eIF3 and Its mRNA-Entry-Channel Arm Contribute to the Recruitment of mRNAs With Long 5′-Untranslated Regions

Abstract

Translation initiation in eukaryotes is a multi-step pathway and the most regulated phase of translation. Eukaryotic initiation factor 3 (eIF3) is the largest and most complex of the translation initiation factors, and it contributes to events throughout the initiation pathway. In particular, eIF3 appears to play critical roles in mRNA recruitment. More recently, eIF3 has been implicated in driving the selective translation of specific classes of mRNAs. However, unraveling the mechanism of these diverse contributions—and disentangling the roles of the individual subunits of the eIF3 complex—remains challenging. We employed ribosome profiling of budding yeast cells expressing two distinct mutations targeting the eIF3 complex. These mutations either disrupt the entire complex or subunits positioned near the mRNA-entry channel of the ribosome and which appear to relocate during or in response to mRNA binding and start-codon recognition. Disruption of either the entire eIF3 complex or specific targeting of these subunits affects mRNAs with long 5′-untranslated regions and whose translation is more dependent on eIF4A, eIF4B, and Ded1 but less dependent on eIF4G, eIF4E, and PABP. Disruption of the entire eIF3 complex further affects mRNAs involved in mitochondrial processes and with structured 5′-untranslated regions. Comparison of the suite of mRNAs most sensitive to both mutations with those uniquely sensitive to disruption of the entire complex sheds new light on the specific roles of individual subunits of the eIF3 complex.

JUNmRNA Translation Regulation is Mediated by Multiple 5’ UTR and Start Codon Features

“…These secondary structure elements may serve potential regulatory roles, similar to the one shown for the eIF3-interacting SL. These results are consistent with previous findings which have correlated long and highly structured 5′ UTRs with complex regulation mediated by eIF3 (Stanciu et al 2022). However, it remains to be determined whether eIF3 interacts directly with these regions.…”

“…Due to its length and complexity, JUN ’s 5′ UTR might present additional layers of translational regulation of its mRNA through novel structural and/or sequence elements. Previously reported involvement of several initiation factors, including eIF3 and eIF4A, in the recruitment of mRNAs with long and structurally complex 5′ UTRs further supports a 5′ UTR-mediated mechanism for JUN translation regulation and suggests that additional factors may be involved in JUN regulation (Stanciu et al 2022). For example, JUN was recently shown to be sensitive to RocA, an anti-cancer drug that clamps eIF4A onto specific polypurine sequences in the 5′ UTRs of a subset of mRNAs (Iwasaki et al 2016, 2019).…”

eIF3 Interacts with Selenoprotein mRNAs

“…No obvious sequence or structure conservation could be found in the 5′UTR of the mRNAs. In yeast, disruption of the eIF3 complex affects the translation of mRNAs with long 5′-UTR regions and whose translation is more dependent on eIF4A, eIF4B, and Ded1 but less dependent on eIF4G, eIF4E, and PABP [ 61 ]. Unlike what was observed in yeast, the size of the 5′UTR of mammalian selenoprotein mRNAs bound to eIF3 was similar to that of unbound mRNAs.…”

JUN mRNA translation regulation is mediated by multiple 5’ UTR and start codon features

“…Due to its length and complexity, JUN ’s 5′ UTR might present additional layers of translational regulation of its mRNA through novel structural and/or sequence elements. Previously reported involvement of several initiation factors, including eIF3 and eIF4A, in the recruitment of mRNAs with long and structurally complex 5′ UTRs further supports a 5′ UTR-mediated mechanism for JUN translation regulation and suggests that additional factors may be involved in JUN regulation [ 58 ]. For example, JUN was recently shown to be sensitive to RocA, an anti-cancer drug that clamps eIF4A onto specific polypurine sequences in the 5′ UTRs of a subset of mRNAs [ 33 , 34 ].…”