A gene-editing system similar to the bacterial CRISPR-Cas system has been discovered in a virus for the first time (Levasseur et al., 2016). The system was discovered in a giant virus called mimivirus, which uses it as a defence against infection by smaller viruses called virophages. The future will reveal whether this, like CRISPR, could be exploited as a tool for genetic manipulation in mammalian cells.
The discovery that a bacterial defence system against virus infection can be repurposed for editing genes in human cells has undoubtedly been one of the biggest achievements in modern science (Jinek et al., 2012, Mali et al., 2013, Cong et al., 2013). This system, called CRISPR-Cas9, allows bacteria to retain a memory of viruses (called bacteriophages) that have infected them in the past so that they can respond to them more efficiently during subsequent encounters. The bacteria essentially cut and paste DNA from the virus into a part of their own DNA called CRISPR. Later, when they encounter the same virus again, this allows them to recognise the virus DNA and cut it up with a pair of molecular scissors called Cas9. Scientists soon recognised that this CRISPR-Cas9 system could be exploited to cut genes inside human cells too: the Cas9 enzyme could be guided to specific human genes and used to cut and edit them in a controlled way.
In traditional gene therapy, viruses are often used as vectors to deliver healthy genes to the cells of people suffering from genetic diseases. For example, this kind of treatment has benefitted patients suffering from severe combined immunodeficiency (SCID) (Hacein-Bey-Abina et al., 2010) caused by a single gene defect. However, these treatments provide a healthy gene rather than fixing a faulty one. Now, instead of simply carrying a healthy gene, the virus could carry the Cas9 enzyme as well as special guide molecules and so provide the cell with the tools required to fix the faulty gene directly.
Scientists tested this idea on mice with the equivalent of the human genetic disease Duchenne muscular dystrophy (DMD), which causes muscle deterioration and premature death. DMD is caused by a fault in the dystrophin gene, which is required for muscle contraction. The scientists found that they could use CRISPR-Cas9 to remove the faulty part of the dystrophin gene and thereby reverse the disease (Nelson et al., 2016, Tabebordbar et al., 2016). There are countless other examples of the power of CRISPR being harnessed to try and treat diseases, for example, to erase HIV DNA from latently infected cells (Hu et al., 2014) or to engineer immune cells that are better at killing cancer cells (Schumann et al., 2015). CRISPR is also invaluable as a tool in basic biomedical research to better understand cellular processes in health and disease.
But CRISPR might have competition. Recently, a team of virologists in France made a striking discovery. Bacteria are not the only microbes with a gene editing system – viruses have one too! The scientists discovered a system analogous to CRISPR-Cas in giant viruses. These giant viruses are called mimiviruses and have been causing a stir in the microbiology field since they were first discovered in 2003 (La Scola et al., 2003). These viruses are so massive that they are larger than some bacteria. In fact, their name “mimi” comes from “mimicking microbe”. Unlike bacteria, however, mimiviruses are entirely dependent on their host cells to replicate and so fit the definition of a virus.
As if giant viruses weren’t crazy enough, a few years later the same research team discovered another interesting phenomenon (La Scola et al., 2008): viruses infecting other viruses! Virophages, as they named them, were viruses that could parasitise the mimivirus in the same way mimivirus and other viruses parasitise cells. Fascinated by this virus-ception, the scientists started looking for more virophages that could infect members of the mimivirus family.
In 2014, the scientists discovered a new virophage (Gaia et al., 2014), which they found particularly intriguing. They named it Zamilon, which is Arabic for “the neighbour”. Zamilon was interesting to the researchers because it could infect some mimiviruses but not others. It became clear that some mimiviruses were resistant to Zamilon and they wanted to find out why.
By comparing mimiviruses that were resistant to Zamilon with those that were susceptible, the scientists noticed something curious: all the mimiviruses that were resistant to Zamilon contained an insertion of Zamilon DNA in one of their genes. When this mimivirus gene was inhibited, the mimiviruses lost their resistance to Zamilon and became infected. This was immediately reminiscent of the CRISPR-Cas system in bacteria, whereby bacteria insert DNA from invading viruses into their own CRISPR DNA. To investigate whether this really was a CRISPR-Cas-like system in the mimiviruses, the scientists looked for proteins similar to Cas9 inside the mimivirus. They found 2 genes nearby the inserted virophage DNA, which encoded proteins that looked very similar to the family of enzymes to which Cas9 belongs. When they tested the functions of these proteins, they found that one of them could cause unwinding of DNA, whereas the other could cut DNA – just like Cas9!
The scientists named this viral CRISPR-Cas-like system MIMIVIRE, for mimivirus virophage resistance element. Further investigation will be required to understand exactly how the MIMIVIRE system works and in particular how the Cas-like proteins are targeted to the virophage DNA.
With a better understanding of how the MIMIVIRE system works, scientists may reveal a new opportunity to harness a microbial mechanism for gene editing. Perhaps MIMIVIRE will be able to complement CRISPR, broadening the gene editing toolkit. This discovery also demonstrates for the first time that viruses, like bacteria, may be capable of retaining a molecular memory of what has infected them before. The parallels with our own immune systems are remarkable given that viruses are not even considered to be truly alive.
Layal Liverpool is a PhD student at University of Oxford and a FameLab Oxford 2016 finalist.
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