Optimization of ribosome structure and function by rRNA base modification

PLoS ONE

Volumn 2, Issue 1, 2007, Pages

  Baxter Roshek, Jennifer L ^a   Petrov, Alexey N ^a   Dinman, Jonathan D ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOACYL TRANSFER RNA; PEPTIDYLTRANSFERASE; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; MUTANT; NONHUMAN; OPEN READING FRAME; PHENOTYPE; RIBOSOME; RIBOSOME STRUCTURE; RNA ANALYSIS; RNA BASE MODIFICATION; RNA BINDING; RNA STRUCTURE; RNA TRANSLATION; STOP CODON; STRUCTURE ANALYSIS; ALLELE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; HUMAN; LARGE RIBOSOMAL SUBUNIT; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; PROTEIN SYNTHESIS;

ALLELES; BASE SEQUENCE; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PEPTIDYL TRANSFERASES; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; RIBOSOME SUBUNITS, LARGE, EUKARYOTIC; RIBOSOMES; RNA, RIBOSOMAL; RNA, TRANSFER, AMINO ACID-SPECIFIC;

EID: 34249868208     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000174     Document Type: Article

References (49)

1. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289: 905-920.
2. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, et al. (2001) Crystal Structure of the Ribosome at 5.5 A Resolution. Science 292: 883-896.
3. Samarsky DA, Fournier MJ (1999) A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. Nucleic Acids Res 27: 161-164.
4. Decatur WA, Fournier MJ (2002) rRNA modifications and ribosome function. Trends Biochem Sci 27: 344-351.
5. Ofengand J, Bakin A, Wrzesinski J, Nurse K, Lane BG (1995) The pseudouridine residues of ribosomal RNA. Biochem Cell Biol 73: 915-924.
6. Green R, Noller HF (1996) In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA 2: 1011-1021.
7. Tollervey D, Lehtonen H, Jansen R, Kern H, Hurt EC (1993) Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72: 443-457.
8. Zebarjadian Y, King T, Fournier MJ, Clarke L, Carbon J (1999) Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA. Mol Cell Biol 19: 7461-7472.
9. Lowe TM, Eddy SR (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283: 1168-1171.
10. Raychaudhuri S, Conrad J, Hall BG, Ofengand J (1998) A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli. RNA 4: 1407-1417.
11. Raychaudhuri S, Niu L, Conrad J, Lane BG, Ofengand J (1999) Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J Biol Chem 274: 18880-18886.
12. Charette M, Gray MW (2000) Pseudouridine in RNA: what, where, how, and why. IUBMB Life 49: 341-351.
13. Helm M (2006) Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res 34: 721-733.
14. Williams DJ, Boots JL, Hall KB (2001) Thermodynamics of 2′-ribose substitutions in UUCG tetraloops. RNA 7: 44-53.
15. Meroueh M, Grohar PJ, Qiu J, SantaLucia J Jr, Scaringe SA, et al. (2000) Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA. Nucleic Acids Res 28: 2075-2083.
16. Sumita M, Desaulniers JP, Chang YC, Chui HM, Clos L, et al. (2005) Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA. RNA 11: 1420-1429.
17. Gustafsson C, Persson BC (1998) Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant. J Bacteriol 180: 359-365.
18. King TH, Liu B, McCully RR, Fournier MJ (2003) Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Molecular Cell 11: 425-435.
19. Bonnerot C, Pintard L, Lutfalla G (2003) Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2′-O-ribose methylation of a conserved rRNA position in yeast. Molecular Cell 12: 1309-1315.
20. Lapeyre B, Purushothaman SK (2004) Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Mol Cell 16: 663-669.
21. Caldas T, Binet E, Bouloc P, Costa A, Desgres J, et al. (2000) The FtsJ/ RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase. J Biol Chem 275: 16414-16419.
22. Bugl H, Fauman EB, Staker BL, Zheng F, Kushner SR, et al. (2000) RNA methylation under heat shock control. Mol Cell 6: 349-360.
