Novel predicted RNA-binding domains associated with the translation machinery

Journal of Molecular Evolution

Volumn 48, Issue 3, 1999, Pages 291-302

  Aravind, L ^a,b   Koonin, Eugene V ^b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Archaeosine transglycosylase; Pseudouridine synthase; Ribosomal protein S4; RNA binding domains; Translation machinery

Indexed keywords

ADENOSINE DERIVATIVE; RIBOSOME RNA; RNA BINDING PROTEIN; RNA METHYLTRANSFERASE; SYNTHETASE; TRANSFER RNA;

ARTICLE; BACTERIUM; ENZYME ACTIVITY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; RNA BINDING; RNA TRANSLATION; YEAST;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 0033046425     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006472     Document Type: Article

References (56)

1. 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
2. Baker A, Draper D (1995) Messenger RNA recognition by fragments of ribosomal protein S4. J Biol Chem 270:22939-22945
3. Becker HF, Motorin Y, Planta RJ, Grosjean H (1997) The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res 25:4493-4499
4. Bork P, Koonin EV (1994) A P-loop-like motif in a widespread ATP pyrophosphatase domain: Implications for the evolution of sequence motifs and enzyme activity. Proteins 20:347-355
5. Brick P, Bhat TN, Blow DM (1989) Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J Mol Biol 208:83-98
6. Tyr interacts with both subunits. Proc Natl Acad Sci USA 83:1189-1192
7. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG (1997) The solution structure of the SI RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88:235-242
8. Dennis PP (1997) Ancient ciphers: translation in Archaea. Cell 89: 1007-1010
9. Doherty AJ, Serpell LC, Ponting CP (1996) The helix-hairpin-helix DNA-binding motif: A structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res 24:2488-2497
10. Edmonds CG, Crain PF, Gupta R, Hashizume T, Hocart CH, Kowalak JA, Pomerantz SC, Stetter KO, McCloskey JA (1991) Posttranscriptional modification of tRNA in thermophilic archaea (Archae-bacteria). J Bacteriol 173:3138-3148
11. Gregson JM, Crain PF, Edmonds CG, Gupta R, Hashizume T, Phillipson DW, McCloskey JA (1993) Structure of the archaeal transfer RNA nucleoside G*-15 (2-amino-4,7-dihydro-4-oxo-7-beta-D-ribofuranosyl-1H-pyrrolo[2,3-d]pyrimidine-5-carboximidamide (archaeosine)). J Biol Chem 268:10076-10086
12. Guez-Ivanier V, Bedouelle H. (1996) Disordered C-terminal domain of tyrosyl transfer-RNA synthetase: Evidence for a folded state. J Mol Biol 255:110-120
13. Heilek GM, Marusak R, Meares CF, Noller HF (1995) Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4. Proc Natl Acad Sci USA 92:1113-1116
14. Heiss NS, Knight SW, Vulliamy TJ, Klauck SM, Wiemann S, Mason PJ, Poustka A, Dokal I (1998) X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nat Genet 19:32-38
15. Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, Söll D (1997a) A euryarchaeal lysyl-tRNA synthetase: Resemblance to class I synthetases. Science 278: 1119-1122
16. Ibba M, Bono JL, Rosa PA, Söll D (1997) Archaeal-type lysyl-tRNA synthetase in the lyme disease spirochete Borrelia burgdorferi. Proc Natl Acad Sci USA 94:14383-14388
17. Jakoi ER, Brown AL, Ho YS, Snyderman R (1989) Molecular cloning of the cDNA for ligatin. J Cell Sci 93:227-232
18. Kagan R, 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
19. Kasperaitis MA, Voorma HO, Thomas AA (1995) The amino acid sequence of eukaryotic translation initiation factor 1 and its similarity to yeast initiation factor SUI1. FEBS Lett 365:47-50
20. Koonin EV (1994) Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120. Nucleic Acids Res 22:2476-2478
21. Koonin EV (1996) Pseudouridine synthases: Four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Acids Res 24:2411-2415
22. Koonin EV, Aravind L (1998) Re-evaluation of translation machinery evolution. Curr Biol 8:R266-R269
23. Koonin EV, Tatusov RL, Rudd KE (1995) Sequence similarity analysis of Escherichia coli proteins: Functional and evolutionary implications. Proc Natl Acad Sci USA 92:11921-11925
24. Kyrpides N, Woese C (1998) Universally conserved translation initiation factors. Proc Natl Acad Sci USA 95:224-228
25. Kyrpides NC, Woese CR, Ouzounis CA (1996) KOW: A novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem Sci 21:425-426
26. Lane BG, Ofengand J, Gray MW (1995) Pseudouridine and O2′-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
27. Limbach PA, Grain PF, McCloskey JA (1994) Summary: The modified nucleosides of RNA. Nucleic Acids Res 22:2183-2196
