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Core flexibility of a truncated metazoan mitochondrial tRNA.

Frazer-Abel AA, Hagerman PJ - Nucleic Acids Res. (2008)

Bottom Line: Thus, the absence of canonical TpsiC-D interactions likely results in greater dispersion of anticodon-acceptor interstem angle than for canonical tRNAs.To test this hypothesis, we have assessed the dispersion of the anticodon-acceptor angle for bovine mtRNA(Ser)(AGY), which lacks the canonical D arm and is thus incapable of forming stabilizing interarm interactions.These results suggest that increased flexibility, in addition to a more open interstem angle, would allow both noncanonical and canonical mtRNAs to utilize the same protein synthetic apparatus.

View Article: PubMed Central - PubMed

Affiliation: National Jewish Health, Denver, CO 80206, USA.

ABSTRACT
Secondary and tertiary structures of tRNAs are remarkably preserved from bacteria to humans, the notable exception being the mitochondrial (m) tRNAs of metazoans, which often deviate substantially from the canonical cloverleaf (secondary) or 'L'-shaped (tertiary) structure. Many metazoan mtRNAs lack either the TpsiC (T) or dihydrouridine (D) loops of the canonical cloverleaf, which are known to confer structural rigidity to the folded structure. Thus, the absence of canonical TpsiC-D interactions likely results in greater dispersion of anticodon-acceptor interstem angle than for canonical tRNAs. To test this hypothesis, we have assessed the dispersion of the anticodon-acceptor angle for bovine mtRNA(Ser)(AGY), which lacks the canonical D arm and is thus incapable of forming stabilizing interarm interactions. Using the method of transient electric birefringence (TEB), and by changing the helical torsion angle between a core mtRNA bend and a second bend of known angle/rigidity, we have demonstrated that the core of mtRNA(Ser)(AGY) has substantially greater flexibility than its well-characterized canonical counterpart, yeast cytoplasmic tRNA(Phe). These results suggest that increased flexibility, in addition to a more open interstem angle, would allow both noncanonical and canonical mtRNAs to utilize the same protein synthetic apparatus.

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Related in: MedlinePlus

Plots τ ratios as a function of the number of phasing base pairs for the bovine mtRNASer(AGY) constructs. Filled circles represent the experimental data. The curve is generated using model values for bend angles (Table 5) with no additional flexibility relative to standard RNA helix (P = 700 Å, C = 3 × 10−19 erg cm). (Insets) Computed curves (solid lines) used to model the experimental data for the two-bend tRNA constructs (circles). Parameters used: (no magnesium) true minimum free energy interstem angle 130°, P = 340 Å, C = 0.06 × 10−19 erg cm; (2 mM magnesium) minimum free energy interstem angle 150°; P = 230 Å, C = 3 × 10−19 erg cm. All theoretical values used were in agreement with the apparent angle measured in the single-bend studies (Table 5).
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Figure 6: Plots τ ratios as a function of the number of phasing base pairs for the bovine mtRNASer(AGY) constructs. Filled circles represent the experimental data. The curve is generated using model values for bend angles (Table 5) with no additional flexibility relative to standard RNA helix (P = 700 Å, C = 3 × 10−19 erg cm). (Insets) Computed curves (solid lines) used to model the experimental data for the two-bend tRNA constructs (circles). Parameters used: (no magnesium) true minimum free energy interstem angle 130°, P = 340 Å, C = 0.06 × 10−19 erg cm; (2 mM magnesium) minimum free energy interstem angle 150°; P = 230 Å, C = 3 × 10−19 erg cm. All theoretical values used were in agreement with the apparent angle measured in the single-bend studies (Table 5).

Mentions: TEB decay (τ ratio) data for the set of noncanonical bovine mtRNASer(AGY) constructs demonstrate only weak phase dependence, indicating that the non-canonical tRNA is flexible (Figure 6). For the canonical yeast tRNAPhe, similar measurements showed a greater than twofold difference between the minimum and maximum τ ratio values in the presence of millimolar quantities of magnesium (6), as predicted for a tRNA core that is as rigid as an equivalent span of duplex RNA helix. For the highly truncated bovine mtRNASer(AGY), there was only a 0.6-fold difference, consistent with a substantially flexible mtRNA core.Figure 6.


