From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses
Abstract
:1. Introduction
2. Results
2.1. Description of N4-Like Viruses
- Podovirus morphology
- Genome size of 59–80 kb
- Linear genome with defined ends (terminal repeats expected)
- Presence of three RNA polymerase genes, including a large (~3500 aa) virion-associated RNA polymerase (vRNAP)
2.2. Proposal of a New Family
2.3. Proposal of New Subfamilies and Genera
3. Discussion
4. Materials and Methods
4.1. vConTACT2 Analysis
4.2. Panproteome Analysis
4.3. VIRIDIC Analysis
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Phage | Subfamily | Genus | Reference |
---|---|---|---|
Achromobacter phage JWAlpha | “Rothmandenesvirinae” | Jwalphavirus | [15] |
Achromobacter phage JWDelta | “Rothmandenesvirinae” | Jwalphavirus | [15] |
Achromobacter phage phiAxp–3 | “Rothmandenesvirinae” | “Dongdastvirus” | [16] |
Achromobacter phage vB_AxyP_19–32_Axy04 | “Rothmandenesvirinae” | “Dongdastvirus” | [17] |
Achromobacter phage vB_AxyP_19–32_Axy10 | “Rothmandenesvirinae” | “Pourcelvirus” | [17] |
Achromobacter phage vB_AxyP_19–32_Axy11 | “Rothmandenesvirinae” | “Pourcelvirus” | [17] |
Achromobacter phage vB_AxyP_19–32_Axy12 | “Rothmandenesvirinae” | “Dongdastvirus” | [17] |
Achromobacter phage vB_AxyP_19–32_Axy13 | “Rothmandenesvirinae” | “Inbricusvirus” | [17] |
Achromobacter phage vB_AxyP_19–32_Axy22 | “Rothmandenesvirinae” | “Pourcelvirus” | [17] |
Achromobacter phage vB_AxyP_19–32_Axy24 | “Rothmandenesvirinae” | “Dongdastvirus” | [17] |
Acinetobacter phage Presley | “Presleyvirus” | [18] | |
Acinetobacter phage VB_ApiP_XC38 | [19] | ||
Delftia phage RG–2014 | “Dendoorenvirus” | [20] | |
Dinoroseobacter phage DFL12phi1 | “Rhodovirinae” | Baltimorevirus | |
Dinoroseobacter phage DS–1410Ws–06 | “Rhodovirinae” | “Sanyabayvirus” | [21] |
Dinoroseobacter phage vBDshPR2C | “Rhodovirinae” | Baltimorevirus | [22] |
Enterobacter phage EcP1 | “Eceepunavirus” | ||
Enterobacteria phage N4 | “Enquatrovirinae” | Enquatrovirus | [3] |
Erwinia phage Ea9–2 | “Erskinevirinae” | Johnsonvirus | |
Erwinia phage phiEaP–8 | “Erskinevirinae” | Yonginvirus | [23] |
Erwinia phage vB_EamP_Frozen | “Erskinevirinae” | Johnsonvirus | [24] |
Erwinia phage vB_EamP_Gutmeister | “Erskinevirinae” | Johnsonvirus | [24] |
Erwinia phage vB_EamP_Rexella | “Erskinevirinae” | Johnsonvirus | [24] |
Erwinia phage vB_EamP–S6 | “Waedenswilvirus” | [25] | |
Escherichia phage Bp4 | “Enquatrovirinae” | Gamaleyavirus | [26] |
Escherichia phage EC1–UPM | “Enquatrovirinae” | Gamaleyavirus | [27] |
Escherichia phage ECBP1 | “Enquatrovirinae” | Gamaleyavirus | [28] |
Escherichia phage IME11 | “Enquatrovirinae” | Gamaleyavirus | [29] |
Escherichia phage OLB145 | “Enquatrovirinae” | Enquatrovirus | |
Escherichia phage PD38 | “Enquatrovirinae” | Gamaleyavirus | |
Escherichia phage PGN829.1 | “Enquatrovirinae” | Gamaleyavirus | |
Escherichia phage phi G17 | “Enquatrovirinae” | Gamaleyavirus | [30] |
Escherichia phage PMBT57 | “Enquatrovirinae” | Enquatrovirus | |
Escherichia phage Pollock | “Humphriesvirinae” | “Pollockvirus” | [31] |
Escherichia phage St11Ph5 | “Enquatrovirinae” | Gamaleyavirus | [32] |
Escherichia phage vB_EcoP_3HA13 | “Enquatrovirinae” | Enquatrovirus | |
Escherichia phage vB_EcoP_G7C | “Enquatrovirinae” | Gamaleyavirus | [33] |
Escherichia phage vB_EcoP_PhAPEC5 | “Enquatrovirinae” | Gamaleyavirus | [34] |