28. Murzin A (1993) OB(oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences. EMBO J 12:861-867
29. Naranda T, MacMillan E, Donahue T, Hershey J (1996) SUI1/p16 is required for the activity of eukaryotic translation initiation factor 3 in Saccharomyces cerevisiae. Mol Cell Biol 16:2307-2313
30. Navaratnam N, Bhattacharya S, Fujino T, Patel D, Jarmuz AL, Scott J (1995) Evolutionary origins of apoB mRNA editing: Catalysis by a cytidine deaminase that has acquired a novel RNA-binding motif at its active site. Cell 81:187-195
31. Neuwald AF, Liu JS, Lawrence CE (1995) Gibbs motif sampling: Detection of bacterial outer membrane protein repeats. Protein Sci 4:1618-1632
32. Ofengand J, Bakin A, Wrzesinski J, Nurse K, Lane BG (1995) The pseudouridine residues of ribosomal RNA. Biochem Cell Biol 73: 915-924
33. Ogura M, Tanaka T (1996) Transcription of Bacillus subtilis degR is sigma D dependent and suppressed by multicopy proB through sigma D. J Bacteriol 178:216-222
34. Romier C, Reuter K, Suck D, Ficner R (1996) Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. EMBO J 15:2850-2857
35. Romier C, Meyer JE, Suck D (1997) Slight sequence variations of a common fold explain the substrate specificities of tRNA-guanine transglycosylases from the three kingdoms. FEBS Lett 416:93-98
36. Rost B, Sander C (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72
37. Rost B, Schneider R, Sander C (1997) Protein fold recognition by prediction-based threading. J Mol Biol 270:471-480
38. Rottman FM, Bokar JA, Narayan P, Shambaugh ME, Ludwiczak R (1994) N6-Adenosine methylation in mRNA: substrate specificity and enzyme complexity. Biochimie 76:1109-1114
39. Schnuchel A, Wiltscheck R, Czisch M, Herrler M, Willimsky G, Graumann P, Marahiel MA, Holak TA (1993) Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature 364: 169-171
40. Schuler GD, Altschul SF, Lipman DJ (1991) A workbench for multiple alignment construction and analysis. Proteins 9:180-190
41. Schwedock JS, Liu C, Leyh TS, Long SR (1994) Rhizobium meliloti NodP and NodQ form a multifunctional sulfate-activating complex requiring GTP for activity. J Bacteriol 176:7055-7064
42. Shamoo Y, Abdul-Manan N, Williams (1995) Multiple RNA binding domains (RBDs) just don't add up. Nucleic Acids Res 23:725-728
43. Smith HC, Sowden MP (1996) Base-modification mRNA editing through deamination - The good, the bad and the unregulated. Trends Genet 12:418-424
44. St Johnston D, Brown NH, Gall JG, Jantsch M (1992) A conserved double-stranded RNA-binding domain. Proc Natl Acad Sci USA 89:10979-10983
45. Tang C, Draper D. (1989) Unusual mRNA pseudoknot structure is recognized by a protein translational represser. Cell 57:531-536
46. Tatusov RL, Altschul SF, Koonin EV (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci USA 91:12091-12095
47. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637
48. ter Huurne AA, Muir S, van Houten M, van der Zeijst BA, Gaastra W, Kusters JG (1994) Characterization of three putative Serpulina hyodysenteriae hemolysins. Microb Pathog 16:269-282
49. Thompson JD, Higgins DC, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
50. Tollervey D, Kiss T (1997) Function and synthesis of small nucleolar RNAs. Curr Opin Cell Biol 9:337-342
51. Tzermia M, Katsoulou C, Alexandraki D (1997) Sequence analysis of a 33.2 kb segment from the left arm of yeast chromosome XV reveals eight known genes and ten new open reading frames including homologues of ABC transporters, inositol phosphatases and human expressed sequence tags. Yeast 13:583-589
52. Watanabe M, Matsuo M, Tanaka S, Akimoto H, Asahi S, Nishimura S, Katze JR, Hashizume T, Grain PF, McCloskey JA, Okada N (1997) Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to archaeal tRNA, proceeds via a pathway involving base replacement on the tRNA polynucleotide chain. J Biol Chem 272:20146-20151
53. Wootton JC, Federhen S (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266:554-573
54. Wrzesinski J, Bakin A, Nurse K, Lane BG, Ofengand J (1995a) Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 34:8904-8913
55. Wrzesinski J, Nurse K, Bakin A, Lane BG, Ofengand J (1995b) A dual-specificity pseudouridine synthase: An Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi32 in tRNA(phe). RNA 1:437-448
56. Yoon H, Donahue T (1992) The suil suppressor locus in Saccharomyces cerevisiae encodes a translation factor that functions during tRNA(iMet) recognition of the start codon. Mol Cell Biol 12:248-260