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Chapter 11 : Biosynthesis and Function of Modified Nucleosides

Author: Glenn R. Björk1
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Affiliations: 1: Department of Microbiology, Umea University, S-90187 Umea, Sweden
Content Type: Monograph
Publication Year: 1995

Category: Microbial Genetics and Molecular Biology

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Abstract:

Modified nucleosides, which are derivatives of the four normal nucleosides, adenosine (A), guanosine (G), cytidine (C), and uridine (U), were found in nucleic acids as early as 1948. Modified nucleosides are contained in tRNA from all three phylogenetic domains—Archaea, Bacteria, and Eucarya—which were formerly called the kingdoms of archaebacteria, eubacteria, and eukaryotes, respectively. Although modified nucleosides are found in various positions in the tRNA, two positions, 34 and 37, contain the largest variety of modified nucleosides. This chapter presents an overview of the coding properties associated with modified nucleosides present in positions 34 and 37. Outside the anticodon, the modified nucleosides are usually “simple” modifications like methylated or thiolated derivatives, whereas all except one (archaeosine in tRNAs from Archaea) of the hypermodified nucleosides are present in the anticodon region and only in positions 34 and 37. Moreover, outside the anticodon region, only one or two kinds of modified nucleosides in each position are present, whereas a large variety of modified nucleosides are present in the anticodon region, especially in positions 34 and 37. During evolution, structural refinements of the individual tRNAs were presumably fulfilled by the evolution of the synthesis of the various modified nucleosides, including the hypermodified nucleoside. Modified nucleosides in the anticodon region exert their functions primarily in the decoding process, whereas modified nucleosides outside this region may primarily be involved in other tRNA interactions, such as interactions with translation factors or as sensors for environmental stress conditions.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11

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Gene Expression and Regulation
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Biosynthesis and Function of Modified Nucleosides
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Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
/content/10.1128/9781555818333.chap11.fig11-1
Figure 1

Genetic organization of region (from reference with permission). FIS = possible FIS binding site; tRNA T-arm homology = a sequence with extensive similarity to the T-loop of tRNAs; AdoMet binding = AdoMet binding site; and catalytic nucleophile = the catalytic nucleophile Cys-324. Also shown are 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 sequence is found in reference .

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Figure 1

Genetic organization of region (from reference with permission). FIS = possible FIS binding site; tRNA T-arm homology = a sequence with extensive similarity to the T-loop of tRNAs; AdoMet binding = AdoMet binding site; and catalytic nucleophile = the catalytic nucleophile Cys-324. Also shown are 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 sequence is found in reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 2

Genetic organization of operon. Figures above the gene symbols indicate the number of protein molecules encoded from the respective genes per genome equivalents in cells grown at k = 1.0 hr. The Ω denotes a -independent terminator. In vitro, 60% to 70% of the transcript terminates at the first such structure ( ). Structures above the operon denote possible stem-loop structures that influence the translation of the and genes, respectively ( ). The sequence is found in reference .

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Figure 2

Genetic organization of operon. Figures above the gene symbols indicate the number of protein molecules encoded from the respective genes per genome equivalents in cells grown at k = 1.0 hr. The Ω denotes a -independent terminator. In vitro, 60% to 70% of the transcript terminates at the first such structure ( ). Structures above the operon denote possible stem-loop structures that influence the translation of the and genes, respectively ( ). The sequence is found in reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 3

Genetic organization of operon. Figures within the parentheses indicate the size of the protein encoded by the respective genes. Dyad symmetries and possible independent terminators are denoted as → ← and Ω, respectively. Transcriptions are shown by wavy lines and the transcription 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 ( ). It is presently unclear whether and are part of the operon ( ). However, a chromosomally encoded transcript covering the intracistronic region between and is present ( ). Furthermore, the -independent terminator present between and is not active ( ), suggesting that transcripts extend to the -independent terminator following the gene. The promoters P, P, and P were located on the chromosome ( ), whereas P was located on a plasmid ( ). The dedD gene seems to have its own promoter located within the gene ( ). The overlap of the asd stop codon with the start codon is also indicated, suggesting translational coupling of the expression of these two genes ( ). The sequence is found in references and .

