The Discovery of phiAGATE, A Novel Phage Infecting Bacillus pumilus, Leads to New Insights into the Phylogeny of the Subfamily Spounavirinae

Abstract

The Bacillus phage phiAGATE is a novel myovirus isolated from the waters of Lake Góreckie (a eutrophic lake in western Poland). The bacteriophage infects Bacillus pumilus, a bacterium commonly observed in the mentioned reservoir. Analysis of the phiAGATE genome (149844 base pairs) resulted in 204 predicted protein-coding sequences (CDSs), of which 53 could be functionally annotated. Further investigation revealed that the bacteriophage is a member of a previously undescribed cluster of phages (for the purposes of this study we refer to it as “Bastille group”) within the Spounavirinae subfamily. Here we demonstrate that these viruses constitute a distinct branch of the Spounavirinae phylogenetic tree, with limited similarity to phages from the Twortlikevirus and Spounalikevirus genera. The classification of phages from the Bastille group into any currently accepted genus proved extremely difficult, prompting concerns about the validity of the present taxonomic arrangement of the subfamily.

Effects of Actin-Like Proteins Encoded by Two Bacillus pumilus Phages on Unstable Lysogeny, Revealed by Genomic Analysis

“…Although phage Bp8p-C and phiAGATE exhibited high genome similarity at 62.5% and baseplate associated genes were found in both genomes, the structure of the baseplate was only observed for phage Bp8p-C virion (Fig. 1C) and not for phiAGATE (16).…”

“…Each of the two phages had an isometric head with a diameter of 88 nm, a 189-nm-long contractile tail, a 60-nm-long tail needle, and a 20-nmlong and 46-nm-wide baseplate. To date, a few phages of B. pumilus have been isolated (17), while only one B. pumilus phage from the Myoviridae family has been morphologically characterized (16).…”

“…In prokaryotes, the actin-like filamentous proteins allow accurate distribution of the plasmids in daughter cells during cell division (51). Actin-like proteins have also been found in several phage genomes such as that of C. botulinum phage c-st (3), B. megaterium phage G (52), Pseudomonas chlororaphis phage 2012-1 (6), and B. pumilus phage phiAGATE (16). The actin-like protein encoded by c-st genome belongs to the type III plasmid segregation system and has been regarded as one of the factors causing unstable lysogeny.…”

“…Because of its ability to convert into latent phage, the Bacillus phage can achieve species conservation by incorporating itself into the host spore. The putative plasmid segregation protein is widely found in the genome of Bacillus myovirus (16,55) and might be a common survival mechanism of the Bacillus myovirus. A further functional analysis of the putative phage-encoding plasmid segregation protein in vivo will illustrate how the protein regulates the state of phage genome, whether the phage genomes are packaged into phage capsids or distribute into daughter cells as phage-plasmid during cell division.…”

“…Before 1981, more than 33 different phages were reported to infect B. pumilus, and a few more have been characterized since (15). In addition, the genome of 10 B. pumilus phages have been characterized to date (16,17); however, the structural proteome of the phage virion has not yet been analyzed.…”