Fig 1.
Electron micrographs of phage Str01 (left) and Str03 (right). Electron micrographs of negatively stained (2% uranyl acetate) phage Str01 (left) and Str03 (right). The scale bar represents 100 nm.
Table 1.
Stability of phages Str01 and Str03 in various temperatures.
Table 2.
Stability of phages Str01 and Str03 in various pH values.
Fig 2.
Result of agarose gel electrophoresis.
(A) PCR with primers targeting sequence specific for Str01 genome. (B) PCR results with primers targeting sequence specific for Str03 genome. Each set of primers was tested with the same set of templates isolated from (left to right): C–E. coli and phage mix as wash protocol control; L–lysogenic strain of PCM 2855 (positive control), P–PCM 2855 host genome, 1 –phage genome Str01, 3 –phage genome Str03, 0 –no template (negative and environmental control).
Table 3.
Basic features of the analyzed genomes.
Fig 3.
Similarities between genomes of Str03 and the most closely related phage.
Genome maps are shown in a pairwise alignment. Arrows indicate genes and are colored according to the gene similarity (grey–identical genes, pink–genes with silent mutations, red–genes with amino acid substitutions in protein products). The middle bar shows DNA sequence similarity between the two genomes. Regions with no alignment are shown as a thin black line.
Fig 4.
Genome organization of phages Str01 and Str03.
Genome organization is shown as a linear map oriented to start at the small terminase subunit gene. Predicted CDSs are marked with arrows colored by predicted function: DNA packaging (violet); head assembly (blue), tail assembly (aquamarine), lysis (red), integration (green) and DNA replication (orange). CDSs with no function assigned are light grey. Genes with protein products detected by mass spectrometry are marked with the “M” or “m” symbol (depending on the confidence level of the finding see columns 6–8 in Table 4 and Table 5). The GC content of the isolated phages differs less than 1% from of the average of S. pyogenes and our phages follow typical features of such phages, like lack of phage-encoded tRNAs coding sequences. The genome maps were exported using Geneious software (v 9.0.5). Minor adjustments in the resulting svg file included realignment of labels (but not labelling itself) for the improved readability and addition of the “MS” symbols. All these adjustments were implemented using InkScape 0.91.
Fig 5.
Similarities between genomes of Str01 and A25.
Genome map of both phages are shown in a pairwise alignment. Arrows indicate genes and are colored according to the gene similarity (grey–identical genes, pink–genes with silent mutations, red–genes with amino acid substitutions in protein products). The middle bar shows DNA sequence similarity between the two genomes. Regions with no alignment are shown as a thin black line.
Fig 6.
Phylogenetic trees showing relations between selected siphoviruses of Gram-positive bacteria.
(A) Approximately maximum-likelihood tree based on alignment of large subunits of terminases. (B) Approximately Neighbor-joining tree based on whole genome comparison. The leaves are colored according to the ICTV classification of each phage. Names of phages Str01 and Str03 are italicized, bolded and marked with asterisk (*). The cone at the top of the tree represent collapsed branch of Leuconostoc phages treated collectively as the outgroup. All phylogenetic trees were visualized using Geneious tree viewer. Legend coloring and shading were added using InkScape 0.91 software.
Table 4.
Proteins of the phage Str01 detected by mass spectrometry.
Table 5.
Proteins of the phage Str03 detected by mass spectrometry.