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10.1128/9781555818333/fig11-3.gif
Image of Figure 3
Figure 3

Genetic organization of operon. Figures within the parentheses indicate the size of the protein encoded by the respective genes. Dyad symmetries and possible independent terminators are denoted as → ← and Ω, respectively. Transcriptions are shown by wavy lines and the transcription 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 ( ). It is presently unclear whether and are part of the operon ( ). However, a chromosomally encoded transcript covering the intracistronic region between and is present ( ). Furthermore, the -independent terminator present between and is not active ( ), suggesting that transcripts extend to the -independent terminator following the gene. The promoters P, P, and P were located on the chromosome ( ), whereas P was located on a plasmid ( ). The dedD gene seems to have its own promoter located within the gene ( ). The overlap of the asd stop codon with the start codon is also indicated, suggesting translational coupling of the expression of these two genes ( ). The sequence is found in references and .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 4

Genetic organization of operon. The sequence is found in reference . The location of the different promoters was established by H.-C. T. Tsui and M. Winkler ( ). Also shown is the region of translational overlap between the and genes and that translation terminates with UGA for both genes.

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10.1128/9781555818333/fig11-4.gif
Image of Figure 4
Figure 4

Genetic organization of operon. The sequence is found in reference . The location of the different promoters was established by H.-C. T. Tsui and M. Winkler ( ). Also shown is the region of translational overlap between the and genes and that translation terminates with UGA for both genes.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 5

Genetic organization of the operon ( ). The sequence is found in reference .

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10.1128/9781555818333/fig11-5.gif
Image of Figure 5
Figure 5

Genetic organization of the operon ( ). The sequence is found in reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 6

Structure of queuosine and its derivatives.

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Figure 6

Structure of queuosine and its derivatives.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 7

Presence of modified nucleosides in position 34 (wobble position). Data compiled from reference . To the left of the different modified nucleosides are bars indicating which codons the tRNA is able to read well (filled circles). An open circle denotes less preferred pairing to that codon. Underlined nucleosides are for tRNAs from . If not otherwise stated N is an uncharacterized modified nucleoside and U* indicates a modified U; V4 = cmnmU; V5 = cmnms2U; V8 = mcnmU; V9 =cmnmUm.

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Image of Figure 7
Figure 7

Presence of modified nucleosides in position 34 (wobble position). Data compiled from reference . To the left of the different modified nucleosides are bars indicating which codons the tRNA is able to read well (filled circles). An open circle denotes less preferred pairing to that codon. Underlined nucleosides are for tRNAs from . If not otherwise stated N is an uncharacterized modified nucleoside and U* indicates a modified U; V4 = cmnmU; V5 = cmnms2U; V8 = mcnmU; V9 =cmnmUm.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 8

Synthesis of msioA37 and mcmoU and the links to the synthesis of chorismic acid.

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Figure 8

Synthesis of msioA37 and mcmoU and the links to the synthesis of chorismic acid.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 9

Presence of modified nucleosides in position 37 (next to the 3-side of the anticodon) and the coding capacities of tRNAs. Note also that contains msioA instead of msiA in corresponding tRNAs (see Fig. 8 ) ( ). For explanation of symbols, see Fig. 1. Y1 (yW) = wybutosine; Y2 (oyW) = wybutoxosine; A4 = iA; A5 = msiA; Z = cis-zeatin or ioA; N for AAG codon is a modified A, probably a tA derivative.

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Image of Figure 9
Figure 9

Presence of modified nucleosides in position 37 (next to the 3-side of the anticodon) and the coding capacities of tRNAs. Note also that contains msioA instead of msiA in corresponding tRNAs (see Fig. 8 ) ( ). For explanation of symbols, see Fig. 1. Y1 (yW) = wybutosine; Y2 (oyW) = wybutoxosine; A4 = iA; A5 = msiA; Z = cis-zeatin or ioA; N for AAG codon is a modified A, probably a tA derivative.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 10

Enzymatic mechanism for the synthesis of mU54. The figure is modified from reference .

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Image of Figure 10
Figure 10

Enzymatic mechanism for the synthesis of mU54. The figure is modified from reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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