The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2'- O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs

RNA

Volumn 5, Issue 1, 1999, Pages 66-81

  Cavaillé, Jérôme ^a   Chetouani, Farid ^a   Bachellerie, Jean Pierre ^a  

^a Université Paul Sabatier   (France)

Author keywords

Gene disruption; In vitro modification of tRNA; RNA modification; spoU; tRNA modifying enzyme; TRP 185

Indexed keywords

RNA METHYLTRANSFERASE;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROCESSING; RNA METHYLATION; RNA PROCESSING; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; FUNGAL PROTEINS; GENES, FUNGAL; GUANOSINE; METHYLTRANSFERASES; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; RESTRICTION MAPPING; RNA, FUNGAL; RNA, TRANSFER; RNA, TRANSFER, SER; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS; ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 0032953571     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299981475     Document Type: Article

References (81)

1. 2+ in RNA structure and function. Prog Nucleic Acid Res Mol Biol 53:79-129.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
4. Aström SU, Byström AS. 1994. Rit1, a tRNA backbone-modifying enzyme that mediates initiator and elongator tRNA discrimination. Cell 79:535-546.
5. Bachellerie JP, Cavaillé J. 1997. Guiding ribose methylation of rRNA. Trends Biochem Sci 22:257-261.
6. Becker HF, Motorin Y, Planta RJ, Grosjean H. 1997a. The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of Ψ55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res 25:4493-4499.
7. Becker HF, Motorin Y, Sissler M, Florentz C, Grosjean H. 1997b. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨC loop of yeast tRNAs. J Mol Biol 274:508-518.
8. Bibb MJ, Bibb MJ, Ward JM, Cohen SN. 1985. Nucleotide sequences encoding and promoting expression of three antibiotic resistance genes indigenous to Streptomyces. Mol Gen Genet 199:26-36.
9. Björk GR. 1995. Biosynthesis and function of modified nucleosides. In: Söll D, RajBhandary UL, eds. tRNA: Structure, biosynthesis and function. Washington, DC: American Society of Microbiology Press. pp 165-206.
10. Bonneaud N, Ozier-Kalogeropoulos O, Li G, Labouesse M, Minvielle-Sebastia L, Lacroute F. 1991. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast 7:609-615.
11. Cavaillé J, Nicoloso M, Bachellerie JP. 1996. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383:732-735.
12. Clark MW, Abelson J. 1987. The subnuclear localization of tRNA ligase in yeast. J Cell Biol 105:1515-1526.
13. Cundliffe E. 1989. How antibiotic-producing organisms avoid suicide. Annu Rev Microbiol 43:207-233.
14. Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, secondary, and tertiary structures of tRNAs. In: Söll D, RajBhandary UL, eds. tRNA: Structure, biosynthesis and function. Washington, DC: American Society of Microbiology Press. pp 93-126.
15. Djordjevic S, Stock AM. 1997. Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine. Structure 75:545-558.
16. Ser. J Mol Biol 206:707-722.
17. Phe: Specificity depends on structural elements outside the anticodon loop. EMBO J 5:1105-1109.
18. Ellis SR, Morales MJ, Li JM, Hopper AK, Martin NC. 1986. Isolation and characterization of the TRM1 locus, a gene essential for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J Biol Chem 261:9703-9709.
19. Filipowicz W, Shatkin AJ. 1983. Origin of splice junction phosphate in tRNAs processed by HeLa cell extract. Cell 32:547-557.
20. Pro restrict interactions in the binary primer/template complex of M-MuLV. J Mol Biol 275:731-746.
21. Fourmy D, Recht MI, Blanchard SC, Puglisi JD. 1996. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274:1367-1371.
22. Ganot P, Bortolin ML, Kiss T. 1997. Site-specific pseudouridine formation in eukaryotic pre-rRNAs is guided by small nucleolar RNAs. Cell 89:799-809.
23. Grosjean H, Edqvist J, Straby KB, Giegé R. 1996. Enzymatic formation of modified nucleosides in tRNA: Dependence on tRNA architecture. J Mol Biol 255:67-85.
24. Grosjean H, Szweykowska-Kulinska Z, Motorin Y, Fasiolo F, Simos G. 1997. Intron-dependent enzymatic formation of modified nucleosides in eukaryotic tRNAs: A review. Biochimie 79:293-302.
