Diversity of archaeosine synthesis in crenarchaeota

ACS Chemical Biology

Volumn 7, Issue 2, 2012, Pages 300-305

  Phillips, Gabriela ^a   Swairjo, Manal A ^b   Gaston, Kirk W ^c   Bailly, Marc ^a   Limbach, Patrick A ^c   Iwata Reuyl, Dirk ^d   De Crécy Lagard, Valérie ^a  

^a UNIVERSITY OF FLORIDA   (United States)

^b WESTERN UNIVERSITY OF HEALTH SCIENCES   (United States)

^c UNIVERSITY OF CINCINNATI   (United States)

^d PORTLAND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

7 CYANO 7 DEAZAGUANINE; ARCHAEOSINE; ARCHAEOSINE SYNTHASE; BACTERIAL ENZYME; GLUTAMINE AMIDOTRANSFERASE; GLYCOSYLTRANSFERASE; NATURAL PRODUCT; QUEUINE TRANSFER RIBONUCLEIC ACID RIBOSYLTRANSFERASE; SYNTHETASE; TRANSFER RNA; TRANSFERASE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BIOTRANSFORMATION; CRENARCHAEOTA; ENZYME MECHANISM; ENZYME SPECIFICITY; EURYARCHAEOTA; GENOMICS; MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; REDUCTION; SYNTHESIS;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; CRENARCHAEOTA; GENOMICS; GUANOSINE; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; EURYARCHAEOTA;

EID: 84857599173     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb200361w     Document Type: Article

References (33)

