NATURAL BIODIVERSITY OF PHAGES AS A TOOL TO STUDY BREX, A NOVEL BACTERIAL DEFENSE SYSTEM

The perpetual arms race between bacteria and phages has resulted in the evolution of efficient resistance systems, such as CRISPR and restriction enzymes, that protect bacteria against phage infection. We have recently discovered a new defense system, BREX¹, which is present in ~10% of the sequenced prokaryotic genomes. We have shown that BREX protects bacteria against an array of phages from multiple families. As BREX defense level varied among different phages, we sought to use this diversity as a tool to understand the mechanism of action of BREX. To this end, we isolated and sequenced a large collection of phages from environmental samples. We used this collection to challenge bacteria containing the full BREX system - comprised of 6 genes - as well as BREX systems with single deletions of BREX proteins.

We found that pglX, an adenine methylase, was essential for the defense against all phages tested. Deletion of brxL, a Lon-like protease, impeded BREX defense against only a subset of phages. Surprisingly, deletion of brxA, a putative RNA-binding protein, was found to improve BREX defense against some phages, leading to the hypothesis that this gene encodes a negative regulator of the system. BREX systems lacking brxB, brxC or pglZ were apparently toxic to the host bacteria. Finally, by sequencing and comparing a set of 44 closely related phages we revealed a putative anti-BREX gene within a subset of the phages, pointing to an ongoing, active BREX-mediated arms race between phages and bacteria.

¹ Goldfarb et al. EMBO J 34:169-183 (2015).