Periodic Reporting for period 2 - DefenseAgainstPhage (Understanding the pan-immune system of bacteria)
Reporting period: 2023-07-01 to 2024-12-31
To survive in the face of perpetual phage attacks, bacteria and archaea have developed a variety of anti-phage defense systems, commonly known as the microbial “immune system". These systems play a major role in shaping the evolution of both phage and bacterial genomes. In the past, the discovery of new defense systems contributed not only to our understanding of the arms race between bacteria and phage, but also provided important molecular tools that proved invaluable for biotechnological utilizations. Defense systems, including CRISPR-Cas and Abi systems, are being used in the dairy industry to protect cheese- and yogurt-producing bacteria against detrimental phage attacks. Moreover, deep mechanistic understanding of the mode of action of individual systems has led to revolutions in molecular biology, as demonstrated by the utilization of restriction enzymes for genetic engineering, and the adaptation of the CRISPR-Cas system into powerful genome editing tools.
The objective of this project is to understand the arsenal of defense mechanisms that are at the disposal of bacteria in their struggle against phages, their evolutionary implications, and the ways by which phages counteract these defenses. The project includes extensive mechanistic characterization of individual defense systems, together with broad mapping of new defense systems within microbial genomes and metagenomes. The project also aims to mine phage genomes to identify phage-encoded inhibitors of bacterial defenses, which will further assist in understanding the mechanism of defense for the systems we discover.
Importance for society: Past discoveries of novel defense systems led to revolutions in molecular biology, because defense systems entail specific molecular recognition and targeting characteristics. Discovery of novel defense systems and understanding their mechanism of action could lead to the development of additional strong molecular tools that would be beneficial to the broad scientific community. Moreover, understanding of bacterial immunity can lead to better understanding of our own immune system.
The objective of this project is to understand the arsenal of defense mechanisms that are at the disposal of bacteria in their struggle against phages, their evolutionary implications, and the ways by which phages counteract these defenses. The project includes extensive mechanistic characterization of individual defense systems, together with broad mapping of new defense systems within microbial genomes and metagenomes. The project also aims to mine phage genomes to identify phage-encoded inhibitors of bacterial defenses, which will further assist in understanding the mechanism of defense for the systems we discover.
Importance for society: Past discoveries of novel defense systems led to revolutions in molecular biology, because defense systems entail specific molecular recognition and targeting characteristics. Discovery of novel defense systems and understanding their mechanism of action could lead to the development of additional strong molecular tools that would be beneficial to the broad scientific community. Moreover, understanding of bacterial immunity can lead to better understanding of our own immune system.
As part of the project we developed a computational platform for the discovery of new defense systems in genomes and metagenomes. Multiple predicted systems were validated experimentally, and a subset of these were studied mechanistically. This resulted in the discovery of a large set of defense systems, understanding the organization of defense system in bacterial genomes, and mechanistic analysis of multiple systems containing sirtuin (SIR2) domains . We also conducted mechanistic studies on a number of new defense systems, including systems triggering ATP depletion in infected cells and systems that install ubiquitin-like molecules on phages. As part of our plans to give special attention to defense systems that show homology to human proteins we found that a small immune molecule originally discovered in a bacterial defense system is also produced by a human protein homologous to the defense system protein. In addition, we initiated computational prediction of phage genes that inhibit bacterial immunity, resulting in the discovery of multiple proteins that inhibit a diversity of bacterial defense systems.
Our work exposed over 25 previously unknown bacterial immune systems. In addition, our studies described new mechanisms of bacterial defense, including depletion of cellular metabolites in response to infection, and utilization of ubiquitin-like proteins in bacterial defenses. Our discovery of new families of phage proteins that inhibit bacterial immunity is another representation for progress beyond the state of the art. Overall, we published so far 10 research papers and 3 review papers supported by this project. We expect that until the end of the project we will described additional new mechanisms of bacterial defenses and phage counter-defenses, as planned in the project outline.