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PMID:30366363
| Citation |
Šimoliūnas, E, Šimoliūnienė, M, Kaliniene, L, Zajančkauskaitė, A, Skapas, M, Meškys, R, Kaupinis, A, Valius, M and Truncaitė, L (2018) Bacteriophage vB_PagS_Vid5: A Low-Temperature Siphovirus That Harbors a Cluster of Genes Involved in the Biosynthesis of Archaeosine. Viruses 10 |
|---|---|
| Abstract |
A novel lowtemperature siphovirus, vB_PagS_Vid5 (Vid5), was isolated in Lithuania using isolate for the phage propagation. The 61,437 bp genome of Vid5 has a G⁻C content of 48.8% and contains 99 probable protein encoding genes and one gene for tRNA. A comparative sequence analysis revealed that 46 out of 99 Vid5 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 33 Vid5 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phagehost interactions, and DNA metabolism. In addition, a cluster of genes possibly involved in the biosynthesis of 7-deazaguanine derivatives was identified. Notably, one of these genes encodes a putative preQ₀/preQ₁ transporter, which has never been detected in bacteriophages to date. A proteomic analysis led to the experimental identification of 11 virion proteins, including nine that were predicted by bioinformatics approaches. Based on the phylogenetic analysis, Vid5 cannot be assigned to any genus currently recognized by ICTV, and may represent a new one within the family of . |
| Links |
PubMed PMC6266253 Online version:10.3390/v10110583 |
| Keywords |
Bacteriophages/genetics; Bacteriophages/metabolism; Bacteriophages/ultrastructure; Cold Temperature; Computational Biology; Genes, Viral; Genome, Viral; Genomics/methods; Guanosine/analogs & derivatives; Guanosine/biosynthesis; Host Specificity; Multigene Family; Pantoea/virology; Phylogeny; Proteomics/methods; Sequence Analysis, DNA; Siphoviridae/genetics; Siphoviridae/metabolism; Viral Proteins/genetics; Viral Proteins/metabolism |
Significance
Annotations
| Gene product | Qualifier | GO Term | Evidence Code | with/from | Aspect | Extension | Notes | Status |
|---|---|---|---|---|---|---|---|---|
| GO:0019012: virion |
ECO:0007184: |
C |
Pg. 583 shows that the portal protein (gp03, ORF03) was found in Pantoea phage vB_PagS_Vid5. LC MS/MS was run on protein, and a molecular weight of 54.818 kDa, with 48 amino acid residues was recorded. Supplementary Table 3 shows results of mass spectrometry. |
complete | ||||
| GO:0019012: virion |
ECO:0007184: protein mass spectrometry evidence used in manual assertion |
C |
Table S3: Liquid Chromatography and Mass Spectroscopy indicate that ORF07 (gp7, Uncharacterized Protein, Vid5_gp07) is present in the organism Pantoea phage vB_PagS_Vid5. |
complete | ||||
| GO:0019012: virion |
ECO:0007184: |
C |
Pg. 583 shows that the tail fiber protein (gp22, ORF22) was found in Pantoea phage vB_PagS_Vid5. LC MS/MS was run on the protein, and a molecular weight of 98.324 kDa, with 7 amino acid residues was recorded. Supplementary Table 3 shows results of mass spectrometry. |
complete | ||||
| GO:0019012: virion |
ECO:0007184: protein mass spectrometry evidence used in manual assertion |
C |
Table S3: Liquid chromatography mass spectrometry evidence identified gp18 (ORF18), a protein of Pantoea Bacteriophage vB_PagS_Vid5, as a component of the virion. |
complete | ||||
| GO:0019012: virion |
ECO:0007184: protein mass spectrometry evidence used in manual assertion |
C |
Table S3 Liquid Chromatography and Mass Spectroscopy indicate that ORF13 (gp13, Neck Protein, Vid5_gp13) is present in the organism Pantoea phage vB_PagS_Vid5. |
complete | ||||
| GO:0019012: virion |
ECO:0007184 : |
C |
Page 583 shows that gp10 (ORF10), a putative EPS depolymerase enzyme, was identified by LC-MS/MS based proteomics as present in the virion of Pantoea Bacteriophage vB_PagS_Vid5. Table S3 shows gp10 to possess a molecular mass of 95.823 kDa. |
complete | ||||
| GO:0019012: virion |
ECO:0007184: protein mass spectrometry evidence used in manual assertion |
C |
Table S3: Liquid Chromatography and Mass Spectroscopy indicate that ORF99 (gp99, Lysis regulatory protein, Vid5_gp99) is present in the organism Pantoea phage vB_PagS_Vid5. |
complete | ||||
| GO:0019012: virion |
ECO:0001582: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion |
C |
The tail fiber protein (gp25, ORF25) is identified through LC-MS/MS in Pantoea phage vB_PagS_Vid5. Supplementary Table 3 shows the data obtained from the LC-MS/MS and identifies the molecular weight as 44.464(KDa). |
complete | ||||
| GO:0019012: virion |
ECO:0001582: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion |
C |
Page 583 shows that gp11 (ORF11), a head-tail adaptor, was identified by LC-MS/MS based proteomics as present in the virion of Pantoea Bacteriophage vB_PagS_Vid5. Table S3 shows that gp11 possesses a molecular mass of 18.734 kDa. |
complete | ||||
| GO:0019012: virion |
ECO:0001582: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion |
C |
The major tail protein (gp15, ORF15) is identified through LC-MS/MS in Pantoea phage vB_PagS_Vid5. Supplementary Table 3 shows the data obtained from the LC-MS/MS and identifies the molecular weight as 33.329(KDa). |
complete | ||||
| GO:0019012: virion |
ECO:0001582: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion |
C |
The major capsid protein (gp06, ORF06) is identified through LC-MS/MS in Pantoea phage vB_PagS_Vid5. Supplementary Table 3 shows the data obtained from the LC-MS/MS and identifies the molecular weight as 39.892 (KDa) |
complete | ||||
Notes
See also
References
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