Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Cultivation Media
2.2. Phage Isolation and Propagation
2.3. Phage Plaque Morphology and Electron Microscopy of Phage Particles
2.4. Biological Properties of KP8 Bacteriophage and Host Range Analysis
2.5. Phage DNA Purification and Sequencing
2.6. Genome Analysis
2.7. Phage Structural Proteins Analysis and Mass Spectrometry
3. Results and Discussion
3.1. Isolation, Morphology, and Host Range
3.2. Biological Properties of KP8
3.3. Genome Structure
3.4. Predicted Gene Products
3.5. Proteomic Analysis
3.6. Phylogenetic Analysis of the KP8 Complete Genome
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Name | Position | ORF a | Regulatory Element Sequence b |
---|---|---|---|
Putative promoter | |||
P1 | 89–110 | 1 | ACGTTGCTCCGCAACCTATGGA |
P2 | 962–983 | 4 | AAGACGCTCCGCGTCTTATGGA |
P3 | 1225–1246 | 5 | GGGCTGCTCCGCAGCCTTTGGA |
P4 | 5965–5984 | 21 | AAGCAGCTCCGCTGCTTGTGGG |
Putative ρ-independent terminator | |||
T | 37311–37349 | 64 | TGCTGAAGAATGGGCAAGTAGTGCCTTAGAGCGACCTTG |
No | ORF | ORF Position (b.p.) | Length of Product (aa)/Predicted Molecular Mass (kDa) | Start Codon/ORF Orientation (+−) | Maximal Identity (%) with GenBank Phage Protein Sequences, according to Algorithm BLASTXa | Predicted Molecular Function | Protein Sequence Coverage, (%) in MS-Analysis |
---|---|---|---|---|---|---|---|
1 | 5 | 1254–1748 | 165/18.2 | ATG/+ | 74.2 (Escherichia virus N4 [YP_950480]) | RNA polymerase 1 subunit A | |
2 | 14 | 3799–4155 | 119/13.3 | ATG/+ | 75.4 (Escherichia phage EC1-UPM [YP_009598285]) | GTP binding protein DUF2493/DNA processing A domain | |
3 | 19 | 5304–5684 | 126/13.89 | ATG/+ | 77.0 (Escherichia virus N4 [YP_950492]) | ADP-ribosylglycohydrolase | |
4 | 22 | 6257–7072 | 272/31.73 | ATG/+ | 74.6 (Escherichia virus N4 [YP_950493]) | RNA polymerase 1 subunit B | |
5 | 25 | 7589–8803 | 404/45.99 | ATG/+ | 74.1 (Escherichia phage PMBT57 [AUV59092]) | RNA polymerase 2 subunit A | |
6 | 26 | 8896–9411 | 171/17.95 | ATG/+ | 48.5 (Erwinia phage phiEaP-8 [AWN06248]) | Capsid decorating protein (Ig-like domain) | 84 |
7 | 29 | 10082–10432 | 116/13.24 | ATG/+ | 88.4 (Escherichia virus N4 [YP_950500]) | HNH-endonuclease | |
8 | 35 | 11890–12942 | 350/35.9 | ATG/+ | 63.0 (Escherichia phage OLB145 [AYR04207]) | ATPase | |
9 | 36 | 12953–14104 | 384/43.8 | ATG/+ | 62.9 (Escherichia phage OLB145 [AYR04209]) | Metallopeptidase | |
10 | 37 | 14112–14639 | 175/19.5 | ATG/+ | 78.7 (Escherichia phage phiG17 [AWY03411]) | dCTP deaminase | |
11 | 40 | 15353–16294 | 313/35.9 | ATG/+ | 67.7 (Escherichia phage PMBT57 [AUV59106]) | FAD-dependent thymidylate synthase | |
12 | 44 | 17167–19689 | 840/95.1 | ATG/+ | 43.5 (Escherichia virus N4 [YP_950511]) | rIIA lysis inhibitor | |
13 | 45 | 19686–21722 | 678/73.69 | ATG/+ | 52.7 (Escherichia virus N4 [YP_950512]) | rIIB lysis inhibitor | |
14 | 46 | 21782–22177 | 131/14.9 | ATG/+ | 84.6 (Escherichia phage PMBT57 [AUV59111]) | DNA-binding domain1 | |
15 | 47 | 22158–22562 | 134/14.8 | GTG/+ | 64.4 (Escherichia phage vB_EcoP_PhAPEC5 [YP_009055545]) | NTP pyrophosphohydrolase | |
16 | 48 | 22599–23906 | 435/49.05 | ATG/+ | 71.3 (Escherichia virus N4 [YP_950515]) | DNA-helicase | |
17 | 50 | 24454–27036 | 860/97.5 | ATG/+ | 74.8 (Escherichia phage vB_EcoP_G7C [YP_004782168.1]) | DNA-polymerase I | |
18 | 51 | 27036–27251 | 71/7.88 | ATG/+ | 47.0 (Klebsiella phage Soft [QEM42165.1]) | Nucleoside/nucleotide kinase1 | |
19 | 53 | 27556–27966 | 136/15.34 | ATG/+ | 79.8 (Escherichia virus N4 [YP_950519.1]) | 3’-phosphatase 5’-polynucleotide kinase | |
