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Chapter 17 : Small RNA Oligonucleotide Substrates for Specific Aminoacylations

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Abstract:

Transfer RNAs fold into a globular two-domain, L-shaped structure with the amino acid acceptor terminus and anticodon at opposite ends. This chapter reports nine examples of sequence-specific aminoacylation of RNA oligonucleotides based on tRNA acceptor stems with both class I and class II tRNA synthetases. The examples are class I aminoacyl-tRNA synthetases for Met, He, Gin, and Val and class II aminoacyl-tRNA synthetases for Ala, His, Asp, Ser, and Gly. In these examples, the aminoacylation activity for RNA oligonucleotide substrates is commonly greater for the class II enzymes. The exception is the class I He tRNA synthetase. This variation in activity may be due to the difference in the way the 3' end of tRNA interacts with the class I enzymes compared with the class II enzymes. The structures of the class I Gln-tRNA synthetase-tRNA complex and the class II Asp-tRNA synthetase-tRNA complex indicate that the binding of the 3' end of the tRNA is fundamentally different. For example, interactions between the minor groove of the acceptor stem of tRNAand Gln tRNA synthetase disrupt the first base pair of the tRNA and induce a hairpin turn of the 3' terminus toward the inside of the L-shaped tRNA. The relationship between the attached amino acids and the sequences of RNA oligonucleotide substrates constitute an operational RNA code for amino acids.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17

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Figures

Image of Figure 1
Figure 1

tRNA. (A) The secondary structure of tRNA is depicted on the left in the cloverleaf form. The right structure illustrates the tertiary folding of the tRNA. (B) The left hairpin helix represents a minihelix substrate, which is composed of the acceptor TΨC stem and TΨC loop. The right hairpin helix is a microhelix substrate comprised of the acceptor stem and TΨC loop.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 2
Figure 2

Minihelix RNA substrates. These RNA hairpin helix acceptor stem substrates are comprised of the acceptor-TΨC stem of the respective tRNA, closed by a TΨC (UUC) loop. Nucleotides in the shaded boxes are identity elements, and nucleotides that are simply boxed are minor identity elements. The + and − signs indicate, respectively, whether the indicated aminoacyl-tRNA synthetase could or could not charge the RNA substrate ( ). The ( + ) designation means that aminoacylation was detectable but at a rate at least 20-fold reduced relative to that in the wild-type sequence. All minihelices are derived from . tRNAs unless otherwise specified. (A) Minihelices tested for alanine acceptance. (B) Minihelices tested for alanine, histidine, methionine, and isoleucine acceptance. Ile refers to the major tRNA isoacceptor, which contains a GAU anticodon. (C) Minihelices tested for valine, serine, and aspartic acid acceptance. The first base or base pair of the minihelix substrates was changed to incorporate a G1 residue to enhance T7 transcription. This mutation did not affect the aminoacylation rates.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 3a
Figure 3a

Microhelix RNA substrates. These RNA hairpin helix acceptor stem substrates contain the acceptor stem of the respective tRNA, closed by a loop. Nucleotides in the shaded boxes are identity elements, and nucleotides that are simply boxed are minor identity elements. The + and − signs indicate, respectively, whether the indicated aminoacyl-tRNA synthetase could or could not charge the RNA substrate ( ). The ( + ) designation means that aminoacylation was detectable but at a rate at least 20-fold reduced relative to that in the wild-type sequence. All microhelices are derived from . tRNA unless otherwise specified. (A) and (B) Microhelices tested for alanine, histidine, glycine, methionine, and glutamine acceptance. (C) Microhelices tested for aspartic acid, glut amine, isoleucine, and serine acceptance. The first base pair of the microhelix substrate was changed to incorporate a G1 residue to enhance T7 transcription. This mutation did not affect the aminoacylation rates ( ). The serine and leucine microhelices are closed by a tetraloop (GAAA). When included, the subscript indicates the number of base pairs in the acceptor stem.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 3b
Figure 3b

Microhelix RNA substrates. These RNA hairpin helix acceptor stem substrates contain the acceptor stem of the respective tRNA, closed by a loop. Nucleotides in the shaded boxes are identity elements, and nucleotides that are simply boxed are minor identity elements. The + and − signs indicate, respectively, whether the indicated aminoacyl-tRNA synthetase could or could not charge the RNA substrate ( ). The ( + ) designation means that aminoacylation was detectable but at a rate at least 20-fold reduced relative to that in the wild-type sequence. All microhelices are derived from . tRNA unless otherwise specified. (A) and (B) Microhelices tested for alanine, histidine, glycine, methionine, and glutamine acceptance. (C) Microhelices tested for aspartic acid, glut amine, isoleucine, and serine acceptance. The first base pair of the microhelix substrate was changed to incorporate a G1 residue to enhance T7 transcription. This mutation did not affect the aminoacylation rates ( ). The serine and leucine microhelices are closed by a tetraloop (GAAA). When included, the subscript indicates the number of base pairs in the acceptor stem.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 4
Figure 4

