Identification of Genes Encoding tRNA Modification Enzymes by Comparative Genomics

Methods in Enzymology

Volumn 425, Issue , 2007, Pages 153-183

  Crécy Lagard, Valérie de ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID DERIVATIVE; NUCLEOSIDE; TRANSFER RNA; ENZYME;

AMINOACYLATION; ANTICODON; BACTERIAL GENE; BASE PAIRING; BIOSYNTHESIS; CODON; ENZYME ANALYSIS; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CODE; GENOMICS; MOLECULAR STABILITY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; QUEC GENE; QUED GENE; QUEE GENE; QUEF GENE; REVIEW; RIBOSOMAL FRAMESHIFTING; RNA SEQUENCE; SEQUENCE HOMOLOGY; TGT GENE; BACTERIUM; COMPARATIVE STUDY; ENZYMOLOGY; GENETICS; METABOLISM; METHODOLOGY;

BACTERIA; ENZYMES; GENOMICS; RNA, TRANSFER;

EID: 34548733710     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)25007-4     Document Type: Review

References (127)

1. Alexandrov A., Martzen M.R., and Phizicky E.M. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8 (2002) 1253-1266
2. Alm E.J., Huang K.H., Price M.N., Koche R.P., Keller K., Dubchak I.L., and Arkin A.P. The MicrobesOnline Web site for comparative genomics. Genome Res. 15 (2005) 1015-1022
3. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl. Acids Res. 25 (1997) 3389-3402
4. Anantharaman V., Koonin E.V., and Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucl. Acids Res. 30 (2002) 1427-1464
5. Anantharaman V., Koonin E.V., and Aravind L. SPOUT: A class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. J. Mol. Microbiol. Biotechnol. 4 (2002) 71-75
6. Aravind L., and Koonin E.V. THUMP-a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Trends Biochem. Sci. 26 (2001) 215-217
7. Barrick J.E., Corbino K.A., Winkler W.C., Nahvi A., Mandal M., Collins J., Lee M., Roth A., Sudarsan N., Jona I., Wickiser J.K., and Breaker R.R. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. USA 101 (2004) 6421-6426
8. Bishop A.C., Xu J., Johnson R.C., Schimmel P., and de Crécy-Lagard V. Identification of the tRNA-dihydrouridine synthase family. J. Biol. Chem. 277 (2002) 25090-25095
9. Björk G.R. Biosynthesis and Function of Modified Nucleosides. In: RajBhandary U.L. (Ed). "tRNA: Structure, Biosynthesis, and Function" (1995), ASM Press, Washington D. C 165-206
10. Björk G.R., and Kohli J. Synthesis and Function of Modified Nucleosides in tRNA. In: Gehrke C., and Kuo K. (Eds). "Chromatography and Modification of Nucleosides. Part B. Biological Roles and Function of Modification" (1990), Elsevier, Amsterdam B13-B67
11. Bobik T.A., and Rasche M.E. Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. J. Biol. Chem. 276 (2001) 37194-37198
12. Bujnicki J.M., Droogmans L., Grosjean H., Purushothaman S.K., and Lapeyre B. Bioinformatics-guided identification of novel RNA methyltransferases. In: Bujnicki J.M. (Ed). "Practical Bioinformatics" Vol. 15 (2004), Springer-Verlag, Berlin Heidelberg 139-168
13. Bujnicki J.M., Oudjama Y., Roovers M., Owczarek S., Caillet J., and Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA 10 (2004) 1236-1242
14. Chen Y.-B., Chattopadhyay A., Bergen P., Gadd C., and Tannery N. The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System-a one-stop gateway to online bioinformatics databases and software tools. Nucl. Acids Res. 35 (2007) D780-D785
15. Date S.V., and Marcotte E.M. Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics 21 (2005) 2558-2559
16. Daugherty M., Polanuyer B., Farrell M., Scholle M., Lykidis A., de Crécy-Lagard V., and Osterman A. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem. 277 (2002) 21431-21439
17. Daugherty M., Vonstein V., Overbeek R., and Osterman A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183 (2001) 292-300
18. De Bie L.G., Roovers M., Oudjama Y., Wattiez R., Tricot C., Stalon V., Droogmans L., and Bujnicki J.M. The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. J. Bacteriol. 185 (2003) 3238-3243
19. de Crécy-lagard V. Bioinformatics leads the path to the identification of missing tRNA modification genes. In: Bujnicki J.M. (Ed). "Practical Bioinformatics" Vol. 15 (2004), Springer-Verlag, Berlin Heidelberg 169-190
20. 1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucl. Acids Res. 31 (2003) 2148-2156
21. Eastwood Leung H.-C., Björk G.R., and Winkler M.E. Genetic locations and database accession numbers of RNA-modifying and -editing enzymes. In: Benne R. (Ed). "Modification and Editing of RNA" (1998), ASM Press, Washington, D.C 561-568 G., H.T.
