# New retron systems from environmental bacteria identify triggers of anti-phage defense and expand tools for genome editing

## TL;DR

This study discovers new retron systems from environmental bacteria, revealing how they defend against phages and expand genome editing tools.

## Contribution

The paper introduces seven new retron systems from environmental bacteria and explores their phage defense and genome editing potential.

## Key findings

- Seven new retron systems were identified from diverse environmental bacterial hosts.
- Two retrons remain functional despite disruptions by other genetic elements.
- Phage genes triggering retron-based defense were identified for two retrons.

## Abstract

Retrons are bacterial immune systems that protect a bacterial population against phages by killing infected hosts. Retrons typically comprise a reverse transcriptase (RT), a template noncoding RNA that is partially reverse transcribed into RT-DNA, and a toxic effector. The reverse transcriptase (RT), noncoding RNA, and RT-DNA complex sequester the toxic effector until triggered by phage infection, at which point the toxin is released to induce cell death. Due to their ability to produce single-stranded DNA in vivo, retrons have also been engineered to produce donor templates for genome editing in both prokaryotes and eukaryotes. However, the current repertoire of experimentally characterized retrons is limited, with most retrons sourced from clinical and laboratory strains of bacteria. To better understand retron biology and natural diversity, and to expand the current toolbox of retron-based genome editors, we developed a pipeline to isolate retrons and their bacterial hosts from a variety of environmental samples. Here, we identify seven new retron systems, each isolated from a different host bacterium. We characterize DNA production by these retrons and test their ability to defend against a panel of Escherichia coli phages. We find that two of these retrons are disrupted by other elements, in one case a group II intron and in another a separate defense system, yet both retrons still produce RT-DNA. For two other retrons, we further unravel their mechanism of defense by identifying the phage genes responsible for triggering abortive infection. Finally, we engineer these retrons for genome editing in E. coli, demonstrating their potential use in a biotechnological application.

Bacteria rely on retrons for phage defense, yet most known systems come from clinical or lab strains. This study identifies new and diverse retrons from environmental bacteria, uncovering their phage defense mechanisms and applying them as genome editing tools.