RT Journal Article
SR Electronic
T1 Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.05.02.490318
DO 10.1101/2022.05.02.490318
A1 Simon Höllerer
A1 Markus Jeschek
YR 2022
UL http://biorxiv.org/content/early/2022/05/02/2022.05.02.490318.abstract
AB Translation is a key determinant of gene expression and an important biotechnological engineering target. In bacteria, 5’-untranslated region (5’-UTR) and coding sequence (CDS) are well-known mRNA parts controlling translation and thus cellular protein levels. However, the complex interaction of 5’-UTR and CDS has so far only been studied for few sequences leading to non-generalisable and partly contradictory conclusions. Herein, we systematically assess the dynamic translation from over 1.2 million 5’-UTR-CDS pairs in Escherichia coli to investigate their collective effect using a new method for ultradeep sequence-function mapping. This allows us to disentangle and precisely quantify effects of known and hypothetical sequence determinants of translation. We find that 5’-UTR and CDS individually account for 53% and 20% of variance in translation, respectively, and show conclusively that, contrary to a common hypothesis, tRNA abundance does not explain expression changes between CDSs with different synonymous codons. Moreover, the obtained large-scale data clearly point to a base-pairing interaction between initiator tRNA and mRNA beyond the anticodon-codon interaction, an effect that is often masked for individual sequences and therefore inaccessible to low-throughput approaches. Our study highlights the indispensability of ultradeep sequence-function mapping to accurately determine the contribution of parts and phenomena involved in gene regulation.Competing Interest StatementThe authors have declared no competing interest.