Anticodon stem loops. These RNA hairpin helix anticodon stem loops of the indicated full-length tRNA were tested for stimulation of acceptor stem substrate aminoacylation rates and/or inhibition of the full-length tRNA charging ( ). The shaded and open boxes represent the anticodon trinucleotides and substituted bases, respectively. The five and six base pair fMet anticodon stem loops are distinguished by the subscripts 5 and 6, respectively.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 5a
Figure 5a

Duplex RNA substrates. Duplex RNA substrates are comprised of two complementary annealed single strands, which are based on the sequence of the acceptor stem and part of the TΨC stem. Unless otherwise specified, each substrate contains nine base pairs. When different from nine bases pairs, the alternative number of base pairs is indicated by a subscript. The + and −signs indicate, respectively, whether the indicated aminoacyl-tRNA synthetase could or could not charge the RNA substrate ( ). The ( + ) designation means that aminoacylation was detectable but at a rate at least 20-fold reduced relative to that in the wild-type sequence. (A) Duplex RNA substrates. Nucleotides in the shaded boxes are identity elements, and nucleotides that are simply boxed are minor identity elements. Ile refers to the minor isoacceptor of tRNA, which contains a lysidine-modified C34 residue in the anticodon ( ). The ? sign for duplex indicates that the alanine acceptance of the RNA substrate could not be determined because the melting temperature of the 4-bp annealed duplex was lower than the aminoacylation reaction temperature ( ). Inosine, deoxyinosine, and 2-aminopurine are abbreviated as I, dI, and 2-AP, respectively ( ). (B) Alanine duplex RNA substrates contain deoxyribose base substitutions ( ). Ribonucleotides and deoxyribonucleotides are abbreviated, respectively, as r and d, where appropriate. (C) Alanine duplex RNA substrates, which contain 2′-O-methyl base substitutions ( ). The open boxes indicate where the substitutions have been made. The 2′-O-methyl group is abbreviated as 2′-O-Me.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 5b
Figure 5b

Duplex RNA substrates. Duplex RNA substrates are comprised of two complementary annealed single strands, which are based on the sequence of the acceptor stem and part of the TΨC stem. Unless otherwise specified, each substrate contains nine base pairs. When different from nine bases pairs, the alternative number of base pairs is indicated by a subscript. The + and −signs indicate, respectively, whether the indicated aminoacyl-tRNA synthetase could or could not charge the RNA substrate ( ). The ( + ) designation means that aminoacylation was detectable but at a rate at least 20-fold reduced relative to that in the wild-type sequence. (A) Duplex RNA substrates. Nucleotides in the shaded boxes are identity elements, and nucleotides that are simply boxed are minor identity elements. Ile refers to the minor isoacceptor of tRNA, which contains a lysidine-modified C34 residue in the anticodon ( ). The ? sign for duplex indicates that the alanine acceptance of the RNA substrate could not be determined because the melting temperature of the 4-bp annealed duplex was lower than the aminoacylation reaction temperature ( ). Inosine, deoxyinosine, and 2-aminopurine are abbreviated as I, dI, and 2-AP, respectively ( ). (B) Alanine duplex RNA substrates contain deoxyribose base substitutions ( ). Ribonucleotides and deoxyribonucleotides are abbreviated, respectively, as r and d, where appropriate. (C) Alanine duplex RNA substrates, which contain 2′-O-methyl base substitutions ( ). The open boxes indicate where the substitutions have been made. The 2′-O-methyl group is abbreviated as 2′-O-Me.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 6
Figure 6

Chemical representation of first 4 bp of the acceptor stem of tRNA. The major determinant, the exocyclic 2-amino group of G3, is indicated by a box and an arrow. Other important identity determinants are highlighted by boxes ( ).

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 7
Figure 7

Tetraloop RNA substrates. These “minimalist substrates” for tRNA are composed of the first 3 to 6 bp of the acceptor stem, the discriminator base, and the CCA 3′ terminus. A tetraloop moiety is incorporated to close the substrate. Nucleotides in the shaded boxes are identity elements, and nucleotides that are simply boxed are minor identity elements ( ).

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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Image of Figure 8
Figure 8

Metazoan mitochondrial tRNAs. Some of the mitochondrial tRNAs contain deletions in the D stem loop, TΨC stem loop, and variable loop ( ). These molecules are naturally occurring contemporary examples that are the closest known in structure to RNA minihelices that are active for aminoacylation.

Citation: Martinis S, Schimmel P. 1995. Small RNA Oligonucleotide Substrates for Specific Aminoacylations, p 349-370. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch17
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