Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Phage Isolation
2.2. Single Plaque Purification
2.3. Large-Scale Amplification of SSBI34
2.4. Phage Stability and One-Step Growth Curve
2.5. Host Range
2.6. Bacterial Growth Reduction Assay
2.7. Transmission Electron Microscopy
2.8. Genome Sequencing and Bioinformatic Analysis
2.9. Phylogenetic Analysis of SSBI34
2.10. Statistical Analysis
3. Results
3.1. Phage Isolation and Characterization
3.2. Genome Characterization of Salmonella-Phage-SSBI34
3.2.1. Structural ORF Analysis of SSBI34
3.2.2. ORFs Involved in RNA Synthesis and Modification
3.2.3. DNA Replication, Modification, and Metabolism
3.2.4. Cell Wall Hydrolases
3.2.5. Phylogenetic Analysis of SSBI34
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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S. No. | Position | ORF | Map Region | Total AA | Putative Function | Query Coverage | Similarity | GB Ac. No. | Organism |
---|---|---|---|---|---|---|---|---|---|
1 | 45,076–46,560 | 80 | II | 494 AA | Phage terminase, large subunit, PBSX family TC | 99% | 85.63% | YP_006383016.1 | Cronobacter phage CR3 |
2 | 46,576–48,087 | 81 | II | 503 AA | Putative portal protein | 99% 99% | 77.51% 76.53% | YP_009014964.1 QQG33308.1 | Cronobacter phage CR9 Pectobacterium phage PcCB7 V |
3 | 48,156–48,733 | 82 | II | 191 AA | Putative prohead protease | 98% 98% | 77.37% 78.42% | QUL77265.1 YP_009014965.1 | Escherichia phage UPEC06 Cronobacter phage CR9 |
4 | 49,814–50,248 | 84 | II | 144 AA | putative head stabilization/decoration protein | 99% | 65.36% 68.06% 66.67% | QEG12074.1 QUL77267.1 YP_009014967.1 | Klebsiella phage vB_KaeM_KaOmega Escherichia phage UPEC06 Cronobacter phage CR9 |
5 | 50,272–51,264 | 85 | II | 330 AA | putative major capsid protein | 99% | 81.21% | YP_009014968.1 ATS9340 | Cronobacter phage CR9 Pectobacterium phage DU_PP_I |
6 | 51,998–55,276 | 89 | II | 1092 AA | Virion structural protein/ Putative tail fiber protein | 99% | 61.63% 60.54 | ARB11484.1 YP_009014970.1 | Pectobacterium phage vB_PatM_CB7 Cronobacter phage CR9 |
7 | 55,317–55,967 | 90 | II | 216 AA | Hypothetical protein (Putative structural protein tail fiber protein collagen triple helix) | 99% | 60.19% 53.46% | ATS9340 ARB11485.1 | Pectobacterium phage DU_PP_I Pectobacterium phage vB_PatM_CB7 |
8 | 55,969–56,316 | 92 | II | 115 AA | Hypothetical protein putative tail fiber protein | 92% | 57.01% | YP_009014972.1 | Cronobacter phage CR9 |
9 | 56,372–57,160 | 93 | II | 262 AA | hypothetical protein tail fiber like protein | 91% | 51.89% | YP_006383026.1 | Cronobacter phage CR3 |
10 | 57,747–58,277 | 94 | II | 176 AA | hypothetical protein CR8 head completion adaptor | 98% | 72.57% | YP_009042249.1 | Cronobacter phage CR8 |
11 | 58,340–58,801 | 95 | II | 153 AA | Putative RNA polymerase/virion morphogenesis protein | 99% | 75.82% 75.16% | ATS93412.1 YP_009014974.1 | Pectobacterium phage DU_PP_I Cronobacter phage CR9 |
12 | 58,816–59,256 | 96 | II | 146 AA | hypothetical protein Putative minor capsid protein | 99% 99% | 75.34% 74.66% | YP_007392682.1 DAM41403.1 | Pectobacterium phage phiTE Myoviridae sp. |
13 | 59,256–59,834 | 97 | II | 192 AA | hypothetical protein putative tail to head joining protein | 95% 90% | 64.13% 66.68% | YP_006383030.1 QUL77277.1 | Cronobacter phage CR3 Escherichia phage UPEC06 |
14 | 59,938–61,353 | 98 | II | 471 AA | Putative structural protein 1 (probable tail sheath protein) | 99% | 78.09% 77.87% | YP_006383031.1 YP_009042253.1 | Cronobacter phage CR3 Cronobacter phage CR8 |
15 | 61,357–61,839 | 99 | II | 160 AA | Hypothetical protein putative tail tube protein | 96% | 76.28% | YP_009014978.1 | Cronobacter phage CR9 |
16 | 61,916–62,389 | 100 | II | 157 AA | Tail assembly chaperon protein | 96% | 74.51% | YP_009042255.1 | Cronobacter phage CR8 |
17 | 62,707–65,178 | 101 | II | 823 AA | Tail tape measure domain (controls tail length) | 99% 84% | 55.58% 60.96% | QEG12088.1 ATS93421.1 | Klebsiella phage vB_KaeM_KaOmega Pectobacterium phage DU_PP_I |
18 | 65,246–60,127 | 102 | II | 293 AA | Putative tail tape measure protein | 98% | 61.17% | QUL77284.1 | Escherichia phage UPEC06 |
