Acids Res., 31, 6524-6535.
16. Galardi,S., Fatica,A., Bachi,A., Scaloni,A., Presutti,C. and Bozzoni,I. (2002) Purified box C/D snoRNPs are able to reproduce site-specific 2′-O-methylation of target RNA in vitro. Mol. Cell. Biol., 22, 6663-6668.
17. Lafontaine,D.L. and Tollervey,D. (1999) Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability. RNA, 5, 455-467.
18. Lyman,S.K., Gerace,L. and Baserga,S.J. (1999) Human Nop5/Nop58 is a component common to the box C/D small nucleolar ribonucleoproteins. RNA, 5, 1597-1604.
19. Newman,D.R., Kuhn,J.F., Shanab,G.M. and Maxwell,E.S. (2000) Box C/D snoRNA-associated proteins: two pairs of evolutionarily ancient proteins and possible links to replication and transcription. RNA, 6, 861-879.
20. Cahill,N.M., Friend,K., Speckmann,W., Li,Z.H., Terns,R.M., Terns,M.P. and Steitz,J.A. (2002) Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J., 21, 3816-3828.
21. Aittaleb,M., Rashid,R., Chen,Q., Palmer,J.R., Daniels,C.J. and Li,H. (2003) Structure and function of archaeal box C/D sRNP core proteins. Nature Struct. Biol., 10, 256-263.
22. Klein,D.J., Schmeing,T.M., Moore,P.B. and Steitz,T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J., 20, 4214-4221.
23. Nottrott,S., Hartmuth,K., Fabrizio,P., Urlaub,H., Vidovic,I., Ficner,R. and Luhrmann,R. (1999) Functional interaction of a novel 15.5kD [U4/ U6.U5] tri-snRNP protein with the 5′ stem-loop of U4 snRNA. EMBO J., 18, 6119-6133.
24. Vidovic,I., Nottrott,S., Hartmuth,K., Luhrmann,R. and Ficner,R. (2000) Crystal Structure of the Spliceosomal 15.5kD Protein Bound to a U4 snRNA Fragment. Mol. Cell, 6, 1331-1342.
25. Ban,N., Nissen,P., Hansen,J., Moore,P.B. and Steitz,T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 289, 905-920.
26. Lescoute,A., Leontis,N.B., Massire,C. and Westhof,E. (2005) Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic Acids Res., 33, 2395-2409.
27. Omer,A.D., Ziesche,S., Ebhardt,H. and Dennis,P.P. (2002) In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc. Natl Acad. Sci. USA, 99, 5289-5294.
28. Moore,T., Zhang,Y., Fenley,M.O. and Li,H. (2004) Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure (Camb.), 12, 807-818.
29. Hamma,T. and Ferre-D'Amare,A.R. (2004) Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution. Structure (Camb.), 12, 893-903.
30. Rozhdestvensky,T.S., Tang,T.H., Tchirkova,I.V., Brosius,J., Bachellerie,J.P. and Huttenhofer,A. (2003) Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res., 31, 869-877.
31. Charpentier,B., Muller,S. and Branlant,C. (2005) Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation. Nucleic Acids Res., 33, 3133-3144.
32. Charron,C., Manival,X., Clery,A., Senty-Segault,V., Charpentier,B., Marmier-Gourrier,N., Branlant,C. and Aubry,A. (2004) 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. Biol., 342, 757-773.
33. Milligan,J.F. and Uhlenbeck,O.C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol., 180, 51-62.
34. Lowe,T.M. and Eddy,S.R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science, 283, 1168-1171.
35. Omer,A.D., Lowe,T.M., Russell,A.G., Ebhardt,H., Eddy,S.R. and Dennis,P.P. (2000) Homologs of small nucleolar RNAs in Archaea. Science, 288, 517-522.
36. Qu,L.H., Meng,Q., Zhou,H., Chen,Y.Q., Liang-Hu,Q., Qing,M., Hui,Z. and Yue-Qin,C. (2001) Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. Nucleic Acids Res., 29, 1623-1630.
37. Qu,L.H., Henras,A., Lu,Y.J., Zhou,H., Zhou,W.X., Zhu,Y.Q., Zhao,J., Henry,Y., Caizergues-Ferrer,M. and Bachellerie,J.P. (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.
38. Gaspin,C., Cavaille,J., Erauso,G. and Bachellerie,J.P. (2000) Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J. Mol. Biol., 297, 895-906.
39. Zago,M.A., Dennis,P.P. and Omer,A.D. (2005) The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Microbiol., 55, 1812-1828.
40. Tang,T.H., Polacek,N., Zywicki,M., Huber,H., Brugger,K., Garrett,R., Bachellerie,J.P. and Huttenhofer,A. (2005) Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol. Microbiol., 55, 469-481.
41. Starostina,N.G., Marshburn,S., Johnson,L.S., Eddy,S.R., Terns,R.M. and Terns,M.P. (2004) Circular box C/D RNAs in Pyrococcus furiosus. Proc. Natl Acad. Sci. USA, 101, 14097-14101.
42. Cohen,G.N., Barbe,V., Flament,D., Galperin,M., Heilig,R., Lecompte,O., Poch,O., Prieur,D., Querellou,J., Ripp,R. et al. (2003) An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol., 47, 1495-1512.
43. Galtier,N. and Lobry,J.R. (1997) Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol., 44, 632-636.
44. Leontis,N.B. and Westhof,E. (2003) Analysis of RNA motifs. Curr. Opin. Struct. Biol., 13, 300-308.