The research performed in this thesis focuses on the understanding on the interactions of bacteria and phages occurring via anti-phage defense system mechanisms. This involved a set of literature research and experimental studies that provide an overview of the diverse defense systems described at the time of submission.

Viruses are, as we have seen over the past year, very proficient at invading a host and subsequently reproducing rapidly. Our adaptive immune system, after a first encounter with a virus, can store information about the outside protein shell and use this information to destroy the virus in later encounters. Bacteria have an adaptive immune system that works on the nucleic acid level (DNA/RNA). The right functioning of the system demands that a fragment of a virus is incorporated into the bacterial genome correctly (adaptation). Subsequently, proteins carrying copies of this fragment have to find and destroy the virus quickly enough after it enters the cell (interference). An obstacle in the interference process is that the cell is filled with host DNA, which has to be scanned to differentiate it from viral DNA. How bacteria are still able to find these viruses fast enough is the subject of my thesis.

For millennia, humanity has been plagued by pathogenic bacteria. Until the advent of antibiotic treatments, seemingly harmless bacterial infections could have fatal consequences. However, in the microcosm that these single celled organisms inhabit, the line between being the invader or being invaded is a thin line. Bacteria and archaea are con¬stantly targeted by their viruses (bacteriophages – from Greek “to de¬vour”-bacteria). Without mechanisms in place to protect the prokar¬yotic cell from infection, bacteriophages would drive whole species to almost extinction. This thesis presents the work in which we applied techniques of molecular biology and biochemistry to investigate the mechanism certain bacterial species use to develop immunity against bacteriophages.