The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges

Hinnebusch, Alan G.; Lorsch, Jon R.

doi:10.1101/cshperspect.a011544

Cited by 444 publications

(482 citation statements)

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“…To obtain a fuller appreciation of where eIF4F fits into the grand scheme of things, the reader may find one or more of the closing references to reviews useful (72)(73)(74)(75)(76)(77)(78)(79)(80)(81)(82)(83)(84)(85) …”

Section: Other Complicationsmentioning

confidence: 99%

eIF4F: A Retrospective

Merrick

2015

Journal of Biological Chemistry

149

156

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The original purification of the heterotrimeric eIF4F was published over 30 years ago (Grifo, J. A., Tahara, S. M., Morgan, M. A., Shatkin, A. J., and Merrick, W. C. (1983) J. Biol. Chem. 258, 5804 -5810). Since that time, numerous studies have been performed with the three proteins specifically required for the translation initiation of natural mRNAs, eIF4A, eIF4B, and eIF4F. These have involved enzymatic and structural studies of the proteins and a number of site-directed mutagenesis studies. The regulation of translation exhibited through the mammalian target of rapamycin (mTOR) pathway is predominately seen as the phosphorylation of 4E-BP, an inhibitor of protein synthesis that functions by binding to the cap binding subunit of eIF4F (eIF4E). A hypothesis that requires the disassembly of eIF4F during translation initiation to yield free subunits (eIF4A, eIF4E, and eIF4G) is presented. The Biology of eIF4FThe initial findings in the study of natural mRNA translation reflected the newly discovered m 7 G cap at the 5Ј end of eukaryotic mRNAs (2). mRNAs lacking this structure were translated with less efficiency than mRNAs that contained this structure (3). This unique structure allowed for specific assays or purifications, many established in the laboratory of Dr. Aaron Shatkin with assists from his colleagues. Two of note were the use of m 7 G-Sepharose for affinity purification (4, 5) and the crosslinking of periodate-oxidized mRNAs to proteins (6).The initial application of these methodologies identified two different molecular weight species (about 25,000 and at least 200,000), although the high molecular weight protein contained the small molecular weight component, now known as eIF4E (7). Given the size of several other known translation factors, the question was whether these contained the small molecular weight subunit (notably eIF3 and eIF4B) (8 -11). Ultimate purification of eIF4F indicated that neither of these were correct but that eIF4F would form stable complexes with either, thus being consistent with the eIF4E component tracking with them. At the same time, it was recognized that the 46,000 molecular weight subunit of eIF4F was eIF4A. By physical analysis, eIF4F was a heterotrimeric complex of eIF4A, eIF4E, and eIF4G (1).The next studies were to attempt to identify the functions of the various proteins required specifically for natural mRNA translation (eIF4A, eIF4B, and eIF4F). The characteristics of these three proteins were very different. In the absence of ATP, binding to RNA could only be well demonstrated with eIF4F (Table 1). eIF4A and eIF4F could hydrolyze ATP in the presence of single-stranded RNA, and eIF4B would enhance both of these activities (12). In terms of mechanism, the coupling of the binding of ATP and RNA was realized in recognizing that eIF4A or eIF4F had the ability to unwind duplex RNA. As noted in Table 1, the "strength" of the helicase activity was greater with eIF4F (14).As the ability to determine amino acid sequence from RNA sequence advanced, it was found that there...

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Section: Other Complicationsmentioning

confidence: 99%

eIF4F: A Retrospective

Merrick

2015

Journal of Biological Chemistry

149

156

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“…Located within transcript leaders of protein coding genes, uORFs are cis-regulatory elements that affect translation of the downstream main ORF (Somers et al 2013;Wethmar 2014;Hinnebusch et al 2016). uORF regulatory effects can be conceptualized through the scanning model of translation initiation, in which the preinitiation complex binds the 5 ′ end of transcript leaders and scans downstream in search of start codons (Hinnebusch and Lorsch 2012). If initiation occurs at a uORF, there are two possible outcomes: The uORF can act as a repressor of translation of the main ORF, potentially triggering mRNA turnover through nonsense-mediated decay; alternatively, uORFs can act as stress-specific enhancers by promoting downstream reinitiation at main ORFs.…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

