Retrons and CRISPR—Two Gene Editing tools - BiopharmaDirect

Retrons and CRISPR—Two Gene Editing tools

The Nobel Prize in Chemistry 2020 was awarded jointly to Emmanuelle Charpentier and Jennifer A. Doudna for their discovery of a method called CRISPR for genome editing. CRISPR is viewed as the genetic scissors that can rewrite the code of life. Researchers use CRISPR to change the DNA of living organisms, which is beneficial to both basic research innovative medical treatments. Now, researchers have found a new gene editing tool called Retrons, which are expected to be used in combination with CRISPR to achieve better performances.

In early November, the Rotem Sorek team from the Weizmann Institute of Science in Israel published an article on Cell, introducing their newly discovered reverse transcriptase-based gene editing tool—Retrons. Similar to CRISPR, this tool can protect microorganisms from phage viruses, and researchers are expected to use it to edit the genes of single-celled organisms.

As early as more than 30 years ago, scientists discovered reverse transcriptase from Myxococcus flavus. This genetic element is composed of DNA, RNA and proteins from certain bacteria, but their role in organisms remains to be a mystery. According to Science reports, in the newly published research, Sorek and other scientists have found reverse transcriptase in many bacteria. They first searched the genomes of nearly 40,000 bacteria and used computer programs to find antiviral structures similar to CRISPR and other known antiviral constructs.

Later, the researchers found a piece of DNA that contains reverse transcriptase and is flanked by DNA fragments that cannot encode any known bacterial proteins. Researchers think that these mysterious sequences may play a role in RNA coding. In addition, DNA with reverse transcription is usually accompanied by a protein-coding gene, and the protein carried by each genetic element is different.

Sorek et al. speculate that these sequence clusters are involved in a new phage defense. In follow-up studies, they further proved that Ec48, an element containing reverse transcriptase, a mixture of DNA and RNA, and proteins, can destroy newly infected cells, making the virus unable to replicate and spread.

Coincidentally, a research team in the European Molecular Biology Laboratory has similar findings. They found toxic protein genes next to the reverse-transcribed coding genes in Salmonella. Under normal circumstances, toxins are encapsulated and are only activated when phage proteins appear. The relevant research was published on the preprint platform bioRxiv in June this year.

Figure 1 Gene-editing pipeline takes off. (Adi Millman, et al., 2020)

In the 1980s, researchers studying soil bacteria were puzzled to find that many short single-stranded DNA sequences were scattered in the cytoplasm of bacteria. Immediately afterwards, the researchers discovered that every piece of DNA would be connected to RNA with complementary base sequences, which made them realize that an enzyme called reverse transcriptase synthesizes DNA from the attached RNA and forms a complex composed of RNA, DNA and enzymes. Later, scientists discovered that this complex is a retron, which is a new bacterial defense system that prevents phage infection.

Researchers can use CRISPR to target and cut target regions in the genome. Despite the fact that CRISPR is highly targeted, so far it has not been a good choice to introduce new codes into target DNA. In contrast, reverse transcriptase can make a large number of copies of the target sequence through reverse transcriptase, and these copies can be effectively spliced into the host genome. Therefore, if the reverse transcriptor can be integrated with CRISPR, a new and more powerful gene editing tool may be developed. But at present, it has not been confirmed as to whether retrons can be used in mammalian cells. Much work remains to be done in the near future.

• Adi Millman, et al. Bacterial Retrons Function in Anti-Phage Defense. Cell. 2020.