eIF3 associates with 80S ribosomes to promote translation elongation, mitochondrial homeostasis, and muscle health

Abstract

eIF3 is a multi-subunit complex with numerous functions in canonical translation initiation, including mRNA recruitment to the 40S ribosome, scanning for the start codon, and inhibition of premature 60S subunit joining 1-3 . eIF3 was also found to interact with 40S and 60S ribosomal proteins and translation elongation factors 4 , but a direct involvement in translation elongation has never been demonstrated. Using ribosome profiling, we found that eIF3 deficiency reduced early ribosomal elongation speed between codons 25 and 75 on a set of ~2,700 mRNAs encoding proteins associated with mitochondrial and membrane functions, resulting in defective synthesis of their encoded proteins. To promote early elongation, eIF3 forms stable protein interactions with 80S ribosomes translating the first ~60 codons and serves as a platform to recruit protein quality control factors, functions required for normal mitochondrial physiology. Accordingly, eIF3e +/knockout mice accumulate defective mitochondria in skeletal muscle and show a progressive decline in muscle strength with age. Hence, in addition to its canonical role in translation initiation, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for mitochondrial physiology and muscle health.The interaction of the 13 subunit eIF3 complex with mRNA is central to all forms of translation initiation, including cap-dependent and cap-independent mechanisms 5-7 . eIF3 promotes ternary complex recruitment, binding of the 43S pre-initiation complex to mRNA, as well as scanning processivity and fidelity 1,2 . Although eIF3 has traditionally been thought to be released from ribosomes upon 40S-60S subunit joining in vitro 8 , recent evidence in yeast 3 suggested that it can remain associated with 80S ribosomes during translation of short uORFs in order to facilitate re-initiation on downstream ORFs 9 . In addition, pull-down experiments indicated that yeast eIF3 forms stable in vivo interactions with factors involved in translation elongation (40S and 60S ribosomal proteins, eukaryotic elongation factors (eEFs), and tRNA synthetases), suggesting an unexplored role in integrating translation initiation with elongation 4 .

Robust T cell activation requires an eIF3-driven burst in T cell receptor translation

“…Importantly, the TCRA and TCRB mRNA 3'-UTR elements are necessary and sufficient to control this burst in translation (Figure 3). Recent evidence suggests that eIF3 can remain associated with translating ribosomes (Bohlen et al, 2020;Lin et al, 2019;Wagner et al, 2020), a phenomenon that seems to be enhanced for the pan-mRNAs identified here. Additional layers of translation regulation also contribute to T cell function (Tan et al, 2017), particularly with respect to mTOR signaling (Miyamoto et al, 2005;Myers et al, 2019) and carbon metabolism (Manfrini et al, 2017;Ricciardi et al, 2018).…”

A burst in T cell receptor translation mediated by eIF3 interactions with T cell receptor mRNAs

“…13a ). Recent evidence suggests that eIF3 can remain associated with translating ribosomes 34,35,36 a phenomenon that may be enhanced for the pan-mRNAs identified here. Notably, additional layers of translation regulation also contribute to T cell function 37 , particularly with respect to mTOR signaling 3, 38 and carbon metabolism 4, 39 .…”

eIF4G is retained on ribosomes elongating and terminating on short upstream ORFs to control reinitiation in yeast

“…While this manuscript was in preparation, a seminal selective 40S/80S ribosome footprinting work from the Teleman's lab revealed that scanning in majority of tested human cell lines occurs in a cap-tethered way and that eIF4G1 and eIF4E components of human eIF4F remain bound to 80S ribosomes during an early elongation phase (with a decay half-length of ∼12 codons) ( 17 ). Since these authors together with the Wolf's lab and us expectedly demonstrated that, besides the eIF4F factors, early human elongation complexes also carry eIF3 ( 12 , 16 ), and earlier evidence suggested an active involvement of mammalian eIF3, eIF4G and eIF4A in promoting REI ( 15 , 22 ), they proposed a simple model explaining the molecular basis of REI in mammals. It postulates that since majority of mammalian uORFs are believed to be permissive for REI ( 6 , 35 , 36 ), the fact that the cap-tethered eIF4F complex and eIF3 are temporarily retained on 80S ribosomes as they translate short uORFs suffices to prevent full ribosomal recycling and allow prompt assembly of the post-termination 48S complex.…”