Heads or Tails? Structural Studies of Host Interaction and Molecular Piracy in Bacteriophages

Abstract

Staphylococcus aureus is an opportunistic human pathogen dependent mainly on bacteriophages (phages) for dissemination of the virulence factors that contribute to its pathogenicity. Most phages have double-stranded DNA (dsDNA) genomes which are packaged into protein capsids attached to tails of varying morphology to form their complete virion structures. S. aureus pathogenicity islands (SaPIs) are highly specialized mobile genetic elements that encode various virulence factors and have been named molecular pirates for their ability to parasitize certain helper phages. SaPI1 is capable of hijacking virions constructed by the helper phage 80α, partly by altering the size of the capsid to only accommodate the smaller SaPI1 dsDNA genome, to ensure the spread of SaPI1 to new host S. aureus cells.

In this dissertation, I applied recent advances in the field of cryo-electron microscopy (cryo-EM) to study the structure of 80α and characterize the process of capsid size redirection. I solved the structure of the 80α baseplate, a complex apparatus at the end of the tail used for interaction with S. aureus cells, which offered unprecedented insight into the tools used by 80α and SaPI1 to identify and penetrate new host cells. I also solved the structures of the 80α and SaPI1 procapsids, precursor capsids formed before being packaged with dsDNA. Comparing them, we found that SaPI1 uses a phage-like scaffolding protein that increase the curvature of the procapsid during assembly, reducing its ultimate size. I fitted atomic models created from the procapsids into matured 80α and SaPI1 capsid cryo-EM reconstructions, revealing how the procapsid changes during dsDNA packaging without compromising stability. Finally, I solved the procapsid structure of P4, a molecular pirate of the Escherichia coli phage P2. Though P4 causes capsid size redirection similarly to SaPI1, it is unrelated to SaPIs and uses a completely different mechanism. This shows that capsid size redirection is an evolutionarily advantageous strategy that diverse molecular pirates have evolved to employ.