The uridine in “U-turn”: Contributions to tRNA-ribosomal binding

Ashraf, S. Salman; Ansari, Ghazala; Guenther, Richard; Sochacka, Elżbieta; Małkiewicz, Andrzej; Agris, Paul F.

doi:10.1017/s1355838299981931

Cited by 57 publications

(70 citation statements)

References 34 publications

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“…1(a) and we do not question this if uridine is considered as a part of a larger system or in condensed phase. 26,27 Figure 2 shows the C 1s photoelectron spectrum of uridine measured with 325 eV photons together with the simulated spectra of the two geometries of Fig. 1.…”

Section: A Ground State Geometry Of Isolated Uridinementioning

confidence: 99%

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Gas-phase study on uridine: Conformation and X-ray photofragmentation

Itälä

Kooser

Rachlew

et al. 2015

The Journal of Chemical Physics

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Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases the C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form. C 2015 AIP Publishing LLC. [http://dx

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Section: A Ground State Geometry Of Isolated Uridinementioning

confidence: 99%

“…Region 3 represents the (27,41), (28,(40)(41)(42)(43), and (29, 40-43) patterns, where the 27, 28, and 29 amu fragments are CHN + , HNCH + /(CO + ) (from the base as in Fig. 4), and COH + (from the sugar), respectively.…”

Section: Fig 3 Pepipico Map Of Uridine the Center Point Of Each Pementioning

confidence: 99%

Gas-phase study on uridine: Conformation and X-ray photofragmentation

Itälä

Kooser

Rachlew

et al. 2015

The Journal of Chemical Physics

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“…Several studies have indicated that tRNAs lacking the highly conserved U33 bind the ribosome with lower efficiency (40,41), although it has also been shown that U33 is not essential for tRNAs to perform in eukaryotic in vitro suppression assays (42). The dedication of tRNA 1 Cys to a function other than protein synthesis would suggest a further linkage between Cys-tRNA Cys synthesis and other aspects of metabolism.…”

Section: Differential Utilization Of Trnamentioning

confidence: 99%

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei

Hauenstein

Perona

2008

Journal of Biological Chemistry

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mazei CysRS and SepRS reveals that each enzyme prefers a distinct tRNACys isoacceptor or pair of isoacceptors. Recognition determinants distinguishing the tRNAs are shown to reside in the globular core of the molecule. Both enzymes also require the S-adenosylmethionedependent formation of m1 G37 in the anticodon loop for efficient aminoacylation. We further report a new, highly sensitive assay to measure the activity of SepCysS under anaerobic conditions. With this approach, we demonstrate that SepCysS functions as a multiple-turnover catalyst with kinetic behavior similar to bacterial selenocysteine synthase and the archaeal/ eukaryotic SepSecS enzyme. Together, these data suggest that both metabolic routes and all three tRNA Cys species in M. mazei play important roles in the cellular physiology of the organism.

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“…As mentioned above, conformational changes in the AC loop are unlikely to affect recognition by EF-Tu, but they may affect tRNA interactions with the ribosome, which establishes extensive contacts with this tRNA region. This hypothesis is supported by the results of previous biochemical studies, showing that the binding affinity of tRNA fragments toward the ribosome is significantly affected by the identity of nucleotides at positions 32 and 38 (Olejniczak et al 2005 and references therein), and the affinity of a yeast tRNA Phe ASL construct containing the U33C substitution for the 30S ribosome subunit is reduced to 5% of the unsubstituted ASL, a result that was ascribed to the loss of the conserved U33 hydrogen bond with the phosphate group of A36 described above (Ashraf et al 1999). Alterations in tRNA affinity for the ribosome might affect the efficiency of protein synthesis and this might contribute, at least in part, to the observed yeast phenotypes (i.e., defects in O 2 consumption and increased percentages of petite cells).…”

Section: Uur (De Luca Et Al 2009)mentioning

confidence: 74%

“…In three-dimensional structures of tRNA molecules in the free state U33 is part of a conserved structural motif called ''U-turn,'' consisting in a change of direction of the polynucleotide backbone and stabilized by three intramolecular non-WC interactions (Ashraf et al 1999; Auffinger and Westhof 2001), which are conserved in tRNA complexes with elongation factor Tu (EF-Tu) or ribosome (see Fig. 6E; Supplemental Table S3).…”

Section: Structure and Sequence Analysismentioning

confidence: 99%

Structural and functional role of bases 32 and 33 in the anticodon loop of yeast mitochondrial tRNA^Ile

Montanari

Luca²,

Micco³

et al. 2011

RNA

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Previous work has demonstrated the usefulness of the yeast model to investigate the molecular mechanisms underlying defects due to base substitutions in mitochondrial tRNA genes, and to identify suppressing molecules endowed with potential clinical relevance. The present paper extends these investigations to two human equivalent yeast mutations located at positions 32 and 33 in the anticodon loop of tRNA Ile . Notwithstanding the proximity of the two T>C base substitutions, the effects of these mutations have been found to be quite different in yeast, as they are in human. The T32C substitution has a very severe effect in yeast, consisting in a complete inhibition of growth on nonfermentable substrates. Conversely, respiratory defects caused by the T33C mutation could only be observed in a defined genetic context. Analyses of available sequences and selected tRNA threedimensional structures were performed to provide explanations for the different behavior of these adjacent mutations. Examination of the effects of previously identified suppressors demonstrated that overexpression of the TUF1 gene did not rescue the defective phenotypes determined by either mutation, possibly as a consequence of the lack of interactions between EF-Tu and the tRNA anticodon arm in known structures. On the contrary, both the cognate IleRS and the noncognate LeuRS and ValRS are endowed with suppressing activities toward both mutations. This allows us to extend to the tRNA Ile mutants the crosssuppression activity of aminoacyl-tRNA synthetases previously demonstrated for tRNA Leu and tRNA Val mutants.

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The uridine in “U-turn”: Contributions to tRNA-ribosomal binding

Cited by 57 publications

References 34 publications

Gas-phase study on uridine: Conformation and X-ray photofragmentation

Gas-phase study on uridine: Conformation and X-ray photofragmentation

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei

Structural and functional role of bases 32 and 33 in the anticodon loop of yeast mitochondrial tRNA^Ile

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The uridine in “U-turn”: Contributions to tRNA-ribosomal binding

Cited by 57 publications

References 34 publications

Gas-phase study on uridine: Conformation and X-ray photofragmentation

Gas-phase study on uridine: Conformation and X-ray photofragmentation

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei

Structural and functional role of bases 32 and 33 in the anticodon loop of yeast mitochondrial tRNAIle

Contact Info

Product

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Structural and functional role of bases 32 and 33 in the anticodon loop of yeast mitochondrial tRNA^Ile