Thermal unfolding of yeast glycine transfer RNA

Hilbers, Cornelis W.; Robillard, George T.; Shulman, Robert G.; Blake, R. D.; Webb, P.; Fresco, Raoul; Riesner, Detlev

doi:10.1021/bi00654a013

Cited by 49 publications

(36 citation statements)

References 20 publications

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“…The conclusion that the low-temperature transition in L-21 Sca I melting is primarily due to disruption of tertiary interactions implies that the tertiary interactions are weaker than the secondary structure interactions. Similar conclusions were derived for melting of tRNAs (Crothers et al, 1974;Riesner & Riimer, 1973;Hilbers et al, 1976). If this result is general, it suggests that a combination of melting and modification experiments may be useful for determining RNA structure.…”

Section: A-u M a T R O W Hit A T 6 Ksupporting

confidence: 69%

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure

Banerjee¹,

Jaeger²,

Turner³

1993

Biochemistry

173

123

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Little is known about the folding pathways of RNA. A particularly interesting RNA is L-21 Sca I, a linear form of the self-splicing intron from the precursor of the Tetrahymena thermophila large subunit (LSU) rRNA. Thermal unfolding of L-21 Sca I is studied by UV absorption and chemical mapping in 50 mM Na+ and 10 mM free Mg2+ at pH 7.5. UV melting experiments identify two major transitions with maxima at 65 and 73 degrees C. Chemical mapping at the beginning and middle of the first transition suggests it primarily involves disruption of tertiary structure. Phylogenetic comparisons suggest a potential tertiary interaction between loops L2.1 and L9.1a. Chemical mapping and melting experiments on a truncated form of the intron lacking P9.1a, L-21 Nhe I, are consistent with this hypothesis. The results indicate that increasing temperature disrupts tertiary interactions before disrupting secondary structure. This suggests tertiary interactions are weaker than secondary interactions in this case. These results support an important assumption for RNA structure prediction: that secondary structure dominates the free energy of folding.

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Section: A-u M a T R O W Hit A T 6 Ksupporting

confidence: 69%

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure

Banerjee¹,

Jaeger²,

Turner³

1993

Biochemistry

173

123

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“…4A). According to detailed studies of the molecular mechanism of thermal unfolding of tRNAs, tRNAs unfold in a few discrete steps as the temperature is raised (37,38). First, the D stem unfolds at the same time as the tertiary structure is lost, followed in succession by the unfolding of the T stem, the anticodon stem and, finally, the acceptor stem.…”

Section: Discussionmentioning

confidence: 99%

tRNA Recognition of tRNA-guanine Transglycosylase from a Hyperthermophilic Archaeon, Pyrococcus horikoshii

Watanabe

Nameki

Matsuo-Takasaki

et al. 2001

Journal of Biological Chemistry

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In the biosynthesis of archaeosine, archaeal tRNAguanine transglycosylase (TGT) catalyzes the replacement of guanine at position 15 in the D loop of most tRNAs by a free precursor base. We examined the tRNA recognition of TGT from a hyperthermophilic archaeon, Pyrococcus horikoshii. Mutational studies using variant tRNA Val transcripts revealed that both guanine and its location (position 15) were strictly recognized by TGT without any other sequence-specific requirements. It appeared that neither the global L-shaped structure of a tRNA nor the local conformation of the D loop contributed to recognition by TGT. A minihelix composed of the acceptor stem and D arm of tRNA Val , designed as a potential minimal substrate, failed to serve as a substrate for TGT. Only a minihelix with mismatched nucleotides at the junction between the two domains served as a good substrate, suggesting that mismatched nucleotides in the helix provide the specific information that allows TGT to recognize the guanine in the D loop. Our findings indicate that the tRNA recognition requirements of P. horikoshii TGT are sufficiently limited and specific to allow the enzyme to recognize efficiently any tRNA species whose structure is not fully stabilized in an extremely high temperature environment.Among the large number of modified nucleosides found in tRNAs, only two hypermodified nucleotides have a 7-deazaguanosine structure, namely, queuosine and archaeosine. Queuosine (Q 1 ; 7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine) has been found at position 34, the wobble position of the anticodon, of four tRNAs with the anticodon sequence GUN (specific for amino acids Asp, Asn, His, and Tyr), but it has been found in most eubacteria and eukaryotes (1-3). Queuosine is involved not only in the fine tuning of translation in eubacteria, as suggested by its location at the wobble position, but also in cellular events such as development, differentiation, aging, and cancer in eukaryotes. However, the mechanisms responsible for such phenomena are not fully understood (for reviews, see Refs. 4 and 5). Archaeosine (G*; 7-formamidino-7-deazaguanosine) has been found at position 15 in the D loop of tRNAs from many archaea (6, 7). In Haloferax volcanii, the archaeon that has been examined in the greatest detail, archaeosine has been identified in more than 15 tRNA species (8, 9), but its role remains unknown.A characteristic feature of the biosynthesis of both queuosine and archaeosine is the base replacement reaction that is catalyzed by tRNA-guanine transglycosylase (TGT) (10 -13). Eubacterial TGTs catalyze the replacement of guanine at position 34 by the free precursor, 7-aminomethyl-7-deazaguanine (preQ 1 ), and archaeal TGT catalyzes that at position 15 by 7-cyano-7-deazaguanine (preQ 0 ). Subsequent modification is catalyzed by two different enzymes to yield the final products in Escherichia coli (14, 15), whereas such reactions are presumably catalyzed by at least one as yet unidentified enzyme in archaea. By contrast, eukar...

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“…The application of proton N M R to the study of the physical chemical properties of nucleic acids has been advanced recently by the combination of N M R and temperature-jump relaxation data (Crothers et al, 1974;Hilbers et al, 1976). The range of relaxation rates for an individual transition monitored by temperature jump is related to the type of "melting" which should be observed in the low-field spectral region of tRNA N M R spectra.…”

Section: Discussionmentioning

confidence: 99%

A nuclear magnetic resonance study of secondary and tertiary structure in yeast tRNAPhe

Robillard¹,

Tarr²,

Vosman³

et al. 1977

Biochemistry

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Thermal unfolding of yeast glycine transfer RNA

Cited by 49 publications

References 20 publications

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure

tRNA Recognition of tRNA-guanine Transglycosylase from a Hyperthermophilic Archaeon, Pyrococcus horikoshii

A nuclear magnetic resonance study of secondary and tertiary structure in yeast tRNAPhe

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