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Chapter 8 : Primary, Secondary, and Tertiary Structures of tRNAs

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Abstract:

This chapter talks about primary, secondary, and tertiary structures of tRNAs. What is striking about the tRNA molecule is its extreme variability in primary and secondary structures. Every single invariant or semi-invariant position has numerous exceptions depending on the origin of the cell from which the tRNA is extracted. Several elements of the classical cloverleaf structure can altogether disappear, evidently as long as the amino acid and anticodon parts are maintained. Thus, the variable region, the D-arm, and the T-arm can be missing or severely amputated without apparent disfunctionality of the tRNA. This diversity at the sequence and 2D-structure levels must clearly manifest fest itself at the 3D-structure level also. This is discernible in some crystal structures and, especially, in recently modelled structures, although in the latter case one cannot reach the same degree of confidence. Nature has tinkered around every tertiary interaction responsible for maintaining the famous L-structure of tRNAs. The tRNA-like structures found at the 3' end of viral RNAs display some of the most extreme cases of divergence from canonical tRNA structure.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8

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Murine leukemia virus
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Figures

Image of Figure 1a
Figure 1a

Cloverleaf structure of tRNA with numbering of nucleotides according to Sprinzl et al. (176) and localization of most modified nucleotides as well as number of tRNAs (in parentheses) where these modified nucleotides have been found. The relationship of symbols to abbreviations and names commonly used is given in Fig. 1b .

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 1b
Figure 1b

Cloverleaf structure of tRNA with numbering of nucleotides according to Sprinzl et al. (176) and localization of most modified nucleotides as well as number of tRNAs (in parentheses) where these modified nucleotides have been found. The relationship of symbols to abbreviations and names commonly used is given below.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 2
Figure 2

Classical cloverleaf structure with numbering of nucleotides.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 3
Figure 3

Structure of Schizosaccharomyces pombe mit tRNA (deduced from gene).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 4
Figure 4

(A) and (B) tRNAs deduced from genes.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 5
Figure 5

Variant of classical -Levitt pair.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 6
Figure 6

Nematode mit tRNA genes shown in presumed secondary structural form of corresponding tRNAs. A: tRNA from corrected according to reference 142, with a TV replacement loop. B: tRNA from Caenorhabditis elegans with a D replacement loop. C: tRNA from .

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 7
Figure 7

Cloverleaf structures of animal mit tRNA and tRNA . Nucleotide sequences of the tRNAs from bovine and mosquito were determined at the RNA level, and those from other animals are deduced from their DNA sequences ( ).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 8a
Figure 8a

Representation of all possible interactions between bases involving at least two H bonds. Some of the non-Watson-Crick interactions (b, c, g, k, 1, m, q, and r) were mentioned by Donohue as early as 1956 ( ). Interactions involving N3 of purines are not considered. A curved arrow on a covalent bond means that a symmetric configuration obtained by a 180° rotation around this bond must be considered. This simplification has not been used in the particular cases of the Watson-Crick (a and b) and Hoogsteen (e and f) pairing between A and U. It should be kept in mind that this figure is only schematic and is not intended to be exact regarding the angles of H bonds. Also, some of these interactions (e.g., s and t) are illustrated for completeness and may not ever be observed in real structures.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 8b
Figure 8b

Representation of all possible interactions between bases involving at least two H bonds. Some of the non-Watson-Crick interactions (b, c, g, k, 1, m, q, and r) were mentioned by Donohue as early as 1956 ( ). Interactions involving N3 of purines are not considered. A curved arrow on a covalent bond means that a symmetric configuration obtained by a 180° rotation around this bond must be considered. This simplification has not been used in the particular cases of the Watson-Crick (a and b) and Hoogsteen (e and f) pairing between A and U. It should be kept in mind that this figure is only schematic and is not intended to be exact regarding the angles of H bonds. Also, some of these interactions (e.g., s and t) are illustrated for completeness and may not ever be observed in real structures.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 9
Figure 9

Stereoviews for the comparison of interaction between T•C and D loops for elongator tRNAs (A) an eukaryotic initiator tRNAs (B).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 10
Figure 10

Stereoviews for the comparison between anticodon loop (A) and TΨC loop (B). The residues that are excluded from the 3' end stacking in a TΨC loop (positions 59 and 60), as well as their counterpart in an anticodon loop (positions 37 and 38), are shown in heavy lines.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 11
Figure 11