Escherichia phage vB_EcoP_PhAPEC7 | “Enquatrovirinae” | Gamaleyavirus | [34] |
Klebsiella phage KP8 | “Enquatrovirinae” | “Kaypoctavirus” | [35] |
Klebsiella phage KpCHEMY26 | “Humphriesvirinae” | “Pylasvirus” | [36] |
Klebsiella phage Pylas | “Humphriesvirinae” | “Pylasvirus” | [37] |
Pectobacterium phage Nepra | “Cbunavirus” | ||
Pectobacterium phage phiA41 | “Cbunavirus” | [38] | |
Pectobacterium phage vB_PatP_CB1 | “Cbunavirus” | [39] | |
Pectobacterium phage vB_PatP_CB3 | “Cbunavirus” | [39] | |
Pectobacterium phage vB_PatP_CB4 | “Cbunavirus” | [39] | |
Pseudoalteromonas phage pYD6-A | “Fuhrmanvirinae” | “Mazuvirus” | |
Pseudomonas phage 98PfluR60PP | “Littlefixvirus” | [40] | |
Pseudomonas phage DL64 | “Migulavirinae” | Litunavirus | [41] |
Pseudomonas phage inbricus | “Rothmandenesvirinae” | “Inbricusvirus” | |
Pseudomonas phage KPP21 | “Migulavirinae” | Luzseptimavirus | [42] |
Pseudomonas phage LIT1 | “Migulavirinae” | Litunavirus | [43] |
Pseudomonas phage Littlefix | “Littlefixvirus” | ||
Pseudomonas phage LP14 | “Migulavirinae” | Litunavirus | [44] |
Pseudomonas phage LUZ7 | “Migulavirinae” | Luzseptimavirus | [43] |
Pseudomonas phage LY218 | “Migulavirinae” | Litunavirus | |
Pseudomonas phage Pa2 | “Migulavirinae” | Litunavirus | |
Pseudomonas phage PA26 | “Migulavirinae” | Litunavirus | [45] |
Pseudomonas phage PEV2 | “Migulavirinae” | Litunavirus | [43] |
Pseudomonas phage phCDa | Shizishanvirus | ||
Pseudomonas phage phi176 | “Migulavirinae” | Litunavirus | [46] |
Pseudomonas phage RWG | “Migulavirinae” | Litunavirus | [46] |
Pseudomonas phage vB_Pae1396P-5 | “Migulavirinae” | Litunavirus | |
Pseudomonas phage vB_Pae575P-3 | “Migulavirinae” | Litunavirus | |
Pseudomonas phage vB_PaeP_C2–10_Ab09 | “Migulavirinae” | Litunavirus | [47] |
Pseudomonas phage vB_PaeP_DEV | “Migulavirinae” | Litunavirus | [48] |
Pseudomonas phage vB_PaeP_MAG4 | “Migulavirinae” | Litunavirus | [49] |
Pseudomonas phage vB_PaeP_PYO2 | “Migulavirinae” | Litunavirus | [48] |
Pseudomonas phage YH30 | “Migulavirinae” | Litunavirus | [50] |
Pseudomonas phage YH6 | “Migulavirinae” | Litunavirus | [51] |
Pseudomonas phage ZC03 | “Zicotriavirus” | [52] | |
Pseudomonas phage ZC08 | “Zicotriavirus” | [52] | |
Pseudomonas phage Zuri | “Zurivirus” | ||
Roseobacter phage RD–1410W1–01 | “Rhodovirinae” | “Aoquinvirus” | [21] |
Roseobacter phage RD–1410Ws–07 | “Rhodovirinae” | “Sanyabayvirus” | [21] |
Roseovarius Plymouth podovirus 1 | “Rhodovirinae” | “Plymouthvirus” | [53] |
Roseovarius sp. 217 phage 1 | “Rhodovirinae” | “Plymouthvirus” | [53] |
Ruegeria phage vB_RpoP–V12 | “Rhodovirinae” | “Aorunvirus” | |
Ruegeria phage vB_RpoP–V13 | “Rhodovirinae” | “Pomeroyivirus” | |
Ruegeria phage vB_RpoP–V14 | “Rhodovirinae” | “Aorunvirus” | |
Ruegeria phage vB_RpoP–V17 | “Rhodovirinae” | “Aorunvirus” | |
Ruegeria phage vB_RpoP–V21 | “Rhodovirinae” | “Aorunvirus” | |
Salmonella phage FSL SP–058 | “Humphriesvirinae” | “Ithacavirus” | [54] |
Salmonella phage FSL SP–076 | “Humphriesvirinae” | “Ithacavirus” | [54] |
Shigella phage pSb–1 | “Enquatrovirinae” | Gamaleyavirus | [55] |
Silicibacter phage DSS3phi2 | “Rhodovirinae” | “Aorunvirus” | [56] |
Sinorhizobium phage ort11 | “Huelvavirus” | [57] | |
Stenotrophomonas phage Pokken | “Pokkenvirus” | [58] | |
Sulfitobacter phage EE36phi1 | “Rhodovirinae” | “Aorunvirus” | [56] |
