Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide

Abstract

In the human genome, translation initiation from non-AUG codons plays an important role in various gene regulation programs. However, mechanisms regulating the non-AUG initiation rate remain poorly understood. Here, we show that the non-AUG initiation rate is nearly consistent under a fixed nucleotide context in various human and insect cells. Yet, it ranges from <1% to nearly 100% compared to AUG translation, depending on surrounding sequences, including Kozak, and possibly additional nucleotide contexts. Mechanistically, this range of non-AUG initiation is controlled in part, by the eIF5-mimic protein (5MP). 5MP represses non-AUG translation by competing with eIF5 for the Met-tRNAi-binding factor eIF2. Consistently, eIF5 increases, whereas 5MP decreases translation of NAT1/EIF4G2/DAP5, whose sole start codon is GUG. By modulating eIF5 and 5MP1 expression in combination with ribosome profiling we identified a handful of previously unknown non-AUG initiation sites, some of which serve as the exclusive start codons. If the initiation rate for these codons is low, then an AUG-initiated downstream ORF prevents the generation of shorter, AUG-initiated isoforms. We propose that the homeostasis of the non-AUG translatome is maintained through balanced expression of eIF5 and 5MP.

DDX 3X and specific initiation factors modulate FMR 1 repeat‐associated non‐AUG‐initiated translation

“…Multiple factors and regulatory pathways converge to govern start codon selection, including EIF1 and EIF5. eIF1 (originally identified as Sui1) is known to increase the specificity of scanning 43S PICs for AUG start codons [58,103], while higher availability and abundance of eIF5 (originally Sui5) have been shown to decrease start codon fidelity [88,104,105]. Consistent with our prediction, we observed that EIF1 overexpression decreased RAN translation in a start codon-dependent manner, while over-expression of EIF5 did the opposite.…”

“…Multiple factors and regulatory pathways converge to govern start codon selection, including EIF1 and EIF5 . eIF1 (originally identified as Sui1) is known to increase the specificity of scanning 43S PICs for AUG start codons , while higher availability and abundance of eIF5 (originally Sui5) have been shown to decrease start codon fidelity .…”

uORF-mediated translational control: recently elucidated mechanisms and implications in cancer

“…Moreover, alternative usage of start codons may impact proteomes, and hence have detrimental effects on cell physiology [86]. In addition, the eIF5-mimic protein (5MP) suppresses non-AUG translation by competing with eIF5 for eIF2 [87]. Therefore, alternative translation initiators or regulators modulate the efficiency of non-AUG uORF activation, which hence impacts main CDS translation.…”

Near-cognate initiation generates FMRpolyG from CGG repeats in Fragile X associated Tremor Ataxia Syndrome

“…Despite this global inhibition, some genes are able to bypass this response, and many do so by initiating at near-cognate codons, rather than the canonical AUG start codon (Starck et al 2016;Ingolia et al 2009;Green et al 2017;Imataka, Olsen, and Sonenberg 1997;Ingolia, Lareau, and Weissman 2011;Kearse et al 2019;Schwab et al 2004). The likelihood that initiation will occur at a near-cognate codon during cellular stress is dependent on a number of factors including efficiency of TC recruitment to the 40S docked on an initiation codon, strength of that codon and its surrounding Kozak sequence, and availability of specific initiation factors (Kolitz, Takacs, and Lorsch 2009;Lind and Aqvist 2016;Tang et al 2017;Kearse and Wilusz 2017). In particular, the eIF2 alternative factor, eIF2A, can facilitate near-cognate codon initiation, and a unlike eIF2, is GTP-independent and upregulated during cellular stress (Starck et al 2016;Starck et al 2012;Komar et al 2005;Kim et al 2018;Sonobe et al 2018).…”