Deciphering the in vivo RNA structure code in regulating protein translation in plants

DING_J22DTP2

Codon optimisation is a common method in synthetic biology to achieve high levels of protein expression. It relies on the creation of so-called “silent” or synonymous mutations within a coding sequence, such that the DNA/RNA sequence is altered but the resulting amino acid sequence remains unchanged. Codon optimisation mainly takes into account codon usage bias (i.e. which of the 61 codons encoding for one of 20 amino acids are preferentially used in a given species), although more sophisticated online tools also use additional parameters such as GC content, mRNA structure, repetitive sequences and inadvertent introduction of regulatory cis-elements.

This project will study the effect of synonymous mutations on in vivo RNA structure and how this can be used to improve codon optimisation to achieve greater control over transgene expression in plants. The project will define the structure of RNA species in vivo and compare this to phenotypic analysis of synonymous mutants in plants. This work will be essential to shed new light on how synonymous mutations influence RNA structure and thus protein function in living cells. The student will receive extensive training in molecular biology, synthetic biology, nucleic acid chemistry and bioinformatics. The successful applicant will enjoy the benefits of working at both the John Innes Centre and the University of East Anglia.

References
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2. Yang, M., Woolfenden, H. C., Zhang, Y., Fang, X., Liu, Q., Vigh, M. L., Cheema, J., Yang, X., Norris, M., Yu, S., Carbonell, A., Brodersen, P., Wang, J. & Ding, Y. Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo. Nucleic Acids Res 48, 8767-8781, (2020).

3. Zhang, H. & Ding, Y. Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants. Biochem Soc Trans 49, 1829-1839, (2021).