Posttranscriptional RNA modifications: Playing metabolic games in a cell's chemical legoland

Chemistry and Biology

Volumn 21, Issue 2, 2014, Pages 174-185

  Helm, Mark ^a   Alfonzo, Juan D ^b  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTICODON; BACTERIA; EUKARYOTIC CELLS; METABOLIC NETWORKS AND PATHWAYS; NUCLEIC ACID CONFORMATION; RNA; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, TRANSFER; URIDINE;

EID: 84894436024     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2013.10.015     Document Type: Review

References (58)

1. M.E. Armengod, I. Moukadiri, S. Prado, R. Ruiz-Partida, A. Benítez-Páez, M. Villarroya, R. Lomas, M.J. Garzón, A. Martínez-Zamora, S. Meseguer, and C. Navarro-González Enzymology of tRNA modification in the bacterial MnmEG pathway Biochimie 94 2012 1510 1520
2. J.F. Atkins, and G.R. Björk A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment Microbiol. Mol. Biol. Rev. 73 2009 178 210
3. A.L. Benko, G. Vaduva, N.C. Martin, and A.K. Hopper Competition between a sterol biosynthetic enzyme and tRNA modification in addition to changes in the protein synthesis machinery causes altered nonsense suppression Proc. Natl. Acad. Sci. USA 97 2000 61 66
4. G.R. Björk, K. Jacobsson, K. Nilsson, M.J. Johansson, A.S. Byström, and O.P. Persson A primordial tRNA modification required for the evolution of life? EMBO J. 20 2001 231 239
5. C. Boland, P. Hayes, I. Santa-Maria, S. Nishimura, and V.P. Kelly Queuosine formation in eukaryotic tRNA occurs via a mitochondria-localized heteromeric transglycosylase J. Biol. Chem. 284 2009 18218 18227
6. D. Brégeon, V. Colot, M. Radman, and F. Taddei Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift Genes Dev. 15 2001 2295 2306
7. J. Cabello-Villegas, M.E. Winkler, and E.P. Nikonowicz Solution conformations of unmodified and A(37)N(6)-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe) J. Mol. Biol. 319 2002 1015 1034
8. E. Calo, and J. Wysocka Modification of enhancer chromatin: what, how, and why? Mol. Cell 49 2013 825 837
9. C.T. Chan, M. Dyavaiah, M.S. DeMott, K. Taghizadeh, P.C. Dedon, and T.J. Begley A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress PLoS Genet. 6 2010 e1001247
10. C.T. Chan, Y.L. Pang, W. Deng, I.R. Babu, M. Dyavaiah, T.J. Begley, and P.C. Dedon Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins Nat. Commun. 3 2012 937
11. Y.C. Chen, A.F. Brooks, D.M. Goodenough-Lashua, J.D. Kittendorf, H.D. Showalter, and G.A. Garcia Evolution of eukaryal tRNA-guanine transglycosylase: insight gained from the heterocyclic substrate recognition by the wild-type and mutant human and Escherichia coli tRNA-guanine transglycosylases Nucleic Acids Res. 39 2011 2834 2844
12. V. de Crécy-Lagard, C. Brochier-Armanet, J. Urbonavicius, B. Fernandez, G. Phillips, B. Lyons, A. Noma, S. Alvarez, L. Droogmans, J. Armengaud, and H. Grosjean Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea Mol. Biol. Evol. 27 2010 2062 2077
13. D. Dominissini, S. Moshitch-Moshkovitz, S. Schwartz, M. Salmon-Divon, L. Ungar, S. Osenberg, K. Cesarkas, J. Jacob-Hirsch, N. Amariglio, and M. Kupiec et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq Nature 485 2012 201 206
14. C.E. Dumelin, Y. Chen, A.M. Leconte, Y.G. Chen, and D.R. Liu Discovery and biological characterization of geranylated RNA in bacteria Nat. Chem. Biol. 8 2012 913 919
15. B. El Yacoubi, B. Lyons, Y. Cruz, R. Reddy, B. Nordin, F. Agnelli, J.R. Williamson, P. Schimmel, M.A. Swairjo, and V. de Crécy-Lagard The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA Nucleic Acids Res. 37 2009 2894 2909
16. B. El Yacoubi, M. Bailly, and V. de Crécy-Lagard Biosynthesis and function of posttranscriptional modifications of transfer RNAs Annu. Rev. Genet. 46 2012 69 95