25. Gustafsson C, Reid R, Greene PJ, Santi DV. 1996. Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes. Nucleic Acids Res 24:3756-3762.
26. Hashimoto S, Sakai M, Muramatsu M. 1975. 2'-O-methylated oligonucleotides in ribosomal 18S and 28S RNA of a mouse hepatoma, MH134. Biochemistry 14:1956-1964.
27. Henikoff S. 1987. Multifunctional polypeptides for purine de novo synthesis. Bioessays 6:8-13.
28. Hodel AE, Gershon PD, Shi X, Quiocho FA. 1996. The 1.85 Å structure of vaccinia protein VP39, a bifunctional protein that participates in the modification of both mRNA ends. Cell 85:247-256.
29. Hopper AK, Furukawa AH, Pham HD, Martin NC. 1982. Defects in modification of cytoplasmic and mitochondrial transfer RNAs are caused by single nuclear mutations. Cell 28:543-550.
30. Ingrosso D, Fowler AV, Bleibaum J, Clarke S. 1989. Sequence of the D-aspartyl/L-isoaspartyl protein methyltransferase from human erythrocytes. J Biol Chem 264:20131-20139.
31. Phe: An in vitro study. Nucleic Acids Res 25:2694-2701.
32. Kagan RM, Clarke S. 1994. Widespread occurrence of three sequence motifs in diverse S-adenosylmethionine-dependent methyltransferases suggests a common structure for these enzymes. Arch Biochem Biophys 310:417-427.
33. Keith G. 1995. Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography. Biochimie 77:142-144.
34. 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.
35. Kisselev LL, Wolfson AD. 1994. Aminoacyl-tRNA synthetases from higher eukaryotes. Prog Nucleic Acid Res Mol Biol 48:83-142.
36. Koonin EV, Rudd KE. 1993. SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases. Nucleic Acids Res 21:5519.
37. Kumagai I, Watanabe K, Oshima T. 1982. A thermostable tRNA(guanosine-2'-)-methyltransferase from Thermus thermophilus HB27 and the effect of ribose methylation on the conformational stability of tRNA. J Biol Chem 257:7388-7395.
38. Lafontaine D, Bousquet-Antonelli C, Henry Y, Caizergues-Ferrer M, Tollervey D. 1998. The box H+ACA snoRNAs carry CbfSp, the putative rRNA pseudouridine synthase. Genes & Dev 12:527-537.
39. Lafontaine D, Vandenhaute J, Tollervey D. 1995. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes & Dev 9:2470-2481.
40. 2'-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins. Biochimie 77:7-15.
41. Lecointe F, Simos G, Sauer A, Hurt EC, Motorin Y, Grosjean H. 1998. Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of ψ38 and ψ39 in tRNA anticodon loop. J Biol Chem 273:1316-1323.
42. Maden BEH, Corbett ME, Heeney PA, Pugh K, Ajuh PM. 1995. Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie 77:22-29.
43. Malone T, Blumenthal RM, Cheng X. 1995. Structure-guided analysis reveals nine sequence motifs conserved among DNA aminomethyl-transferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253:618-632.
44. Mason TL, Pan C, Sanchirico ME, Sirum-Connolly K. 1996. Molecular genetics of the peptidyl transferase center and the unusual Var1 protein in yeast mitochondrial ribosomes. Experientia 52:1148-1157.
45. Massenet S, Mougin A, Branlant C. 1998. Post-transcriptional modifications in the small nuclear UsnRNAs. In: Grosjean H, Benne R, eds. Modification and editing of RNA: The alteration of RNA structure and function. Washington, DC: American Society of Microbiology Press. pp 201-228.
46. Matsumoto T, Ohta T, Kumagai I, Oshima T, Murao K, Hasegawa T, Ishikura H, Watanabe K. 1987. A thermostable Gm-methylase recognizes the tertiary structure of tRNA. J Biochem 101:1191-1198.
47. Mirande M. 1991. Aminoacyl-tRNA synthetase family from prokaryotes and eukaryotes: Structural domains and their implications. Prog Nucleic Acid Res Mol Biol 40:95-142.
48. Motorin Y, Keith G, Simon C, Foiret D, Simos G, Hurt E, Grosjean H. 1998. The yeast tRNA:pseudouridine synthase Pus1 p displays a multisite substrate specificity. RNA 4:856-869.
49. Narayan P, Rottman FM. 1992. Methylation of mRNA. Adv Enzymol & Rel Areas Mol Biol 65:255-285.
50. Ni J, Tien AL, Fournier MJ. 1997. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89:565-573.
51. Nicoloso M, Qu LH, Michot B, Bachellerie JP. 1996. Intron-encoded, antisense small nucleolar RNAs: The characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs. J Mol Biol 260:178-195.
52. Peebles CL, Gegenheimer P, Abelson J. 1983. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell 32:525-536.