et al. 2017

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Upstream open reading frames (uORFs), located in transcript leaders (5′ UTRs), are potent cis-acting regulators of translation and mRNA turnover. Recent genome-wide ribosome profiling studies suggest that thousands of uORFs initiate with non-AUG start codons. Although intriguing, these non-AUG uORF predictions have been made without statistical control or validation; thus, the importance of these elements remains to be demonstrated. To address this, we took a comparative genomics approach to study AUG and non-AUG uORFs. We mapped transcription leaders in multiple Saccharomyces yeast species and applied a novel machine learning algorithm (uORF-seqr) to ribosome profiling data to identify statistically significant uORFs. We found that AUG and non-AUG uORFs are both frequently found in Saccharomyces yeasts. Although most non-AUG uORFs are found in only one species, hundreds have either conserved sequence or position within Saccharomyces. uORFs initiating with UUG are particularly common and are shared between species at rates similar to that of AUG uORFs. However, non-AUG uORFs are translated less efficiently than AUG-uORFs and are less subject to removal via alternative transcription initiation under normal growth conditions. These results suggest that a subset of non-AUG uORFs may play important roles in regulating gene expression.

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“…60 eIF1 (12.7 kDa) and eIF1A (16.5 kDa) are 2 proteins that work in tandem to ensure correct start codon recognition. 27,61 eIF1 suppresses initiation from non-cognate codons or start codons in improper context. 61 Directed hydroxyl radical probing and X-ray analyses (»7.9-9.0 A ) involving mammalian 40S and eIF1 showed that eIF1 binds to helices 44, 24 and 45 of the 18S rRNA near the P-site.…”

Section: E999576-6mentioning

confidence: 99%

“…Poly(A)-binding protein (PABP) is believed to enforce a "closed loop" mRNA conformation via interaction with eIF4G. Following recognition of the start codon and eIF5-induced irreversible hydrolysis of eIF2- 26,27 However, the exact mechanism by which the mRNA threads through the narrow mRNA channel in the 40S ribosomal subunit remains a mystery. The 'open' scanningcompetent conformation of the 40S subunit allows sampling of non-AUG triplets during movement of the initiation complex, but does not lead to efficient codon-anticodon base pairing.…”

Section: Introductionmentioning

confidence: 99%

“…The 'open' scanningcompetent conformation of the 40S subunit allows sampling of non-AUG triplets during movement of the initiation complex, but does not lead to efficient codon-anticodon base pairing. 27,28 During scanning, eIF1 acts as a gatekeeper and blocks the release of Pi from partially hydrolyzed eIF2 GTP into eIF2 GDP Pi induced by eIF5 and maintains the 'open' 40S conformation. Upon recognition of a start AUG codon, factors are rearranged and eIF1 is released.…”

Section: Introductionmentioning

confidence: 99%

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Eukaryote-specific extensions in ribosomal proteins of the small subunit: Structure and function

Ghosh

Komar

2015

Translation

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Keywords: conserved ribosomal proteins, eukaryotic/yeast ribosome, eukaryote-specific extensions, eukaryotic translation initiation factors, protein synthesis, small ribosomal subunitHigh-resolution structures of yeast ribosomes have improved our understanding of the architecture and organization of eukaryotic rRNA and proteins, as well as eukaryote-specific extensions present in some conserved ribosomal proteins. Despite this progress, assignment of specific functions to individual proteins and/or eukaryotespecific protein extensions remains challenging. It has been suggested that eukaryote-specific extensions of conserved proteins from the small ribosomal subunit may facilitate eukaryote-specific reactions in the initiation phase of protein synthesis. This review summarizes emerging data describing the structural and functional significance of eukaryotespecific extensions of conserved small ribosomal subunit proteins, particularly their possible roles in recruitment and spatial organization of eukaryote-specific initiation factors.

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The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges

Cited by 444 publications

References 133 publications

eIF4F: A Retrospective

eIF4F: A Retrospective

Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

Eukaryote-specific extensions in ribosomal proteins of the small subunit: Structure and function

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