Bacteria and their mobile genetic elements (MGEs), such as plasmids and phages, are locked in a constant evolutionary arms race. Horizontal gene transfer (HGT) is a major driver of bacterial evolution and a source of adaptive traits. However, MGE invasion can be fatal for a bacterial cell and therefore has to be tightly controlled. As a result, bacteria have evolved a plethora of dedicated immune defense systems to control the impact of MGEs. Amidst these, there is a wide variety of innate defense systems, such as those executing abortive infection (Abi), or restriction-modification (R-M). Additionally, a large proportion of bacteria carry CRISPR-Cas systems, which are the only known adaptive immune systems in bacteria. These defenses are effective in excluding MGEs, however, MGEs have evolved a variety of strategies to counteract such defenses and therefore often overcome bacterial immunity.

The conventional picture of the bacteria-MGE arms race depicts bacteria utilizing multiple defense strategies to protect themselves from MGEs, while MGEs employ strategies to overcome these defenses and evade immunity. In reality, their relationship is much more nuanced, and it has become evident that MGEs themselves frequently carry defense systems or defense components in favor of their own evolutionary trajectory. This adds yet another layer to the multifaceted interactions between bacteria and their MGEs.

The work presented in my thesis sheds light on the relationship between bacteria and their MGEs, the interplay among MGEs, and the defense strategies they employ to cope with one another. In Manuscript 1, we investigate a type IV-A3 CRISPR-Cas system encoded by a Klebsiella pneumoniae (K. pneumoniae) plasmid. This study not only enhances our understanding of the molecular mechanisms behind type IV CRISPR-Cas systems but also provides valuable insights into their involvement in inter-plasmid conflicts. In Manuscript 2, we examine the first known RNA-based CRISPR-Cas inhibitors encoded by a diverse range of phages and other MGEs, which we refer to as RNA-based anti-CRISPRs (Racrs). We reveal that Racrs can confer a significant replicative advantage to the MGEs that carry them when targeted by CRISPR-Cas systems. This phenomenon extends across different CRISPR-Cas classes, including various types and subtypes. Lastly, in Manuscript 3, we conduct a comprehensive review of immune inhibition strategies employed by MGEs to overcome host defenses. We discuss the current challenges in the field, describe the methods used for their discovery as well as their biotechnological applications, and finally provide insights into future directions for research in this area.