Cryo-EM structure of bacteriophage Nocturne116: insights into the architecture of c2-like Lactococcus viruses

Abstract

ABSTRACT Nocturne116 is a small bacterial virus with a prolate head and a flexible, non-contractile tail that infects an insect-associated strain of Lactococcus lactis. Nocturne116 has little sequence similarity to other bacteriophages and represents a diverged virus lineage that includes the Lactococcus phage Q54 and phages of the Ceduovirus genus. To better understand the molecular architecture of this group of viruses, we determined the three-dimensional structure of the Nocturne116 virion. The head of the Nocturne116 phage is composed of two types of capsid proteins: the major capsid protein, which assembles into 50 hexamers, and a dedicated vertex protein, which forms 11 pentamers. The particle is stabilized by covalent isopeptide bonds, which result in topologically interlocked capsomer rings in the cylindrical midsection, while in the hemispherical caps, the chainmail-like structure is incomplete. An end vertex of the capsid is occupied by a portal complex, which is connected to the tail via a series of three neck protein rings. The genomic DNA extends through the neck channel up to the second tail tube ring, where it encounters the tail tape measure protein. The tail shaft is built of 26 hexameric rings of the tail tube protein and is capped by an assembly of three minor structural proteins that form a dome-shaped structure at the tail tip. The tail tip lacks characteristic receptor-binding proteins and represents the simplest host-attachment device of any studied Lactococcus phage, suggestive of an unusual mechanism by which the virus recognizes and infects its bacterial host. IMPORTANCE Viruses that infect the widely used food fermenter Lactococcus lactis can cause major problems in the food industry, but despite considerable effort, there are still gaps in the understanding of these viruses. Knowledge of their three-dimensional structure is important for understanding aspects such as particle-stabilizing mechanisms that they employ, or the host recognition mechanisms that these viruses use. The three-dimensional structure of Lactococcus phage Nocturne116 reveals a number of unusual features such as two types of capsid proteins making up the head, covalently crosslinked capsomers which, to our knowledge, are the first such observation in a prolate-shaped virus, or a minimalist tail tip which starkly contrasts with the elaborate machinery of other previously studied Lactococcus phages. Our results also shed light on the general structure of related ceduoviruses which, despite being the third-largest lactococcal virus group, have remained poorly understood from a structural perspective. Viruses that infect the widely used food fermenter Lactococcus lactis can cause major problems in the food industry, but despite considerable effort, there are still gaps in the understanding of these viruses. Knowledge of their three-dimensional structure is important for understanding aspects such as particle-stabilizing mechanisms that they employ, or the host recognition mechanisms that these viruses use. The three-dimensional structure of Lactococcus phage Nocturne116 reveals a number of unusual features such as two types of capsid proteins making up the head, covalently crosslinked capsomers which, to our knowledge, are the first such observation in a prolate-shaped virus, or a minimalist tail tip which starkly contrasts with the elaborate machinery of other previously studied Lactococcus phages. Our results also shed light on the general structure of related ceduoviruses which, despite being the third-largest lactococcal virus group, have remained poorly understood from a structural perspective.