By Dr Heather Hendrickson, Senior Lecturer, Massey University
The microbial world is an invisible war zone where tiny combatants – bacteria, viruses, molds and amoebae – are fiercely competing for resources.
In this microbial melee there are no pulled punches and anything goes. The viruses that attack bacterial cells are called bacteriophages and there are estimated to be ~10 of these menacing each bacterial cell at any given time. Bacteriophages will inject their DNA into bacterial cells, take over and force the cell to replicate them, ultimately being burst open to release the bacteriophages.
CRISPR-Cas is the bacterial adaptive immune system and it allows bacterial cells under attack by bacteriophages or other selfish genetic elements (like plasmids) to recognize and destroy invasive DNA quickly in order to protect their genetic integrity and stay alive and about half of bacteria appear to have this system (Fig 1A).
In a series of elegant experiments published in Nature Microbiolgy, Pawluk and colleagues were previously able to demonstrate the existence of anti-CRISPR systems, able to shut down the adaptive immune system. Bacteriophages or plasmids that carry these genes can infect bacteria even when they should be recognized and eliminated by the CRISPR-Cas system, a little like a “get out of jail, free” card. Previously, they discovered a family of these anti-CRISPR genes but they were not widely distributed.
This new study shows that there are several versions of these types of anti-CRISPR genes and that they appear to have completely separate origins (they are not related to one another) and therefore appear to have evolved multiple times, from scratch. Intriguingly, there are two flavours of the CRISPR-Cas system and in this study they were surprised to discover an anti-CRISPR gene system that can confer immunity to either CRISPR-Cas system.
Implications for Horizontal Gene Transfer
The introduction and the discussion of the paper focus on the Horizontal Gene Transfer (HGT) implications of the anti-CRISPR systems. HGT is the transfer of DNA, often across species boundaries. Importantly, genes that are transferred via HGT can be anything including virulence factors and antibiotic resistance. HGT happens in a few different ways, the two that are most relevant to this discussion are plasmid or bacteriophage mediated transfer (Fig 1B). Plasmids are tiny loops of DNA that can sometimes self-mobilize; building tunnels between bacterial cells, copying themselves and moving.
HGT via bacteriophages occurs primarily when bacteriophages accidentally package bacterial DNA and inject it into cells they are attempting to infect, rather than injecting their own DNA. The CRISPR-Cas adaptive immunity relies on the system keeping, replenishing and referring to a library of DNA fragments that have been harvested from previously encountered infectious elements. Generally, a CRISPR-Cas library will have a selection of short segments from various bacteriophages and plasmids. However, when bacteriophages transfer genetic material between bacterial strains, the viral particles generally do not contain any bacteriophage DNA. This makes the relationship between bacteriophage defenses (like CRISPR-Cas) and the frequency of gene transfer two essentially unrelated topics. CRISPR-Cas, targets bacteriophage DNA and HGT by bacteriophages specifically involves the absence of that bacteriophage DNA.
The anti-CRISPR systems reported in this paper involve bacteriophages that have integrated into the bacterial genome after successfully infecting the cell. These have been found to have previously un-described genes with anti-CRISPR activity.
This study increases our understanding of the offensive and defensive strategies in the invisible world. These findings are exciting because by understanding how invasive elements are able escape destruction we increase our own arsenal of tools that we can use to manipulate bacteria. The idea that bacteriophages sometimes carry these “get out of jail, free” cards that allow them to out-maneuver bacterial defenses is intriguing and makes sense from an evolutionary point of view. We should not be surprised when we discover that bacteria have also found ways of overcoming these anti-CRISPR systems, such is the nature of the microbial arms race.
Featured image: Transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall; the magnification is approximately 200,000. Credit: Dr Graham Beards.