1. Grosjean, H. (2009) Nucleic acids are not boring long polymers of only four types of nucleotides, In DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution (Grosjean, H., Ed.), pp 1-18, Landes Bioscience, Austin.
2. Iwata-Reuyl, D. (2003) Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA Bioorg. Chem. 31, 24-43 (Pubitemid 36416604)
3. His influences " in vivo " decoding properties EMBO J. 4, 823-827
4. Gregson, J. M., Crain, P. F., Edmonds, C. G., Gupta, R., Hashizume, T., Phillipson, D. W., and McCloskey, J. A. (1993) Structure of Archaeal transfer RNA nucleoside G*-15 (2-amino-4,7-dihydro-4-oxo-7-β- d -ribofuranosyl-1 H -pyrrolo[2,3- d ]pyrimidine-5-carboximidamide (Archaeosine)) J. Biol. Chem. 268, 10076-10086 (Pubitemid 23150184)
5. 2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs RNA 13, 1427-1436 (Pubitemid 47347413)
6. Phillips, G., El Yacoubi, B., Lyons, B., Alvarez, S., Iwata-Reuyl, D., and de Crécy-Lagard, V. (2008) Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP Cyclohydrolase I J. Bacteriol. 190, 7876-7884
7. Reader, J. S., Metzgar, D., Schimmel, P., and de Crécy-Lagard, V. (2004) Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine J. Biol. Chem. 279, 6280-6285 (Pubitemid 38248760)
8. 0 from guanosine 5′-triphosphate in four steps Biochemistry 48, 3847-3852
9. Blaby, I. K., Phillips, G., Blaby-Haas, C. E., Gulig, K. S., El Yacoubi, B., and de Crécy-Lagard, V. (2010) Towards a systems approach in the genetic analysis of archaea: accelerating mutant construction and phenotypic analysis in Haloferax volcanii Archaea 2010, 426239
10. Watanabe, M., Matsuo, M., Tanaka, S., Akimoto, H., Asahi, S., Nishimura, S., Katz, J. R., Hashizume, T., Crain, P. F., McCloskey, J. A., and Okada, N. (1997) Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to Archaeal tRNA, proceeds via a pathway involving base replacement of the tRNA polynucleotide chain J. Biol. Chem. 272, 20146-20151 (Pubitemid 27340122)
11. Bai, Y., Fox, D. T., Lacy, J. A., Van Lanen, S. G., and Iwata-Reuyl, D. (2000) Hypermodification of tRNA in Thermophilic archaea. Cloning, overexpression, and characterization of tRNA-guanine transglycosylase from Methanococcus jannaschii J. Biol. Chem. 275, 28731-28738
12. Van Lanen, S. G., Reader, J. S., Swairjo, M. A., de Crécy-Lagard, V., Lee, B., and Iwata-Reuyl, D. (2005) From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold Proc. Natl. Acad. Sci. U.S.A. 102, 4264-4269 (Pubitemid 40397100)
13. Noguchi, S., Nishimura, Y., Hirota, Y., and Nishimura, S. (1982) Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA J. Biol. Chem. 257, 6544-6550 (Pubitemid 12059948)
14. Slany, R. K., Bosl, M., and Kersten, H. (1994) Transfer and isomerization of the ribose moiety of AdoMet during the biosynthesis of queuosine tRNAs, a new unique reaction catalyzed by the QueA protein from Escherichia coli Biochimie 76, 389-393
15. Miles, Z. D., McCarty, R. M., Molnar, G., and Bandarian, V. (2011) Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification Proc. Natl. Acad. Sci. U.S.A. 108, 7368-7372
16. Phillips, G., Chikwana, V. M., Maxwell, A., El-Yacoubi, B., Swairjo, M. A., Iwata-Reuyl, D., and de Crécy-Lagard, V. (2010) Discovery and characterization of an amidotransferase involved in the modification of archaeal tRNA J. Biol. Chem. 285, 12706-12713
17. Edmonds, C. G., Crain, P. F., Gupta, R., Hashizume, T., Hocart, C. H., Kowalak, J. A., Pomerantz, S. C., Stetter, K. O., and McCloskey, J. A. (1991) Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria) J. Bacteriol. 173, 3138-3148
18. McCloskey, J. A., Liu, X.-H., Crain, P. F., Bruenger, E., Guymon, R., Hashizume, T., and Stetter, K. O. (2000) Posttranscriptional modification of transfer RNA in the submarine hyperthermophile Pyrolobus fumarii Nucleic Acids Symp. Ser. 44, 267-268
19. Massiere, F. and Badet-Denisot, M. A. (1998) The mechanism of glutamine-dependent amidotransferases Cell. Mol. Life Sci. 54, 205-222
20. Colloc'h, N., Poupon, A., and Mornon, J. P. (2000) Sequence and structural features of the T-fold, an original tunnelling building unit Proteins 39, 142-154 (Pubitemid 30176481)
21. Kim, Y., Zhou, M., Moy, S., Morales, J., Cunningham, M. A., and Joachimiak, A. (2010) High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism J. Mol. Biol. 404, 127-137
22. Kowalak, J. A., Pomerantz, S. C., Crain, P. F., and McCloskey, J. A. (1993) A novel method for the determination of posttranscriptional modification in RNA by mass spectrometry Nucleic Acids Res. 21, 4577-4585 (Pubitemid 23292724)
23. Mandal, D., Kohrer, C., Su, D., Russell, S. P., Krivos, K., Castleberry, C. M., Blum, P., Limbach, P. A., Söll, D., and RajBhandary, U. L. (2010) Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine Proc. Natl. Acad. Sci. U.S.A. 107, 2872-2877
24. Sekiya, T., Mori, M., Takahashi, N., and Nishimura, S. (1980) Sequence of the distal tRNA1Asp gene and the transcription termination signal in the Escherichia coli ribosomal RNA operon rrnF (or G) Nucleic Acids Res. 8, 3809-3828
25. 1 Biochemistry 34, 15381-15387
26. Overbeek, R, Begley, T, Butler, R. M., Choudhuri, J. V., Chuang, H. Y., Cohoon, M, de Crécy-Lagard, V, Diaz, N, Disz, T, Edwards, R, Fonstein, M, Frank, E. D., Gerdes, S, Glass, E. M., Goesmann, A, Hanson, A, Iwata-Reuyl, D, Jensen, R, Jamshidi, N, Krause, L, Kubal, M, Larsen, N, Linke, B, McHardy, A. C., Meyer, F, Neuweger, H, Olsen, G, Olson, R, Osterman, A, Portnoy, V, Pusch, G. D., Rodionov, D. A., Rückert, C, Steiner, J, Stevens, R, Thiele, I, Vassieva, O, Ye, Y, Zagnitko, O, and Vonstein, V. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes Nucleic Acids Res. 33, 5691-5702 (Pubitemid 41548835)
27. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25, 3389-3402 (Pubitemid 27359211)
28. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G., and Thompson, J. D. (2003) Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res. 31, 3497-3500 (Pubitemid 37442184)
29. Kelley, L. A. and Sternberg, M. J. E. (2009) Protein structure prediction on the Web: a case study using the Phyre server Nat. Protoc. 4, 363-371
30. Shatsky, M., Nussinov, R., and Wolfson, H. J. (2004) A method for simultaneous alignment of multiple protein structures Proteins: Struct., Funct., Bioinf. 56, 143-156 (Pubitemid 38720846)
31. Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript Bioinformatics 15, 305-308 (Pubitemid 29213756)
32. de Crécy-Lagard, V., Brochier-Armanet, C., Urbonavicius, J., Fernandez, B., Phillips, G., Lyons, B., Noma, A., Alvarez, S., Droogmans, L., Armengaud, J., and Grosjean, H. (2010) Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea Mol. Biol. Evol. 2062-2077
33. Rinehart, J., Krett, B., Rubio, M. A. T., Alfonzo, J. D., and Söll, D. (2005) Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion Genes Dev. 19, 583-592 (Pubitemid 40314990)