The DOI matches its Crossref record; 283 of the 283 references it cites were found in a registry or an index.
Transfer RNA Modification
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6 -threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t 6 A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Complete Genome Sequence of Escherichia coli K-12
Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997) · Science · doi:10.1126/science.277.5331.1453 · Cited by 7,452
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128
Codon—anticodon pairing: The wobble hypothesis
Crick, F. H. C. (1966) · Journal of Molecular Biology · doi:10.1016/s0022-2836(66)80022-0 · Cited by 2,029
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
McClelland, M., Sanderson, K. E., Spieth, J., Clifton, S. W., Latreille, P., Courtney, L., Porwollik, S., Ali, J., Dante, M., Du, F., et al. (2001) · Nature · doi:10.1038/35101614 · Cited by 1,837
Sofia, H. J. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.5.1097 · Cited by 1,019
Many paths to methyltransfer: a chronicle of convergence
Schubert, H. L., Blumenthal, R. M., & Cheng, X. (2003) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(03)00090-2 · Cited by 876
Ikemura, T. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90363-6 · Cited by 875
Stadtman, T. C. (1996) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.65.070196.000503 · Cited by 829
Universal rules and idiosyncratic features in tRNA identity
Giege, R., Sissler, M., & Florentz, C. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.22.5017 · Cited by 769
THE QUANTITATIVE SEPARATION OF PURINES, PYRIMIDINES, AND NUCLEOSIDES BY PAPER CHROMATOGRAPHY
Hotchkiss, R. D. (1948) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)57261-6 · Cited by 766
Sampson, J. R., & Uhlenbeck, O. C. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.4.1033 · Cited by 604
The Small RNA Regulators of Escherichia coli : Roles and Mechanisms
Gottesman, S. (2004) · Annual Review of Microbiology · doi:10.1146/annurev.micro.58.030603.123841 · Cited by 586
Biological Methylation: Selected Aspects
Cantoni, G. L. (1975) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.44.070175.002251 · Cited by 556
Global analysis of small RNA and mRNA targets of Hfq
Zhang, A., Wassarman, K. M., Rosenow, C., Tjaden, B. C., Storz, G., & Gottesman, S. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03734.x · Cited by 544
Summary: the modified nucleosides of RNA
Limbach, P. A., Crain, P. F., & McCloskey, J. A. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.12.2183 · Cited by 523
Improvement of reading frame maintenance is a common function for several tRNA modifications
Urbonavicius, J. (2001) · The EMBO Journal · doi:10.1093/emboj/20.17.4863 · Cited by 499
AdoMet-dependent methylation, DNA methyltransferases and base flipping
Cheng, X. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.18.3784 · Cited by 485
Muramatsu, T., Nishikawa, K., Nemoto, F., Kuchino, Y., Nishimura, S., Miyazawa, T., & Yokoyama, S. (1988) · Nature · doi:10.1038/336179a0 · Cited by 457
Schwartz, C. J., Giel, J. L., Patschkowski, T., Luther, C., Ruzicka, F. J., Beinert, H., & Kiley, P. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.251550898 · Cited by 443
RIBONUCLEIC ACIDS FROM YEAST WHICH CONTAIN A FIFTH NUCLEOTIDE
Davis, F. F., & Allen, F. W. (1957) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)70770-9 · Cited by 435
Cohn, W. E. (1960) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)69432-3 · Cited by 407
Minor Components in Transfer RNA: Their Characterization, Location, and Function
Nishimuka, S. (1972) · Progress in Nucleic Acid Research and Molecular Biology · doi:10.1016/s0079-6603(08)60659-5 · Cited by 402
Role of modifications in tyrosine transfer RNA: A modified base affecting ribosome binding
Gefter, M. L., & Russell, R. L. (1969) · Journal of Molecular Biology · doi:10.1016/0022-2836(69)90339-8 · Cited by 394
Tsui, H. T., Leung, H. E., & Winkler, M. E. (1994) · Molecular Microbiology · doi:10.1111/j.1365-2958.1994.tb00400.x · Cited by 389
MARCK, C., & GROSJEAN, H. (2002) · RNA · doi:10.1017/s1355838202022021 · Cited by 376
E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo.
