Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation

Abstract

Highlights d RCP-seq allows the study of both scanning and translating ribosomal complexes d Threading of mRNA through the small ribosomal subunit loads the subunits onto the 5 0 UTR d Processivity of small ribosomal subunits is high while scanning 5 0 UTRs d Direct measurements of initiation redefine optimal start codon context

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

“…One of the reasons underlying this correlation lies in a higher potential of long 5 0 UTRs to create secondary RNA structures. Indeed, a mere extension of 5 0 UTR without introduction of secondary RNA structures does not significantly impact translation (Hinnebusch, 2011), which agrees with data suggesting comparable ribosome scanning efficiency on 5 0 UTRs of different lengths (Giess et al, 2020). The presence of secondary structures negatively correlates with TE of the respective mRNA in cells of multiple origins, from bacteria to humans (Araujo et al, 2012;Yus et al, 2017;Leppek et al, 2018;Li et al, 2019).…”

“…For instance, when MEF cells are starved for glucose, mRNAs bearing either A or G nucleotides at the cap-proximal residue recruit eIF4E more efficiently, promoting the initiation of their translation (Tamarkin-Ben-Harush et al, 2017). A recent genome-wide study of translation initiation in the developing zebrafish embryo reported similar observations, suggesting that mRNAs having cytosine at the +1 position, particularly those followed by the TOP motif (see below), exhibit less efficient 43S scanning (Giess et al, 2020). Collectively, these findings support the notion that the first transcribed nucleotide, stemming from either use of alternative promoters or as a part of clustered transcription initiation sites, is a critical determinant regulating the efficiency of mRNA translation.…”

“…While additional studies revealed differential translation initiation factor requirements for TISU-mediated translation (Haimov et al, 2017(Haimov et al, , 2018, establishing it as a noncanonical mode of translation initiation, the mechanism enabling translation upon energy stress is not entirely understood. Indeed, this feature is in contrast to the particularly strong translational arrest of TISU-containing mRNAs upon eIF4E inhibition (Elfakess et al, 2011;Giess et al, 2020). Importantly, TSS-seq of free and polysome-associated mRNAs revealed that scanning-independent translation of short 5 0 UTR mRNAs that operate without or with minimal scanning comprises a significant part of the translatome, highlighting the importance of this form of translation initiation (Haimov et al, 2017).…”

“…However, also in normal conditions, mRNA isoforms harboring TOP motifs are translated less efficiently (Wang et al, 2016). A recent genome-wide analysis of translation initiation in the developing zebrafish embryo showed that this phenomenon could stem from the less efficient recruitment of the scanning 43S structures to mRNAs with TOP motifs (Giess et al, 2020). The less efficient translation initiation may have an essential role in the overall efficiency of the translation process.…”

DENR promotes translation reinitiation via ribosome recycling to drive expression of oncogenes including ATF4

“…To this end, we employed 40S ribosome footprinting, which captures the positions of 40S ribosomes during scanning and recycling 47 . We and others recently adapted this method for animal cells 29,48,49 . This revealed that loss of DENR causes a strong accumulation of 40S recycling intermediates on stop codons of both main ORFs (mORFs) (Fig.…”