Characterization of a Novel Thermobifida fusca Bacteriophage P318
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolation and Purification of P318
2.2. One Step Growth Cycle of P318
2.3. Phylogenetic Analysis
2.4. Genome Organization of P318
2.5. COS Site of P318
2.6. Identification of Proteins Associated with P318 Virions
3. Results and Discussion
3.1. Isolation and Purification of P318
3.2. Morphology and Infectivity of P318
3.3. Genome Structure of P318
3.4. Putative Proteins Encoded by P318
3.5. Comparison between P318 and P1312 Genomes
4. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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ORF | Start (nt) | End (nt) | Size (kDa) a | Predicted Functions | BLASTP (Best Match) | LC-M/M b |
---|---|---|---|---|---|---|
1 | 1255 | 827 | 15.8 | ssDNA binding protein | YP_009269232.1 Gordonia phage Smoothie | |
2 | 1461 | 1240 | 8.2 | hypothetical protein | WP_015060945.1 Streptomyces sp. | |
3 | 2142 | 1534 | 22.4 | RNA ligase | YP_008859155.1 Mycobacterium phage Zaka | |
4 | 3163 | 2312 | 31.3 | FAD-dependent thymidylate synthase | WP_043914404.1 Kitasatospora griseola | 15 |
5 | 5103 | 3340 | 64.7 | DNA polymerase | OEV28665.1 Streptomyces nanshensis | |
6 | 5717 | 5181 | 19.7 | phage protein | SBO90589.1 Nonomuraea gerenzanensis | |
7 | 8719 | 5762 | 109.6 | ribonucleoside-triphosphate reductase | OEV28666.1 Streptomyces nanshensis | 4 |
8 | 9570 | 8872 | 25.7 | putative sigma factor | AIS73726.1 Mycobacterium phage Quinnkiro | |
9 | 10365 | 9580 | 28.4 | phosphoesterase | YP_008051820.1 Mycobacterium phage Severus | 29 |
10 | 10676 | 10362 | 11.6 | hypothetical protein | OEV28668.1 Streptomyces nanshensis | |
11 | 10950 | 10669 | 10.5 (V) | hypothetical protein | WP_093886506.1 Streptosporangium canum | |
12 | 11769 | 11149 | 22.8 (V) | DNA primase | ASZ75224.1 Mycobacterium phage MissWhite | |
13 | 12347 | 11955 | 14.5 | resolvase | AYN59122.1 Arthrobacter phage Yang | |
14 | 13164 | 12322 | 31.0 | DnaB-like helicase | AFF28358.1 Mycobacterium phage Twister | |
15 | 14397 | 13441 | 35.1 | exonuclease | AOT25428.1 Mycobacterium phage BabyRay | |
16 | 15206 | 15394 | 7.0 (V) | cystathionine β-synthase | WP_087442904.1 Paenibacillus thiaminolyticus | |
17 | 15851 | 16300 | 16.5 | terminase small subunit | AYN58482.1 Arthrobacter phage Maureen | |
18 | 16740 | 17888 | 42.2 | terminase large subunit | SFI82078.1 Streptosporangium canum | |
19 | 17902 | 19350 | 54.1 | phage portal protein | WP_093886565.1 Streptosporangium canum | 17 |
20 | 19402 | 20007 | 22.3 | phage scaffold protein | AWN05292.1 Streptomyces phage Ibantik | 7 |
21 | 20023 | 21084 | 39.0 | phage major capsid protein | AWN05293.1 Streptomyces phage Ibantik | 47 |
22 | 21166 | 21432 | 7.8 | hypothetical protein | OEV28690.1 Streptomyces nanshensis | 18 |
23 | 21435 | 21800 | 13.4 | phage gp6-like head-tail connector protein | WP_018564996.1 Streptomyces sp. | 9 |
24 | 21797 | 22111 | 11.6 | hypothetical protein | WP_055523439.1 Streptomyces graminilatus | 25 |
25 | 22147 | 22557 | 15.1 | hypothetical protein | WP_039630012.1 Streptomyces | 14 |
