eIF1 Controls Multiple Steps in Start Codon Recognition during Eukaryotic Translation Initiation

Nanda, Jagpreet S.; Cheung, Yuen Nei; Takacs, Julie E.; Martín-Marcos, Pilar; Saini, Adesh K.; Hinnebusch, Alan G.; Lorsch, Jon R.

doi:10.1016/j.jmb.2009.09.017

Cited by 120 publications

(162 citation statements)

References 40 publications

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“…8, cf. E, eIF5/eIF1, and C, WT), consistent with the previously reported effects of eIF5 on TC binding affinity (Nanda et al 2009). Remarkably, replacing WT eIF5 with eIF5-G31R dramatically reduced the k off for mRNA(UUG) while slightly eIF1:AUG eIF1:UUG eIF2β-S264Y:AUG eIF2β-S264Y:UUG eIF5-G31R:AUG eIF5-G31R:UUG FIGURE 7.…”

Section: Ssusupporting

confidence: 90%

“…This alteration should contribute to the increased UUG:AUG initiation ratio conferred by SUI3-2 in vivo (Huang et al 1997) by preferentially reducing initiation at AUG codons. Interestingly, this latter mechanism was described previously for the eIF1 Sui − substitution G107R, which also delays eIF1 dissociation specifically at AUG codons (Nanda et al 2009). Again, the effect of the S264Y substitution on eIF1 dissociation kinetics occurs in the absence of GTP hydrolysis, implicating the zinc-binding domain of eIF2β (harboring WT S264) in regulating the open/P OUT -to-closed/ P IN transition of the PIC and attendant eIF1 release apart from any effects on GTP hydrolysis/P i release.…”

Section: Ssusupporting

confidence: 68%

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Enhanced eIF1 binding to the 40S ribosome impedes conformational rearrangements of the preinitiation complex and elevates initiation accuracy

Martín-Marcos

Nanda

Luna

et al. 2013

RNA

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In the current model of translation initiation by the scanning mechanism, eIF1 promotes an open conformation of the 40S subunit competent for rapidly loading the eIF2·GTP·Met-tRNA i ternary complex (TC) in a metastable conformation (P OUT ) capable of sampling triplets entering the P site while blocking accommodation of Met-tRNA i in the P IN state and preventing completion of GTP hydrolysis (P i release) by the TC. All of these functions should be reversed by eIF1 dissociation from the preinitiation complex (PIC) on AUG recognition. We tested this model by selecting eIF1 Ssu − mutations that suppress the elevated UUG initiation and reduced rate of TC loading in vivo conferred by an eIF1 (Sui − ) substitution that eliminates a direct contact of eIF1 with the 40S subunit. Importantly, several Ssu − substitutions increase eIF1 affinity for 40S subunits in vitro, and the strongest-binding variant (D61G), predicted to eliminate ionic repulsion with 18S rRNA, both reduces the rate of eIF1 dissociation and destabilizes the P IN state of TC binding in reconstituted PICs harboring Sui − variants of eIF5 or eIF2. These findings establish that eIF1 dissociation from the 40S subunit is required for the P IN mode of TC binding and AUG recognition and that increasing eIF1 affinity for the 40S subunit increases initiation accuracy in vivo. Our results further demonstrate that the GTPase-activating protein eIF5 and β-subunit of eIF2 promote accuracy by controlling eIF1 dissociation and the stability of TC binding to the PIC, beyond their roles in regulating GTP hydrolysis by eIF2.

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Section: Ssusupporting

confidence: 90%

Section: Ssusupporting

confidence: 68%

Enhanced eIF1 binding to the 40S ribosome impedes conformational rearrangements of the preinitiation complex and elevates initiation accuracy

Martín-Marcos

Nanda

Luna

et al. 2013

RNA

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“…The majority of our detected uORFs had no AUG start codons. eIF1 and eIF5 are the factors that control the recognition of start codons during translation initiation in eukaryotes (25,26). We suggest that hydrogen peroxide impairs the fidelity of these factors, which normally restrict initiation to AUG codons, thereby facilitating non-AUG initiation of translation as the ribosome scans the mRNA.…”

Section: Discussionmentioning

confidence: 94%

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

Gerashchenko

Lobanov

Gladyshev

2012

Proc. Natl. Acad. Sci. U.S.A.

275

294

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Information on unique and coordinated regulation of transcription and translation in response to stress is central to the understanding of cellular homeostasis. Here we used ribosome profiling coupled with next-generation sequencing to examine the interplay between transcription and translation under conditions of hydrogen peroxide treatment in Saccharomyces cerevisiae . Hydrogen peroxide treatment led to a massive and rapid increase in ribosome occupancy of short upstream ORFs, including those with non-AUG translational starts, and of the N-terminal regions of ORFs that preceded the transcriptional response. In addition, this treatment induced the synthesis of N-terminally extended proteins and elevated stop codon read-through and frameshift events. It also increased ribosome occupancy at the beginning of ORFs and potentially the duration of the elongation step. We identified proteins whose synthesis was regulated rapidly by hydrogen peroxide posttranscriptionally; however, for the majority of genes increased protein synthesis followed transcriptional regulation. These data define the landscape of genome-wide regulation of translation in response to hydrogen peroxide and suggest that potentiation (coregulation of the transcript level and translation) is a feature of oxidative stress.

