Deconstructing the individual steps of vertebrate translation initiation

Giess, Adam; Cleuren, Yamila N. Torres; Tjeldnes, Håkon; Krause, Maximilian; Bizuayehu, Teshome Tilahun; Hiensch, Senna; Okon, Aniekan; Wagner, Carston R.; Valen, Eivind

doi:10.1101/811810

Cited by 3 publications

(8 citation statements)

References 51 publications

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“…Data are normalized to a no-uORF start codon control without a synthetic uORF. , but these requirements are at odds with the typically short and poorly initiating nature of known uORFs [1,3,4,[8][9][10][11]. Indeed, when we use parameters specific to UL4 uORF2 for the 80S-hit model (Table 1), namely that uORF2 initiates poorly, re-initiates well, and is not very long, buffering is no longer predicted (S2B Fig).…”

Section: Discussionmentioning

confidence: 99%

“…uORFs can regulate gene expression via the biological activity of the uORF peptide, but they also often cis-regulate translation of the downstream main ORF [6,7]. Despite having poor initiation sequence contexts, many eukaryotic uORFs repress main ORF translation [1,3,4,[7][8][9][10][11]. uORF mutations are implicated in several human diseases via changes to main ORF translation [12,13].…”

Section: Introductionmentioning

confidence: 99%

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Translational buffering by ribosome stalling in upstream open reading frames

et al. 2022

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Upstream open reading frames (uORFs) are present in over half of all human mRNAs. uORFs can potently regulate the translation of downstream open reading frames through several mechanisms: siphoning away scanning ribosomes, regulating re-initiation, and allowing interactions between scanning and elongating ribosomes. However, the consequences of these different mechanisms for the regulation of protein expression remain incompletely understood. Here, we performed systematic measurements on the uORF-containing 5′ UTR of the cytomegaloviral UL4 mRNA to test alternative models of uORF-mediated regulation in human cells. We find that a terminal diproline-dependent elongating ribosome stall in the UL4 uORF prevents decreases in main ORF protein expression when ribosome loading onto the mRNA is reduced. This uORF-mediated buffering is insensitive to the location of the ribosome stall along the uORF. Computational kinetic modeling based on our measurements suggests that scanning ribosomes dissociate rather than queue when they collide with stalled elongating ribosomes within the UL4 uORF. We identify several human uORFs that repress main ORF protein expression via a similar terminal diproline motif. We propose that ribosome stalls in uORFs provide a general mechanism for buffering against reductions in main ORF translation during stress and developmental transitions.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Translational buffering by ribosome stalling in upstream open reading frames

et al. 2022

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“…S2A, yellow-green line) in the 80S-hit model (Fig. 1B), but these requirements are at odds with the typically short and poorly initiating nature of known uORFs 1,3,4,[8][9][10][11] . Consequently, when we use parameters speci c to UL4 uORF2 for the 80S-hit model (Table 1), namely that uORF2 initiates poorly, re-initiates well, and is not very long, buffering is no longer predicted (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Longer uORFs offer more time for elongating ribosomes to catch up, hit, and knock off 3′ scanning ribosomes. Nevertheless, most eukaryotic uORFs only weakly initiate translation and are short 1,3,4,[8][9][10][11]31 . UL4 uORF2 is 22 codons long, and we estimate reinitiation to be frequent (Table 1).…”

Section: Computational Modeling Predicts That Different Models Of Uorf Regulation Have Unique Parameters Important For Bufferingmentioning

confidence: 99%

“…uORFs can regulate gene expression via the biological activity of the uORF peptide, but they also often cis-regulate translation of the downstream main ORF 6,7 . Despite having poor initiation sequence contexts, many eukaryotic uORFs repress main ORF translation 1,3,4,[7][8][9][10][11] . uORF mutations are implicated in several human diseases via changes to main ORF translation 12,13 .…”

Section: Introductionmentioning

confidence: 99%

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Translational buffering by ribosome stalling in upstream open reading frames

Bottorff

Geballe

Subramaniam

2022

Preprint

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Upstream open reading frames (uORFs) are present in over half of all human mRNAs. uORFs can potently regulate the translation of downstream open reading frames by several mechanisms: siphoning away scanning ribosomes, regulating re-initiation, and allowing interactions between scanning and elongating ribosomes. However, the consequences of these different mechanisms for the regulation of protein expression remain incompletely understood. Here, we performed systematic measurements on the uORF-containing 5′ UTR of the cytomegaloviral UL4 mRNA to test alternative models of uORF-mediated regulation in human cells. We find that a terminal diproline-dependent elongating ribosome stall in the UL4 uORF prevents decreases in main ORF translation when ribosome loading onto the mRNA is reduced. This uORF-mediated buffering is insensitive to the location of the ribosome stall along the uORF. Computational kinetic modeling based on our measurements suggests that scanning ribosomes dissociate rather than queue when they collide with stalled elongating ribosomes within the UL4 uORF. We identify several human uORFs that repress main ORF translation via a similar terminal diproline motif. We propose that ribosome stalls in uORFs provide a general mechanism for buffering against reductions in main ORF translation during stress and developmental transitions.

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The differential effect of SARS-COV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage and virus evolution

Berlanga,

Matamoros,

Pulido

et al. 2024

Preprint

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SummaryThe non-structural protein 1 (NSP1) of SARS-CoV-2 blocks the mRNA entry channel of the 40S ribosomal subunit, causing inhibition of translation initiation and subsequent degradation of host mRNAs. However, target mRNA specificity and the way in which viral mRNAs escape NSP1-mediated degradation have not been clarified to date. Here we found that NSP1 acts as a translational switch capable of blocking or enhancing translation depending on how preinitiation complex 43S-PIC is recruited to the mRNA, whereas NSP1-mediated mRNA degradation mostly depends on codon usage bias. Thus, fast-translating mRNAs with optimal codon usage for human cells that preferentially recruit 43S-PIC by threading, showed a dramatic sensitivity to NSP1. On the contrary, slow-translating mRNAs with suboptimal codon usage and 5’ UTR that enabled slotting on 43S-PIC were resistant to or even enhanced by NSP1. Translation of SARS-CoV-2 mRNAs escapes NSP1-mediated inhibition by a proper combination of suboptimal codon usage and slotting-prone 5’ UTR that also confers efficient translation. Thus, the prevalence of non-optimal codons found in SARS-CoV-2 and other coronavirus genomes is favored by the distinctive effect that NSP1 plays on translation and mRNA stability.

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Deconstructing the individual steps of vertebrate translation initiation

Cited by 3 publications

References 51 publications

Translational buffering by ribosome stalling in upstream open reading frames

Translational buffering by ribosome stalling in upstream open reading frames

Translational buffering by ribosome stalling in upstream open reading frames

The differential effect of SARS-COV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage and virus evolution

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