Stereoview showing the possible structure of yeast initiator anticodon loop as derived from x-ray study ( ). It should be recalled that these authors did not draw any firm conclusion regarding the unusual structure of this loop because there was an important crystalline disorder (see text).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 12
Figure 12

Stereoviews illustrating the detailed molecular mechanism of the wobble as examined with option PUCK ( ) added in graphics program FRODO ( ). (A) The usual H bond between O2' (i) and O4' (i + 1) for the residues 34 and 35 (arrow) is absent because the distance between these two atoms is too great ( ). The lack of such an H bond allows the movement of residue 34 relative to the two other residues of the anticodon. The origin of this movement is analyzed in the next figure. (B) A crankshaft motion about the covalent bonds P-O5', O5'-C5', and C5'-C4' of residue 35 (thick bonds) can cause a dangling of residue 34, the first residue of the anticodon. This results in modification of the distance between it and the third residue of the codon. However, this distance tuning is accompanied by misorientation of the base of residue 34, which can be counterbalanced by modification of the phase of pseudorotation of its ribose. This results in a rotation of the base about an axis defined by O2'-O4' (thin segment and curved arrow), which is roughly parallel to the previous axis. The extreme positions of the bases shown in this figure result from a pseudorotation phase change between 0° and 40°. Finally, further tuning can be achieved through an analogous pseudorotation phase change for the last residue of the codon, which results in movement of its base in the plane, contrary to the previous movement out of the plane for residue 34 of the anticodon.

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 13
Figure 13

Stereoview showing the location of spermine molecule in major groove of acceptor stem of tRNAAsp ( ). The corresponding part of the Fourier difference map is shown and clearly reveals an elongated peak into which an elongated spermine molecule could be fitted. The two black spheres within the peak correspond to putative solvent molecules. In a Fourier difference map, the calculated electron density corresponding to the macromolecule (here the tRNA) has been subtracted from the total electron density. Such maps therefore allow the identification of solvent molecules (water, ions, spermine, etc.).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 14
Figure 14

Schematic drawing of tertiary interactions in core of class I tRNAs. Broken lines indicate nonstandard base pairing. Classically, residues 45 and 46 of the variable loop form triple interactions with base pairs 10-25 and 13-22 in the deep and narrow groove of the D helix. Residue 46 is intercalated between residues 9 and 21, while residue 9 is intercalated between residues 45 and 46. Two other triples occur: one between residue 9 and base pair 12-23 and another between residue 21 and the trans-Hoogsteen U8-A14 base pair. The trans-Watson-Crick pair between R15 and Y48, known as the Levitt pair, is shown at the top. Drawing from Dock-Bregeon et al. ( ).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 15
Figure 15

Schematic drawing for proposed tertiary interactions in core of class II tRNAs. Residue 45 interacts now with a residue in the variable helix and thus does not form a triple with base pair 12-23. Base pair 13-22 is unusual purine-purine pair. Drawing from Dock-Bregeon et al. ( ).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 16
Figure 16

Schematic drawing for proposed tertiary interactions in prokaryotic selenocysteine-inserting tRNASec. Again, residue 45 pairs to form the start of the variable helix, but residue 9 cannot form a triple with 12-23. There is now a U14-A21 Watson-Crick pair extending the D helix, as well as a 15-20a pair. Residue 8 interacts with the Hoogsteen sites of residue 21. An unusual pyrimidine-pyrimidine interaction is suggested between residues 16 and 59 of the D and T loops. Residue 48 presents only stacking interaction on this figure, although a tertiary pair with base pair 15-20a cannot be excluded. Drawing from Baron et al. ( ).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Image of Figure 17
Figure 17

Stereo view of model of selenocysteine-inserting tRNA as deduced from chemical and enzymatic mapping in solution (drawing after Sturchler et al. [ ]).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8
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Tables

