Structure and DNA delivery mechanism of gene transfer agent of Rhodobacter capsulatus

Pavol Bárdy¹ , Tibor Füzik^{2 ,} Dominik Hrebík² , Roman Pantůček¹ , Pavel Plevka²

¹Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic

²Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic

bardy.pavol@mail.muni.cz

Gene transfer agents (GTAs) are extracellular particles that enable high-frequency horizontal gene transfer among prokaryotes and thus accelerate their evolution. GTAs are derived from phages that were independently acquired by several bacterial and archaeal lineages. In spite of their importance for adaptation and diversification of prokaryotes, the structure and mechanism of DNA delivery of GTA are unknown. Here we used cryo-electron microscopy to show that GTA of Rhodobacter capsulatus resembles bacteriophage from the family Siphoviridae with several unique features. The DNA-containing head of the GTA is shortened in the direction of GTA tail relative to the regular icosahedral heads of phages. This results in T3 compressed icosahedron with ~50% reduction of the DNA packaging capacity. It represents the smallest possible size of a capsid, which can be assembled in portal-containing viruses. Unlike in the previously studied phages, attachment of the GTA tail to the head is reinforced by the interaction of the neck adaptor protein with the capsid. Tape-measure protein, which determines the length of the GTA tail, exhibits similarities to the structural features of tape-measure proteins of phages with both short and long tails and may, therefore, correspond to their common ancestor. DNA-delivery commences by the GTA attaching to the host capsule by head-spike and tail-fibres. Subsequently, the baseplate interacts with the outer membrane, irreversibly disassembles and releases the cell-wall hydrolase, located inside the baseplate. The tape-measure protein is no longer held in the virion and ejects together with DNA into the periplasm, from where DNA is uptaken to the cytoplasm by cell transformation complex. Our results reveal important structural features in tailed phage virion and describe novel DNA-delivery mechanism present in GTAs and related phages.

Figure 1. DNA-delivery mechanism of Rhodobacter capsulatus gene transfer agent (GTA).

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/0958/2018).