Predicting the efficiency of UAG translational stop signal through studies of physicochemical properties of its composite mono- and dinucleotides

Mao, Pei-Lin; Liu, Tie-Fei; Kueh, Kelly; Wu, Peng

doi:10.1016/j.compbiolchem.2004.05.003

Cited by 2 publications

(1 citation statement)

References 39 publications

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“…The downstream fourth (+4) nt (relative to the uridine of the PTC) virtually has no effect on PTC readthrough It has been reported that a short downstream flanking sequence, especially the identity of the fourth (+4) nt (relative to the uridine [+1] of a stop codon) is crucial in influencing rare stop codon readthrough, which occurs during translation of some mRNAs (Li and Rice 1993;Bonetti et al 1995;McCaughan et al 1995;Tate et al 1996;Mao et al 2004;Loughran et al 2014;Wei and Xia 2017;Cridge et al 2018;Yu et al 2019;Wangen and Green 2020). However, according to published work, the impact of the fourth nucleotide on stop codon readthrough is not entirely consistent.…”

Section: ψ-Mediated Ptc Readthrough Occurs Regardless Of Where the Ptc Is Placed Within The Coding Region Of A Genementioning

confidence: 99%

Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context–independent

Adachi

2020

RNA

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We have previously shown that when the uridine of a stop codon (UAA, UAG, or UGA) is pseudouridylated, the ribosome reads through the modified stop codon. However, it is not clear as to whether or not the pseudouridine (Ψ)-mediated readthrough is dependent on the sequence context of mRNA. Here, we use several different approaches and the yeast system to address this question. We show that when a stop codon (premature termination codon, PTC) is introduced into the coding region of a reporter mRNA at several different positions (with different sequence contexts) and pseudouridylated, we detect similar levels of readthrough. Using mutational and selection/screen analyses, we also show that the upstream sequence (relative to PTC) as well as the nucleotides surrounding the PTC (upstream and downstream) play a minimal role (if at all) in Ψ-mediated ribosome readthrough. Interestingly, we detect no suppression of NMD (nonsense-mediated mRNA decay) by targeted PTC pseudouridylation in the yeast system. Our results indicate that Ψ-mediated nonsense suppression occurs at the translational level, and that the suppression is sequence context-independent, unlike some previously characterized rare stop codon readthrough events.

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Section: ψ-Mediated Ptc Readthrough Occurs Regardless Of Where the Ptc Is Placed Within The Coding Region Of A Genementioning

confidence: 99%

Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context–independent

Adachi

2020

RNA

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Translational tuning optimizes nascent protein folding in cells

Kim

Yoon

Shishido

et al. 2015

Science

192

223

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In cells, biosynthetic machinery coordinates protein synthesis and folding to optimize efficiency and minimize off-pathway outcomes. However, it has been difficult to delineate experimentally the mechanisms responsible. Using fluorescence resonance energy transfer, we studied cotranslational folding of the first nucleotide-binding domain from the cystic fibrosis transmembrane conductance regulator. During synthesis, folding occurred discretely via sequential compaction of N-terminal, α-helical, and α/β-core subdomains. Moreover, the timing of these events was critical; premature α-subdomain folding prevented subsequent core formation. This process was facilitated by modulating intrinsic folding propensity in three distinct ways: delaying α-subdomain compaction, facilitating β-strand intercalation, and optimizing translation kinetics via codon usage. Thus, de novo folding is translationally tuned by an integrated cellular response that shapes the cotranslational folding landscape at critical stages of synthesis.

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Predicting the efficiency of UAG translational stop signal through studies of physicochemical properties of its composite mono- and dinucleotides

Cited by 2 publications

References 39 publications

Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context–independent

Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context–independent

Translational tuning optimizes nascent protein folding in cells

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