BREX is a novel phage resistance system widespread in microbial genomes

Abstract

The perpetual arms race between bacteria and phage has resulted in the evolution of efficient resistance systems that protect bacteria from phage infection. Such systems, which include the CRISPR-Cas and restriction-modification systems, have proven to be invaluable in the biotechnology and dairy industries. Here, we report on a six-gene cassette in Bacillus cereus which, when integrated into the Bacillus subtilis genome, confers resistance to a broad range of phages, including both virulent and temperate ones. This cassette includes a putative Lon-like protease, an alkaline phosphatase domain protein, a putative RNAbinding protein, a DNA methylase, an ATPase-domain protein, and a protein of unknown function. We denote this novel defense system BREX (Bacteriophage Exclusion) and show that it allows phage adsorption but blocks phage DNA replication. Furthermore, our results suggest that methylation on non-palindromic TAGGAG motifs in the bacterial genome guides self/non-self discrimination and is essential for the defensive function of the BREX system. However, unlike restriction-modification systems, phage DNA does not appear to be cleaved or degraded by BREX, suggesting a novel mechanism of defense. Pan genomic analysis revealed that BREX and BREX-like systems, including the distantly related Pgl system described in Streptomyces coelicolor, are widely distributed in~10% of all sequenced microbial genomes and can be divided into six coherent subtypes in which the gene composition and order is conserved. Finally, we detected a phage family that evades the BREX defense, implying that anti-BREX mechanisms may have evolved in some phages as part of their arms race with bacteria.

Evolutionary Ecology of Prokaryotic Immune Mechanisms

“…Bioinformatics analyses predict the existence of many more immune mechanisms, often clustered together in defense islands (112). One such mechanism, coined bacteriophage exclusion (BREX), is widely distributed across bacteria and appears to share some mechanistic features with RM systems (261). We are starting to understand how all these different immune mechanisms work, but the next challenge is to examine when these mechanisms are favored over one another and how they are integrated during antiviral responses.…”

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

“…lacusprofundi (Goldfarb et al, 2015), with a portion of the BREX genes contained on a~14 kb HIR present only in DL31 and Hrr. lacusprofundi, and FR coverage was low for the region containing the pglX gene (Supplementary Figure S7 Figure S7).…”

“…lacusprofundi also potentially provide an additional mechanism for modulating the impact of viruses (Goldfarb et al, 2015), but much remains to be learned about the activity, viral specificity and dissemination of this system. Surveys of bacterial and archaeal genomes have shown that the pglX gene is prone to variation, including gene disruption, duplication and possible phase variation (Goldfarb et al, 2015). The metagenome FR data reveal that a high level of withinpopulation variation exists for pglX in Hrr.…”

“…To date, analyses of CRISPR systems of haloarchaeal communities have only been examined using DNA sequence data of environmental samples, and not from functional studies (for example, metaproteomics) which have the added potential to inform about the genes expressed by active members of the communities (both hosts and viruses), and the molecular mechanisms of ongoing interactions. Recently, Bacteriophage Exclusion (BREX) systems were described that function in Bacillus species by preventing viral replication (Goldfarb et al, 2015). BREX gene clusters are present in~10% of sequenced bacterial and archaeal genomes, including the Type 5 system which has only been identified in haloarchaea, including DL31 and Hrr.…”

“…BREX gene clusters are present in~10% of sequenced bacterial and archaeal genomes, including the Type 5 system which has only been identified in haloarchaea, including DL31 and Hrr. lacusprofundi (Goldfarb et al, 2015).…”