Identifying novel vulnerabilities in M. tuberculosis using proteomics and genomic approaches

I aim to use genetics and proteomics to discover how bacteria combat bacteriophage lysis.

Driving this goal is the desire to combat phage resistance mechanisms to make bacteria more susceptible to phage predation.

My group will first tackle the problem by employing genetic methods to interrogate the role of M tuberculosis (Mtb) genes in limiting phage replication and bacterial lysis.

Using CRISPRi, my group will conduct the first study in the Mtb to determine whether gene knockdown can positively impact phage replication.

To increase our understanding of the physical underpinnings of phage resistance, we will create a physical map of the protein-protein interactions between the phage and the bacterium using whole cell fractionation proteomics. This is critical as many phage proteins are of unknown function might interact with essential bacterial complexes.

Lastly, I suspect that phage “accessory genes” represent a treasure trove of modulators of host processes, which could be useful genetic fodder for enhancing future phage therapeutics.

Using conventional affinity-purification MS, my group will identify the interactor partners of the phage accessory proteins and validate their phenotype with phage replication assays.

My goal is to shift the paradigm of phage therapy by identifying essential pathways and complexes in the host that can be inhibited with small molecules or phage engineering to boost lysis and retard the emergence of resistant bacteria during phage therapy.