Sequence and Structural Characterization of Great Salt Lake Bacteriophage CW02, a Member of the T7-Like Supergroup

Abstract

Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpDlike densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.

Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

“…Although they have diverged to the point that they do not always have easily recognizably similar AA sequence similarities, very divergent tailed phage MCPs have been examined and found to have similar protein folds (Parent et al , 2012; Shen et al , 2012; Zhang et al , 2013; Rizzo et al , 2014; Grose et al , 2014 and references therein). Thus, although they are amazingly diverse, all tailed phage MCPs are almost certainly very ancient homologues.…”

Morphology, Physiological Characteristics, and Complete Sequence of Marine Bacteriophage ϕRIO-1 Infecting Pseudoalteromonas marina

“…Only two other phages were found that could be considered to have shared a common ancestor end to end with intervening insertions and deletions. These were Pseudomonas phage PA11 (14) and Salinivibrio phage CW02 (15). The method was also used to explore the relationship of RIO-1 to the two marine phages SIO1 and VpV262, which are known to be organized similarly to each other but have greatly divergent replicative genes (8).…”

“…Its most closely related relatives are Pseudomonas phage PA11 (14) and Salinivibrio phage CW02 (15). It contains a suite of genes that have predicted activities related to synthesizing and breaking unusual peptide linkages, first discussed by Iyer et al (16) as possibly being involved in modifying cell wall metabolism, and that are more fully described here.…”

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

“…The N-terminal domain (yellow), cross-linking arm (green), A domain (blue), and P domain (red) are shown. As in a previous study (47), only the A and P domains were used in the fitting into the Basilisk capsid density. Coordinates omitted from the CW02 fitting (yellow, green, light red, and light blue) are indicated.…”

“…UCSF Chimera was also used to fit coordinates of the bacteriophage HK97 major capsid protein (46) into the Basilisk capsid density. Only the core of the HK97 protein was fitted (47). HK97 coordinates were first fit into the Tϭ9 capsid of halophilic bacteriophage NS01 (D. Eng, P. Shen, M. Domek, D. Belnap, unpublished results), and this fit was used as a starting point for the fit into the Basilisk structure.…”