19 | 66,483–67,451 | 104 | II | 322 AA | Putative tail protein CR9 | 99% | 73.62% | YP_009014984.1 | Cronobacter phage CR9 |
20 | 67,461–68,108 | 105 | II | 215 AA | Putative base plate assembly protein | 97% | 66.23% | QEG12092.1 | Klebsiella phage vB_KaeM_KaOmega |
21 | 68,118–68,642 | 106 | II | 174 AA | Putative tail lysozyme/part of base plate wedge protein | 99% | 72.32% 71.19% | QEG12093.1 ARB11502.1 | Klebsiella phage vB_KaeM_KaOmega Pectobacterium phage vB_PatM_CB7 |
22 | 68,737–70,224 | 107 | II | 495 AA | Putative base plate assembly protein | 99% | 76.97% | YP_009188994.1 | Cronobacter phage PBES 02 |
23 | 70,236–70,883 | 108 | II | 215 AA | Putative base plate wedge protein | 97% 97% | 81.99% 78.20% | YP_009014988.1 QQG33332.1 | Cronobacter phage CR9 Pectobacterium phage PcCB7V |
24 | 70,897–72,417 | 109 | II | 506 AA | XXXCH domain containing protein (Putative tail fiber domain) | 99% | 50.90% 50.09% | QEG12096.1 YP_009042265.1 | Klebsiella phage vB_KaeM_KaOmega Cronobacter phage CR8 |
25 | 72,420–72,935 | 110 | II | 171 AA | Putative tail fiber assembly protein | 98% 98% | 59.76% 57.65% | QUL77293.1 QEG12097.1 | Escherichia phage UPEC06 Klebsiella phage vB_KaeM_KaOmega |
26 | 73,313–73,774 | 112 | II | 153 AA | Putative membrane protein | 99% | 57.52% 55.56% | QEG12099.1 YP_009042268.1 | Klebsiella phage vB_KaeM_KaOmega Cronobacter phage CR8 |
27 | 73,794–74,066 | 113 | II | 90 AA | Putative membrane protein | 91% | 73.49% | YP_009851591.1 | Erwinia phage pEp_SNUABM_01 |
28 | 74,059–77,580 | 114 | II | 1173 AA | Putative tail fiber protein 2 | 99% 99% | 32.98% 33.92% | QQG33338.1 YP_009189001.1 | Pectobacterium phage PcCB7V Cronobacter phage PBES |
Phage | Total ORF | Genome Size (bp) | G + C Content (%) | Accession No. | Querry Coverage | Shared Proteins (%) ** |
---|---|---|---|---|---|---|
Identity (%) * | ||||||
SE-Phage-SSBI34 | 234 | 141,095 | 44% | MZ520832 | 100 | 100% |
100 | ||||||
Klebsiella phage vB_KaeM_KaOmega, | 317 | 149,489 | 50.5 | MN013077.1 | 7% | 8.11% |
77.94% | ||||||
Cronobacter phage CR9 | 281 | 151,924 | 50.6 | JQ691611.1 | 5% | 17.52% |
74.78% | ||||||
Pectobacterium phage DU_PP_I | 267 | 144,959 | 50.1 | MF979560.1 | 5% | 2.99% |
77.25% | ||||||
Pectobacterium phage PcCB7V | 269 | 146,054 | 50.4% | MW367417.1 | 4% | 6% |
77.78% | ||||||
Cronobacter phage PBES 02 | 270 | 149,732 | 50.7 | KT353109.1 | 4% | 5.55% |
76.56% | ||||||
Cronobacter phage CR8, | 269 | 149,162 nt | 50.8 | KC954774.1 | 4% | 7.69% |
76.44% | ||||||
Cronobacter phage CR3 | 265 | 149,273 | 50.9 | JQ691612.1 | 4% | 15% |
76.46% | ||||||
Pectobacterium phage DU_PP_IV | 268 | 145,233 | 50.3 | MF979563.1 | 3% | 0 |
76.49% | ||||||
Pectobacterium phage phiTE | 242 | 142,349 | 50.1 | JQ015307.1 | 2% | 6.83% |
76.23% | ||||||
Acinetobacter phage ABPH49 | 252 | 149,960 | 50.8 | MH533020.1 | 1% | 0.85% |
72.87% | ||||||
Escherichia phage UPEC06 | 318 | 143,140 | 41.2 | MW250786.1 | 1% | 8.54% |
76.50% |
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Sattar, S.; Ullah, I.; Khanum, S.; Bailie, M.; Shamsi, B.; Ahmed, I.; Abbas Shah, T.; Javed, S.; Ghafoor, A.; Pervaiz, A.; et al. Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae. Viruses 2022, 14, 241. https://doi.org/10.3390/v14020241
Sattar S, Ullah I, Khanum S, Bailie M, Shamsi B, Ahmed I, Abbas Shah T, Javed S, Ghafoor A, Pervaiz A, et al. Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae. Viruses. 2022; 14(2):241. https://doi.org/10.3390/v14020241
Chicago/Turabian StyleSattar, Sadia, Inam Ullah, Sofia Khanum, Marc Bailie, Bushra Shamsi, Ibrar Ahmed, Tahir Abbas Shah, Sundus Javed, Aamir Ghafoor, Amna Pervaiz, and et al. 2022. "Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae" Viruses 14, no. 2: 241. https://doi.org/10.3390/v14020241
APA StyleSattar, S., Ullah, I., Khanum, S., Bailie, M., Shamsi, B., Ahmed, I., Abbas Shah, T., Javed, S., Ghafoor, A., Pervaiz, A., Sohail, F., Imdad, K., Tariq, A., Bostan, N., Ali, I., & Altermann, E. (2022). Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae. Viruses, 14(2), 241. https://doi.org/10.3390/v14020241