Core flexibility of a truncated metazoan mitochondrial tRNA.

Frazer-Abel AA, Hagerman PJ - Nucleic Acids Res. (2008)

Plots τ ratios as a function of the number of phasing base pairs for the bovine mtRNASer(AGY) constructs. Filled circles represent the experimental data. The curve is generated using model values for bend angles (Table 5) with no additional flexibility relative to standard RNA helix (P = 700 Å, C = 3 × 10−19 erg cm). (Insets) Computed curves (solid lines) used to model the experimental data for the two-bend tRNA constructs (circles). Parameters used: (no magnesium) true minimum free energy interstem angle 130°, P = 340 Å, C = 0.06 × 10−19 erg cm; (2 mM magnesium) minimum free energy interstem angle 150°; P = 230 Å, C = 3 × 10−19 erg cm. All theoretical values used were in agreement with the apparent angle measured in the single-bend studies (Table 5).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553581&req=5

Figure 6: Plots τ ratios as a function of the number of phasing base pairs for the bovine mtRNASer(AGY) constructs. Filled circles represent the experimental data. The curve is generated using model values for bend angles (Table 5) with no additional flexibility relative to standard RNA helix (P = 700 Å, C = 3 × 10−19 erg cm). (Insets) Computed curves (solid lines) used to model the experimental data for the two-bend tRNA constructs (circles). Parameters used: (no magnesium) true minimum free energy interstem angle 130°, P = 340 Å, C = 0.06 × 10−19 erg cm; (2 mM magnesium) minimum free energy interstem angle 150°; P = 230 Å, C = 3 × 10−19 erg cm. All theoretical values used were in agreement with the apparent angle measured in the single-bend studies (Table 5).
Mentions: TEB decay (τ ratio) data for the set of noncanonical bovine mtRNASer(AGY) constructs demonstrate only weak phase dependence, indicating that the non-canonical tRNA is flexible (Figure 6). For the canonical yeast tRNAPhe, similar measurements showed a greater than twofold difference between the minimum and maximum τ ratio values in the presence of millimolar quantities of magnesium (6), as predicted for a tRNA core that is as rigid as an equivalent span of duplex RNA helix. For the highly truncated bovine mtRNASer(AGY), there was only a 0.6-fold difference, consistent with a substantially flexible mtRNA core.Figure 6.

Bottom Line: Thus, the absence of canonical TpsiC-D interactions likely results in greater dispersion of anticodon-acceptor interstem angle than for canonical tRNAs.To test this hypothesis, we have assessed the dispersion of the anticodon-acceptor angle for bovine mtRNA(Ser)(AGY), which lacks the canonical D arm and is thus incapable of forming stabilizing interarm interactions.These results suggest that increased flexibility, in addition to a more open interstem angle, would allow both noncanonical and canonical mtRNAs to utilize the same protein synthetic apparatus.

View Article: PubMed Central - PubMed

Affiliation: National Jewish Health, Denver, CO 80206, USA.

ABSTRACT
Secondary and tertiary structures of tRNAs are remarkably preserved from bacteria to humans, the notable exception being the mitochondrial (m) tRNAs of metazoans, which often deviate substantially from the canonical cloverleaf (secondary) or 'L'-shaped (tertiary) structure. Many metazoan mtRNAs lack either the TpsiC (T) or dihydrouridine (D) loops of the canonical cloverleaf, which are known to confer structural rigidity to the folded structure. Thus, the absence of canonical TpsiC-D interactions likely results in greater dispersion of anticodon-acceptor interstem angle than for canonical tRNAs. To test this hypothesis, we have assessed the dispersion of the anticodon-acceptor angle for bovine mtRNA(Ser)(AGY), which lacks the canonical D arm and is thus incapable of forming stabilizing interarm interactions. Using the method of transient electric birefringence (TEB), and by changing the helical torsion angle between a core mtRNA bend and a second bend of known angle/rigidity, we have demonstrated that the core of mtRNA(Ser)(AGY) has substantially greater flexibility than its well-characterized canonical counterpart, yeast cytoplasmic tRNA(Phe). These results suggest that increased flexibility, in addition to a more open interstem angle, would allow both noncanonical and canonical mtRNAs to utilize the same protein synthetic apparatus.

Show MeSH
Related in: MedlinePlus