Ross, W., Thompson, J. F., Newlands, J. T., & Gourse, R. L. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07586.x · Cited by 365
Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase
Rould, M. A., Perona, J. J., & Steitz, T. A. (1991) · Nature · doi:10.1038/352213a0 · Cited by 360
The role of modifications in codon discrimination by tRNALysUUU
Murphy, F. V., Ramakrishnan, V., Malkiewicz, A., & Agris, P. F. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb861 · Cited by 360
Decoding the genome: a modified view
Agris, P. F. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh185 · Cited by 341
Nucleoside-5′-Phosphates from Ribonucleic Acid
COHN, W. E., & VOLKIN, E. (1951) · Nature · doi:10.1038/167483a0 · Cited by 335
An Adenosine Deaminase that Generates Inosine at the Wobble Position of tRNAs
Gerber, A. P., & Keller, W. (1999) · Science · doi:10.1126/science.286.5442.1146 · Cited by 321
Belcourt, M. F., & Farabaugh, P. J. (1990) · Cell · doi:10.1016/0092-8674(90)90371-k · Cited by 298
Nucleotide Sequence of N-Formyl-methionyl-transfer RNA
DUBE, S. K., MARCKER, K. A., CLARK, B. F. C., & CORY, S. (1968) · Nature · doi:10.1038/218232a0 · Cited by 293
tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli
Wolf, J. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf362 · Cited by 287
The influence of codon context on genetic code translation
Bossi, L., & Roth, J. R. (1980) · Nature · doi:10.1038/286123a0 · Cited by 284
Transfer of Sulfur from IscS to IscU during Fe/S Cluster Assembly
Urbina, H. D., Silberg, J. J., Hoff, K. G., & Vickery, L. E. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m106907200 · Cited by 278
Structure of yeast phenylalanine transfer RNA at 2.5 A resolution.
Ladner, J. E., Jack, A., Robertus, J. D., Brown, R. S., Rhodes, D., Clark, B. F., & Klug, A. (1975) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.72.11.4414 · Cited by 277
On the physical basis for ambiguity in genetic coding interactions.
Grosjean, H. J., de Henau, S., & Crothers, D. M. (1978) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.75.2.610 · Cited by 274
Yokoyama, S., Watanabe, T., Murao, K., Ishikura, H., Yamaizumi, Z., Nishimura, S., & Miyazawa, T. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.15.4905 · Cited by 271
Cocrystal Structure of a tRNA Ψ55 Pseudouridine Synthase
Hoang, C., & Ferré-D'Amaré, A. R. (2001) · Cell · doi:10.1016/s0092-8674(01)00618-3 · Cited by 270
"Two out of three": an alternative method for codon reading.
Lagerkvist, U. (1978) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.75.4.1759 · Cited by 269
A primordial tRNA modification required for the evolution of life?
Bjork, G. R. (2001) · The EMBO Journal · doi:10.1093/emboj/20.1.231 · Cited by 260
Accurate Translation of the Genetic Code Depends on tRNA Modified Nucleosides
Yarian, C., Townsend, H., Czestkowski, W., Sochacka, E., Malkiewicz, A. J., Guenther, R., Miskiewicz, A., & Agris, P. F. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m200253200 · Cited by 248
Prevention of Translational Frameshifting by the Modified Nucleoside 1-Methylguanosine
Björk, G. R., Wikström, P. M., & Byström, A. S. (1989) · Science · doi:10.1126/science.2471265 · Cited by 245
Self-citationBiosynthesis and Function of Modified Nucleosides
Björk, G. R. (2014) · tRNA · doi:10.1128/9781555818333.ch11 · Cited by 244
Self-citationKawai, G., Yamamoto, Y., Kamimura, T., Masegi, T., Sekine, M., Hata, T., Iimori, T., Watanabe, T., Miyazawa, T., & Yokoyama, S. (1992) · Biochemistry · doi:10.1021/bi00119a012 · Cited by 239
Anticodon Switching Changes the Identity of Methionine and Valine Transfer RNAs
Schulman, L. H., & Pelka, H. (1988) · Science · doi:10.1126/science.3055296 · Cited by 234
Chen, G.-F. T., & Inouye, M. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.6.1465 · Cited by 225
Koonin, E. V. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.12.2411 · Cited by 224
An RNA-Modifying Enzyme that Governs Both the Codon and Amino Acid Specificities of Isoleucine tRNA