17. V. Emilsson, A.K. Näslund, and C.G. Kurland Thiolation of transfer RNA in Escherichia coli varies with growth rate Nucleic Acids Res. 20 1992 4499 4505
18. D.M. Goodenough-Lashua, and G.A. Garcia tRNA-guanine transglycosylase from E. coli: a ping-pong kinetic mechanism is consistent with nucleophilic catalysis Bioorg. Chem. 31 2003 331 344
19. E.M. Gustilo, F.A. Vendeix, and P.F. Agris tRNA's modifications bring order to gene expression Curr. Opin. Microbiol. 11 2008 134 140
20. N.A. Hawkes, G. Otero, G.S. Winkler, N. Marshall, M.E. Dahmus, D. Krappmann, C. Scheidereit, C.L. Thomas, G. Schiavo, and H. Erdjument-Bromage et al. Purification and characterization of the human elongator complex J. Biol. Chem. 277 2002 3047 3052
21. R.M. Hoskinson, and H.G. Khorana Studies on polynucleotides, XLI. Purification of phenylalanine-specific transfer ribonucleic acid from yeast by countercurrent distribution J. Biol. Chem. 240 1965 2129 2134
22. B. Huang, M.J. Johansson, and A.S. Byström An early step in wobble uridine tRNA modification requires the Elongator complex RNA 11 2005 424 436
23. G.L. Igloi Interaction of tRNAs and of phosphorothioate-substituted nucleic acids with an organomercurial. Probing the chemical environment of thiolated residues by affinity electrophoresis Biochemistry 27 1988 3842 3849
24. G.L. Igloi, and H. Kössel Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid Nucleic Acids Res. 13 1985 6881 6898
25. K. Ishida, T. Kunibayashi, C. Tomikawa, A. Ochi, T. Kanai, A. Hirata, C. Iwashita, and H. Hori Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus Nucleic Acids Res. 39 2011 2304 2318
26. D. Iwata-Reuyl Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA Bioorg. Chem. 31 2003 24 43
27. M. Kato, Y. Araiso, A. Noma, A. Nagao, T. Suzuki, R. Ishitani, and O. Nureki Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification Nucleic Acids Res. 39 2011 1576 1585
28. S.H. Kim, F.L. Suddath, G.J. Quigley, A. McPherson, J.L. Sussman, A.H. Wang, N.C. Seeman, and A. Rich Three-dimensional tertiary structure of yeast phenylalanine transfer RNA Science 185 1974 435 440
29. J.A. Kowalak, J.J. Dalluge, J.A. McCloskey, and K.O. Stetter The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles Biochemistry 33 1994 7869 7876
30. T.N. Lamichhane, N.H. Blewett, and R.J. Maraia Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases RNA 17 2011 1846 1857
31. S. Leidel, P.G. Pedrioli, T. Bucher, R. Brost, M. Costanzo, A. Schmidt, R. Aebersold, C. Boone, K. Hofmann, and M. Peter Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA Nature 458 2009 228 232
32. S. Li, and P.A. Limbach Method for comparative analysis of ribonucleic acids using isotope labeling and mass spectrometry Anal. Chem. 84 2012 8607 8613
33. M.A. Machnicka, K. Milanowska, O. Osman Oglou, E. Purta, M. Kurkowska, A. Olchowik, W. Januszewski, S. Kalinowski, S. Dunin-Horkawicz, and K.M. Rother et al. MODOMICS: a database of RNA modification pathways - 2013 update Nucleic Acids Res. 41 Database issue 2013 D262 D267
34. C. Mehlgarten, D. Jablonowski, U. Wrackmeyer, S. Tschitschmann, D. Sondermann, G. Jäger, Z. Gong, A.S. Byström, R. Schaffrath, and K.D. Breunig Elongator function in tRNA wobble uridine modification is conserved between yeast and plants Mol. Microbiol. 76 2010 1082 1094
35. S. Meyer, S. Böhme, A. Krüger, H.J. Steinhoff, J.P. Klare, and A. Wittinghofer Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy PLoS Biol. 7 2009 e1000212
36. K.D. Meyer, Y. Saletore, P. Zumbo, O. Elemento, C.E. Mason, and S.R. Jaffrey Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons Cell 149 2012 1635 1646
37. K. Miyauchi, S. Kimura, and T. Suzuki A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification Nat. Chem. Biol. 9 2013 105 111