20 | 54 | 27950–28921 | 323/37.33 | GTG/+ | 78.0 (Escherichia virus N4 [YP_950520.1]) | PD-(D/E)XK nuclease superfamily protein | |
21 | 55 | 28921–31068 | 715/81.8 | ATG/+ | 80.7 (Escherichia phage PMBT57 [AUV59047]) | DNA primase | |
22 | 56 | 31126–31884 | 252/28.68 | ATG/+ | 86.9 (Escherichia phage PGN829.1 [AXY82607.1]) | Nucleoside triphosphate hydrolase | |
23 | 57 | 31927–32721 | 264/28.45 | ATG/+ | 57.7 (Escherichia virus N4 [YP_950523.1]) | ssDNA-binding protein | |
24 | 58 | 32721–33278 | 185/20.3 | ATG/+ | 73.5 (Escherichia virus N4 [YP_950524.1]) | Holliday junction resolvase | |
25 | 68 | 37968–48392 | 3474/379.07 | ATG/− | 69.9 (Escherichia phage OLB145 [AYR04234.1]) | Virion RNA polymerase | 8 |
26 | 69 | 48494–50443 | 649/70 | ATG/− | 69.3 (Escherichia phage vB_EcoP_PhAPEC7 [YP_009056187.1]) | Putative structural protein | 78 |
27 | 70 | 50453–50893 | 146/15.5 | ATG/− | 66.4 (Escherichia phage ECBP1 [YP_006908829]) | Putative structural protein | |
28 | 72 | 53569–54399 | 276/30.3 | ATG/− | 85.6 (Escherichia phage IME11 [YP_006990617]) | Putative structural protein | |
29 | 74 | 55147–56352 | 401/44.1 | ATG/− | 90.5 (Escherichia phage vB_EcoP_PhAPEC5 [YP_009055570.1) | Major coat protein | 91 |
30 | 75 | 56365–57594 | 409/45 | ATG/− | 66.3 (Escherichia phage IME11 [YP_006990614]) | Tape measure protein | |
31 | 77 | 57976–60261 | 761/85.1 | ATG/− | 76.9 (Escherichia phage PGN829 [AXY82589]) | Portal protein | 57 |
32 | 78 | 60270–60767 | 165/18.8 | ATG/− | 65.9 (Escherichia phage IME11 [YP_006990611]) | Rz/RzI spanin protein | |
33 | 79 | 60751–61389 | 212/22.8 | ATG/− | 81.8 (Escherichia phage vB_EcoP_PhAPEC7 [YP_009056197]) | N-acetylmuramidase | |
34 | 80 | 61373–61699 | 108/12.6 | ATG/− | 56.6 (Shigella phage pSb-1 [YP_009008416]) | Holin | |
35 | 81 | 61624–61956 | 110/12.3 | ATG/− | 97.8 (Escherichia phage IME11 [YP_006990608]) | Tail length tape-measure protein | |
36 | 83 | 62259–64526 | 755/82.25 | ATG/− | 23.7 (Klebsiella phage K64-1 [YP_009153195]) | Tail spike protein/endo-N-acetylneuraminidase | 64 |
37 | 84 | 64598–67075 | 825/89.3 | ATG/− | 30.1 (Escherichia phage IME11 [YP_006990695]) | Tail fiber protein/SGNH-esterase domain 1 | 56 |
38 | 85 | 67072–67779 | 235/61 | ATG/− | 97.0 (Escherichia phage IME11 [YP_006990694]) | Head completion adaptor | |
39 | 86 | 67786–69378 | 530/60.7 | ATG/− | 89.4 (Escherichia virus N4 [YP_950546]) | Terminase large subunit | |
40 | 87 | 69371–70063 | 230/25.6 | ATG/− | 86.1 (Escherichia virus N4 [YP_950547]) | Terminase small subunit |
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Morozova, V.; Babkin, I.; Kozlova, Y.; Baykov, I.; Bokovaya, O.; Tikunov, A.; Ushakova, T.; Bardasheva, A.; Ryabchikova, E.; Zelentsova, E.; et al. Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8. Viruses 2019, 11, 1115. https://doi.org/10.3390/v11121115
Morozova V, Babkin I, Kozlova Y, Baykov I, Bokovaya O, Tikunov A, Ushakova T, Bardasheva A, Ryabchikova E, Zelentsova E, et al. Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8. Viruses. 2019; 11(12):1115. https://doi.org/10.3390/v11121115
Chicago/Turabian StyleMorozova, Vera, Igor Babkin, Yuliya Kozlova, Ivan Baykov, Olga Bokovaya, Artem Tikunov, Tatyana Ushakova, Alevtina Bardasheva, Elena Ryabchikova, Ekaterina Zelentsova, and et al. 2019. "Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8" Viruses 11, no. 12: 1115. https://doi.org/10.3390/v11121115
APA StyleMorozova, V., Babkin, I., Kozlova, Y., Baykov, I., Bokovaya, O., Tikunov, A., Ushakova, T., Bardasheva, A., Ryabchikova, E., Zelentsova, E., & Tikunova, N. (2019). Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8. Viruses, 11(12), 1115. https://doi.org/10.3390/v11121115