The secret of microbes helps defeat DNA viruses – and it has the potential for genome-editing

Seven years ago, an understanding of nature inspired a revolutionary new technology, while the defense system used by researchers to insert viruses into a gene-editing tool is now known as CRISPR. But understanding for other emerging gene editors has lagged behind apps. For many years, researchers have been adapting to the mysterious complex of DNA, RNA and proteins found in some bacteria – a potentially powerful return to the genome of single-celled organisms. Now, biology is catching on, as two groups provide evidence that, like CRISPR, retron is part of a bacterial immune arsenal that protects microorganisms from viruses called phages.

Last week Cell, A team described how a particular retron protects against bacteria, triggering newly infected cells to self-repel so that the virus does not replicate and spread to others. This Cell Paper is the first to determine the natural function of the retron, says Anna Simon, an artificial biologist at Strand Therapeutics who studies bacterial oddities. Another paper, which has so far only appeared as a printprint, reports the same discovery.

A new understanding of the natural function of the retro may accelerate the efforts to employ them. Retron is “a very efficient tool for accurate and efficient genome acquisition,” says Rotem Sorek, a microbial genomist and author of the Wittzmann Institute of Science. Cell Study. But they have yet to compete with CRISPR, in part because the technology to work in mammalian cells has not been developed.

In the 1980’s, researchers studying the soil bacterium were surprised to find many copies of a short series of single-strand DNA that spreads to cells. A lot of mystery came to light when they found out that every bit of DNA is connected to RNA with a complementary base sequence. Eventually they realized that an enzyme called reverse transcriptus made DNA from attached RNA, and that all three molecules, RNA, DNA, and the enzyme, formed a complex.

Similar constructions, dub return for reverse transcript, were found in many bacteria. “They’re really a remarkable biological entity, even though no one knew what they were for,” says a biophysicist at the University of Texas at Austin.

When Sorek came to an early sign of his work when he and his colleagues discovered 38,000 bacterial genomes for genes used to fight phases. Such genes are close to each other, and his team developed a computer program that sought new defense systems alongside genes for CRISPR and other well-known antiviral constructs. A portion of the DNA was found by Weizmann graduate student Adi Millman, as it contained a gene for transcripts by contrast to the strands of DNA that did not code any known bacterial proteins. By chance, he came across a paper about the previous ones and realized that the mysterious sequence encoded one of their RNA components. “It was an ineffective jump,” Sorek says.

The team then observed that DNA encoding retron components often come with a protein-coding gene, and the protein varies from retron to retron. The team decided to test its kunda that the sequence cluster introduced a new phase defense. They showed that bacteria needed all three components – reverse transcript, DNA-RNA hybrids and other proteins – to defeat various viruses.

For a retron named Akek 48, Sorek and colleagues showed that the associated protein delivers the rebellion de grease by entering the outer membrane of the bacterium and changing its permeability. The researchers concluded that the retron somehow “protects” the second molecular complex, which is the bacterium’s first line of antiviral defense. Several phases deactivate the complex, triggering the retron to release the membrane-destroying protein and kill the infected cell, Millman, Sorek, and his team reported on November 6. Cell.

The second group has reached similar conclusions. Led by the European Molecular Biology Laboratory (EMBL), Heidelberg-based microbiologist Athanasius Types, the group realized that the genes coding for retron at the front Salmonella The bacterium was a gene for toxic proteins Salmonella. The team found that retrone usually keeps the toxin under wraps, but activates it in the presence of phage protein.

Types says the two groups met at an EMBL meeting in the summer of 2019. Teams simultaneously post preprints on their work on Byroxiv in June. (Review of the second group’s paper is ongoing in the journal.)

Even before these discoveries, other researchers took advantage of the then-mysterious features of the people behind the creation of new gene editors. CRISPR easily targets and binds or cuts off desired regions of the genome, but it is not yet very adept at introducing new code into target DNA. Returns, combined with elements of the CRISPR, are able to make more thanks to their contrasting transcripts: they can make multiple copies of the desired sequence, which can be effectively calibrated in the host genome. “Because CRISPR-based systems and returns have different strengths, combining them is a very promising strategy,” says Simon.

In 2018, researchers at Hunter Fraser’s Stanford University lab introduced a retron-derived base editor called CRSPY (C-9 Retroneous Parallel Acquisition by C Homology). First, they created backbones whose RNA matched the fermentation genes, but mutated with a single base. They linked them to the “guide RNA” of CRISPR, which is located on the target DNA, and the CAS9 enzyme that acts as the nuclear scissors of CISPR. Once CAS9 cut the DNA, the cell’s DNA repair mechanisms replaced the fermented gene with DNA produced by the transcript opposite the retron.

Crispy enabled Stanford graduate student Shi-And Na Anderson Chen and his colleagues to effectively create thousands of yeast mutants, each separated by just one base. Let them determine, for example, what bases were needed for fermentation to thrive in glucose. “Crispy is very cool and very powerful,” says Harmeet Malik, an evolutionary biologist at the Fred Hutchinson Cancer Research Center. This year, two other teams led by Harvard University geneticist George Church and Massachusetts Institute of Technology synthetic biologist Timothy Luni have described similar feats in bacteria in bioroxivative prints.

Researchers are excited about retrons, but caution they have a lot to learn about how to turn these bacteria plows into swords. “It could be that people as backward as CRISPR would be radical,” says Simon. “But it’s hard to say until we understand more about natural biology and the artificial behavior of people in the past.”