Bacteriophage-host interactions in Mycobacterium and related actinobacteria

Every year, Mycobacterium tuberculosis (Mtb), the causative agent of the disease tuberculosis kills nearly two million people globally. In recent times this public health emergency has been exacerbated by acquired antibiotic resistance. Even though this was one of the first etiologic agents of disease to be discovered, many aspects of the physiology of Mtb remain unknown. Mycobacteriophages, viruses that can infect Mtb and closely related bacteria may be useful tools to both combat and study Mtb. In this work, I address three aspects relating to the dynamics between phages that infect Mtb and related bacteria in the phylum Actinobacteria. First, the therapeutic potential of mycobacteriophages is explored by elucidating the susceptibility to phage infection for a set of strains of Mtb that is representative of the global genetic diversity of this pathogen. This investigation led to propose a five-phage cocktail that is able to both infect and kill representative strains of Mtb. Secondly, as resistance occurs with antibiotics, phage resistance can also arise. Phage resistance can occur through spontaneous mutations that alter host-factors that are required for phages to successfully infect their host. In Mycobacterium few of the host-factors associated with phage resistance have been elucidated. Through the work presented here, several host-factors associated with phage resistance in Mycobacterium are presented and characterized, including the nucleoid associated protein Lsr2 in M. smegmatis, as well as genes of the methylglucose lipopolysaccharide (MGLP) pathway that cause phage resistance in both M. smegmatis and Mtb. Finally, I describe tRNA-dependent lysogeny, an unusual and previously uncharacterized lysogenization mechanism that depends on a phage-encoded tRNA. Phages that encode tyrosine integrases frequently integrate into tRNA genes in their host and reconstitute the 3’ end of the tRNA gene upon integration. Phages that employ tRNA-dependent lysogeny do not reconstitute the tRNA, and instead use a tRNA present on their own genome to complement the loss of the host tRNA. This new strategy of lysogeny is employed by phages that infect the Actinobacterial hosts Mycobacterium and Gordonia and in many ways is counter to the model for integration and lysogeny that was established in E. coli phage Lambda.