22. El Yacoubi B., Bonnett S., Anderson J.N., Swairjo M.A., Iwata-Reuyl D., and de Crécy-Lagard V. Discovery of a new prokaryotic type I GTP cyclohydrolase family. J. Biol. Chem. 281 (2006) 37586-37593
23. Enault F., Suhre K., Poirot O., Abergel C., and Claverie J.M. Phydbac2: Improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. Nucl. Acids Res. 32 (2004) W336-W339
24. Enright A.J., Iliopoulos I., Kyrpides N.C., and Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402 (1999) 86-90
25. Fernandez-Ricaud L., Warringer J., Ericson E., Glaab K., Davidsson P., Nilsson F., Kemp G.J.L., Nerman O., and Blomberg A. PROPHECY-a yeast phenome database, update 2006. Nucl. Acids Res. 35 (2007) D463-D467
26. Field D., Feil E.J., and Wilson G.A. Databases and software for the comparison of prokaryotic genomes. Microbiology 151 (2005) 2125-2132
27. Finn R.D., Mistry J., Schuster-Bockler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., Eddy S.R., Sonnhammer E.L.L., et al. Pfam: Clans, web tools and services. Nucl. Acids Res. 34 (2006) D247-D251
28. Galperin M.Y., and Brenner S.E. Using metabolic pathway databases for functional annotation. Trends Genet. 14 (1998) 332-333
29. Galperin M.Y., and Koonin E.V. Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol. 1 (1998) 55-67
30. Galperin M.Y., and Koonin E.V. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18 (2000) 609-613
31. Gaur R., and Varshney U. Genetic analysis identifies a function for the queC (ybaX) gene product at an initial step in the queuosine biosynthetic pathway in Escherichia coli. J. Bacteriol. 187 (2005) 6893-6901
32. Geer L.Y., Domrachev M., Lipman D.J., and Bryant S.H. CDART: Protein Homology by Domain Architecture. Genome Res. 12 (2002) 1619-1623
33. Gelfand M.S., Koonin E.V., and Mironov A.A. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucl. Acids Res. 28 (2000) 695-705
34. Gelfand M.S., Novichkov P.S., Novichkova E.S., and Mironov A.A. Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform. 1 (2000) 357-371
35. Gerdes S.Y., Kurnasov O.V., Shatalin K., Polanuyer B., Sloutsky R., Vonstein V., Overbeek R., and Osterman A.L. Comparative genomics of NAD biosynthesis in Cyanobacteria. J. Bacteriol. 188 (2006) 3012-3023
36. Gerlt J.A., and Babbitt P.C. Can sequence determine function?. Genome Biol. 1 (2000) 1-10
37. Goldovsky L., Janssen P., Ahren D., Audit B., Cases I., Darzentas N., Enright A.J., Lopez-Bigas N., Peregrin-Alvarez J.M., Smith M., Tsoka S., Kunin V., and Ouzounis C.A. CoGenT++: An extensive and extensible data environment for computational genomics. Bioinformatics 21 (2005) 3806-3810
38. Graham D.E., Graupner M., Xu H., and White R.H. Identification of coenzyme M biosynthetic 2-phosphosulfolactate phosphatase. A member of a new class of Mg2+-dependent acid phosphatases. Eur. J. Biochem. 268 (2001) 5176-5188
39. Grosjean H., Keith G., and Droogmans L. Detection and quantification of modified nucleotides in RMA using thin-layer chromatography. In: Gott J. (Ed). "Methods in Molecular Biology" Vol. 265 (2004), Humana Press, Totowa, NJ 357-391
40. His. Genes Dev. 17 (2003) 2889-2901
41. Gustafsson C., Reid R., Greene P.J., and Santi D.V. Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes. Nucl. Acids Res. 24 (1996) 3756-3762
42. Haft D.H., Selengut J.D., Brinkac L.M., Zafar N., and White O. Genome Properties: A system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 21 (2005) 293-306
43. Heath R.J., and Rock C.O. A triclosan-resistant bacterial enzyme. Nature 406 (2000) 145-146