Soma, A., Ikeuchi, Y., Kanemasa, S., Kobayashi, K., Ogasawara, N., Ote, T., Kato, J.-I., Watanabe, K., Sekine, Y., & Suzuki, T. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00346-0 · Cited by 215
Relaxation of a transfer RNA specificity by removal of modified nucleotides
Perret, V., Garcia, A., Grosjean, H., Ebel, J.-P., Florentz, C., & Giegé, R. (1990) · Nature · doi:10.1038/344787a0 · Cited by 215
Tsui, H. C., Feng, G., & Winkler, M. E. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.23.7476-7487.1997 · Cited by 215
Divergent promoters, a common form of gene organization
Beck, C. F., & Warren, R. A. J. (1988) · Microbiological Reviews · doi:10.1128/mmbr.52.3.318-326.1988 · Cited by 213
Ollagnier-de-Choudens, S., Mattioli, T., Takahashi, Y., & Fontecave, M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m102902200 · Cited by 211
Promoter Sequence for Stringent Control of Bacterial Ribonucleic Acid Synthesis
Travers, A. A. (1980) · Journal of Bacteriology · doi:10.1128/jb.141.2.973-976.1980 · Cited by 210
Brown, L., & Elliott, T. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.13.3763-3770.1996 · Cited by 210
Beier, H., Barciszewska, M., Krupp, G., Mitnacht, R., & Gross, H. J. (1984) · The EMBO Journal · doi:10.1002/j.1460-2075.1984.tb01810.x · Cited by 208
Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria)
Edmonds, C. G., Crain, P. F., Gupta, R., Hashizume, T., Hocart, C. H., Kowalak, J. A., Pomerantz, S. C., Stetter, K. O., & McCloskey, J. A. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.10.3138-3148.1991 · Cited by 206
Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic growth conditions
Jeter, R. M., Olivera, B. M., & Roth, J. R. (1984) · Journal of Bacteriology · doi:10.1128/jb.159.1.206-213.1984 · Cited by 205
Sulfur Transfer from IscS to IscU: The First Step in Iron−Sulfur Cluster Biosynthesis
Smith, A. D., Agar, J. N., Johnson, K. A., Frazzon, J., Amster, I. J., Dean, D. R., & Johnson, M. K. (2001) · Journal of the American Chemical Society · doi:10.1021/ja016757n · Cited by 194
Flint, D. H. (1996) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)48580-8 · Cited by 190
Translational Efficiency of Transfer RNA's: Uses of an Extended Anticodon
Yarus, M. (1982) · Science · doi:10.1126/science.6753149 · Cited by 188
Sylvers, L. A., Rogers, K. C., Shimizu, M., Ohtsuka, E., & Soll, D. (1993) · Biochemistry · doi:10.1021/bi00066a002 · Cited by 183
Queuosine modification of the wobble base in tRNAHis influences ‘in vivo’ decoding properties.
Meier, F., Suter, B., Grosjean, H., Keith, G., & Kubli, E. (1985) · The EMBO Journal · doi:10.1002/j.1460-2075.1985.tb03704.x · Cited by 182
Muramatsu, T., Yokoyama, S., Horie, N., Matsuda, A., Ueda, T., Yamaizumi, Z., Kuchino, Y., Nishimura, S., & Miyazawa, T. (1988) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)76533-8 · Cited by 182
Modified Nucleosides and Codon Recognition+
Yokoyama, S., & Nishimura, S. (2014) · tRNA · doi:10.1128/9781555818333.ch12 · Cited by 180
Escherichia coli genes whose products are involved in selenium metabolism
Leinfelder, W., Forchhammer, K., Zinoni, F., Sawers, G., Mandrand-Berthelot, M. A., & Böck, A. (1988) · Journal of Bacteriology · doi:10.1128/jb.170.2.540-546.1988 · Cited by 180
Nucleotide Sequences in the Yeast Alanine Transfer Ribonucleic Acid
Holley, R. W., Everett, G. A., Madison, J. T., & Zamir, A. (1965) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)97435-1 · Cited by 180
The occurrence of methylated guanines in ribonucleic acids from several sources
Smith, J. D., & Dunn, D. B. (1959) · Biochemical Journal · doi:10.1042/bj0720294 · Cited by 177
Glass, R. S., Singh, W. P., Jung, W., Veres, Z., Scholz, T. D., & Stadtman, T. (1993) · Biochemistry · doi:10.1021/bi00210a001 · Cited by 176
Additional components in ribonucleic acid of rat-liver fractions
Dunn, D. B. (1959) · Biochimica et Biophysica Acta · doi:10.1016/0006-3002(59)90274-4 · Cited by 176
Model for regulation of the histidine operon of Salmonella.
