Gene transfer agents (GTA), the virus-like particles of certain alpha-proteo-bacteria, represent the most sophisticated system of horizontal gene transfer in prokaryotes discovered to date. Here, we report the structure of Rhodobacter capsulatus GTA.
A novel purification method of GTA was developed, combining anion-exchange chromatography on methacrylate monolith columns with ultracentrifugation in sucrose gradient. This method resulted in >95% pure sample of full and empty GTA particles with ratio = 2:3. Cryo-EM studies revealed functionally important differences between GTA and bacteriophages in the capsid geometry. There are two types of GTA particles. The minor one (1 % of all particles) possess icosahedral head, with the triangulation number T = 3. The more prevalent one (99 % of all particles) possess oblate head (icosahedron shortened along fivefold axis), with the triangulation number for the center body Q = 3, resulting in the compression value in respect to spherical capsid of dQ = -3. To our knowledge this is the first structure with negative dQ value ever observed.
The capsid is composed out of major capsid protein with HK97 fold, decorated with head spikes on the capsid pentons. The portal and the tail proteins are homologous to those of phages from the family Siphoviridae. The tail of GTA contains 6 hexamer rings, with an estimated rise of 38.1 Å, the relative twist of the disks is yet undetermined. The portal, neck, and tail of the full GTA particle contain internal central density of unknown origin, which is not observable in the empty particle. Similar structure is not present in phages and may play a role in transducing of a signal to initiate genome-release. This differs from the conformational changes of baseplate, tail, and neck that trigger the genome release of phages.
The baseplate of GTA possess C3 symmetry and has been reconstructed to the resolution of 6.1 Å. It is the only part of GTA structural locus with higher than 50% sequence similarity to known phages. Gp12 forms hexamer disc at the tip of the tail, gp13 forms central hub, and gp15 forms receptor binding trimers connected to the hub. The tail fiber is encoded in genome locus distinct from that, which encodes the rest of the baseplate, revealing complex evolution of the baseplate assembly.
Our results show more distant evolutionary relationship between GTAs and phages then previously thought, and reveal a strategy that enabled bacteria to utilize its parasite for own purposes.
CIISB research infrastructure project – LM2015043, IT4Innovations National Supercomputing Center – LM2015070, and the National Grid Infrastructure MetaCentrum – LM2015042 funded by by The Ministry of Education, Youth and Sports of the Czech Republic are gratefully acknowledged. This work was supported by Grant Agency of the Masaryk University (MUNI/A/0824/2017).