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“…Assays of ␤-galactosidase activity in whole-cell extracts (WCEs) were performed as described previously (32). For Western analysis, WCEs were prepared by trichloroacetic acid extraction as previously described (39), and immunoblot analysis was conducted as described previously (33) with antibodies against eIF1 (48), eIF2Bε/Gcd6 (4) or myc epitope (Sigma). Enhanced chemiluminescence or the Odyssey infrared imaging system (Li-Cor) was used to visualize immune complexes, and signal intensities were quantified by densitometry using NIH ImageJ software or with the Odyssey application software, respectively.…”

Section: Yeast Strain Constructionsmentioning

confidence: 99%

“…Although the reduced 40S occupancy of a Sui Ϫ eIF1 mutant decreases the rate of TC loading, since this reaction occurs in the open 40S conformation, once TC is bound it can isomerize more readily to the fully accommodated mode of P-site binding in the absence of a perfect codon-anticodon match, e.g., at UUG codons, thus accounting for the Sui Ϫ phenotype (8,33). We presume that the novel Sui Ϫ mutations in eIF1 described here similarly reduce its affinity for the 40S because they exhibit the hallmark of this class of eIF1 mutations, that their Sui Ϫ phenotypes are suppressed by overexpressing the mutant proteins (unpublished observations).…”

mentioning

confidence: 99%

Functional Elements in Initiation Factors 1, 1A, and 2β Discriminate against Poor AUG Context and Non-AUG Start Codons

Martín-Marcos

Cheung

Hinnebusch

2011

Molecular and Cellular Biology

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136

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Yeast eIF1 inhibits initiation at non-AUG triplets, but it was unknown whether it also discriminates against AUGs in suboptimal context. As in other eukaryotes, the yeast gene encoding eIF1 (SUI1) contains an AUG in poor context, which could underlie translational autoregulation. Previously, eIF1 mutations were identified that increase initiation at UUG codons (Sui ؊ phenotype), and we obtained mutations with the opposite phenotype of suppressing UUG initiation (Ssu ؊ phenotype). Remarkably, Sui ؊ mutations in eukaryotic translation initiation factor 1 (eIF1), eIF1A, and eIF2␤ all increase SUI1 expression in a manner diminished by introducing the optimal context at the SUI1 AUG, whereas Ssu ؊ mutations in eIF1 and eIF1A decrease SUI1 expression with the native, but not optimal, context present. Therefore, discrimination against weak context depends on specific residues in eIFs 1, 1A, and 2␤ that also impede selection of non-AUGs, suggesting that context nucleotides and AUG act coordinately to stabilize the preinitiation complex. Although eIF1 autoregulates by discriminating against poor context in yeast and mammals, this mechanism does not prevent eIF1 overproduction in yeast, accounting for the hyperaccuracy phenotype afforded by SUI1 overexpression.Bacterial translation initiation factor 3 (IF3) promotes the fidelity of initiation at AUG codons by discriminating against non-AUG triplets as start sites (17,26,40,45). This discriminatory function forms the basis for IF3's ability to negatively autoregulate translation of its mRNA, which initiates with an AUU start codon (5, 6). IF3 also destabilizes initiation complexes formed on AUG codons at the 5Ј ends of leaderless mRNAs (47), which lack the Shine-Dalgarno sequence that stabilizes mRNA association with the small (30S) ribosomal subunit at the AUG codon.In eukaryotes, the 43S preinitiation complex (PIC), harboring the eIF2-GTP-Met-tRNA i Met ternary complex (TC) and various other eIFs, attaches to the capped 5Ј end of the mRNA and identifies the AUG codon by scanning the mRNA leader base-by-base for complementarity with the anticodon of MettRNA i Met. Efficient initiation is influenced by the sequence immediately upstream from the AUG, but it is unclear how this sequence context is recognized or regulates AUG selection (20,36). The functional counterpart of IF3 in eukaryotes appears to be eIF1 (Sui1 in yeast). eIF1 and IF3 occupy analogous locations on the platform of the small ribosomal subunit (11,27,38) and, similar to IF3, eIF1 blocks formation of stable 48S PICs at near-cognate start codons (20, 36). eIF1/Sui1 and eIF1A (Tif11 in yeast) cooperate to promote an open conformation of the 40S subunit (34) thought to be conducive to scanning (35), and eIF1 also blocks the final step of GTP hydrolysis by the TC, the release of P i from eIF2-GDP-P i , until an AUG enters the P site (1). AUG recognition triggers dissociation of eIF1 from the 40S subunit (30), enabling P i release and stabilizing a closed conformation of the 40S subunit that is incompatible with ...

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eIF1 Controls Multiple Steps in Start Codon Recognition during Eukaryotic Translation Initiation

Cited by 120 publications

References 40 publications

Enhanced eIF1 binding to the 40S ribosome impedes conformational rearrangements of the preinitiation complex and elevates initiation accuracy

Enhanced eIF1 binding to the 40S ribosome impedes conformational rearrangements of the preinitiation complex and elevates initiation accuracy

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

Functional Elements in Initiation Factors 1, 1A, and 2β Discriminate against Poor AUG Context and Non-AUG Start Codons

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