Johnston, H. M., Barnes, W. M., Chumley, F. G., Bossi, L., & Roth, J. R. (1980) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.77.1.508 · Cited by 175
Durant, P. C., & Davis, D. R. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2297 · Cited by 173
Pierrel, F., Douki, T., Fontecave, M., & Atta, M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m408562200 · Cited by 169
MnmA and IscS Are Required for in Vitro 2-Thiouridine Biosynthesis in Escherichia coli
Kambampati, R., & Lauhon, C. T. (2003) · Biochemistry · doi:10.1021/bi026536+ · Cited by 168
Palenchar, P. M., Buck, C. J., Cheng, H., Larson, T. J., & Mueller, E. G. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.12.8283 · Cited by 168
Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift
Brégeon, D., Colot, V., Radman, M., & Taddei, F. (2001) · Genes & Development · doi:10.1101/gad.207701 · Cited by 162
5-Ribosyl uracil, a carbon-carbon ribofuranosyl nucleoside in ribonucleic acids
Cohn, W. E. (1959) · Biochimica et Biophysica Acta · doi:10.1016/0006-3002(59)90644-4 · Cited by 161
Durand, J. M. B., Dagberg, B., Uhlin, B. E., & Björk, G. R. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01767.x · Cited by 161
Self-citationAminoacyl-tRNAs: setting the limits of the genetic codePreprint
Ibba, M., & Söll, D. G. (2004) · Genes & Development · doi:10.1101/gad.1187404 · Cited by 160
Identification of Four Genes Necessary for Biosynthesis of the Modified Nucleoside Queuosine
Reader, J. S., Metzgar, D., SCHIMMEL, P. R., & de Crécy‐Lagard, V. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m310858200 · Cited by 158
Kambampati, R., & Lauhon, C. T. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.15.10727 · Cited by 154
Normal tRNAs promote ribosomal frameshifting
Atkins, J. F., Gesteland, R. F., Reid, B. R., & Anderson, C. W. (1979) · Cell · doi:10.1016/0092-8674(79)90225-3 · Cited by 153
Kumar, R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.6.1272 · Cited by 152
In vitrostudy ofE.colitRNAArgand tRNALysidentity elements
Tamura, K., Himeno, H., Asahara, H., Hasegawa, T., & Shimizu, M. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.9.2335 · Cited by 151
Biosynthesis of Pseudouridine in Transfer Ribonucleic Acid
Cortese, R., Kammen, H. O., Spengler, S. J., & Ames, B. N. (1974) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)42947-5 · Cited by 148
Stern, L., & Schulman, L. H. (1978) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)34590-8 · Cited by 148
Huang, L., Pookanjanatavip, M., Gu, X., & Santi, D. V. (1998) · Biochemistry · doi:10.1021/bi971874+ · Cited by 147
Lecointe, F., Simos, G., Sauer, A., et al. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.3.1316 · Cited by 145
Mechanism of growth delay induced in Escherichia coli by near ultraviolet radiation.
Ramabhadran, T. V., & Jagger, J. (1976) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.73.1.59 · Cited by 145
Anantharaman, V., Koonin, E. V., & Aravind, L. (2002) · PubMed · Cited by 142
Cusack, S., Yaremchuk, A. D., & Tukalo, M. A. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb01022.x · Cited by 141
Okada, N., Noguchi, S., Kasai, H., Shindo‐Okada, N., Ohgi, T., Goto, T., & Nishimura, S. (1979) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)30183-7 · Cited by 141
Selenophosphate synthetase. Enzyme properties and catalytic reaction.
Veres, Z., Kim, I. Y., SCHOLZ, T. D., & Stadtman, T. C. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)34101-7 · Cited by 139
Gustafsson, C., Reid, R., Greene, P. J., & Santi, D. V. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.19.3756 · Cited by 138
Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition
Ahn, H. J., Kim, H., Yoon, H., et al. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg269 · Cited by 137
Structure of an unmodified tRNA molecule
Hall, K. B., Sampson, J. R., Uhlenbeck, O. C., & Redfield, A. G. (1989) · Biochemistry · doi:10.1021/bi00440a014 · Cited by 137
The photochemistry of 4-thiouridine in escherichia coli t-RNAİVal
Favre, A., Yaniv, M., & Michels, A. M. (1969) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(69)90729-3 · Cited by 135
Pan, H., Agarwalla, S., Moustakas, D. T., Finer-Moore, J. S., & Stroud, R. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2135585100 · Cited by 135
Frey, B., MCCLOSKEY, J. A., Kersten, W., & Kersten, H. (1988) · Journal of Bacteriology · doi:10.1128/jb.170.5.2078-2082.1988 · Cited by 134
Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA
Iwata‐Reuyl, D. (2003) · Bioorganic Chemistry · doi:10.1016/s0045-2068(02)00513-8 · Cited by 134
Krüger, M. K., Pedersen, S. B., Hagervall, T. G., & Sørensen, M. A. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2196 · Cited by 133
Self-citationPossibilities for the Evolution of the Genetic Code from a Preceding Form
Jukes, T. H. (1973) · Nature · doi:10.1038/246022a0 · Cited by 131
The Role of the Cysteine Residues of ThiI in the Generation of 4-Thiouridine in tRNA
Mueller, E. G., Palenchar, P. M., & Buck, C. J. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m104067200 · Cited by 130
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase
Roovers, M., Wouters, J., Bujnicki, J. M., Tricot, C., Stalon, V., Grosjean, H., & Droogmans, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh191 · Cited by 128
Singly and Bifurcated Hydrogen-bonded Base-pairs in tRNA Anticodon Hairpins and Ribozymes
Auffinger, P., & Westhof, É. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3080 · Cited by 127
Identification of a gene involved in the generation of 4-thiouridine in tRNA
Mueller, E. G., Buck, C. J., Palenchar, P. M., Barnhart, L. E., & Paulson, J. L. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.11.2606 · Cited by 126
Agris, P. F. (1991) · Biochimie · doi:10.1016/0300-9084(91)90163-u · Cited by 125
Hopfield, J. J. (1978) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.75.9.4334 · Cited by 125
Hypermodified Nucleosides in the Anticodon of tRNALys Stabilize a Canonical U-Turn Structure,
Sundaram, M., Durant, P. C., & Davis, D. R. (2000) · Biochemistry · doi:10.1021/bi0014655 · Cited by 124
RNA Methyltransferases Utilize Two Cysteine Residues in the Formation of 5-Methylcytosine
King, M. Y., & Redman, K. L. (2002) · Biochemistry · doi:10.1021/bi026055q · Cited by 123
Bork, P., & Koonin, E. V. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340200407 · Cited by 123
Functional Diversity of the Rhodanese Homology Domain
Wolfe, M. D., Ahmed, F., Lacourciere, G. M., Lauhon, C. T., Stadtman, T. C., & Larson, T. J. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m310442200 · Cited by 121
Nureki, O., Niimi, T., Muramatsu, T., Kanno, H., Kohno, T., Florentz, C., Giegé, R., & Yokoyama, S. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1184 · Cited by 121
Requirement for IscS in Biosynthesis of All Thionucleosides in Escherichia coli
Lauhon, C. T. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.24.6820-6829.2002 · Cited by 121
Auxilien, S., Crain, P. F., Trewyn, R. W., & Grosjean, H. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0527 · Cited by 121
Wild-type tRNATyrG reads the TMV RNA stop codon, but Q base-modified tRNATyrQ does not
Bienz, M., & Kubli, E. (1981) · Nature · doi:10.1038/294188a0 · Cited by 120
Footprints of aminoacyl-tRNA synthetases are everywhere
SCHIMMEL, P. R., & de Pouplana, L. R. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01553-x · Cited by 120
Hydrogen bonding in yeast phenylalanine transfer RNA.
Quigley, G. J., Wang, A. H. ‐., Seeman, N. C., Suddath, F. L., Rich, A., Sussman, J. L., & Kim, S. (1975) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.72.12.4866 · Cited by 118
NovelE. colimutants deficient in blosynthesis of 5-methylamlnomethyl-2-thiouridine
Elseviers, D., Petrullo, L. A., & Gallagher, P. J. (1984) · Nucleic Acids Research · doi:10.1093/nar/12.8.3521 · Cited by 118
Madore, É., Florentz, C., Giegé, R., Sekine, S., Yokoyama, S., & Lapointe, J. (1999) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.1999.00965.x · Cited by 117
Crystal structure of tRNA‐guanine transglycosylase: RNA modification by base exchange.
Romier, C., Reuter, K., Suck, D., & Ficner, R. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00646.x · Cited by 116
Näsvall, J., Chen, P., & Björk, G. R. (2004) · RNA · doi:10.1261/rna.7106404 · Cited by 116
Self-citationm 5 C RNA and m 5 C DNA methyl transferases use different cysteine residues as catalysts
Liu, Y., & Santi, D. V. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.15.8263 · Cited by 115
Hoff, K. G., Ta, D. T., Tapley, T. L., Silberg, J. J., & Vickery, L. E. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m202814200 · Cited by 114
Persson, B. C., Jäger, G., & Gustafsson, C. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.20.4093 · Cited by 114
Growth rate dependence of transfer RNA abundance in Escherichia coli.
