Bacteria are not sterile to viruses: that is one of the main issues of the big food chain companies that need to use those bacteria. They are used in many food industries, in healthy ways: you need bacteria to ferment dairy products such as cheese and yogurt.
This is where, in 2013, the scientists discovered how bacteria create their immune response from viruses that infect them. The company Danisco was the first to work with bacteria and research new ways of protecting bacteria.
The viruses that infect bacteria are called bacteriophage. If, for example, one strain that makes cheese gets infected with a bacteriophage, you need to retire the strain, because industrially, you can’t sell it. As such, you need to develop cultures that are resistant to bacteriophages.
Take, as such, a bacterium population and expose it to a new virus: the virus comes in and kills the vast majority, but there is a small subset of the population that will survive. Why? That was the new variant: they possessed characteristics that made them able to withstand the bacteriophage.
Look here at this image: the bacteria was infected with a virus: the virus killed almost all the population, but some small subsets (transparent dots) survived the attack.
This is where genetic sequencing of the variant comes in: when scientists compared the genetic strand of the variant to that of the normal bacteria, they were 99.9999% identical across the 2 million DNA letters. The only difference that was observed was right at the CRISPR array.
What is the CRISPR array?
CRISPR (from Clustered Regularly Interspaced Short Palindromic Repeats) is the DNA adaptive immune system. If infected by a virus, it keeps a part of its DNA and stores it. It is a combination of a repeat section and a spacer: the repeat is the identical part of the DNA that is used to then encode proteins. However, the spacers are all unique, and will not encode any proteins.
Coming back to the initial experience of the bacteria population that survived: the striking difference was that at the end of the variant that survives, there is one more repeat and a spacer.
And most importantly, the spacer sequence that gets added every time the bacteria survives an infection of a phage corresponds exactly to the DNA sequence of the phage that is used.
As such, if you add synthetically a spacer, the bacteria will become resistant to the phage of which sequence you used. Opposedly, if you remove the spacer, the bacteria loses its resistant abilities.
But the only thing is that the CRISPR sequence is not alone: before the spacers, we find some Crispr-Associated-Genes, called CAS genes. If we modify those CAS genes, does it have an impact on the expression of CRISPR?
So we know there are 4 Cas molecules before the CRISPR array: those are cas1, cas2, cns2 and cas9. If you inactive the cas9 molecule, the ability to be resistant will also be lost even if the spacer is still there. As such, the spacer is not enough, but you also need the CAS genes. If you knock out Csn2, you don’t lose resistance, but you lose the ability to acquire new spacers. So the CAS genes don’t only allow you to be immune, but they also help for immunization.
Photo sources:
Phage plaques on an Erwinia lawn.
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