44. Hegyi H., and Gerstein M. Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins. Genome Res. 11 (2001) 1632-1640
45. Helgadottir S., Rosas-Sandoval G., Soll D., and Graham D.E. Biosynthesis of phosphoserine in the Methanococcales. J. Bacteriol. 189 (2007) 575-582
46. Hiley S.L., Jackman J., Babak T., Trochesset M., Morris Q.D., Phizicky E., and Hughes T.R. Detection and discovery of RNA modifications using microarrays. Nucl. Acids Res. 33 (2005) e2
47. Hoang C., and Ferre-D'Amare A.R. Cocrystal structure of a tRNA Psi55 pseudouridine synthase: Nucleotide flipping by an RNA modifying enzyme. Cell 107 (2001) 929-939
48. Hopper A.K., and Phizicky E.M. tRNA transfers to the limelight. Genes Dev. 17 (2003) 162-180
49. Huynen M.A., Snel B., Mering C., and Bork P. Function prediction and protein networks. Curr. Opin Cell. Biol. 15 (2003) 191-198
50. Huynen M.A., Snel B., and van Noort V. Comparative genomics for reliable protein-function prediction from genomic data. Trends Genet. 20 (2004) 340-344
51. Ikeuchi Y., Shigi N., Kato J., Nishimura A., and Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol. Cell. 21 (2006) 97-108
52. Ishitani R., Nureki O., Fukai S., Kijimoto T., Nameki N., Watanabe M., Kondo H., Sekine M., Okada N., Nishimura S., and Yokoyama S. Crystal structure of archaeosine tRNA-guanine transglycosylase. J. Mol. Biol. 318 (2002) 665-677
53. Jager G., Leipuviene R., Pollard M.G., Qian Q., and Björk G.R. The conserved Cys-X1-X2-Cys motif present in the TtcA protein is required for the thiolation of cytidine in position 32 of tRNA from Salmonella enterica serovar Typhimurium. J. Bacteriol. 186 (2004) 750-757
54. Jeltsch A., Nellen W., and Lyko F. Two substrates are better than one: Dual specificities for Dnmt2 methyltransferases. Trends Biochem. Sci. 31 (2006) 306
55. Jensen L.J., Lagarde J., von Mering C., and Bork P. ArrayProspector: A web resource of functional associations inferred from microarray expression data. Nucl. Acids Res. 32 (2004) W445-W448
56. Kahraman A., Avramov A., Nashev L.G., Popov D., Ternes R., Pohlenz H.-D., and Weiss B. PhenomicDB: A multi-species genotype/phenotype database for comparative phenomics. Bioinformatics 21 (2005) 418-420
57. Kalhor H.R., Penjwini M., and Clarke S. A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA. Bioch. Bioph. Res. Com. 334 (2005) 433
58. Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K.F., Itoh M., Kawashima S., Katayama T., Araki M., and Hirakawa M. From genomics to chemical genomics: New developments in KEGG. Nucl. Acids Res. 34 (2006) D354-D357
59. Katz J.E., Dlakic M., and Clarke S. Automated Identification of Putative Methyltransferases from Genomic Open Reading Frames. Mol. Cell. Proteomics 2 (2003) 525-540
60. Kaya Y., and Ofengand J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 9 (2003) 711-721
61. Kersten H., and Kersten W. Biosynthesis and Function of Queuine and Queuosine tRNAs. In: Kuo K.C.T. (Ed). "Chromatography and Modification of Nucleosides Part B" (1990), Elsevier, Amsterdam B69-B108
62. Kharchenko P., Chen L., Freund Y., Vitkup D., and Church G. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7 (2006) 177
63. Kitagawa M., Ara T., Arifuzzaman M., Ioka-Nakamichi T., Inamoto E., Toyonaga H., and Mori H. Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res. 12 (2005) 291-299
64. Kobayashi K., Ehrlich S.D., Albertini A., Amati G., Andersen K.K., Arnaud M., Asai K., Ashikaga S., Aymerich S., Bessieres P., Boland F., Brignell S.C., et al. Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100 (2003) 4678-4683
