Oral Presentation Australasian RNA Biology and Biotechnology Association 2025 Conference

Synthetic RNA-binding proteinsĀ for controlling gene expression (129723)

Ian Small 1 , Farley Kwok van der Giezen 1 , Michael Dennis 1 , Su Yi Low 1 , Amy Viljoen 1 , Anuradha Pullakhandam 1 , Charlie Bond 1
  1. University of Western Australia, Crawley, WA, Australia

RNA has an essential role in gene expression as a template for protein translation and a platform for post-transcriptional regulatory controls. Programmable RNA-targeting technologies would have many biotechnological and therapeutic applications, but achieving high specificity and efficiency remains challenging. Pentatricopeptide repeat (PPR) proteins are a superfamily of RNA-binding proteins that sequence-specifically recognize RNA via particular amino acid combinations in each repeat. Their modular nature and relatively well-understood RNA base recognition characteristics make them an attractive target for protein design. Although especially prevalent in plant organelles, they also function effectively in heterologous systems including bacteria and mammalian cytosol. As RNA-binding specificity is encoded in the peptide sequence, this gives them an advantage for targeting organellar RNA as it avoids the necessity to transport guide RNAs through organelle membranes. We have developed a MoClo-compatible kit for high-throughput synthesis of custom PPR proteins and demonstrated its utility by creating and testing a set of PPR-based RNA editing enzymes in a cell-free expression system. We are currently working towards developing switches for chloroplast gene expression based on PPRs that catalyse translation-enabling RNA editing events (creating translation start codons or removing premature stop codons), thus mimicking the novel mechanisms for control of organelle gene expression found in ferns, lycophytes and hornworts. These proteins have exciting potential in synthetic biology for tight control of the translatability of target mRNAs.

  1. GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins https://doi.org/10.1101/2025.06.29.661641