Eukaryotic Wobble Uridine Modifications Promote a Functionally Redundant Decoding System

Johansson, Marcus; Esberg, Anders; Huang, Bo; Björk, Glenn R.; Byström, Andeŕs S.

doi:10.1128/mcb.01542-07

Cited by 237 publications

(333 citation statements)

References 54 publications

(116 reference statements)

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“…Therefore, one may speculate that the hydroxylation of mcm 5 U into mchm 5 U improves the reading of non-cognate codons; a typical feature of wobble uridine modifications found on family box tRNAs 3,4 . This ability may be of particular importance in higher eukaryotes, for example, mammals, which consist of a wide diversity of specialized cells, such as elongated neurons.…”

Section: Discussionmentioning

confidence: 99%

“…The nucleotide at the wobble position in the anticodon loop of tRNA interacts with the third nucleotide of the codon in mRNA, and wobble uridines are usually modified, both in bacteria and eukaryotes 1,2 . Modification of wobble uridines ensures efficient decoding of both cognate and non-cognate codons 3,4 , and prevents misreading of codons from 'split' boxes, where purine-and pyrimidine-ending codons encode different amino acids 1 .…”

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confidence: 99%

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ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

et al. 2011

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Mammals have nine different homologues (ALKBH1-9) of the Escherichia coli DNA repair demethylase AlkB. ALKBH2 is a genuine DNA repair enzyme, but the in vivo function of the other ALKBH proteins has remained elusive. It was recently shown that ALKBH8 contains an additional transfer RNA (tRNA) methyltransferase domain, which generates the wobble nucleoside 5-methoxycarbonylmethyluridine (mcm 5 U) from its precursor 5-carboxymethyluridine (cm 5 U). In this study, we report that (R)-and (S)-5-methoxycarbonylhydroxymethyluridine (mchm 5 U), hydroxylated forms of mcm 5 U, are present in mammalian tRNA UCG Arg , and tRNA UCC Gly , respectively, representing the first example of a diastereomeric pair of modified RNA nucleosides. Through in vitro and in vivo studies, we show that both diastereomers of mchm 5 U are generated from mcm 5 U, and that the AlkB domain of ALKBH8 specifically hydroxylates mcm 5 U into (S)-mchm 5 U in tRNA UCC Gly . These findings expand the function of the ALKBH oxygenases beyond nucleic acid repair and increase the current knowledge on mammalian wobble uridine modifications and their biogenesis.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

et al. 2011

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“…73 These analyses revealed that mcm 5 and ncm 5 side chains promote pairing with G-ending codons in most codon boxes and that concurrent mcm 5 and s 2 groups improve reading of both A-and G-ending codons. 73 A second in vivo strategy is to quantify the role of wobble uridine modifications in a tRNA isoacceptor decoding the cognate A or the near cognate G ending codon using reporter systems. The SUP4-encoded ochre suppressor tRNA, where the primary anticodon sequence is UUA, has a mcm 5 side chain at U 34 .…”

Section: -73mentioning

confidence: 99%

Elongator, a conserved complex required for wobble uridine modifications in Eukaryotes

Karlsborn

Tükenmez

Mahmud³

et al. 2014

RNA Biology

109

104

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“…Because translation is accomplished with fewer tRNA identities than there are codon identities, some codonanticodon interactions involve non-Watson-Crick base-pairings [7,8]. These so-called wobble pairings are thought to modulate the speed of decoding [9][10][11][12]. Once a tRNA has arrived and base-paired, the speed of peptide bond formation between the C-terminal amino acid in the nascent chain and an incoming amino acid may be influenced by chemical properties of these amino acids [13].…”

Section: Introductionmentioning

confidence: 99%

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

Hussmann

Patchett

Johnson

et al. 2015

Preprint

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Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs. These snapshots can be used to make inferences about translation dynamics. Recent ribosome profiling studies in yeast, however, have reached contradictory conclusions regarding the average translation rate of each codon. Some experiments have used cycloheximide (CHX) to stabilize ribosomes before measuring their positions, and these studies all counterintuitively report a weak negative correlation between the translation rate of a codon and the abundance of its cognate tRNA. In contrast, some experiments performed without CHX report strong positive correlations. To explain this contradiction, we identify unexpected patterns in ribosome density downstream of each type of codon in experiments that use CHX. These patterns are evidence that elongation continues to occur in the presence of CHX but with dramatically altered codon-specific elongation rates. The measured positions of ribosomes in these experiments therefore do not reflect the amounts of time ribosomes spend at each position in vivo. These results suggest that conclusions from experiments in yeast using CHX may need reexamination. In particular, we show that in all such experiments, codons decoded by less abundant tRNAs were in fact being translated more slowly before the addition of CHX disrupted these dynamics. Author SummaryRibosome profiling measures the precise locations of millions of actively translating ribosomes on mRNAs. In theory, the frequency with which ribosomes are observed positioned over each type of codon can be used to quantify the speed with which each codon is translated. In practice, ribosome profiling experiments in yeast that use translation inhibitors to arrest translation before measuring the positions of ribosomes report very different Data Availability Statement: Sequencing data has been deposited to the SRA with accession number SRP060588.Funding: This work was supported by NIH grant R01-GM-093086 to SS and NIH grant GM053655 to AJ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Competing Interests: The authors have declared that no competing interests exist.apparent translation speeds for each codon than experiments that do not use inhibitors.To explain this inconsistency, we show that a previously unappreciated mechanism causes experiments using translation inhibitors to not measure ribosomes at each position on mRNAs in proportion to the actual amount of time spent there in vivo. Understanding this mechanism reveals that experiments without inhibitors more accurately measure translation dynamics and provides guidance for the design and interpretation of future ribosome profiling experiments.

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Eukaryotic Wobble Uridine Modifications Promote a Functionally Redundant Decoding System

Cited by 237 publications

References 54 publications

ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

Elongator, a conserved complex required for wobble uridine modifications in Eukaryotes

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

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