Structures of phage 812 neck suggest a mechanism for genome retention and release in Herelleviridae

Zuzana Cieniková1, Jiří Nováček1, Marta Šiborová1, Barbora Břenková1, Tibor Füzik1, Martin Benešík2, Pavel Plevka1

1CEITEC Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic

2Masaryk University, Faculty of Science, Kamenice 753/5, 625 00 Brno, Czech Republic

Herelleviridae phage 812 infects a wide range of S. aureus strains and is considered a promising candidate for phage therapy against bacterial infections, including those resistant to antibiotics. The virion is formed by an icosahedral capsid enclosing a double-stranded DNA genome, and a double layered contractile tail terminated by a baseplate. The neck region joins the capsid to the tail and functions in capsid assembly, genome packaging, its retention, and release. The neck consists of four protein complexes forming the DNA channel: portal, adaptor, stopper, and tail terminator. We determined the structural features of the neck in virion, genome-releasing intermediate and empty particle using cryo-electron microscopy, as well as the structure of a closed conformation of the stopper complex by X-ray crystallography. The portal provides a dodecameric DNA binding site anchoring the genomic end inside the capsid. This high-avidity binding site recognizes B-form DNA shape with locally narrowed minor groove. The DNA binding may be important during the initial stages of genome packaging to prevent DNA escape from the capsid caused by packaging terminase slippage. In the late stages of packaging, high genome pressure inside the phage head hinders DNA escape by inducing a compression of the portal crown which obstructs the opening of portal tunnel valve loops. The stopper hexamer blocks genome escape in the packaging intermediate particle prior to tail attachment. The stopper gating function involves a shifting of a zinc-ribbon loop and a strand-to-helix conformational switching of the gating valve loop. After the attachment of the tail, the stopper adopts an open conformation and primes the DNA for release by allowing its descent toward the tail. The study of structural changes in phage 812 neck proteins throughout stages of phage life cycle thus expands our understanding of the functions fulfilled by the head-to-tail joining region of the viral particle.