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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

Outline of the construction of double-bend tRNA–A5 bulge constructs. (A) Construction of the tRNA core and A5 bulge. The phasing bases are indicated as N. The additional extensions are indicated as (dotted line). (B) Schematic representation of the phase constructs for a rigid tRNA core, and (C) for a flexible tRNA core.
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Figure 3: Outline of the construction of double-bend tRNA–A5 bulge constructs. (A) Construction of the tRNA core and A5 bulge. The phasing bases are indicated as N. The additional extensions are indicated as (dotted line). (B) Schematic representation of the phase constructs for a rigid tRNA core, and (C) for a flexible tRNA core.

Mentions: The construction of the single-bend construct of the bovine mtRNASer(AGY) has been described in detail (1). The sequences of the oligonucleotides used to create the single-bend and the two-bend tRNA–A5 bulge constructs, with the varied spacing (n), are contained in Table 1. The current approach, depicted in Figure 3, is essentially that used in Friederich et al. (6), except for the inclusion of three additional phasing sizes: n = 14, n = 16 and n = 18.Figure 3.


Core flexibility of a truncated metazoan mitochondrial tRNA.

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

Outline of the construction of double-bend tRNA–A5 bulge constructs. (A) Construction of the tRNA core and A5 bulge. The phasing bases are indicated as N. The additional extensions are indicated as (dotted line). (B) Schematic representation of the phase constructs for a rigid tRNA core, and (C) for a flexible tRNA core.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Outline of the construction of double-bend tRNA–A5 bulge constructs. (A) Construction of the tRNA core and A5 bulge. The phasing bases are indicated as N. The additional extensions are indicated as (dotted line). (B) Schematic representation of the phase constructs for a rigid tRNA core, and (C) for a flexible tRNA core.
Mentions: The construction of the single-bend construct of the bovine mtRNASer(AGY) has been described in detail (1). The sequences of the oligonucleotides used to create the single-bend and the two-bend tRNA–A5 bulge constructs, with the varied spacing (n), are contained in Table 1. The current approach, depicted in Figure 3, is essentially that used in Friederich et al. (6), except for the inclusion of three additional phasing sizes: n = 14, n = 16 and n = 18.Figure 3.

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