Establishing a Standardized Genetic Toolkit for the Radiation-Resistant Extremophile Deinococcus radiodurans

Deinococcus radiodurans is a highly radiation-resistant extremophile with potential for biomanufacturing and bioremediation in harsh environments including extraterrestrial settings. However, engineering in this organism has been constrained by limited genetic tools. Here, we establish a comprehensive genetic toolkit for D. radiodurans that enables tunable gene regulation with genome engineering tools. We have standardized a library of 32 constitutive promoter sequences sourced from the native D. radiodurans genome and from synthetic sources, spanning a 45-fold range of gene expression in the context of plasmid-based expression. We have also identified 125 variants of ribosome binding sites (RBS), using a high-throughput screen for precise translational control across a 963-fold range of expression when used in our plasmid-based system. Additionally, we have developed a codon-optimizer script that we leverage to improve the function of four fluorescent proteins in D. radiodurans. Next, we characterized 9 small-molecule-inducible promoter systems and identified four key inducible promoter systems that achieve between 3-fold and 12-fold signal amplification, as well as titratability across induction concentrations in D. radiodurans. To engineer the D. radiodurans genome, we present a method for gene integration, compatible with de novo sequences, up to 3 kB in length, doing so with 70% efficiency. Lastly, we repurpose the RNA-directed nuclease, TnpB, as a novel post-transcriptional tool for programmable gene repression analogous to CRISPRi-based systems, and this tool can achieve between 40% and 70% repression of its target. Collectively, this toolkit provides modular, standardized components for both plasmid engineering and chromosomal engineering in D. radiodurans to improve its genetic tractability and facilitate its deployment.