YSD1 is a lytic bacteriophage that infects and kills Salmonella enterica serovar Typhi, the causative agent of typhoid fever. Over 13 million cases of Typhoid fever are reported annually with >200,000 deaths worldwide.
YSD1 is a Siphoviridae related to bacteriophage chi. We have shown by electron microscopy (EM) that YSD1 attaches to flagella and hypothesise that, like bacteriophage chi, the virion moves down to the bacterial membrane where it injects its genome. Deletion of the flagellum genes of S. Typhi prevents infection. Although the chi (χ) bacteriophage was discovered in 1936, there are no high-resolution structures of the structural proteins of flagella-binding bacteriophages.
To elucidate the structure of YSD1, purified virions were isolated from cultures of Salmonella typhimurium and imaged by cryo-EM. Single-particle analysis of the motion-corrected movies generated a structure of the T=7 icosahedral head at 4.7 Å. The organisation of the major capsid protein YSD17 was modelled using our 2.8 Å x-ray crystallography structure, while a model of the minor capsid protein, YSD16, was determined by modelling in the EM map. YSD16 forms a trimeric complex which acts as a cementing protein stabilising the icosahedral shell formed by the major capsid protein.
Helical processing of the phage tail produced a 3.8 Å reconstruction that reveals the fold and organisation of the major tail protein, YSD22. A beta-barrel domain forms the core of the C6 helix, while a small beta-sandwich domain decorates the periphery of the tail tube. The stability of the assembly is maintained by extended beta-hairpins projecting on either side of the hexameric ring.
The fold of the major tail protein is homologous to the tube protein of the Type VI secretion system found in gram-negative bacteria. These structures give us insight into the assembly and infection mechanisms used by flagella-binding bacteriophages.