Regulatory elements in eIF1A control the fidelity of start codon selection by modulating tRNA(i)(Met) binding to the ribosome

Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
Genes & development (Impact Factor: 10.8). 01/2010; 24(1):97-110. DOI: 10.1101/gad.1871910
Source: PubMed

ABSTRACT eIF1A is the eukaryotic ortholog of bacterial translation initiation factor IF1, but contains a helical domain and long unstructured N-terminal tail (NTT) and C-terminal tail (CTT) absent in IF1. Here, we identify elements in these accessory regions of eIF1A with dual functions in binding methionyl initiator tRNA (Met-tRNA(i)(Met)) to the ribosome and in selecting AUG codons. A pair of repeats in the eIF1A CTT, dubbed Scanning Enhancer 1 (SE1) and SE2, was found to stimulate recruitment of Met-tRNA(i)(Met) in the ternary complex (TC) with eIF2.GTP and also to block initiation at UUG codons. In contrast, the NTT and segments of the helical domain are required for the elevated UUG initiation occurring in SE mutants, and both regions also impede TC recruitment. Remarkably, mutations in these latter elements, dubbed scanning inhibitors SI1 and SI2, reverse the defects in TC loading and UUG initiation conferred by SE substitutions, showing that the dual functions of SE elements in TC binding and UUG suppression are mechanistically linked. It appears that SE elements enhance TC binding in a conformation conducive to scanning but incompatible with initiation, whereas SI elements destabilize this conformation to enable full accommodation of Met-tRNA(i)(Met) in the P site for AUG selection.

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Available from: Adesh Saini, Feb 25, 2014
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    • "Through the global expression analysis, we have noticed that a eukaryotic translation initiation factor 1A (Eif1a) is highly up-regulated in the Zscan4+ state of ES cells compared with the Zscan4− state.10 Studies using a yeast model have shown that, together with Eif1, Eif1a plays an important role in the identification of translation initiation codon in eukaryotes.11,12 According to the Mouse Genome Informatics database13 at The Jackson Laboratory, Eif1a was originally identified as a mouse eukaryotic elongation factor Tu in erythroleukemic cells.14 "
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    DNA Research 05/2013; 20(4). DOI:10.1093/dnares/dst018 · 5.48 Impact Factor
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    • "Capitalizing on different eIF1A dissociation kinetics between the open and closed states, individual mutations altering eIF1A or eIF5 (within its NTD) were shown to manipulate the closed and open states of the AUG-or UUG-bound PIC (Maag et al., 2006). Any mutation that favors the closed PIC and allows initiation at a faulty UUG codon would promote translation initiation at the expense of lower fidelity, leading to a suppressor of initiation codon mutation (Sui − ) phenotype, whereas a mutation that favors the open complex and block faulty initiation at a UUG codon would increase the fidelity of translation initiation, a suppressor of Sui − (Ssu − ) phenotype (Saini et al., 2010). Thus Sui − mutations stabilize the closed state, whereas Ssu − mutations favor the open state of the PIC (summarized in Table S1). "
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    Cell Reports 06/2012; 1(6):689-702. DOI:10.1016/j.celrep.2012.04.007 · 8.36 Impact Factor
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    • "While greater defects in tRNA binding do not result in lethality in E. coli (McClory et al., 2010; Zaher and Green, 2010), similarly large changes may not be tolerated in yeast because of the presence of the nonfunctional ribosome decay (NRD) apparatus present in eukaryotic cells (LaRiviere et al., 2006). Furthermore , mutations in trans-acting eukaryotic initiation factors have been reported to strongly affect recruitment of initiator tRNA (Saini et al., 2010) or IRES elements to the small ribosomal subunit (Otto and Puglisi, 2004; Ji et al., 2004) without affecting cell viability. However, large changes in affinities for RNA ligands in the large subunit itself are probably unobtainable, and the observed $40% decreases in ribosome affinity for RNA ligands promoted by D95A mutant ribosomes likely approach the tolerable limits for the viability of this single-celled microorganism. "
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    Molecular cell 11/2011; 44(4):660-6. DOI:10.1016/j.molcel.2011.09.017 · 14.02 Impact Factor
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