An experimental census of retrons for DNA production and genome editing
Retrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) they produce encodes an editing donor. Retrons are quite common in bacteria: thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally, for RT-DNA production or genome editing. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons and quantified their RT-DNA production; identified the natural sequence of RT-DNA they produce; and quantified the relative rates of editing using retron-derived donors in bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons. We find that top performing editors outperform those used in previous studies, and are not drawn randomly from the retron phylogeny.