Old Bacterial structures has some new anti-Phage defense strategy

The function of unusual bacterial structures called retrons has remained unclear for over three decades. Now, the long-standing mystery has been solved by a team: Retrons are 'guards' of the immune system that ensure the bacterial colony's survival when it is infected by viruses. In addition to revealing a new method used by bacteria to defend themselves from viral infection, one that is remarkably close to that used by plant immune systems, the study revealed several new retrons that could contribute to the genome-editing toolkit in the future.

This research is published in the Cell "Bacterial Retrons Function In Anti-Phage Defense". The study, conducted by Adi Millman and Avigail Stokar-Avihail, two graduate students, and Aude Bernheim, PhD, a postdoc in the laboratory, was conducted in the laboratory of Rotem Sorek, PhD, full professor , Department of Molecular Genetics, Weizmann Institute of Science.

Retrons, commonly found in bacteria, consist of a reverse transcriptase (RT) and a non-coding RNA (ncRNA) as genetic elements. The RT uses ncRNA as a template, generating a molecule of chimeric RNA / DNA in which the components of RNA and DNA are covalently linked.

The team did not set out to solve the mystery of the retron; they were looking for new elements of the immune system of bacteria, specifically elements that help prevent viral infection from bacteria. Their search was made easier by their recent discovery that genes in the immune system of bacteria tend to cluster together within so-called defence islands in the genome. The team decided to investigate further when they uncovered the unique signature of a retron within a bacterial defence island.

Their initial research showed that this retron was definitely involved in protecting bacteria from viruses infecting bacteria from bacteriophages. As the researchers looked more closely at extra retrons located near known defence genes, they found that the retrons were always connected to one other gene, physically and functionally. The bacteria were less successful in fighting phage infection when either the accompanying gene or the retron had been mutated.

The researchers then set out to look at defence islands for more such complexes. They eventually identified some 5,000 retrons, many of them new, of numerous bacterial species in various defence islands.

The researchers transplanted many retrons, one by one, into laboratory bacterial cells that lacked retrons, to check whether these retrons function, generally, as immune mechanisms. As they suspected, they found retrons in a large number of these cells that were protecting the bacteria from phage infection.

How is this done by retrons? The research team discovered that its function is to cause the infected cell to commit suicide by focusing back on one specific type of retron and tracing its actions in the face of phage infection. If the suicide mechanism works fast enough to kill the cell before the virus finishes making copies of itself and spreading to other cells , cell suicide, once thought to belong exclusively to multicellular organisms, is a last-ditch way of aborting widespread infection.

Further research showed that retrons do not feel the invasion of the phage itself, but rather keep watch over another part of the immune system known as RecBCD, which is one of the first lines of defence of the bacterium. The retron activates its programme through the second, linked genes to kill the infected cell and protect the rest of the colony if it realises that the phage has tampered with the cell's RecBCD.

It's a smart approach, and we've found that it works in a similar way to a guard mechanism used in plant cells,' Sorek says. Phages come equipped with a variety of inhibitors to block assorted parts of the cell's immune response, just like viruses that infect plants. The retron does not need to be able to identify all possible inhibitors, like a guard mechanism known to exist in plants, it just has to have a handle on the functioning of one specific immune complex. This 'abortive infection' method is applied by infected plant cells, killing off a small region of a leaf or root in an effort to save the plant itself. Since most bacteria live in colonies, even at the expense of individual members, this same strategy can promote the survival of the group. 

Retrons are helpful for biotechnology because they start with a piece of RNA, which is the DNA strand synthesis template. This template in the retron sequence can be swapped for any desired DNA sequence and used to manipulate genes in various ways, sometimes in conjunction with another tool borrowed from the bacterial immune toolkit, CRISPR. Sorek and his team believe that more than a few may be hiding within the diverse list of retrons they identified that could provide better templates for specific needs for gene editing.