Hollerer, Simon and Jeschek, Markus (2023) Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript. NUCLEIC ACIDS RESEARCH, 51 (5). pp. 2377-2396. ISSN 0305-1048, 1362-4962
Full text not available from this repository. (Request a copy)Abstract
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 various 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 provide clear experimental evidence for 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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | SHINE-DALGARNO SEQUENCE; RIBOSOME BINDING-SITES; ESCHERICHIA-COLI; MESSENGER-RNA; GENE-EXPRESSION; SECONDARY STRUCTURE; PROTEIN EXPRESSION; START CODON; USAGE BIAS; EFFICIENCY; |
| Subjects: | 500 Science > 570 Life sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Biochemie, Genetik und Mikrobiologie > Lehrstuhl für Mikrobiologie (Archaeenzentrum) > Prof. Dr. Dina Grohmann |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 12 Mar 2024 10:19 |
| Last Modified: | 12 Mar 2024 10:19 |
| URI: | https://pred.uni-regensburg.de/id/eprint/59711 |
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