Emilsson, V., & Kurland, C. G. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07885.x · Cited by 113
Xie, W., Liu, X., & Huang, R. H. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb976 · Cited by 111
A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya
KAYA, Y., & Ofengand, J. (2003) · RNA · doi:10.1261/rna.5230603 · Cited by 111
The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA
Gu, X., Liu, Y., & Santi, D. V. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.25.14270 · Cited by 110
Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons
Takai, K. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg839 · Cited by 110
Enzymatic Modification of tRNAs
Pierrel, F., Björk, G. R., Fontecave, M., & Atta, M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.c100609200 · Cited by 110
Self-citationIdentification of the tRNA-Dihydrouridine Synthase Family
Bishop, A. C., Xu, J., Johnson, R. C., SCHIMMEL, P. R., & de Crécy‐Lagard, V. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m203208200 · Cited by 110
Santi, D. V., & Hardy, L. W. (1987) · Biochemistry · doi:10.1021/bi00400a016 · Cited by 109
Buck, M., & Ames, B. N. (1984) · Cell · doi:10.1016/0092-8674(84)90245-9 · Cited by 109
Davanloo, P., Sprinzl, M., Watanabe, K., Albani, M., & Kersten, H. (1979) · Nucleic Acids Research · doi:10.1093/nar/6.4.1571 · Cited by 108
Cabedo, H., Macián, F., Villarroya, M., Escudero, J. C., Martínez‐Vicente, M., Knecht, E., & Armengod, M. ‐. (1999) · The EMBO Journal · doi:10.1093/emboj/18.24.7063 · Cited by 107
Transfer RNA modifications that alter +1 frameshifting in general fail to affect −1 frameshifting
Urbonavičius, J., Stahl, G., Durand, J. M. B., Salem, S. N. B., QIAN, Q., Farabaugh, P. J., & Björk, G. R. (2003) · RNA · doi:10.1261/rna.5210803 · Cited by 107
Self-citationByström, A. S., Hjalmarsson, K., Wikström, P. M., & Björk, G. R. (1983) · The EMBO Journal · doi:10.1002/j.1460-2075.1983.tb01519.x · Cited by 106
Self-citationGenetic Dissection of Synthesis and Function of Modified Nucleosides in Bacterial Transfer RNA
Björk, G. R. (1995) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60817-x · Cited by 105
Self-citationFunctional Evidence for Indirect Recognition of G·U in tRNA Ala by Alanyl-tRNA Synthetase
Gabriel, K., Schneider, J., & McClain, W. H. (1996) · Science · doi:10.1126/science.271.5246.195 · Cited by 103
Studies of an isomer of uridine isolated from ribonucleic acids
Yu, C.-T., & Allen, F. W. (1959) · Biochimica et Biophysica Acta · doi:10.1016/0006-3002(59)90612-2 · Cited by 103
Ribosomal Frameshifting from -2 to +50 Nucleotides
Weiss, R. B., Dunn, D. M., Atkins, J. F., & Gesteland, R. F. (1990) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60626-1 · Cited by 101
A New Model for Phenotypic Suppression of Frameshift Mutations by Mutant tRNAs
Qian, Q., Li, J.-N., Zhao, H. G., Hagervall, T. G., Farabaugh, P. J., & Björk, G. R. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80048-9 · Cited by 101
Self-citationPersson, B. C., Gustafsson, C., Berg, D. E., & Björk, G. R. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.9.3995 · Cited by 100
Self-citationBiological function of 2-thiouridine in Escherichia coli glutamic acid transfer ribonucleic acid
Agris, P. F., Soell, D., & Seno, T. (1973) · Biochemistry · doi:10.1021/bi00746a005 · Cited by 100
Missense misreading of asparagine codons as a function of codon identity and context.