65. Koonin E.V., and Galperin M.Y. "SEQUENCE-EVOLUTION-FUNCTION. Computational approaches in comparative genomics." (2003), Kluwer Academic Publishers, Dordrecht, Netherlands
66. Krieger C.J., Zhang P., Mueller L.A., Wang A., Paley S., Arnaud M., Pick J., Rhee S.Y., and Karp P.D. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucl. Acids Res. 32 (2004) D438-D442
67. Kuchino Y., Kasai H., Nihei K., and Nishimura S. Biosynthesis of the Modified Nucleoside Q in Transfer RNA. Nucl. Acids Res. 3 (1976) 393-398
68. Kurowski M., Sasin J., Feder M., Debski J., and Bujnicki J. Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures. BMC Bioinformatics 4 (2003) 9
69. Levin I., Giladi M., Altman-Price N., Ortenberg R., and Mevarech M. An alternative pathway for reduced folate biosynthesis in bacteria and halophilic archaea. Mol. Microbiol. 54 (2004) 1307-1318
70. Loh K.D., Gyaneshwar P., Markenscoff Papadimitriou E., Fong R., Kim K.S., Parales R., Zhou Z., Inwood W., and Kustu S. A previously undescribed pathway for pyrimidine catabolism. Proc. Natl. Acad. Sci. USA 103 (2006) 5114-5119
71. Makarova K., and Koonin E. Comparative genomics of archaea: How much have we learned in six years, and what's next?. Genome Biol. 4 (2003) 115
72. Martzen M.R., McCraith S.M., Spinelli S.L., Torres F.M., Fields S., Grayhack E.J., and Phizicky E.M. A Biochemical Genomics Approach for Identifying Genes by the Activity of Their Products. Science 286 (1999) 1153-1155
73. McNeil L.K., Reich C., Aziz R.K., Bartels D., Cohoon M., Disz T., Edwards R.A., Gerdes S., Hwang K., Kubal M., Margaryan G.R., Meyer F., et al. The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucl. Acids Res. 35 (2007) D347-D353
74. Mittl P.R., and Grutter M.G. Structural genomics: Opportunities and challenges. Curr. Opin. Chem. Biol. 5 (2001) 402-408
75. 5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme. RNA 5 (1999) 1105-1118
76. Muramatsu T., Yokoyama S., Horie N., Matsuda A., Ueda T., Yamaizumi Z., Kuchino Y., Nishimura S., and Miyazawa T. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J. Biol. Chem. 263 (1988) 9261-9267
77. Nash R., Weng S., Hitz B., Balakrishnan R., Christie K.R., Costanzo M.C., Dwight S.S., Engel S.R., Fisk D.G., Hirschman J.E., Hong E.L., Livstone M.S., et al. Expanded protein information at SGD: New pages and proteome browser. Nucl. Acids Res. 35 (2007) D468-D471
78. 5UGG) promotes reading of all four proline codons in vivo. RNA 10 (2004) 1662-1673
79. Noguchi S., Nishimura Y., Hirota Y., and Nishimura S. Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA. J. Biol. Chem. 257 (1982) 6544-6550
80. Noma A., Kirino Y., Ikeuchi Y., and Suzuki T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142-2154
81. Okada N., Noguchi S., Nishimura S., Ohgi T., Goto T., Crain P.F., and McCloskey J.A. Structure Determination of a Nucleoside Q Precursor Isolated from E. coli tRNA: 7-(aminomethyl)-7-deazaguanosine. Nucl. Acids Res. 5 (1978) 2289-2296
82. Osterman A., and Begley T. A subsystems based approach to the identification of drug targets in bacterial pathogens. In: Boshoff H.I., and Barrry C.E.I. (Eds). "Progress in Drug Research" Vol. 64 (2006), Birkhauser Verlag, Basel (Switzerland) 133-170
83. Osterman A., and Overbeek R. Missing genes in metabolic pathways: A comparative genomics approach. Curr. Opin. Chem. Biol. 7 (2003) 238-251
84. 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., et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucl. Acids Res. 33 (2005) 5691-5702
85. Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H.Y., Cohoon M., de Crecy-Lagard V., Diaz N., Disz T., Edwards R., Fonstein M., Frank E.D., et al. The ERGO Genome Analysis and Discovery System. Nucleic Acids Res. 31 (2003) 1-8
86. Overbeek R., Fonstein M., D'Souza M., Pusch G.D., and Maltsev N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96 (1999) 2896-2901
87. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., and Yeates T.O. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96 (1999) 4285-4288
88. Peng W.-T., Robinson M.D., Mnaimneh S., Krogan N.J., Cagney G., Morris Q., Davierwala A.P., Grigull J., Yang X., and Zhang W. A panoramic view of yeast noncoding RNA processing. Cell 113 (2003) 919
89. Perez-Arellano I., Rubio V., and Cervera J. Dissection of Escherichia coli glutamate 5-kinase: Functional impact of the deletion of the PUA domain. FEBS Lett. 579 (2005) 6903
90. Pintard L., Lecointe F., Bujnicki J.M., Bonnerot C., Grosjean H., and Lapeyre B. Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop. Embo J. 21 (2002) 1811-1820
91. Purta E., van Vliet F., Tkaczuk K.L., Dunin-Horkawicz S., Mori H., Droogmans L., and Bujnicki J.M. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol. Biol. 7 (2006) 23
92. Purushothaman S.K., Bujnicki J.M., Grosjean H., and Lapeyre B. Trm11p and Trm112p Are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Mol. Cell. Biol. 25 (2005) 4359-4370
93. Reader J.S., Metzgar D., Schimmel P., and de Crécy-Lagard V. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J. Biol. Chem. 279 (2004) 6280-6285
94. Renalier M.-H., Joseph N., Gaspin C., Thebault P., and Mougin A. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2′-O-methylase, or a C/D sRNP. RNA 11 (2005) 1051-1063
95. Reuter K., Slany R., Ullrich F., and Kersten H. Structure and Organization of E. coli Genes Involved in Biosynthesis of the Deazaguanine Derivative Queuine, a Nutrient Factor for Eukaryotes. J. Bacteriol. 173 (1991) 2256-2264
96. Rhee S.Y., Beavis W., Berardini T.Z., Chen G., Dixon D., Doyle A., Garcia-Hernandez M., Huala E., Lander G., Montoya M., Miller N., Mueller L.A., et al. The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucl. Acids Res. 31 (2003) 224-228
97. Rodionov D.A., Hebbeln P., Gelfand M.S., and Eitinger T. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: Evidence for a novel group of ATP-binding cassette transporters. J. Bacteriol. 188 (2006) 317-327
98. Roovers M., Hale C., Tricot C., Terns M.P., Terns R.M., Grosjean H., and Droogmans L. Formation of the conserved pseudouridine at position 55 in archaeal tRNA. Nucl. Acids Res. 34 (2006) 4293-4301
99. Sauerwald A., Zhu W., Major T.A., Roy H., Palioura S., Jahn D., Whitman W.B., Yates III J.R., Ibba M., and Söll D. RNA-dependent cysteine biosynthesis in Archaea. Science 307 (2005) 1969-1972
100. Selkov E., Maltsev N., Olsen G.J., Overbeek R., and Whitman W.B. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 197 (1997) GC11-GC26
101. Slany R.K., Bosl M., and Kersten H. 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 (1994) 389-393
102. Soma A., Ikeuchi Y., Kanemasa S., Kobayashi K., Ogasawara N., Ote T., Kato J., Watanabe K., Sekine Y., Suzuki T., Muramatsu T., Nishikawa K., et al. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell 12 (2003) 689-698
103. Sprinzl M., Vassilenko K.S., Emmerich J., and Bauer F. tRNA Compilation 2000 (1999). http://www.uni-bayreuth.de/departments/biochemie/trna/
104. Suhre K., and Claverie J.-M. FusionDB: A database for in-depth analysis of prokaryotic gene fusion events. Nucl. Acids Res. 32 (2004) D273-D276