53. Persson BC. 1993. Modification of tRNA as a regulatory device. Molec Microbiol 8:1011-1016.
54. Persson BC, Gustafsson C, Berg DE, Björk GR. 1992. The gene for Hk a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli. Proc Natl Acad Sci USA 89:3995-3998.
55. Persson BC, Jagerand G, Gustafsson C. 1997. The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA(Gm18) 2'-O-methyltransferase activity. Nucleic Acids Res 25:3969-3973.
56. Ser1(IGA). Cancer Res 41:2863-2867.
57. Rogg H, Müller P, Keith G, Staehelin M. 1977. Chemical basis for brain-specific serine transfer RNAs. Proc Natl Acad Sci USA 74:4243-4247.
58. Rose AM, Belford HG, Shen WC, Greer CL, Hopper AK, Martin NC. 1995. Location of N2,N2-dimethylguanosine-specific tRNA methyltransferase. Biochimie 77:45-53.
59. Rose AM, Joyce PB, Hopper AK, Martin NC. 1992. Separate information required for nuclear and subnuclear localization: Additional complexity in localizing an enzyme shared by mitochondria and nuclei. Mol Cell Biol 12:5652-5658.
60. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
61. Schluckebier G, O'Gara M, Saenger W, Cheng X. 1995. Universal catalytic domain structure of AdoMet-dependent methyltransferases. J Mol Biol 247:16-20.
62. Sheline CT, Milocco LH, Jones KA. 1991. Two distinct nuclear transcription factors recognize loop and bulge residues of the HIV-1 TAR RNA hairpin. Genes & Dev 5:2508-2520.
63. Sherman F. 1991. Getting started with yeast. Methods Enzymol 194:3-23.
64. Shi X, Yao P, Jose T, Gershon PD. 1996. Methyltransferases specific domains within VP39, a bifunctional protein that participates in the modification of both mRNA ends. RNA 2:88-101.
65. Simos G, Tekotte H, Grosjean H, Segref A, Sharma K, Tollervey D, Hurt EC. 1996. Nuclear pore proteins are involved in the biogenesis of functional tRNA. EMBO J 15:2270-2284.
66. Sirum-Connolly K, Mason TL 1993. Functional requirement of a site-specific ribose methylation in ribosomal RNA. Science 262:1886-1889.
67. Sirum-Connolly K, Peltier JM, Crain PF, McCloskey JA, Mason TL. 1995. Implications of a functional large ribosomal RNA with only three modified nucleotides. Biochimie 77:30-39.
68. Smith S. 1994. The animal fatty acid synthase: One gene, one polypeptide, seven enzymes. FASEB J 8:1248-1259.
69. Smith JE, Cooperman BS, Mitchell P. 1992. Methylation sites in E. coli ribosomal RNA: Localization and identification of four new sites of methylation in 23S rRNA. Biochemistry 31:10825-10834.
70. Smith CM, Steitz JA. 1997. Sno storm in the nucleolus: New roles for myriad small RNPs. Cell 89:669-672.
71. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S. 1998. Compilation of tRNA sequences and sequences of tRNA genes. NuB cleic Acids Res 26:148-153.
72. Stäheli P, Agris P, Niederberger P, Gehrke CW, Hutter R. 1982. Accumulation of 2'-O-methylguanosine deficient tRNATrp in tryptophan limited Saccharomyces cerevisiae. J Gen Microbiol 128: 2591-2600.
73. Strobel MC, Abelson J. 1986. Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo. Mol Cell Biol 6:2662-2673.
74. Thompson J, Schmidt F, Cundliffe E. 1982. Site of action of a ribosomal RNA methylase conferring resistance to thiostreptron. J Biol Chem 257:7915-7917.
75. Tollervey D, Mattaj IW. 1987. Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U-snRNPs. EMBO J 6:469-476.
76. Warner JR. 1991. Labeling of RNA and phosphoproteins in Saccharomyces cerevisiae. Methods Enzymol 194:423-428.
77. Phe. RNA 1:437-448.
78. Wu F, Garcia J, Sigman D, Gaynor R. 1991. Tat regulates binding of the human immunodeficiency virus trans-activating region RNA loop-binding protein TRP-185. Genes & Dev 5:2128-2140.
79. Wu-Baer F, Lane WS, Gaynor RG. 1995a. The cellular factor TRP-185 regulates RNA polymerase II binding to HIV-1 TAR RNA. EMBO J 14:5995-6009.
80. Wu-Baer F, Sigman D, Gaynor RG. 1995b. Specific binding of RNA polymerase II to the human immunodeficiency virus trans-activating region RNA is regulated by cellular cofactors and Tat. Proc Natl Acad Sci USA 92:7153-7157.
81. Wu-Baer F, Lane WS, Gaynor RG. 1996. Identification of a group of cellular cofactors that stimulate the binding of RNA polymerase II and TRP-185 to Human Immunodeficiency Virus 1 TAR RNA. J Biol Chem 271:4201-4208.