Precup, J. W., & Parker, J. (1987) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)60966-4 · Cited by 99
Tsui, H. C., Feng, G., & Winkler, M. E. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.19.5719-5731.1996 · Cited by 98
Campo, M. D., Kaya, Y., & Ofengand, J. (2001) · PubMed · Cited by 98
Senger, B., Auxilien, S., ENGLISCH, U., Cramer, F., & Fasiolo, F. (1997) · Biochemistry · doi:10.1021/bi970206l · Cited by 97
Lim, K., Zhang, H., Tempczyk, A., Krajewski, W. W., Bonander, N., Toedt, J. M., Howard, A. J., Eisenstein, E., & Herzberg, O. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10323 · Cited by 97
An extended structural signature for the tRNA anticodon loop
Auffinger, P., & Westhof, É. (2001) · RNA · doi:10.1017/s1355838201002382 · Cited by 96
Connolly, D. M., & Winkler, M. E. (1989) · Journal of Bacteriology · doi:10.1128/jb.171.6.3233-3246.1989 · Cited by 95
Bouadloun, F., Srichaiyo, T., Isaksson, L. A., & Björk, G. R. (1986) · Journal of Bacteriology · doi:10.1128/jb.166.3.1022-1027.1986 · Cited by 95
Self-citationSlany, R. K., Boesl, M., Crain, P. F., & Kersten, H. (1993) · Biochemistry · doi:10.1021/bi00081a028 · Cited by 94
Agris, P. F., Gracz, H. S., Smith, W. S., Małkiewicz, A. J., Sochacka, E., & Nawrot, B. (1992) · Journal of the American Chemical Society · doi:10.1021/ja00033a044 · Cited by 93
Petrullo, L. A., Gallagher, P. J., & Elseviers, D. (1983) · Molecular and General Genetics MGG · doi:10.1007/bf00330653 · Cited by 93
Cabello‐Villegas, J., Winkler, M. E., & Nikonowicz, E. P. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00382-0 · Cited by 92
Wittwer, A. J., Tsai, L., Ching, W. M., & Stadtman, T. C. (1984) · Biochemistry · doi:10.1021/bi00315a021 · Cited by 91
Weissenbach, J., & Grosjean, H. (1981) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1981.tb05320.x · Cited by 90
TRANSFER RNA INVOLVEMENT IN THE REGULATION OF ENZYME SYNTHESIS
Brenchley, J. E., & Williams, L. S. (1975) · Annual Review of Microbiology · doi:10.1146/annurev.mi.29.100175.001343 · Cited by 90
Adenosylmethionine as a source of 5′-deoxyadenosyl radicals
Fontecave, M., Mulliez, E., & de Choudens, S. O. (2001) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(00)00237-4 · Cited by 90
The effect of an Escherichia coli regulatory mutation on transfer RNA structure
Eisenberg, S. P., Yarus, M., & Soll, L. (1979) · Journal of Molecular Biology · doi:10.1016/0022-2836(79)90343-7 · Cited by 90
Specificity of yeast glutamic acid transfer RNA for codon recognition
Sekiya, T., Takeishi, K., & Ukita, T. (1969) · Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis · doi:10.1016/0005-2787(69)90192-0 · Cited by 90
Sullivan, M. A., Cannon, J. F., Webb, F. H., & Bock, R. M. (1985) · Journal of Bacteriology · doi:10.1128/jb.161.1.368-376.1985 · Cited by 89
Li, J.-N., Esberg, B., Curran, J. F., & Björk, G. R. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1176 · Cited by 89
Self-citationHarada, F., & Nishimura, S. (1974) · Biochemistry · doi:10.1021/bi00699a011 · Cited by 88
Davis, D. R., & Poulter, C. D. (1991) · Biochemistry · doi:10.1021/bi00231a017 · Cited by 88
Vi, L., & Curran, J. F. (2001) · RNA · doi:10.1017/s135583820100214x · Cited by 86
The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I.
Stroud, R. M., Foster, P., Huang, L., & Santi, D. V. (2000) · Nature Structural Biology · doi:10.1038/71219 · Cited by 85
Brierley, I., Meredith, M., Bloys, A. J., & Hagervall, T. G. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1134 · Cited by 83
Self-citationSchön, A., Böck, A., Ott, G., & Söll, D. G. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.18.7159 · Cited by 82
Nilsson, K. L., Lundgren, H. K., Hagervall, T. G., & Björk, G. R. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.24.6830-6835.2002 · Cited by 82
Self-citationEricson, J. U., & Björk, G. R. (1986) · Journal of Bacteriology · doi:10.1128/jb.166.3.1013-1021.1986 · Cited by 81
Self-citationIron mediated methylthiolation of tRNA as a regulator of operon expression inEscherichia coli
Buck, M., & Griffiths, E. (1982) · Nucleic Acids Research · doi:10.1093/nar/10.8.2609 · Cited by 80
The structure of the TrmE GTP‐binding protein and its implications for tRNA modification
Scrima, A., Vetter, I. R., Armengod, M. ‐., & Wittinghofer, A. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600507 · Cited by 80
Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA Phe
Stuart, J. W., Koshlap, K. M., Guenther, R. H., & Agris, P. F. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.09.058 · Cited by 80