Sulfitobacter phage phiCB2047-B | “Rhodovirinae” | “Raunefjordvirus” | [59] |
Vibrio phage 1.025.O._10N.222.46.B6 | “Pontosvirinae” | “Nahantvirus” | |
Vibrio phage 1.026.O._10N.222.49.C7 | “Pontosvirinae” | “Nahantvirus” | |
Vibrio phage 1.097.O._10N.286.49.B3 | “Pontosvirinae” | “Dorisvirus” | |
Vibrio phage 1.150.O._10N.222.46.A6 | “Pontosvirinae” | “Nahantvirus” | |
Vibrio phage 1.152.O._10N.222.46.E1 | “Pontosvirinae” | “Nahantvirus” | |
Vibrio phage 1.169.O._10N.261.52.B1 | Mukerjeevirus | ||
Vibrio phage 1.188.A._10N.286.51.A6 | Mukerjeevirus | ||
Vibrio phage 1.224.A._10N.261.48.B1 | Mukerjeevirus | ||
Vibrio phage 1.261.O._10N.286.51.A7 | Mukerjeevirus | ||
Vibrio phage 2.130.O._10N.222.46.C2 | “Pontosvirinae” | “Nahantvirus” | |
Vibrio phage JA–1 | “Pacinivirus” | [60] | |
Vibrio phage JSF3 | “Pacinivirus” | [61] | |
Vibrio phage phi 1 | “Pacinivirus” | [62] | |
Vibrio phage phi50–12 | |||
Vibrio phage pVa5 | “Pontosvirinae” | “Galateavirus” | [63] |
Vibrio phage pVco–5 | [64] | ||
Vibrio phage VBP32 | “Fuhrmanvirinae” | “Stoningtonvirus” | |
Vibrio phage VBP47 | “Fuhrmanvirinae” | “Stoningtonvirus” | |
Vibrio phage VCO139 | “Pacinivirus” | [60] | |
Vibrio virus vB_VspP_SBP1 | |||
Xanthomonas phage RiverRider | “Riverridervirus” | [65] | |
From metagenomes | |||
Podoviridae sp. isolate ctda_1 | |||
Podoviridae sp. ctLUJ1 | |||
Siphoviridae sp. isolate 355 | “Enquatrovirinae” | Gamaleyavirus |
# | N4_Product | N4 Locus Tag | N4 Protein Accession | PIRATE | Proteinortho_30 | CoreGenes 5.0 |
---|---|---|---|---|---|---|
1 | RNAP 1 | EPNV4_gp15 | YP_950493.1 | Y | Y | Y |
2 | RNAP 2 | EPNV4_gp16 | YP_950494.1 | N | Y | Y |
3 | AAA+ ATPase | EPNV4_gp24 | YP_950502.1 | * | Y | Y |
4 | gp25 | EPNV4_gp25 | YP_950503.1 | N | N | Y |
5 | DNA polymerase | EPNV4_gp39 | YP_950517.1 | Y | Y | Y |
6 | gp42 | EPNV4_gp42 | YP_950520.1 | Y | Y | Y |
7 | DNA primase | EPNV4_gp43 | YP_950521.1 | Y | Y | Y |
8 | gp44 | EPNV4_gp44 | YP_950522.1 | Y | Y | Y |
9 | vRNAP | EPNV4_gp50 | YP_950528.1 | N | N | Y |
10 | 16.5 kDa protein | EPNV4_gp52 | YP_950530.1 | Y | Y | Y |
11 | gp54 | EPNV4_gp54 | YP_950532.1 | N | N | Y |
12 | Major capsid protein | EPNV4_gp56 | YP_950534.1 | Y | Y | Y |
13 | gp57 (tape measure) | EPNV4_gp57 | YP_950535.1 | N | * | Y |
14 | 94 kDa protein (portal vertex protein) | EPNV4_gp59 | YP_950537.1 | Y | Y | Y |
15 | 30 kDa protein | EPNV4_gp67 | YP_950545.1 | N | N | Y |
16 | Terminase, large subunit | EPNV4_gp68 | YP_950546.1 | Y | Y | Y |
17 | gp69 | EPNV4_gp69 | YP_950547.1 | Y | N | Y |
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Wittmann, J.; Turner, D.; Millard, A.D.; Mahadevan, P.; Kropinski, A.M.; Adriaenssens, E.M. From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses. Antibiotics 2020, 9, 663. https://doi.org/10.3390/antibiotics9100663
Wittmann J, Turner D, Millard AD, Mahadevan P, Kropinski AM, Adriaenssens EM. From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses. Antibiotics. 2020; 9(10):663. https://doi.org/10.3390/antibiotics9100663
Chicago/Turabian StyleWittmann, Johannes, Dann Turner, Andrew D. Millard, Padmanabhan Mahadevan, Andrew M. Kropinski, and Evelien M. Adriaenssens. 2020. "From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses" Antibiotics 9, no. 10: 663. https://doi.org/10.3390/antibiotics9100663