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Chapter 7 : Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction

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Abstract:

The anticodon stem loop of tRNA is one of the most remarkable hairpins in RNAs that present several modified nucleotides arising by posttranscriptional processes. Many different modifications have been identified at position 34. These modifications are considered to be important for the specificity, fidelity, and efficiency of the tRNA functions, mainly in decoding the genetic message during translation on the ribosome. This chapter summarizes the information available about the role of modified nucleotides present at positions 34 and 37 in modulating tRNA anticodon-anticodon interaction. Implications for codon-anticodon interaction and comparison with other types of RNA-RNA interacting systems are also discussed in this chapter. One way to evaluate the effect of modified nucleotides on the stability and dynamic properties of anticodon-anticodon complexes is the temperature-jump relaxation technique. The chapter describes two RNA loop-loop interacting systems that do not involve modified nucleotides. Their comparison with the loop-loop interacting systems involving hairpins of tRNA molecules described in this chapter are interesting to better understand how modified nucleotides can restrict the interaction to only a few selected nucleotides within the interacting RNA loops. Comparison to other types of loop-loop complexes involving RNAs other than tRNAs, the so-called "kissing" complexes, is also made. The main difference between these different types of loop-loop complexes is the extent of base pairing between the nucleotides of the interacting loops.

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7

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Figures

Image of Figure 1
Figure 1

Type and location of modified nucleotides in the anticodon stem and loop of tRNAs. The upper part is a schematic representation of the three-dimensional architecture of tRNA. Numbering of nucleotide positions are those universally adopted (see Appendix 5 by Auffinger and Westhof). The anticodon nucleotides corresponding to positions 34, 35, and 36 are shown as square boxes in the anticodon hairpin representation (lower part of the figure). Symbols for modified nucleotides are those defined in Appendix 1 by Motorin and Grosjean. The information is derived from the tRNA data bank of Sprinzl et al. (1996). Frequency of modified nucleotides at specific positions can be obtained from the compilation of and from the data in Appendix 5 by Auffinger and Westhof. Almost all of the hyper-modified nucleotides characterized so far occur exclusively in position 34 (the so-called wobble base) or in position 37 (3′-adjacent to the anticodon); see also Appendix 6 by Björk. Notice also that all positions of the anticodon hairpin (except positions 33, 42, and 43) are potential sites for modification, especially for pseudouridylation (Ψ).

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Figure 2

Schematic representation of complexes formed between two tRNAs having complementary anticodons. Only the nucleotides present in the 7-member anticodon loops are indicated. However, the invariant uridine-33, 5′-adjacent to the wobble base, is omitted for better clarity of the figure. Out of the 60 anticodon-anticodon complexes we have studied, only those having their 3 anticodon nucleotides engaged in canonical A•U, G•C or l•C Watson-Crick base pairs are represented (no mismatch base pairs). Symbols for modified nucleotides are defined in Appendix 1 by Motorin and Grosjean. U* at position 34 of tRNA designates a yet unidentified modified uridine (possibly a derivative of nmU or mnmU). Sequence information originates from the tRNA data bank of Sprinzl et al., 1998.

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Image of Figure 3
Figure 3

Comparison of complexes formed between complementary sequences in various polynucleotides, (a) Two triplets mimicking the anticodons of tRNA and tRNA. (b) Anticodon triplet corresponding to tRNA and its complementary sequence within an anticodon hairpin of yeast tRNA (harboring naturally occurring modified nucleotides). Only the anticodon loop and the proximal anticodon stem are represented, despite the fact that the experiments described in the text concern the entire yeast tRNAPhe, (c) The complementary sequences are both part of the anticodon loop of the entire tRNAs ( tRNA and yeast tRNA) (again only the anticodon loop and proximal anticodon stem are presented), (d) The interaction between a fragment of tRNA (10-mer) and fragment of yeast tRNA (12-mer) is shown, both fragments bearing their respective anticodon sequence. These fragments were obtained after purification of the RNase T hydrolysate of the corresponding tRNAs. Association constants were determined at ionic strength 0.1, 10 mM Mg at pH 6.8, by the T-jump relaxation technique. Symbols for modified nucleotides are those of Appendix 1 by Motorin and Grosjean. For more details see and .