26 | 22557 | 22937 | 11.4 | DUF3168 domain-containing protein | WP_120720997.1 Streptomyces hundungensis | 27 |
27 | 22941 | 23573 | 23.3 | phage major tail protein | SBO90565.1 Nonomuraea gerenzanensis | 31 |
28 | 23667 | 23963 | 10.9 | tail assembly chaperone | YP_009302776.1 Gordonia phage BetterKatz | |
29 | 23978 | 24397 | 15.4 | tail assembly chaperone | AXH45781.1 Gordonia phage GEazy | |
30 | 24417 | 30116 | 207.5 | tape measure domain -containing protein | SMB97758.1 Thermanaeromonas toyohensis | 24 |
31 | 30128 | 31168 | 38.2 | phage tail protein | WP_079249051.1 Streptomyces sp. | 8 |
32 | 31168 | 32589 | 52.2 | phage tail minor protein | ASM62305.1 Arthrobacter phage Nightmare | 21 |
33 | 32582 | 33700 | 41.1 | hypothetical protein | WP_033100528.1 Thermoactinomyces daqus | 34 |
34 | 33717 | 34019 | 11.2 (V) | hypothetical protein | WP_004938179.1 Streptomyces mobaraensis | |
35 | 34016 | 34828 | 29.9 | N-acetylmuramoyl-L-alanine amidase | ALA06408.1 Thermobifida phage P1312 | |
36 | 34880 | 35098 | 8.1 | hypothetical protein | WP_026415462.1 Actinomadura oligospora | 15 |
37 | 35098 | 36045 | 34.8 | phage tail protein | WP_079733063.1 Acinetobacter baumannii | 25 |
38 | 36045 | 36992 | 34.8 | Peptidoglycan binding domain containing protein | WP_013490242.1 Bacillus cellulosilyticus | 5 |
39 | 38528 | 37050 | 54.3 | DUF3987 domain-containing protein | WP_012850795.1 Thermomonospora curvata | 13 |
40 | 37395 | 38753 | 49.9 | putative methyltransferase | EUA88088.1 Mycobacterium ulcerans str. Harvey | |
41 | 39792 | 38629 | 42.7 | hypothetical protein | ONK09418.1 Streptomyces sp. MP131-18 | |
42 | 40601 | 39894 | 28.9 | hypothetical protein P1312_051 | ALA06416.1 Thermobifida phage P1312 | 8 |
43 | 41401 | 40742 | 23.6 | hypothetical protein | OEV28683.1 Streptomyces nanshensis | |
44 | 42099 | 41398 | 25.8 (V) | recombinase | WP_098165210.1 Bacillus pseudomycoides | |
45 | 42541 | 42224 | 11.7 | MerR family transcriptional regulator | WP_003947861.1 Streptomyces | |
46 | 42863 | 42630 | 8.6 | peptidoglycan editing factor PgeF | WP_069300862.1 Neptunicoccus sediminis | |
47 | 43590 | 43108 | 17.8 | hypothetical protein | XP_005789494.1 Emiliania huxleyi CCMP1516 | 4 |
48 | 43997 | 43731 | 9.8 (V) | hypothetical protein | WP_060729217.1 Streptomyces albus | |
49 | 44740 | 44102 | 23.5 | No match | ||
50 | 45599 | 45249 | 12.9 | hypothetical protein | WP_071806278.1 Couchioplanes caeruleus | |
51 | 46086 | 45673 | 15.2 | No match | ||
52 | 46447 | 46124 | 11.9 | DUF305 domain-containing protein | WP_009082635.1 Actinobacteria |
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Cheepudom, J.; Lin, T.-L.; Lee, C.-C.; Meng, M. Characterization of a Novel Thermobifida fusca Bacteriophage P318. Viruses 2019, 11, 1042. https://doi.org/10.3390/v11111042
Cheepudom J, Lin T-L, Lee C-C, Meng M. Characterization of a Novel Thermobifida fusca Bacteriophage P318. Viruses. 2019; 11(11):1042. https://doi.org/10.3390/v11111042
Chicago/Turabian StyleCheepudom, Jatuporn, Tzu-Ling Lin, Cheng-Cheng Lee, and Menghsiao Meng. 2019. "Characterization of a Novel Thermobifida fusca Bacteriophage P318" Viruses 11, no. 11: 1042. https://doi.org/10.3390/v11111042