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Table 1

Invariant and semi-invariant nucleotides in different organisms

Asterisks indicate one or two exceptions to the invariant and semi-invariant nucleotides. Exceptions are as follows. H. volcanii: position 15, A in Gly (UCC); position 16, A in Phe (GAA) and no nucleotide in Ala (GGC); position 21, U in lie (GAU); position 32, A in Pro (GGG); position 48, U in Gly (UCC); position 52, * in one Lys (UUU) and C in Tyr (GUA); position 59, G in Met (CAU); position 60, in Met (CAU). M. capripolum: position 10, C in Ser (GCU and UGA); position 11, A in Arg (ICG) and fMet (CAU); position 21, G in Leu (CAA, UAA, and UAG); position 22, U in Asp (GUC); position 24, U in Arg (ICG) and fMet (CAU); position 25, G in Ser (GCU and UGA); position 26, U in Gly (UCC) and Val (UAC). B. subtilis: position 11, G in Leu (CAG) and A in fMet (CAU); position 21, G in Leu (UAA, CAG and CAA); position 24, C in Leu (CAG) and U in fMet (CAU); position 26, U in Asn (GUU) and C in Gly (UCC); position 32, A in Leu (CAG) and in Thr (GGU); position 62, U in Gly (UCC) and Tyr GUA). E. coli: position 11, A in fMet (CAU); position 21, G in Leu (CAG, GAG, UAG, UAA, and CAA); position 24, U in fMet (CAU); position 26, C in Gly (UCC) and in His (GUG); position 32, A in Ala (GGC) and Pro (GGG); position 48, G in Cys (CGA). S. cerevisiae (mitochondria): position 8, A in Pro (UGG); position 10, U in His (GUG) and Tyr (GUA); position 11, A in Gin (UUG) and G in Gly (UCC); position 12, G in Leu (UAA) and Metj (CAU); position 14, U in Cys (GCA) and in Ser (GCU); position 18, A in Asp (GUC); position 24, U in Gin (UUG) and C in Gly (UCC); position 25, A in His (GUG) and Try (GUA); position 26, U in Cys (GCA) and no nucleotide in Ser (GCU); position 33, C in Glu (UUC); position 54, G in Asp (GUC). S. cerevisiae (cytoplasm): position 16, A in Pro (IGG); position 52, U in Phe (GAA) and C in Tyr (GUA); position 54, A in Met( (CAU); position 56, G in Metj (CAU); position 60, A in Metj (CAU); position 62, A in Phe (GAA) and Tyr (GUA). D. discoideum (mitochondria): position 10, A in Met (CAU); position 16, A in Ala (AGC) and G in Met (CAU); position 20, A in Arg (ACG and UCU); position 24, C in Leu (UAA); position 25, U in Trp (CCA) and Met CAU); position 26, U in Glu (UUC) and C in Gin (UUG); position 48, A in Ala (AGC); position 52, U in Thr (CGU); position 54, A in Arg (UCU) and Met (CAU); position 57, A in Trp (CCA); position 62, A in Thr (CGU). Plant (cytoplasm): position 15, U in Ala (UGC) from Arabidopsis thaliana; position 22, U in Val (AAC) from A. thaliana and Lupinus luteus and Pro (UGG) from Phaseolus vulgaris and Pro (AGG) from L. luteus; position 26, U in Pro (AGG) from L. luteus and Pro (UGG and AGG) from P. vulgaris; position 33, C in Meti (CAU); position 48, A in tRNAAla (UGC) from A. thaliana; position 54, A in Mets (CAU) from wheat germ, L. luteus, and P. vulgaris; position 57, C in mutant of Phe (GAA) from A. thaliana; position 60, A in Met; (CAU) from wheat germ, L. luteus, and P. vulgaris and Val (AAC) from A. thaliana and L. luteus. Mammals (cytoplasm): position 9, C in mouse His (GUC); position 10, A in mouse, bovine, and human HeLa cell Ser (UCA) and in bovine Ser (CCA); position 14, U in mouse and human HeLa cell Ser (UCA) and in bovine Ser (CCA); position 15, C in mouse and human HeLa cell Ser (UCA) and in bovine Ser (CCA); position 21, G in mouse and human HeLa cell Ser (UCA) and U in bovine Ser (NCA), C in bovine Ser (CCA), and U in bovine Ser (NCA); position 33, C in all animal Mets (CAU); position 48, G in mouse, bovine , and human HeLa cell Ser (UCA) and in bovine Ser (CCA); position 52, U in one out of four human Cys (GCA), U in bovine liver Trp (CUG); position 54, A in all animal Metj (CAU); position 57, U in one out of two human Metj (CAU); position 60, A in all Met; and in Val; position 61, U in 1 out of 4 human Cys (GCA).

Citation: Dirheimer G, Keith G, Dumas P, Westhof E. 1995. Primary, Secondary, and Tertiary Structures of tRNAs, p 93-126. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch8

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