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Image of Figure 4
Figure 4

Comparison of relaxation time constants (lifetimes) of different types of nucleic acid associations at 20°C. The left part of the figure shows data concerning duplex formation using synthetic oligoribonucleotides. They were kindly provided by D. Pörschke(MPI of Göttingen, Germany ). On the right part of the figure are the data concerning tRNA anticodon-anticodon complexes. Only a few selected examples are illustrated on this figure: the complete set of tRNA pairs are given in Fig. 2 ; see also Grosjean et al., 1978; Vacher et al., 1984; Houssier and Grosjean, 1985; and Romby et al., 1985). The time scale is logarithmic. Relaxation time constants of the bimolecular reactions are given at zero concentration and correspond to the reverse of the kinetic rate constants of the dissociation of the complexes.

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Image of Figure 5
Figure 5

Schematic representation of complexes formed between two tRNAs having complementary anticodons. In boxes are the nucleotides for which the effect of alteration of the chemical structure or substitution by another nucleotide have been measured (see Table 1 ). Only the nucleotides present in positions 34–38 of the anticodon loops are indicated. W* stands for wobble base-34; R* stands for purine 37; all other symbols for modified nucleotides are as in Appendix 1 by Motorin and Grosjean. The different tRNA pairs are as follows, (a) tRNA (wild type or chemically treated to oxidize the thiol group in mnmsU, ) and yeast tRNA (wild type or chemically treated under acidic conditions to remove the Wye base; ). (b) tRNA (wild type) and tRNA or tRNA (both wild type; ). (c) tRNA (wild type) and tRNA (wild type or the mutant lacking the msi group on A; ). (d) tRNA (wild type) and tRNA or yeast tRNA (both wild type; ). (e) tRNA (wild type) and yeast tRNA (species I and II). Both species were purified from the same yeast strain; species II was shown to lack the t group on A ( ). Notice that in this example, a G•U wobble occurs within the anticodon-anticodon complex, (f) tRNA (wild type) and tRNA or yeast tRNA (both wild type; ). Here, two parameters vary (G and mG in the yeast tRNA versus Q and mA in the tRNA). Therefore, the data obtained with this tRNA pair cannot be interpreted solely on the basis of one nucleotide difference, as in all of the other cases above. The T-jump relaxation technique was used to compare the relative stability of the different tRNA pairs (wild types and mutants; see Table 1 ).

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Figure 6

Correlation between the relative order of the stacking energy of base pairs (a) and the presence of modified bases located at position 37 of the anticodon loop of tRNA (b). (a) Classification of the 10 possible Watson-Crick base paired nearest-neighbor sequences (notice that GG•CC and CC•GG as well as UU•AA and AA•UU are identical) according to measured thermodynamic parameters taken from Borer et al., 1974, and largely confirmed later ( ). (b) Correlation between the nucleotide at position 36 of anticodon in tRNA (cardinal nucleotide; ) and the type of modified nucleotide found at position 37 of tRNA from different origins. Î’, E, and A in parentheses stand for eubacteria, eukaryotes, and archaea, respectively; , mitochondria, and chloroplasts have been excluded from the compilation. Symbols for modified nucleotides are those defined in Appendix 1 by Motorin and Grosjean. The most frequent modified nucleotides are doubly underlined. Ν stands for any nucleotide. For more detailed information see Appendix 6 by Björk or Sprinzl et al., 1998.

