The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus

Molecular Microbiology

Volumn 55, Issue 6, 2005, Pages 1812-1828

  Zago, Maria A ^a   Dennis, Patrick P ^b   Omer, Arina D ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b NATIONAL SCIENCE FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; CELL EXTRACT; COMPLEMENTARY DNA; COMPLEMENTARY RNA; PROTEIN L7AE; RIBOSE; SMALL NUCLEOLAR RNA; UNCLASSIFIED DRUG;

ARTICLE; CELL FUNCTION; COMPLEX FORMATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STABILITY; RNA SEQUENCE; SEQUENCE ANALYSIS; SULFOLOBUS SOLFATARICUS; THERMOPHILIC BACTERIUM;

BASE SEQUENCE; DNA, ARCHAEAL; DNA, COMPLEMENTARY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBONUCLEOPROTEINS; RIBOSOMAL PROTEINS; RNA, ARCHAEAL; RNA, UNTRANSLATED; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, DNA; SULFOLOBUS SOLFATARICUS;

ARCHAEA; SULFOLOBUS SOLFATARICUS;

EID: 15944384666     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2005.04505.x     Document Type: Article

References (40)

1. 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. Nat Struct Biol 10: 256-263.
2. Bachellerie, J.P., Nicoloso, M., Qu, L.H., Michot, B., Caizergues-Ferrer, M., Cavaille, J., and Renalier, M.H. (1995) Novel intron-encoded small nucleolar RNAs with long sequence complementarities to mature rRNAs involved in ribosome biogenesis. Biochem Cell Biol 73: 835-843.
3. Balakin, K.V., Korshun, V.A., Prokhorenko, I.A., Maleev, G.V., Kudelina, I.A., Gontarev, S.V., and Berlin Iu, A. (1997) Novel reagent for labeling of biomolecules-activated derivative of pyrene dichromophore with excimeric fluorescence. Bioorg Khim 23: 33-41.
4. 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.
5. Bhuiyan, S.H., Gowda, K., Hotokezaka, H., and Zwieb, C. (2000) Assembly of archaeal signal recognition particle from recombinant components. Nucleic Acids Res 28: 1365-1373.
6. Dennis, P.P., Omer, A., and Lowe, T. (2001) A guided tour: small RNA function in Archaea. Mol Microbiol 40: 509-519.
7. Diener, J.L., and Wilson, C. (2000) Role of SRP19 in assembly of the Archaeoglobus fulgidus signal recognition particle. Biochemistry 39: 12862-12874.
8. Eddy, S.R. (2002) Computational genomics of noncoding RNA genes. Cell 109: 137-140.
9. Eichler, J., and Moll, R. (2001) The signal recognition particle of Archaea. Trends Microbiol 9: 130-136.
10. Fatica, A., and Tollervey, D. (2002) Making ribosomes. Curr Opin Cell Biol 14: 313-318.
11. Ganot, P., Bortolin, M.L., and Kiss, T. (1997) Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89: 799-809.
12. 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.
13. Halic, M., Becker, T., Pool, M.R., Spann, C.M., Grassucci, R.A., Frank, J., and Beckmann, R. (2004) Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427: 808-814.
14. Herskovits, A.A., and Bibi, E. (2000) Association of Escherichia coli ribosomes with the inner membrane requires the signal recognition particle receptor but is independent of the signal recognition particle. Proc Natl Acad Sci USA 97: 4621-4626.
15. Keenan, R.J., Freymann, D.M., Stroud, R.M., and Walter, P. (2001) The signal recognition particle. Annu Rev Biochem 70: 755-775.
16. Kiss, T. (2001) Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J 20: 3617-3622.
17. 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.
18. 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.
19. Klein, R.J., Misulovin, Z., and Eddy, S.R. (2002) Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci USA 99: 7542-7547.
20. 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.
21. Maden, B.E. (1990) The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucl Acid Res Mol Biol 39: 241-303.
22. Massenet, S., Ansmant, I., Motorin, Y., and Branlant, C. (1999) The first determination of pseudouridine residues in 23S ribosomal RNA from hyperthermophilic Archaea Sulfolobus acidocaldarius. FEBS Lett 462: 94-100.
23. Mattick, J.S. (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25: 930-939.
24. Ni, J., Tien, A.L., and Fournier, M.J. (1997) Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89: 565-573.
25. Nottrott, S., Urlaub, H., and Luhrmann, R. (2002) Hierarchical, clustered protein interactions with U4/U6 snRNA: a biochemical role for U4/U6 proteins. EMBO J 21: 5527-5538.
26. Ofengand, J., and Bakin, A. (1997) Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J Mol Biol 266: 246-268.
27. Ofengand, J., and Fournier, M. (1998) The pseudouridine residues of rRNA: number, location, biosynthesis and function. In Modification and Editing of RNA. Grosjean, H., and Benne, R. (eds). Washington, DC: AMS Press, pp. 229-253.
28. 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.
29. 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.
30. Rashid, R., Aittaleb, M., Chen, Q., Spiegel, K., Demeler, B., and Li, H. (2003) Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. J Mol Biol 333: 295-306.
31. 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.
32. Speckmann, W.A., Li, Z.H., Lowe, T.M., Eddy, S.R., Terns, R.M., and Terns, M.P. (2002) Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus. Curr Biol 12: 199-203.
33. Tang, T.H., Bachellerie, J.P., Rozhdestvensky, T., Bortolin, M.L., Huber, H., Drungowski, M., et al. (2002a) Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci USA 99: 7536-7541.
34. Tang, T.H., Rozhdestvensky, T.S., d'Orval, B.C., Bortolin, M.L., Huber, H., Charpentier, B., et al. (2002b) RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res 30: 921-930.
35. Tollervey, D., and Kiss, T. (1997) Function and synthesis of small nucleolar RNAs. Curr Opin Cell Biol 9: 337-342.
36. 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.
37. Wagner, E.G., Altuvia, S., and Romby, P. (2002) Antisense RNAs in bacteria and their genetic elements. Adv Genet 46: 361-398.
38. Wassarman, K.M. (2002) Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell 109: 141-144.
39. Watkins, N.J., Segault, V., Charpentier, B., Nottrott, S., Fabrizio, P., Bachi, A., et al. (2000) A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell 103: 457-466.
40. Weinstein, L.B., and Steitz, J.A. (1999) Guided tours: from precursor snoRNA to functional snoRNP. Curr Opin Cell Biol 11: 378-384.