Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions

J Biol Chem. 2016 Jan 1;291(1):215-26. doi: 10.1074/jbc.M115.696260. Epub 2015 Nov 16.


Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal "trimer of hairpins" tip. Although the length and composition of tail needles vary significantly in Podoviridae, unexpectedly, the amino acid sequence of the N-terminal tip is exceptionally conserved in more than 200 genomes of P22-like phages and prophages. In this paper, we used x-ray crystallography and EM to investigate the neutral pH structure of three tail needles from bacteriophage P22, HK620, and Sf6. In all cases, we found that the N-terminal tip is poorly structured, in stark contrast to the compact trimer of hairpins seen in gp26 crystallized at acidic pH. Hydrogen-deuterium exchange mass spectrometry, limited proteolysis, circular dichroism spectroscopy, and gel filtration chromatography revealed that the N-terminal tip is highly dynamic in solution and unlikely to adopt a stable trimeric conformation at physiological pH. This is supported by the cryo-EM reconstruction of P22 mature virion tail, where the density of gp26 N-terminal tip is incompatible with a trimer of hairpins. We propose the tail needle N-terminal tip exists in two conformations: a pre-ejection extended conformation, which seals the portal vertex after genome packaging, and a postejection trimer of hairpins, which forms upon its release from the virion. The conformational plasticity of the tail needle N-terminal tip is built in the amino acid sequence, explaining its extraordinary conservation in nature.

Keywords: DNA packaging; bacteriophage; hydrogen-deuterium exchange; infection; protein folding; tail needle; trimer of hairpins; viral genome ejection; x-ray crystallography.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacteriophages / chemistry
  • Circular Dichroism
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Deuterium Exchange Measurement
  • Genome, Viral*
  • Hydrogen-Ion Concentration
  • Mass Spectrometry
  • Negative Staining
  • Podoviridae / genetics*
  • Protein Multimerization
  • Viral Tail Proteins / chemistry*
  • Viral Tail Proteins / ultrastructure
  • Virion / genetics*
  • Virus Assembly*


  • Viral Tail Proteins

Associated data

  • PDB/1LKT
  • PDB/1VT0
  • PDB/2POH
  • PDB/3C9I
  • PDB/3LJ4
  • PDB/3TH0
  • PDB/4ZKP
  • PDB/4ZKU
  • PDB/4ZXQ
  • PDB/5BU5
  • PDB/5BU8
  • PDB/5BVZ