Fig 1.
Liquid phage lysate was incubated on a carbon coated copper grid, stained with 4% uranyl acetate and visualized at 180,000-fold magnification by a transmission electron microscope. Scale bar represent 50 nm. The average capsid height measurement for DLP6 was 99 nm, average tail length of 144 nm and average tail width of 23 nm.
Fig 2.
The scale (in bp) is shown in the outermost periphery of the genome along with late viral promoters (dark green) and terminators (dark red), as predicted by the algorithims in the software programs PHIRE and ARNold, respectively. Assigned functions for each predicted open reading frame are as follows: auxiliary metabolism (black), lysis (red), gene expression (light blue), phage morphogenesis (dark purple), DNA replication/repair (lilac), tRNA (bright green), repeat region (pink) and hypothetical (grey). Due to space constraints, genes are located either inside of or outside the circle thereby reducing overlap. The bp numbering of the circular map takes into account annealing of the direct repeats, reducing the genome length from 168,489 bp (- 229 bp) to 168,260 bp.
Fig 3.
Predicted promoter sequence in DLP6.
Putative phage promoter consensus sequence identified using PHIRE [39] and plotted using WebLogo 3 [40].
Table 1.
Predicted Rho-independent terminators in DLP6.
Rho-independent terminators were identified using the ARNold [36, 37] program and putative terminators with a ΔG value of -10 kcal/mol or less were retained. DNA that is predicted to form the loop in the RNA is in emboldened, whereas DNA that is predicted to encode an RNA stem is underlined.
Fig 4.
Unrooted gp20 (portal vertex protein: AAY80_011) tree.
FastTree was used to generate the tree from a MUSCLE alignment between DLP6 gp20 and the top 250 BLASTP sequences. The local support value for each branch is shown on the tree and the bar is a marker of branch distance length. The clades featuring gp20 of T4 and gp20 of T4-superfamily cyanophages are indicated.
Fig 5.
Circos plot of DLP6 and ΦM12 PROmer comparisons.
Green ribbons indicate regions of similarity between the two genomes at the protein level encoded on the same strand, and representing a similarity of greater than 32%, with an average similarity of 56%. Red ribbons indicate regions of similarity at the protein level encoded on opposite strands, representing a similarity of greater than 32%, with an average similarity of 56%. The scale (in kbp) is shown on the periphery of the plots. PROmer parameters: breaklen = 60, maxgap = 30, mincluster = 10, minmatch = 3.
Table 2.
MUSCLE alignment percent identity score of full-length protein sequences of DLP6 against universal core and nearly universal core proteins of 18 T4-superfamily phages.
Numbers indicate percent similarity to the related DLP6 protein.
Table 3.
MUSCLE alignment percent identity score of DLP6 amino acid sequences against T4-superfamily cyanophage accessory core proteins.
DLP6 contains six of the 25 T4-superfamily cyanophage core proteins. Numbers indicate percent similarity to the related DLP6 protein.
Table 4.
MUSCLE alignment percent identity score of DLP6 amino acid sequences against T4-superfamily non-cyanophage core proteins.
This table includes 10 of the 32 non-cyanophage core proteins. Numbers indicate percent similarity to the related DLP6 protein.