How do the bacteria distinguish 'between enemy and lover'?

Scientists from Tel Aviv University and the Weizmann Institute of Science have revealed mechanisms of action of the bacterial immune system, which may in the future be used to cure a variety of human diseases. The research was published in the journal Nature

A few years ago, researchers discovered that bacteria, which are single-celled creatures, have an immune system similar to that of all living things: an 'adaptive' system, which knows how to remember and identify enemies that penetrate the cell body, and attack them. The bacterial immune mechanism, called CRISPR, is used by bacteria mainly to protect against their main enemies, invading viruses called phages, but humans also know how to mobilize it to their advantage: already today, CRISPR is used to protect 'good' bacteria in the yogurt and cheese production processes; And in the future it may be an effective and available tool for 'editing' the human genome, which will be applied in curing many diseases.

In order for us to be able to use the bacterial immune system, an in-depth understanding of its mechanisms of action is required, and the subject currently occupies many researchers all over the world. An important step in this effort was recently made by Prof. Udi Kimron from the Department of Microbiology and Clinical Immunology at the Tel Aviv University School of Medicine and Prof. Rotem Sorek from the Department of Molecular Genetics at the Weizmann Institute of Science, who discovered how CRISPR performs a fundamental action, which is essential for any immune system: distinguishing between the DNA of the bacterium itself and the DNA of the invading virus, with the aim of attacking the enemy only.

The study was published on April 13.4 in the journal Nature.

hostile environment
"Most bacteria live in a very hostile environment," explains Prof. Sorek. "Usually in nature, the amount of phages is 10 times greater than the number of bacteria. The phages use the host bacterium's own replication machinery to replicate themselves, and are constantly developing new ways to do so. In order to survive in the face of the constant attack, the bacteria need a highly effective and active immune system."

In the never-ending war of survival, the first task of the bacterial immune system (the CRISPR) is to remember enemies it has already met in the past, in order to identify and eliminate them in the next encounter. Prof. Kimron was one of the pioneers of the research activity that revealed several years ago how the immune system remembers its enemies: it takes a short sequence from the DNA of the phage that has penetrated the bacterial cell, and stores it in a special area designated for this within the genome of the bacterium itself. Gradually, action by action, the memory of the immune system is formed in this way. Now, every time an invading bacterium of a known type is penetrated, the CRISPR uses its DNA segments preserved in the bacterial genome, and uses them to produce short strands of RNA adapted to the genetic sequence of the invading phage. Specific protein compounds that attach to the RNA recognize the phage's DNA, and destroy it.

But what happens when the immune system makes a mistake, and stores in its memory a section of the bacteria's own DNA? In previous studies Prof. Sorek showed that in such a case the bacterium will suffer from a type of autoimmune disease, in which it attacks and even kills its own DNA. Prof. Kimron previously discovered that the bacterium overcomes the autoimmune disease when it learns to distinguish between its own DNA and foreign DNA. The ability of the immune system to distinguish 'between enemy and lover' - that is, between foreign DNA and one's own DNA - is therefore essential for the survival of the bacterium; But the mechanism that enables this distinction has remained a mystery for a long time.

Identify the enemy
Now, in their new study, the researchers wanted to get to the bottom of the discrimination mechanism of the bacterial immune system, and reveal its mode of action. For this purpose Prof. Kimron and his research student Moran Goren teamed up with Prof. Shurk and his student Assaf Levy. The researchers created plasmids in the lab - round pieces of DNA that mimic viruses - and injected them into bacteria. Indeed, the observations revealed that the CRISPR system of the bacteria was able to incorporate the DNA of the plasmids into the memory of the immune system within the bacterial genome, while the bacteria's own DNA was only rarely incorporated into this memory. In total, about 38 million vaccination events were recorded in the study.

"The CRISPR takes in and stores segments of foreign DNA using two proteins - Cas1 and Cas2," explains Prof. Kimron. "When we examined the results of our research in depth, we discovered that the two proteins manage to locate the phage by identifying the point where its replication process ends. And since the phages replicate themselves at a rapid rate inside the host bacterium, the proteins can find many points where the replication process occurs and ends. In fact, it can be said that the bacterial immune system utilizes the survival mechanism of the 'enemy' to identify it."

self marking
In addition to the mechanism used by the immune system to identify the 'enemy', the researchers discovered another mechanism, which actually identifies the 'lover' - that is, the bacteria's own DNA. This is a unique marking of the bacterial DNA, which signals to the messenger proteins of the immune system: "I'm a friend, don't touch me!"

"In the DNA of bacteria there are unique sequences called Chi, which are not usually found in phages," says Prof. Kimron, "The Chi sequences have an important and well-known role in repairing DNA breaks, but we discovered that they also have a central role In the immune system: we found that the Cas1 and Cas2 proteins form a compound with enzymes that recognize the Chi sequences, and thus when they encounter a Chi sequence, they know that it is the bacteria's own DNA, and immediately cease their action. In other words: they recognize the unique marking of the friendly DNA, and do not take a segment from it to store in the memory of the immune system."

"In our research, we were able to discover two discrimination mechanisms, through which the bacterial immune system succeeds in distinguishing between 'enemy and lover,'" Prof. Sorek concludes. "Thanks to these smart mechanisms, the system manages to store in its memory almost exclusively fragments of foreign DNA, and knows how to attack them when the time comes, and at the same time it avoids self-attacks that cause autoimmune diseases. This is basic research that may in the future be used as an infrastructure for the development of drugs for various diseases related to the human genome."

These days, researchers are working on deciphering the molecular aspects of the memory mechanism of the bacterial immune system.