105. Tatusov R., Fedorova N., Jackson J., Jacobs A., Kiryutin B., Koonin E., Krylov D., Mazumder R., Mekhedov S., Nikolskaya A., Rao B.S., Smirnov S., et al. The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4 (2003) 41
106. Tatusov R.L., Koonin E.V., and Lipman D.J. A genomic perspective on protein families. Science 278 (1997) 631-637
107. Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., Kiryutin B., Galperin M.Y., Fedorova N.D., and Koonin E.V. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucl. Acids Res. 29 (2001) 22-28
108. Tian W., and Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. J. Mol. Biol. 333 (2003) 863-882
109. Tian W., and Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. J. Mol. Biol. 333 (2003) 863-882
110. Uchiyama I. MBGD: A platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucl. Acids Res. 35 (2007) D343-D346
111. Umeda N., Suzuki T., Yukawa M., Ohya Y., Shindo H., Watanabe K., and Suzuki T. 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
112. 5U methyltransferase in bacteria-evolutionary implications. Nucl. Acids Res. 33 (2005) 3955-3964
113. Van Lanen S.G., Reader J.S., Swairjo M.A., de Crécy-Lagard V., Lee B., and Iwata-Reuyl D. From cyclohydrolase to oxidoreductase: Discovery of nitrile reductase activity in a common fold. Proc. Natl. Acad. Sci. USA 102 (2005) 4264-4269
114. Veitia R. Rosetta Stone proteins: "Chance and necessity"?. Genome Biology 1001 (2002) 1-3
115. von Mering C., Huynen M., Jaeggi D., Schmidt S., Bork P., and Snel B. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 31 (2003) 258-261
116. von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., and Bork P. STRING 7-recent developments in the integration and prediction of protein interactions. Nucl. Acids Res. 35 (2007) D358-D362
117. Waas W.F., Crécy-Lagard. d., and Schimmel P. Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. J. Biol. Chem. 280 (2005) 37616-37622
118. Watanabe Y.-i., and Gray M.W. Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: Cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria. Nucl. Acids Res. 28 (2000) 2342-2352
119. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H., Chu A.M., Connelly C., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285 (1999) 901-906
120. Wolf J., Gerber A.P., and Keller W. tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J. 21 (2002) 3841-3851
121. Wolfe M.D., Ahmed F., Lacourciere G.M., Lauhon C.T., Stadtman T.C., and Larson T.J. Functional diversity of the rhodanese homology domain: The Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase. J. Biol. Chem. 279 (2004) 1801-1809
122. Xing F., Hiley S.L., Hughes T.R., and Phizicky E.M. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J. Biol. Chem. 279 (2004) 17850-17860 Epub 2004 Feb 16
123. Xing F., Martzen M.R., and Phizicky E.M. A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA 8 (2002) 370-381
124. Xu X.M., Carlson B.A., Mix H., Zhang Y., Saira K., Glass R.S., Berry M.J., Gladyshev V.N., and Hatfield D.L. Biosynthesis of Selenocysteine on Its tRNA in Eukaryotes. PLoS Biol. 5 (2006) e4
125. Yakunin A.F., Yee A.A., Savchenko A., Edwards A.M., and Arrowsmith C.H. Structural proteomics: A tool for genome annotation. Curr. Opin. Chem. Biol. 8 (2004) 42-48
126. Yang C., Rodionov D.A., Li X., Laikova O.N., Gelfand M.S., Zagnitko O.P., Romine M.F., Obraztsova A.Y., Nealson K.H., and Osterman A.L. Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J. Biol. Chem. 281 (2006) 29872-29885
127. Ye Y., and Godzik A. Multiple flexible structure alignment using partial order graphs. Bioinformatics 21 (2005) 2362-2369