eIF3 mRNA selectivity profiling reveals eIF3k as a cancer‐relevant regulator of ribosome content

Abstract

eIF3, whose subunits are frequently overexpressed in cancer, regulates mRNA translation from initiation to termination, but mRNAselective functions of individual subunits remain poorly defined. Using multiomic profiling upon acute depletion of eIF3 subunits, we observed that while eIF3a, b, e, and f markedly differed in their impact on eIF3 holo-complex formation and translation, they were each required for cancer cell proliferation and tumor growth. Remarkably, eIF3k showed the opposite pattern with depletion promoting global translation, cell proliferation, tumor growth, and stress resistance through repressing the synthesis of ribosomal proteins, especially RPS15A. Whereas ectopic expression of RPS15A mimicked the anabolic effects of eIF3k depletion, disruption of eIF3 binding to the 5 0 -UTR of RSP15A mRNA negated them. eIF3k and eIF3l are selectively downregulated in response to endoplasmic reticulum and oxidative stress. Supported by mathematical modeling, our data uncover eIF3k-l as a mRNA-specific module which, through controlling RPS15A translation, serves as a rheostat of ribosome content, possibly to secure spare translational capacity that can be mobilized during stress.

Perturbations in eIF3 subunit stoichiometry alter expression of ribosomal proteins and key components of the MAPK signaling pathways

“…This speculation can be supported by the impact of all knock-downs on translation efficiency of different E3 ubiquitin ligases, as described for eIF3h KD (Supplementary Table S5). Similar effect of increased RPs production was recently reported also for eIF3k KD (Duan et al, 2023). Of note, eIF3e KD also decreases protein levels of eIF3k and eIF3l and thus this RP- specific effect could be attributed to the loss of eIF3k.…”

“…Overall, our results suggest that eIF3e and, to some extent, its binding partner eIF3d maintain control over production of RPs in the cell. A similar role has recently been attributed to eIF3k, which has been shown to specifically repress the synthesis of the small ribosomal protein RPS15A, and cells depleted of eIF3k showed increased ribosomal content (Duan et al, 2023). As mentioned above, targeting eIF3e with siRNA results in co-downregulation of not only eIF3e and eIF3d, but also of eIF3k and eIF3l (Wagner et al, 2016).…”

“…Ten of the twelve eIF3 subunits have been linked to human cancers, many due to overexpression (a, b, c, d, g, h, m or i), some due to underexpression (e and f) (reviewed in (de la Parra et al, 2018b; Gomes-Duarte et al, 2018; Hershey, 2015; Valasek et al, 2017; Zhang et al, 2007)). In this regard it is worth stressing that some eIF3 subunits have been shown to directly interact with specific mRNAs (Lee et al, 2015), eIF3d together with DAP5 was shown to facilitate alternate form of cap-dependent mRNA translation (de la Parra et al, 2018a), and eIF3k was recently proposed to serve as a regulator of the balanced ribosome content (Duan et al, 2023). Despite all these relevant observations, the exact mechanism(s) by which eIF3 affects various pathologies is virtually unknown.…”