Investigating the architecture of a bacteriophage using cryo-EM, SAXS, and X-ray crystallography
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.
YSD1 is a lytic bacteriophage that infects and kills Salmonella enterica serovar Typhi, the causative agent of typhoid fever. YSD1 is a Siphoviridae homologous with the bacteriophage chi, which uses a flagella-dependent infection mechanism. We have shown by electron microscopy (EM) that YSD1 attaches to flagella through its tail proteins. Currently, there are no high-resolution structures of flagella-dependent bacteriophages. To elucidate the structure of YSD1, purified virions were isolated from cultures of Salmonella typhimurium and imaged by cryo-EM. A 2.8 Å x-ray crystallography structure combined with the 4.7 Å EM map revealed a T=7 icosahedral capsid similar to the HK-97 and T7 phages. However, in contrast to HK-97, which uses crosslinking to reinforce the capsid, YSD1 has an additional cementing protein stabilising the icosahedral shell formed by the major capsid protein. Helical reconstruction of the tail produced a 3.8 Å map which revealed a C6 helical tube related to Type VI secretion systems and the tails of T4 and T5 phages. The YSD1 tail is composed of a central beta-barrel domain decorated by two peripheral domains. A beta-sandwich domain, unique to Chi-like phages, has structural similarity with bacterial adherence factors. The C-terminal domain is flexible and not well resolved in the helical reconstruction. The Ig-like fold and organisation of this domain was determined using modelling and small-angle x-ray scattering (SAXS). The determination of the structure of YSD1 gives us an insight into the assembly and evolution of flagella-dependent bacteriophages.