Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation

Wang, Jinfan; Shin, Byung‐Sik; Alvarado, Carlos; Kim, Joo-Ran; Bohlen, Jonathan; Dever, Thomas E.; Puglisi, Joseph D.

doi:10.1016/j.cell.2022.10.005

Cited by 43 publications

(40 citation statements)

References 75 publications

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“…This position of eIF4A agrees well with previous biochemical, cross-link mass spectrometry, and proximity labelling data ( 4, 17, 18 ). Moreover, recent single-molecule data revealed FRET between eIF4A and ribosomal uS19 ( 50 ); the latter is located within FRET distance of this second eIF4A in our structure.…”

Section: Resultssupporting

confidence: 65%

See 1 more Smart Citation

The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A

Querido

Sokabe

Díaz-López

et al. 2022

Preprint

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Canonical initiation of translation in eukaryotes involves recruitment of the 43S pre-initiation complex to the 5′ end of mRNA by the cap-binding complex eIF4F to form the 48S initiation complex (48S), followed by scanning along the mRNA until the start codon is selected. We had previously shown that eIF4F binds near the mRNA channel exit site of the 43S. Here we describe a human 48S positioned at the start codon which reveals a second molecule of eIF4A at the mRNA entry site and provides a mechanism for how it facilitates scanning of the 5′ UTR of mRNA. The significantly improved resolution for eIF4F reveals universally conserved interactions with mRNA and the 43S, shedding light on its role in recruitment and scanning.

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Section: Resultssupporting

confidence: 65%

“…A recent study proposed that these mRNAs may use the slotting mechanism as well ( 62 ). However, this would require a backward movement of the 43S (3′ to 5′) rather than the small oscillations that that are known to exist ( 50 ). Thus, it is more likely that those transcripts use alternative recruitment pathway.…”

Section: Resultsmentioning

confidence: 99%

The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A

Querido

Sokabe

Díaz-López

et al. 2022

Preprint

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“…Apparently, this interference can occur when a faster ribosome complex bumps into a slower downstream ribosome or another obstacle. The most likely impediments for the scanning complex are the slower post-scanning initiating ( Wang et al 2022 ) or terminating ribosomes. Collisions between scanning and elongating ribosomes can also occur.…”

Section: Proposed Mechanisms Of Eif4g2 Operation In Translation Initi...mentioning

confidence: 99%

“…All translation elongation rate estimates fall in the ballpark of around 5 codons per second ( Gerashchenko et al 2021 ), while attempts to estimate a scanning rate are less coherent. A recent observation of extremely fast scanning (over 100 nt/sec) ( Wang et al 2022 ) suggests that a scanning complex can potentially catch up ribosomes that translate the uORF. From a structural point of view, eIF4G1 resides on the periphery of the 48S complex, equidistant from either the entry and the exit of the mRNA channel ( Querido et al 2020 ), and any frontal or rearal bumping can arguably make eIF4G1 dissociate.…”

Section: Proposed Mechanisms Of Eif4g2 Operation In Translation Initi...mentioning

confidence: 99%

Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story

Shestakova

Smirnova

Shatsky

et al. 2022

RNA

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The eukaryotic initiation factor 4G2 (eIF4G2, DAP5, Nat1, p97) was discovered in 1997. Over the past two decades, dozens of papers have presented contradictory data on eIF4G2 function. Since its identification, eIF4G2 has been assumed to participate in noncanonical translation initiation mechanisms, but recent results indicate that it can be involved in scanning as well. In particular, eIF4G2 provides leaky scanning through some upstream open reading frames (uORFs), which are typical for long 5’ UTRs of mRNAs from higher eukaryotes. It is likely the protein can also help the ribosome overcome other impediments during scanning of the 5’ UTRs of animal mRNAs. This may explain the need for eIF4G2 in higher eukaryotes, as many mRNAs that encode regulatory proteins have rather long and highly structured 5’ UTRs. Additionally, they often bind to various proteins, which also hamper the movement of scanning ribosomes. This review discusses the suggested mechanisms of eIF4G2 action, denotes obscure or inconsistent results, and proposes ways to uncover other fundamental mechanisms in which this important protein factor may be involved in higher eukaryotes.

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“…eIF4F then recruits the 43S pre-initiation complex (PIC), which is comprised of the 40S small ribosomal subunit, eIF1, eIF1A, eIF3, eIF5, and the ternary complex (eIF2•GTP•Met-tRNAi Met ). The 43S PIC then scans 5ʹ to 3ʹ in search of an AUG start codon (Brito Querido et al 2020;Wang et al 2022). The 48S initiation complex is formed after start codon recognition and eIF2 subsequently hydrolyzes GTP to release Met-tRNAi Met .…”

Section: Introductionmentioning

confidence: 99%

Translation re-initiation after uORFs does not fully protect mRNAs from nonsense-mediated decay

Russell

Slivka

Boyle³

et al. 2022

Preprint

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It is estimated that nearly 50% of mammalian transcripts contain at least one upstream open reading frame (uORF), which are typically one to two orders of magnitude smaller than the downstream main ORF. Most uORFs are thought to be inhibitory as they sequester the scanning ribosome, but in some cases allow for translation re-initiation. However, termination in the 5ʹ UTR at the end of uORFs resembles pre-mature termination that is normally sensed by the nonsense-mediated mRNA decay (NMD) pathway. Translation re-initiation has been proposed as a method for mRNAs to prevent NMD. Here we test how uORF length influences translation re-initiation and mRNA stability. Using custom 5ʹ UTRs and uORF sequences, we show that re-initiation can occur on heterologous mRNA sequences, favors small uORFs, and is supported when initiation occurs with more initiation factors. After determining reporter mRNA half-lives and mining available mRNA half-life datasets for cumulative uORF length, we conclude that translation re-initiation after uORFs is not a robust method for mRNAs to evade NMD. Together, these data support a model where uORFs have evolved to balance coding capacity, translational control, and mRNA stability.

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Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation

Cited by 43 publications

References 75 publications

The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A

The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A

Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story

Translation re-initiation after uORFs does not fully protect mRNAs from nonsense-mediated decay

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