23. Hansen TM, Baranov PV, Ivanov IP, Gesteland RF, Atkins JF (2003) Maintenance of the correct open reading frame by the ribosome. Embo Reports 4: 499-504.
24. Carrasco L, Barbacid M, Vazquez D (1973) The tricodermin group of antibiotics, inhibitors of peptide bond formation by eukaryotic ribosomes. Biochim et Biophys Acta 312: 368-376.
25. Grollman AP (1967) Inhibitors of protein biosynthesis. II. Mode of action of anisomycin. J Biol Chem 242: 3226-3233.
26. Schindler D (1974) Two classes of inhibitors of peptidyltransferase activity in eukaryotes. Nature 249: 38-41.
27. Hansen JL, Moore PB, Steitz TA (2003) Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J Mol Biol 330: 1061-1075.
28. Herner AE, Goldberg IH, Cohen LB (1969) Stabilization of N-acetylphenylalanyl transfer ribonucleic acid binding to ribosomes by sparsomycin. Biochemistry 8: 1335-1344.
29. Jayaraman J, Goldberg IH (1968) Localization of sparsomycin action to the peptide-bond-forming step. Biochemistry 7: 418-421.
30. Moazed D, Noller HF (1991) Sites of interaction of the CCA end of peptidyl-tRNA with 23S rRNA. Proc Natl Acad Sci U S A 88: 3725-3728.
31. 1 double-stranded RNA virus propagation. J Virology 66: 3669-3676.
32. Wickner RB (1996) Double-stranded RNA viruses of Saccharomyces cerevisiae. Microbiol Rev 60: 250-265.
33. Harger JW, Dinman JD (2003) An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae. RNA 9: 1019-1024.
34. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, et al. (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science 310: 827-834.
35. Katunin VI, Muth GW, Strobel SA, Wintermeyer W, Rodnina MV (2002) Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome. Mol Cell 10: 339-346.
36. Sanbonmatsu KY, Joseph S, Tung CS (2005) Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A 102: 15854-15859.
37. Dinman JD, Wickner RB (1994) Translational maintenance of frame: mutants of Saccharomyces cerevisiae with altered - 1 ribosomal frameshifting efficiencies. Genetics 136: 75-86.
38. Ohtake Y, Wickner RB (1995) Yeast virus propagation depends critically on free 60S ribosomal subunit concentration. Mol Cell Biol 15: 2772-2781.
39. Belcourt MF, Farabaugh PJ (1990) Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell 62: 339-352.
40. Hirabayashi N, Sato NS, Suzuki T (2006) Conserved loop sequence of helix 69 in Escherichia coli 23 S rRNA is involved in A-site tRNA binding and translational fidelity. J Biol Chem 281: 17203-17211.
41. Mochizuki Y, He J, Kulkarni S, Bessler M, Mason PJ (2004) Mouse dyskerin mutations affect accumulation of telomerase RNA and small nucleolar RNA, telomerase activity, and ribosomal RNA processing. Proc Natl Acad Sci U S A 101: 10756-10761.
42. Yoon A, Peng G, Brandenburger Y, Zollo O, Xu W, et al. (2006) Impaired control of IRES-mediated translation in X-linked dyskeratosis congenita. Science 312: 902-906.
43. Inoue H, Nojima H, Okayama H (1990) High efficiency transformation of Escherichia coli with plasmids. Gene 96: 23-28.
44. Ito H, Fukuda Y, Murata K, Kimura A (1983) Transformation of intact yeast cells treated with alkali cations. J Bacteriol 153: 163-168.
45. Jacobs JL, Dinman JD (2004) Systematic analysis of bicistronic reporter assay data. Nucleic Acids Res 32: e160-e170.
46. Meskauskas A, Dinman JD (2001) Ribosomal protein L5 helps anchor peptidyl-tRNA to the P-site in Saccharomyces cerevisiae. RNA 7: 1084-1096.
47. Meskauskas A, Petrov AN, Dinman JD (2005) Identification of functionally important amino acids of ribosomal protein L3 by saturation mutagenesis. Molecular & Cellular Biology 25: 10863-10874.
48. Kiparisov S, Petrov A, Meskauskas A, Sergiev PV, Dontsova OA, et al. (2005) Structural and functional analysis of 5S rRNA. Molecular Genetics and Genomics 27: 235-247.
49. Rakauskaite R, Dinman JD (2006) An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome. Mol Cell Biol 26: 8992-9002.