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Figure 7

Structural model for the tRNA anticodon-anticodon interaction. The case of duplex formation with yeast tRNA is illustrated because the crystal structure of this duplex at a 3-Å resolution is known ( ). (A) Nucleotide sequences of the interacting anticodon hairpins; (B) stereo view of the interacting anticodon loops of yeast tRNA (only the segment from Ψ to A is shown). In this complex, the three bases of the anticodon stack in a helical conformation (Α-form) with the purine 37 and the pyrimidine 38 on their 3′ side. The two pyrimidines on the 5′ side of the loop are stacked together but separated from the other stacked bases by a short bend. The two-fold rotational axis is perpendicular to this paper, through the bond joining the two middle bases of the anticodon (here a U•U mismatch). The double helix composed of the three anticodon base pairs is sandwiched (coaxially stacked) into an almost continuous double helix (Α-form) which includes the anticodon stems of both tRNAs. The extensive stacking interactions generated in this structure explain the stabilizing effects of the anticodon stems and of the modified purine (often hypermodified residues) 3′-adjacent to the anticodon ending with A or U (see Fig. 6 ). The crystal structure (as discussed in ) fully confirmed the earlier model proposed by .

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Image of Figure 9
Figure 9

Structural model for the loop-loop interaction formed by two complementary hairpin loops (in fact, an “inverted” loop) found in the antisense RNA-I transcript and its target site (mRNA-II) in the ColE1 plasmid. (A) Nucleotide sequences of the interacting hairpins. (B) Corresponding schematic model as proposed by . The phosphodiester backbone of the RNA-RNA complex is shown as a shaded ribbon (Α-form RNA helix). The seven base pairs of the loop and of the proximal stems are indicated by crossed rods. This complex has also a dyad axis of symmetry located perpendicular to the paper, through the bond joining the pairing central bases of the seven-member loop (here a C•G). Determinants of the instability of such RNA hairpin loop-loop complexes have been extensively studied by and . More detailed model building shows that the helix bends to accommodate the full complementarity of the seven base pairs within the loop ( ). Such bending is further stabilized by protein (see text). (C) Secondary structure of the anticodon domain of tRNA (isoacceptors 1 and 3). The chemical structure of the modified nucleotide (A*) at position 37 of tRNA is not known but could be a derivative of tA.

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Figure 8

Modulation of codon-anticodon binding. The anticodon hairpin in tRNAs is schematically represented. Ζ stands for any nucleotide in the anticodon loop or in the proximal anticodon stem, R stands for purine 37 located 3′-adjacent to the anticodon, and W stands for the anticodon wobble base 34. Asterisks show positions where the bases or the ribose are most frequently modified (see Fig. 1 ). (a and b) Modulation of the strength of binding occurs by the loop constraint. Here the nature of the bases (Z) in the proximal anticodon stem and loop plays a role in the flexibility and hence the preferential conformation adopted by the anticodon when it binds to a complementary codon (conformational switches). The 3′-stacked conformation is schematically represented in panel b because it is the predominant conformation in solution ( ; and ) and the only conformation in the crystal (discussed in ). However, major contributions of the “ribosomal milieu” as well as of divalent cations have also to be taken into account, (c) Modulation occurs by the immediate context of the codon-anticodon pairing. Here the purine (R) 3′-adjacent to the anticodon (and possibly the base 3′-adjacent to the codon) plays a role in the stabilization of the base pair between the third anticodon base and the first codon base ( ). Certain modified bases such as tA, msiA and Y base (designated by the symbol R*) are particularly important because of their stacking potential (this chapter), (d) Modulation occurs by the so-called wobble base (W). Here the strength of the binding depends on the possibility of forming a stable Watson-Crick type base pair rather than a less stable “mismatched” pair (modulation by third codon choice). It also depends on the stabilizing effect (stacking) of the wobble base (modified or not) on the strength of pairing in the middle position of the codon-anticodon complex.

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7
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Tables

Generic image for table
Table 1

Thermodynamic and kinetic parameters of selected tRNA anticodon-anticodon complexes, as determined by the temperature-jump relaxation technique

Citation: Grosjean H, Houssier C, Romby P, Marquet R. 1998. Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction, p 113-133. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch7

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