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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

Transfer RNA Modification

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  • Authors: Glenn R. Björk1, and Tord G. Hagervall2
  • Editor: Susan T. Lovett3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Molecular Biology, Umeå University, S-90187 Umeå University, Sweden; 2: Department of Molecular Biology, Umeå University, S-90187 Umeå University, Sweden; 3: Brandeis University, Waltham, MA
  • Received 02 December 2004 Accepted 18 February 2005 Published 25 July 2005
  • Address correspondence to Glenn R. Björk glenn.bjork@molbiol.umu.se
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  • Abstract:

    Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from 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-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, tA, 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.

  • Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2

Key Concept Ranking

Gene Expression and Regulation
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Aromatic Amino Acids
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Amino Acid Addition
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Integral Membrane Proteins
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An updated version has been published for this content:
Transfer RNA Modification: Presence, Synthesis, and Function

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/content/journal/ecosalplus/10.1128/ecosalplus.4.6.2
2005-07-25
2017-11-23

Abstract:

Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from 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-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, tA, 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.

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Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 2

Data compiled from reference 17 . Yellow positions are those at which modified nucleosides are present. Numbers within parentheses show the number of tRNA species having the indicated modified nucleoside and if found in only one tRNA the amino acid specificity of that tRNA is also shown (one-letter code; Sec denotes selenocysteine). The underlined modified nucleoside msioA is found in tRNA from serovar Typhimurium but not tRNA from ; (c)mnmsU denotes either cmnmsU or mnmsU.

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 3

Letters outside the box, to the left, above and to the right indicate the first, second, and third position of the codon. Circles connected by a line, or a single circle, represent one tRNA species. A filled circle indicates the capability of that tRNA to base pair with a particular codon, either by Watson-Crick or by wobble according to the revised wobble hypothesis (Table 5 ). Red and yellow circles indicate tRNAs that are sequenced at the RNA level while green circles represent tRNAs for which only the DNA sequence is known. These appear dark, light, and medium grey, respectively, when printed in black-and-white. A red or green circle indicates efficient base pairing while a yellow circle indicates a restricted wobble. An open (white) circle suggests base pairing that is not allowed according to the rules above. However, data in vivo from mutants where only this tRNA is left to decode all codons in the codon box, suggest that the tRNA in fact is able to read that codon. To the right of each tRNA the modification pattern in positions 32, 34, 37, and 38–40 is shown. Positions 32 and 38–40 are listed only when a modified base is present. Data are compiled from reference 17 . (a) This tRNA has been shown to have cmnmUm in position 34 ( 36 ). (b) Although this tRNA is not sequenced it contains Cm in position 34 ( 36 ). (c) The three tRNAs which read codons starting with C have an unidentified G in position 37. However, mutations in the gene, the structural gene for tRNA(mG)methyltransferase, affect the chromatographic properties of these three tRNA species (K. J. Hjalmarsson [] and P. M. Wikström [serovar Typhimurium], unpublished results). Therefore, the modified G is most likely mG, alternatively a derivative of mG. (d) The methylester of cmoU, mcmoU, is base labile and will thus be converted to cmoU during most of the analyses of modified nucleosides. If so, this may be an example of tRNA editing in . (f) Sroga et al. ( 37 ) has revised the sequence of this tRNA compared with However, tRNA and tRNA but not tRNA are substrates for the tRNA(mcmoU)methyltranseferase ( 38 ), suggesting that at least some of the tRNAs specific for serine and alanine may normally have mcmoU. (e) Two tRNA (species I and V) differ only in position 20 in the D loop; Ser I has a C in position 20 whereas Ser V has D ( 39 ). Only one gene codes for these tRNAs and the DNA sequence agrees with C20 in the tRNA, suggesting a certain degree of deamination of C20 to U20, which may then be modified to D20. the sequence in the Sprinzl data base ( 17 ). (g) Transfer RNA from has moU ( 17 ). Because this G organism has moU in the tRNAs where has cmoU, cmoU is predicted to be present in the nonsequenced tRNA. (h) The nonsequenced tRNA and tRNA (CCU) are predicted to contain tA since all tRNA-reading codons starting with A have tA although initiator tRNA contains A37. (i) Analysis of purified tRNA has tentatively shown that this tRNA contains mainly cmnmsU but also mnmsU (G. R. Björk and P. Chen, unpublished results). (j) Because the GluQ in tRNA is alkaline labile, this tRNA population may contain both Q and GluQ and the proportion of it may depend on the physiology of the bacteria. (k) The majority of this tRNA contains mnmU34 but there is also a small amount of cmnmU34 (T. Suzuki, Tokyo, personal communication).

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2