Two Distinct Conformations of the Conserved RNA-rich Decoding Center of the Small Ribosomal Subunit Are Recognized by tRNAs and Release Factors

Youngman, Elaine M.; Cochella, Luisa; Brunelle, Julie L.; He, Shan; Green, R.

doi:10.1101/sqb.2006.71.036

Cited by 16 publications

(11 citation statements)

References 25 publications

(31 reference statements)

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“…Moreover, despite the obvious overlaps in the binding sites of the tRNAs and class I release factors on the ribosome, the molecular binding determinants for recognition/function are strikingly distinct, at least in the small ribosome subunit. These observations are consistent with biochemical predictions based on mutational analysis and antibiotic sensitivity profiles for the two processes (Youngman et al, 2006). …”

Section: The Specificity Of Peptide Releasesupporting

confidence: 90%

Fidelity at the Molecular Level: Lessons from Protein Synthesis

Zaher

Green

2009

Cell

348

358

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The faithful and rapid translation of genetic information into peptide sequences is an indispensable property of the ribosome. Mechanistic understanding of strategies utilized by the ribosome in achieving both speed and fidelity during translation results from nearly a half century of biochemical and structural studies. Emerging from these studies is the common theme that the ribosome utilizes local as well as remote conformational switches to govern induced-fit mechanisms that ensure accuracy in codon recognition during both tRNA selection and translation termination.

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Section: The Specificity Of Peptide Releasesupporting

confidence: 90%

Fidelity at the Molecular Level: Lessons from Protein Synthesis

Zaher

Green

2009

Cell

348

358

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“…7). This supports the results of the structural and biochemical studies suggesting that peptide release, which is regulated by proteinmRNA and not tRNA-mRNA interactions, utilizes a distinct mechanism to recognize the codon than those used for aa-tRNA selection (Youngman et al 2006;Korostelev et al 2008;Laurberg et al 2008;Weixlbaumer et al 2008). Moreover, these findings lend further mechanistic insights into the process by which m 6 G affects decoding of sense codons.…”

Section: Kinetics Of Peptide-bond Formation and Proofreadingsupporting

confidence: 78%

O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity

Hudson

Zaher

2015

RNA

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Nucleic acids are under constant assault from endogenous and environmental agents that alter their physical and chemical properties. O6-methylation of guanosine (m 6 G) is particularly notable for its high mutagenicity, pairing with T, during DNA replication. Yet, while m 6 G accumulates in both DNA and RNA, little is known about its effects on RNA. Here, we investigate the effects of m 6 G on the decoding process, using a reconstituted bacterial translation system. m 6 G at the first and third position of the codon decreases the accuracy of tRNA selection. The ribosome readily incorporates near-cognate aminoacyltRNAs (aa-tRNAs) by forming m 6 G-uridine codon-anticodon pairs. Surprisingly, the introduction of m 6 G to the second position of the codon does not promote miscoding, but instead slows the observed rates of peptide-bond formation by >1000-fold for cognate aa-tRNAs without altering the rates for near-cognate aa-tRNAs. These in vitro observations were recapitulated in eukaryotic extracts and HEK293 cells. Interestingly, the analogous modification N6-methyladenosine (m 6 A) at the second position has only a minimal effect on tRNA selection, suggesting that the effects on tRNA selection seen with m 6 G are due to altered geometry of the base pair. Given that the m6G:U base pair is predicted to be nearly indistinguishable from a WatsonCrick base pair, our data suggest that the decoding center of the ribosome is extremely sensitive to changes at the second position. Our data, apart from highlighting the deleterious effects that these adducts pose to cellular fitness, shed new insight into decoding and the process by which the ribosome recognizes codon-anticodon pairs.

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“…These results are consistent with published data showing that Lys-tRNA Lys can miscode on the AAU codon. In addition, paromomycin inhibited the RF-mediated peptide release reaction (data not shown), as previously reported in the bacterial system (Brown et al 1993;Youngman et al 2006). Our data suggest that yeast ribosomes qualitatively respond to paromomycin in the same manner as bacterial ribosomes, arguing for the presence of core structural features that dictate the events of translation elongation.…”

Section: Effects Of Paromomycin On Miscodingsupporting

confidence: 74%

Distinct response of yeast ribosomes to a miscoding event during translation

Eyler¹,

Green²

2011

RNA

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Numerous mechanisms have evolved to control the accuracy of translation, including a recently discovered retrospective quality control mechanism in bacteria. This quality control mechanism is sensitive to perturbations in the codon:anticodon interaction in the P site of the ribosome that trigger a dramatic loss of fidelity in subsequent tRNA and release factor selection events in the A site. These events ultimately lead to premature termination of translation in response to an initial miscoding error. In this work, we extend our investigations of this mechanism to an in vitro reconstituted Saccharomyces cerevisiae translation system. We report that yeast ribosomes do not respond to mismatches in the P site by loss of fidelity in subsequent substrate recognition events. We conclude that retrospective editing, as initially characterized in Escherichia coli, does not occur in S. cerevisiae. These results highlight potential mechanistic differences in the functional core of highly conserved ribosomes.

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Two Distinct Conformations of the Conserved RNA-rich Decoding Center of the Small Ribosomal Subunit Are Recognized by tRNAs and Release Factors

Cited by 16 publications

References 25 publications

Fidelity at the Molecular Level: Lessons from Protein Synthesis

Fidelity at the Molecular Level: Lessons from Protein Synthesis

O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity

Distinct response of yeast ribosomes to a miscoding event during translation

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