Jäger, G., Leipuvienė, R., Pollard, M. G., Qian, Q., & Björk, G. R. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.3.750-757.2004 · Cited by 80
Self-citationLeung, H.-C. E., Chen, Y., & Winkler, M. E. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.20.13073 · Cited by 80
Connolly, D. M., & Winkler, M. E. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.5.1711-1721.1991 · Cited by 79
Hagervall, T. G., Pomerantz, S. C., & McCloskey, J. A. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2162 · Cited by 78
Self-citationAn iron-dependent modification of several transfer RNA species in Escherichia coli
Rosenberg, A. H., & Gefter, M. L. (1969) · Journal of Molecular Biology · doi:10.1016/0022-2836(69)90197-1 · Cited by 77
Gaál, T., Barkei, J. J., Dickson, R., deBoer, H. A., deHaseth, P. L., Alavi, H., & Gourse, R. L. (1989) · Journal of Bacteriology · doi:10.1128/jb.171.9.4852-4861.1989 · Cited by 75
Caillet, J., & Droogmans, L. (1988) · Journal of Bacteriology · doi:10.1128/jb.170.9.4147-4152.1988 · Cited by 75
Mutagenesis and growth delay induced in Escherichia coli by near-ultraviolet radiations
Favre, A., Hajnsdorf, E., Thiam, K., & de Araújo, A. C. (1985) · Biochimie · doi:10.1016/s0300-9084(85)80076-6 · Cited by 75
Stahl, G., McCarty, G., & Farabaugh, P. J. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02064-9 · Cited by 75
Physiological Effects of Near-Ultraviolet Radiation on Bacteria
Jagger, J. (1983) · Springer eBooks · doi:10.1007/978-1-4684-4505-3_1 · Cited by 75
Nonet, M. L., Marvel, C. C., & Tolan, D. R. (1987) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)45338-0 · Cited by 73
Grosjean, H., NICOGHOSIAN, K., Haumont, E., Söll, D. G., & Cedergren, R. (1985) · Nucleic Acids Research · doi:10.1093/nar/13.15.5697 · Cited by 73
Urbonavičius, J., Durand, J. M. B., & Björk, G. R. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.19.5348-5357.2002 · Cited by 73
Self-citationBognar, A. L., Osborne, C., & Shane, B. (1987) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)45358-6 · Cited by 72
Oda, K., Kimura, F., Harada, F., & Nishimura, S. (1969) · Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis · doi:10.1016/0005-2787(69)90125-7 · Cited by 72
An anticodon change switches the identity of E.coli tRNA mMet from methionine to threonine
Schulman, L. H., & Pelka, H. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.2.285 · Cited by 72
Vacher, J., Grosjean, H., Houssier, C., et al. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90460-1 · Cited by 72
Hagervall, T. G., Edmonds, C. G., McCloskey, J. A., & Björk, G. R. (1987) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)47440-6 · Cited by 70
Self-citationWilson, R. K., & Roe, B. A. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.2.409 · Cited by 70
Anantharaman, V., Koonin, E. V., & Aravind, L. (2001) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2001.tb10606.x · Cited by 70
Reflections on the Origin of the Genetic Code: a Hypothesis
Di Giulio, M. (1998) · Journal of Theoretical Biology · doi:10.1006/jtbi.1997.0580 · Cited by 69
Kawakami, K., Jönsson, Y. H., Björk, G. R., Ikeda, H., & Nakamura, Y. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.15.5620 · Cited by 67
Self-citationSCANNELL, J. P., Crestfield, A. M., & Allen, F. W. (1959) · Biochimica et Biophysica Acta · doi:10.1016/0006-3002(59)90613-4 · Cited by 67
Cited by
Extreme genome reduction in symbiotic bacteria
McCutcheon, J. P., & Moran, N. A. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2670 · Cited by 1,464
Zhong, S., Li, H., Bodi, Z., Button, J., Vespa, L., Herzog, M., & Fray, R. G. (2008) · The Plant Cell · doi:10.1105/tpc.108.058883 · Cited by 668
Summary: the modified nucleosides of RNA
Limbach, P. A., Crain, P. F., & McCloskey, J. A. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.12.2183 · Cited by 523
Tetracyclines: Antibiotic action, uptake, and resistance mechanisms
Schnappinger, D., & Hillen, W. (1996) · Archives of Microbiology · doi:10.1007/s002030050339 · Cited by 484
The RNA Modification Database: 1999 update
Rozenski, J., Crain, P. F., & McCloskey, J. A. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.196 · Cited by 389
Metadata
- Authors
- Björk, G. R., & Hagervall, T. G.
- Venue
- EcoSal Plus
- Publisher
- American Society for Microbiology
- Published
- 2005-01-12
- Volume
- 1
- Issue
- 2
- Pages
- 263-87
- ISSN
- 2324-6200 (ISSN-L)
- OpenAlex
- W1971559304
- Cited by
- 340
- References
- 283
- FWCI
- 4.38
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.