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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

Transfer RNA Modification

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • Authors: Glenn R. Björk1, and Tord G. Hagervall2
  • Editor: Susan T. Lovett3
    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 [email protected]
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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
Aromatic Amino Acids
Amino Acid Addition
Integral Membrane Proteins

Article Version

An updated version has been published for this content:
Transfer RNA Modification: Presence, Synthesis, and Function


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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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Figure 1

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
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Figure 4

Possible ρ-independent terminators are denoted as Ω. Transcription is shown by wavy lines and its pattern is only tentative, since none of the transcripts has been shown to exist in vivo. The pattern is deduced from S1 mapping of a few areas of the operon, primer extension analysis and analysis of polarity ( 58 , 57 , 59 ). The overlap of the stop codon with the start codon is also shown, suggesting translational coupling of the expression of these two genes ( 65 ).

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 5

“FIS,” “tRNA T-arm homology,” “AdoMet binding,” and “Catalytic cysteine” denote positions of a possible FIS-binding site, a sequence with extensive identity to the TΨC loop of tRNAs, the AdoMet-binding site, and the catalytic nucleophile Cys324, respectively. Also shown is the similarity between the P and the P1 promoter of genes and the transcriptional terminator (T) shared with the gene. The gene is the structural gene for the vitamin B receptor. The figure is modified from reference 77 .

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 6

Figures below the gene symbols indicate the number of protein molecules encoded from the respective genes per genome equivalent in cells grown at = 1.0 hr. Ω denotes a ρ-independent terminator. At the first of these 60 to 70% of the transcripts terminate in vitro ( 61 ). Structures above the operon show possible stem-loop structures that might influence the translation of the and genes, respectively ( 81 ).

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 7

Shown is the region of translational overlap between the and genes and that translation of both mRNAs terminates with UGA.

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 8

( 123 ). The enzymatic reaction proceeds in the following steps: (i) the SH group of Cys324 of the enzyme reacts with the 6-carbon of U54 of tRNA to produce a nucleophilic centre at the 5-carbon of U54 (enol or enolate; compound II); (ii) a methyl transfer from AdoMet to the 5-carbon of U54 (compound III); (iii) a β-elimination produces mU54 and free enzyme (compound IV). The proton exchange in the absence of AdoMet requires formation of compound IIa, which can be formed by tautomerization of intermediate II. Compound IIa has also been trapped as covalently bound to FUra-tRNA in the absence of AdoMet and has an apparent MW of 63,000 similar to the intermediate (II) formed in the presence of AdoMet and FUra-tRNA. Furthermore, the methyl group is directly displaced from AdoMet by the C5 of U54 and not by a double displacement reaction whereby the methyl group is first transferred to a nucleophile on the enzyme and then to U54. The figure is modified from reference 117 .

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 9

Following the action of IscS, the flow occurs either in an [Fe-S] cluster-independent way (sU8 and mnmsU34) or in a pathway that is dependent on [Fe-S] cluster proteins (sC32 and msioA37). The figure is modified from reference 47 .

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 10

In both panels A and B the U in tRNA is shown after the activation by ATP to form the activated AMP-U derivative. (A) The persulfide group on Cys456 of ThiI attacks the activated U, the AMP is released, a reductant (here shown as dithiothreitol) reduces the persulfide formed between ThiI and U resulting in sU and ThiI containing a disulfide bond between Cys456 and Cys344. Following reduction and sulfur transfer from IscS the ThiI is ready for a new catalytic cycle. (B) Disulfide bond formation between Cys456 and Cys344 of ThiI generates hydrogen sulfide, which attacks the activated U. The figure is modified from reference 150 .

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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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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Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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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 11

The dashed reaction arrows indicate the link between the synthesis of cmoU and chorismic acid. The arrow denoted A is according to Hagervall et al. ( 213 ), and the arrows denoted B and C are the suggested link between chorismic acid and the synthesis of cmoU34 according to Näsvall et al. ( 214 ). X? indicates a possible unknown derivative of chorismic acid.

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 12

The gene products QueC, D, and E, participate prior to the formation of Que and QueF prior to Que ( 48 , 224 ). The glutamylqueosine (GluQ) contains a Glu attached to Q, but the hydroxyl group of the cyclopentene diol to which the Glu is attached has not been established.

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Figure 13

(A) A hypomodified tRNA is defective in the aa-tRNA selection step, thereby allowing a wild-type near-cognate tRNA to be accepted instead in the A site. After a three-nucleotide translocation, the near-cognate tRNA slips into the +1 frame provided that there is a pause before the next tRNA enters the A site. (B) The hypomodified cognate tRNA is slow in entering the A site and thereby inducing a pause that allows the wild-type cognate peptidyl-tRNA to slip into the +1 frame. (C) The hypomodified cognate aa-tRNA is accepted in the A site as fast as the wild-type counterpart and after a normal three-nucleotide translocation, the hypomodification of the peptidyl-tRNA induces a slip into the +1 frame. For clarity only one or two tRNAs is depicted on the ribosome, although two tRNAs are always present in either A and P sites or P and E sites.

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Table 1

Genes influencing modifications in positions 8 to 32 in tRNA of and serovar Typhimurium

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

Genes influencing modifications in position 34 in tRNA of and serovar Typhimurium

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

Genes influencing modifications in position 37 (next to and 3′ of the anticodon) in tRNA of and serovar Typhimurium

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Table 4

Genes influencing modifications in positions 38 to 65 in tRNA of and serovar Typhimurium

Citation: Björk G, Hagervall T. 2005. Transfer RNA Modification, EcoSal Plus 2005; doi:10.1128/ecosalplus.4.6.2
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Table 5

Suggested wobble rules 1966 to 2004

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

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