The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria

Abstract

The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ϳ3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis. M. abscessus subsp. bolletii was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the M. abscessus subsp. bolletii prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to Siphoviridae and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram ؊ ) or Gram ؉ bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.

Structure, Adsorption to Host, and Infection Mechanism of Virulent Lactococcal Phage p2

“…The tail flexibility of siphophages prevented electron microscopy studies of p2 virions as a whole, which is in contrast with the compact podophages (22). We thus reconstructed the p2 virion as four separate regions using the appropriate local symmetry (capsid, connector complex, tail, and baseplate) ( Table 1) before recapitulating in silico the whole phage using a low-resolution reconstruction obtained from a few straight phages, as described previously (16,28) (Fig. 3).…”

“…We devised a strategy to obtain a topological template for the tail reconstruction and especially to obtain the number of tail MTP (ORF-11) rings in the p2 virion. We selected a few hundred phages with almost straight tails and used them for reconstruction of a low-resolution-scaffold 6-fold-averaged map (16,28). In a following step, small tail segments were boxed and combined into one data set that was subsequently processed with the appropriate helical symmetry at a 22-Å resolution, using 2,171 particles (Table 1).…”

“…The structures of some Siphoviridae phages are also available, such as those of Escherichia coli phage T5 (24), Bacillus subtilis phage SPP1 (25)(26)(27), phage TP901-1 (16), and mycobacteriophage Araucaria (28). Due to the inherent flexibility of siphophages, their EM structure determinations have relied on a "divide-and-conquer" approach, where the different parts of the virion are reconstructed independently and then combined to yield the structure of the whole phage (16,28).…”

Cryo-Electron Microscopy Structure of Lactococcal Siphophage 1358 Virion

“…5E). Decorations also have been identified in the tail of other phages, e.g., SPP1 (51), (57), Araucaria (41), and p2 (19). They have been postulated to participate in nonspecific and reversible adhesion of the phage to its host surface polysaccharides, as is the case for the capsid decorations.…”

“…The tail. In order to construct the full-length structure of the tail, we applied a two-step procedure previously used with lactococcal phage TP901-1 (3) and mycobacteriophage Araucaria (41). In the first step, we produced a 6-fold-averaged reconstruction of the whole phage from a selection of virions with a straight tail (Fig.…”