Ribosome rearrangements at the onset of translational bypassing

Agirrezabala, Xabier; Samatova, Ekaterina; Klimova, Mariia; Zamora, Miguel; Gil, David; Rodnina, Marina V.; Valle, Mikel

doi:10.1126/sciadv.1700147

Cited by 37 publications

(62 citation statements)

References 54 publications

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“…Overall, our data are consistent with the idea that the major mechanism of inhibition on most of these inhibitory codon pairs is through impairment of tRNA binding/accommodation. Interestingly, a similar A-site hairpin was observed previously in a structure implicated in translational bypassing (Agirrezabala et al, 2017). In our cryo-EM structures of ribosome-nascent chain complexes stalled on the CGA-CGA or CGA-CCG codon pairs, we identified several structural details that likely directly affect tRNA binding/ accommodation activity.…”

Section: Discussionsupporting

confidence: 78%

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Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

et al. 2019

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Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall-and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes.

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Section: Discussionsupporting

confidence: 78%

“…This structure may be particular to this reporter mRNA sequence since no equivalent stable mRNA secondary structure is formed in the case of the CGA-CGA-stalled RNC. Interestingly, a similar A-site hairpin was observed previously in a structure implicated in translational bypassing (Agirrezabala et al, 2017).…”

Section: Discussionsupporting

confidence: 77%

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

et al. 2019

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“…This structure may be particular to this reporter mRNA sequence since no equivalent stable mRNA secondary structure is formed in the case of the CGA-CGA stalled RNC. Interestingly, a similar A site hairpin was observed previously in a structure implicated in translational bypassing (Agirrezabala, Samatova et al, 2017).…”

Section: Discussionsupporting

confidence: 77%

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

Těšina

Lessen

Buschauer

et al. 2019

Preprint

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Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo‐EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base‐pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo‐EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding‐incompatible conformations of mRNA in the A sites of all studied stall‐ and collision‐inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA‐induced mechanisms of translational stalling in eukaryotic ribosomes.

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“…The subsequent codon is a stop codon UAG, but instead of terminating protein synthesis, the ribosome slides over a 50 nt-long non-coding gap, lands at a distal GGA codon and resumes translation to the end of ORF2 (132). Gene 60 mRNA elements that stimulate bypassing are located 5 of the take-off site, in the take-off SL and 3 of the landing site (132)(133)(134)(135)(136). Remarkably, the key bypassing signals, such as the take-off SL element and the matching take-off and landing codons, are present also in yeast mitochondrial bypassing mRNAs (129), suggesting a similar mechanism of bypassing to that in bacteriophage T4.…”

Section: Translational Bypassingmentioning

confidence: 99%

“…Another remarkable feature of the take-off complex is a short dynamic SL formed by the mRNA in the decoding site of the SSU (133) ( Figure 6B). The short SL hinders access of the translation termination factor or near-cognate aa-tRNAs into the A site (133). In addition, the SL serves as a mimic of an A-site tRNA to help EF-G to promote a pseudo-translocation event ( Figure 6C).…”

Section: Translational Bypassingmentioning

confidence: 99%

Translational recoding: canonical translation mechanisms reinterpreted

Rodnina

Korniy

Klimova

et al. 2019

Nucleic Acids Research

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During canonical translation, the ribosome moves along an mRNA from the start to the stop codon in exact steps of one codon at a time. The collinearity of the mRNA and the protein sequence is essential for the quality of the cellular proteome. Spontaneous errors in decoding or translocation are rare and result in a deficient protein. However, dedicated recoding signals in the mRNA can reprogram the ribosome to read the message in alternative ways. This review summarizes the recent advances in understanding the mechanisms of three types of recoding events: stop-codon readthrough, -1 ribosome frameshifting and translational bypassing. Recoding events provide insights into alternative modes of ribosome dynamics that are potentially applicable to other non-canonical modes of prokaryotic and eukaryotic translation.

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Ribosome rearrangements at the onset of translational bypassing

Abstract: Cryo–electron microscopy shows how the ribosome prepares for take-off to bypass a noncoding mRNA stretch.

Cited by 37 publications

References 54 publications

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

Translational recoding: canonical translation mechanisms reinterpreted

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