How potent is the eTIS in modulating start codon recognition?
Very potent!🦾
An mRNA with a strong distal eTIS and a weak TIS outperforms an mRNA with a strong TIS and a weak distal eTIS!
In conclusion, we identify a ~80-nt sequence region extending across both the 5’UTR and coding sequence, which we term the extended TIS (eTIS), and show that the eTIS determines translation initiation efficiency at start codons.
Curious to hear your thoughts!
How does the eTIS contribute to start codon recognition?
Single-molecule imaging by Carlos Alverado from the Puglisi lab revealed that the distal eTIS stimulates both initial start codon recognition and subsequent steps in translation initiation.
A subset of optimal eTIS residues directly engages the 48S initiation complex via nucleotide-specific interactions.
The +6 position, a strong hit in our RiboScan data, is one example, revealing a underappreciated role for this residue in translation.
Key +6G stabilizes 48S at the start codon.
Finally, could the eTIS be used to improve start codon recognition?
Yes, it can!
Optimizing the eTIS in endogenous mRNAs, as well as in mRNAs designed for therapeutic use, reduced leaky scanning and enhanced protein production.
Can we predict start codon recognition from sequence alone?
Together with @luciabarmar.bsky.social and Jeroen de Ridder, we built RiboScanner, a deep convolutional neural network trained on our RiboScan data, to do exactly that.
We find that the eTIS engages the initiation machinery in a spatially coordinated manner along the mRNA trajectory, integrating interactions at the decoding center with mRNA engagement at the ribosomal periphery.
In a great collaboration, @david-liedtke.bsky.social and @niels-fischer.bsky.social then went on to solve the structure of initiation complexes loaded on different mRNAs with different eTIS contexts using cry-EM.
The sequence logic we uncovered is not just visible in our assay... it is written into genomes!
Nucleotides that stimulate start codon recognition are enriched in genomic sequences, and this enrichment is evolutionarily conserved.🚶♂️🐭🪰
Thanks to all collaborators🙏, @david-liedtke.bsky.social and Valentyn from @niels-fischer.bsky.social lab, @luciabarmar.bsky.social from the de Ridder group, Carlos from the Puglisi lab, Michał Świrski and @edv.bsky.social, @michamuller.bsky.social and @marvintanenbaum.bsky.social!
