Abstract
Translation initiation is the rate-limiting step of protein synthesis that is downregulated during the Integrated Stress Response (ISR). Previously, we demonstrated that most human mRNAs that are resistant to this inhibition possess translated upstream open reading frames (uORFs), and that in some cases a single uORF is sufficient for the resistance. Here we developed a computational model of Initiation Complexes Interference with Elongating Ribosomes (ICIER) to gain insight into the mechanism. We explored the relationship between the flux of scanning ribosomes upstream and downstream of a single uORF depending on uORF features. Paradoxically, our analysis predicts that reducing ribosome flux upstream of certain uORFs increases initiation downstream. The model supports the derepression of downstream translation as a general mechanism of uORF-mediated stress resistance. It predicts that stress resistance can be achieved with long slowly decoded uORFs that do not favor translation reinitiation and that start with initiators of low leakiness.
Highlights
In eukaryotes, canonical translation initiation begins with the recognition of the m7G cap structure found at the 5’ end of mRNAs
What designates some upstream open reading frames (uORFs) as providers of stress resistance? To explore this, we developed a simple stochastic model of Initiation Complexes Interference with Elongating Ribosomes (ICIER) that is based on the Totally Asymmetric Simple Exclusion Process (TASEP)
Using ICIER under different parameters, we explored how the rate of scanning ribosomes arriving at the end of the lattice rout depends on the rate with which scanning ribosomes are loaded at the beginning of the lattice rin. rin corresponds to the rate of preinitiation complex (PIC) assembly at the 5’ end of mRNA, which depends on TC availability which is reduced upon eIF2 phosphorylation. rout corresponds to the rate of scanning ribosomes arrival to the start of the annotated coding ORFs (acORFs)
Summary
Canonical translation initiation begins with the recognition of the m7G cap structure found at the 5’ end of mRNAs. EIF4F recruits the 40S loaded with eIF2*tRNA*GTP (the so-called ternary complex, TC), eIF1, eIF1A and eIF5, along with the multi-subunit scaffold eIF3 to form a preinitiation complex (PIC). After the initiation codon is recognized, the chain of events leads to large ribosome subunit joining and initiation of polypeptide synthesis. Not all translation initiation events lead to the synthesis of annotated functional proteins. Many codons that are recognized as the starting points of translation occur upstream of annotated coding ORFs (acORFs) encoding functional proteins in many eukaryotic organisms (Pueyo et al, 2016; Johnstone et al, 2016; Wethmar, 2014; von Arnim et al, 2014; Barbosa et al, 2013; Somers et al, 2013; Vilela and McCarthy, 2003). Leader length varies greatly in mammalian mRNAs and at least 20% possess evolutionarily conserved AUG triplets upstream of acORFs
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