38. I. Moukadiri, S. Prado, J. Piera, A. Velázquez-Campoy, G.R. Björk, and M.E. Armengod Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions Nucleic Acids Res. 37 2009 7177 7193
39. A. Noma, and T. Suzuki Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis Nucleic Acids Symp. Ser. (Oxf) 50 2006 65 66
40. A. Noma, Y. Kirino, Y. Ikeuchi, and T. Suzuki Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA EMBO J. 25 2006 2142 2154
41. P. Perche-Letuvée, V. Kathirvelu, G. Berggren, M. Clemancey, J.M. Latour, V. Maurel, T. Douki, J. Armengaud, E. Mulliez, and M. Fontecave et al. 4-Demethylwyosine synthase from Pyrococcus abyssi is a radical-S-adenosyl-L- methionine enzyme with an additional [4Fe-4S](+2) cluster that interacts with the pyruvate co-substrate J. Biol. Chem. 287 2012 41174 41185
42. S. Prado, M. Villarroya, M. Medina, and M.E. Armengod The tRNA-modifying function of MnmE is controlled by post-hydrolysis steps of its GTPase cycle Nucleic Acids Res. 41 2013 6190 6208
43. U.L. Rajbhandary, S.H. Chang, A. Stuart, R.D. Faulkner, R.M. Hoskinson, and H.G. Khorana Studies on polynucleotides, lxviii the primary structure of yeast phenylalanine transfer RNA Proc. Natl. Acad. Sci. USA 57 1967 751 758
44. T. Rakovich, C. Boland, I. Bernstein, V.M. Chikwana, D. Iwata-Reuyl, and V.P. Kelly Queuosine deficiency in eukaryotes compromises tyrosine production through increased tetrahydrobiopterin oxidation J. Biol. Chem. 286 2011 19354 19363
45. J.D. Robertus, J.E. Ladner, J.T. Finch, D. Rhodes, R.S. Brown, B.F. Clark, and A. Klug Structure of yeast phenylalanine tRNA at 3 A resolution Nature 250 1974 546 551
46. M. Sakurai, T. Yano, H. Kawabata, H. Ueda, and T. Suzuki Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome Nat. Chem. Biol. 6 2010 733 740
47. A. Scrima, I.R. Vetter, M.E. Armengod, and A. Wittinghofer The structure of the TrmE GTP-binding protein and its implications for tRNA modification EMBO J. 24 2005 23 33
48. N. Shigi, Y. Sakaguchi, S. Asai, T. Suzuki, and K. Watanabe Common thiolation mechanism in the biosynthesis of tRNA thiouridine and sulphur-containing cofactors EMBO J. 27 2008 3267 3278
49. J.E. Squires, H.R. Patel, M. Nousch, T. Sibbritt, D.T. Humphreys, B.J. Parker, C.M. Suter, and T. Preiss Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA Nucleic Acids Res. 40 2012 5023 5033
50. T. Suzuki, T. Suzuki, T. Wada, K. Saigo, and K. Watanabe Novel taurine-containing uridine derivatives and mitochondrial human diseases Nucleic Acids Res. Suppl. Suppl 2001 257 258
51. Y. Suzuki, A. Noma, T. Suzuki, R. Ishitani, and O. Nureki Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4 Nucleic Acids Res. 37 2009 2910 2925
52. J.Q. Svejstrup Elongator complex: how many roles does it play? Curr. Opin. Cell Biol. 19 2007 331 336
53. N. Shyh-Chang, J.W. Locasale, C.A. Lyssiotis, Y. Zheng, R.Y. Teo, S. Ratanasirintrawoot, J. Zhang, T. Onder, J.J. Unternaehrer, and H. Zhu et al. Influence of threonine metabolism on S-adenosylmethionine and histone methylation Science 339 2013 222 226
54. N. Umeda, T. Suzuki, M. Yukawa, Y. Ohya, H. Shindo, K. Watanabe, and T. Suzuki Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases J. Biol. Chem. 280 2005 1613 1624
55. J. Urbonavicius, G. Stahl, J.M. Durand, S.N. Ben Salem, Q. Qian, P.J. Farabaugh, and G.R. Björk Transfer RNA modifications that alter +1 frameshifting in general fail to affect -1 frameshifting RNA 9 2003 760 768
56. Phe H. Grosjean, DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution 2009 Landes Biosciences Texas 423 435
57. A.P. Young, and V. Bandarian Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine Biochemistry 50 2011 10573 10575
58. W.F. Waas, Z. Druzina, M. Hanan, and P. Schimmel Role of a tRNA base modification and its precursors in frameshifting in eukaryotes J. Biol. Chem. 282 2007 26026 26034