Lactococcus Ceduovirus Phages Isolated from Industrial Dairy Plants—From Physiological to Genomic Analyses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains, Bacteriophages, and Culture Conditions
2.2. Bacteriophage Propagation
2.3. Electron Microscopy
2.4. Host Range Studies
2.5. One-Step Growth Assay
2.6. PCR-Based Typing
2.7. Phage Genome Sequencing
2.8. Bioinformatic Analyses
2.9. Construction of Phage Ori+ Plasmids
2.10. Functional Analysis of Putative Phage Ori Regions
3. Results
3.1. Phage Classification and Morphological Analysis
3.2. Phage-Host Interactions
3.3. Infection Dynamics in One-Step Growth Tests
3.4. Phage Genome Sequencing and Comparative Analysis
3.5. Identification and Functional Analysis of the Origin of Phage Replication
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Bacterial Strains | Relevant Features | Source/Reference |
IL1403 | L. lactis subsp. lactis wild-type strain | [26] |
MG1363 | L. lactis subsp. cremoris wild-type strain | [27] |
NZ9000 | L. lactis subsp. cremoris MG1363 derivative pepN::nisRnisK strain | MoBiTec® |
ER2655 | E. coli strain F- λ- fhuA2 [lon] ompT lacZ::T7p07 gal sulA11 Δ(mcrC-mrr)114::IS10 R(mcr-73::miniTn10-TetS)2 R(zgb-210::Tn10)(TetS) endA1 [dcm] | NEB® |
IBB338, 339, 342, 695-700, 704, 732-739, 741-758, 760-764, 1219, 1267, 1280, 1283, 1298, 1784, 1787-1792, 1796 | L. lactis strains | IBB PAS collection |
Plasmids | Relevant Features | Source/Reference |
pG+host3 | E. coli vector, Ts derivative of pGK12, catR | [28] |
pUN121 | E. coli vector, tetR, ampR non-replicative in L. lactis cells | [29] |
pUN121:catR:ori27 | recombinant plasmid with putative ori from L. lactis phage 27, catR | this study |
pUN121:catR:ori94p4 | recombinant plasmid with putative ori from L. lactis phage 94p4, catR | this study |
pUN121:catR:orip6/4 | recombinant plasmid with putative ori from L. lactis phage p6/4, catR | this study |
pUN121:catR:oric2 | recombinant plasmid with putative ori from L. lactis phage c2, catR | this study |
Bacteriophages | GenBank Accession Number* | Source/Reference |
bIL67 | NC_001629.1 | [7] |
c2 | NC_001706.1 | [8] |
bIBB_L81 (L81) | MH779526 * | this study |
bIBB_12 (12) | MH779518 * | “ |
bIBB_14 (14) | MH779519 * | “ |
bIBB_94p4 (94p4) | MH779521 * | “ |
bIBB_27 (27) | MH779520 * | “ |
bIBB_p6/4 (p6/4) | MH779527 * | “ |
bIBB_A3 (A3) | MH779522 * | “ |
bIBB_D4 (D4) | MH779524 * | “ |
bIBB_Am4 (Am4) | MH779523 * | “ |
bIBB_E1 (E1) | MH779525 * | “ |
Name | 5′-3′ Sequence * |
---|---|
c-2for | CAGGTGTAAAAGTTCGAGAACT |
c-2rev | CAGATAATGCACCTGAATCA |
ori27_F | CCGGAATTCCAAGCTATCAAATATTTC |
ori27_R | CCCAAGCTTCATACCAACAAAAG |
orip6/4_F | CCCGATATCCAATGTGTTTTTGTG |
orip6/4_R | CCCAAGCTTCCTACAAAAAATTTAG |
ori94p4_F | CCGGAATTCTARTTACYTTGCTAAAGGG |
ori94p4_R | CCCAAGCTTTCCCTCWTTGATTATG |
oric2_F | CCGGAATTCTARTTACYTTGCTAAAGGG |
oric2_R | CCCAAGCTTTCCCTCWTTGATTATG |
catR_F | CGCGGATCCATGAAGAAAGCAGACAAGTAAG |
catR_R | ACGCGTCGACGTAAAAAGTACAGTC |
pUN121_F | GTCTGGCTATGCAGAAATCC |
pUN121_R | GCTTATAACGCCGCATTGCT |
pUN121_catR_F | TATCGACTACGCGATCATGG |
pUN121_catR_R | GCGTGCAAGATTCCGAATAC |
CWPS_Afor | GTGCCTATGCTCCGTTAGTC |
CWPS_Arev | CGAGGGCCAATCTCTTTACC |
CWPS_Bfor | GATTCAGTTGCACGGCCG |
CWPS_Brev | AGTAAGGGGGCGGATTGTG |
CWPS_Cfor | AAAGCTCATCTTTCCCCTGTTGT |
CWPS_Crev | GCACCATAGTCTGGAATAAGACC |
CTL_for (U-type) | GTACACTATGTTTATAACAATCATCCAG |
CTL_rev (U-type) | GCAAACCAGATTCAAAGTCAGTATG |
Phage | Burst Size * [Plaques Per Infected Cell] | Latent Period * [min] | Burst Time * [min] | Plaque Diameter [mm] | Halo [mm] |
---|---|---|---|---|---|
14 | 66 ± 3 | 20 ± 0 | 32 ± 1 | 2.5 | 0.5 |
27 | 67 ± 2 | 20 ± 0 | 29 ± 3 | 2 | 0.5 |
94p4 | 64 ± 3 | 28 ± 0 | 31 ± 0 | 2 | nd |
L81 | 32 ± 3 | 20 ± 0 | 27 ± 2 | 2 | 1 |
p6/4 | 34 ± 3 | 22 ± 3 | 29 ± 1 | 1.5 | nd |
12 | 197 ± 17 | 22 ± 3 | 29 ± 2 | 3 | nd |
E1 | 109 ± 8 | 26 ± 2 | 33 ± 0 | 5.3 | nd |
D4 | 94 ± 4 | 19 ± 2 | 28 ± 3 | 5 | 1 |
Am4 | 33 ± 3 | 20 ± 0 | 29 ± 2 | 3.5 | 0.5 |
A3 | 91 ± 3 | 23 ± 3 | 33 ± 0 | 4 | 0.5 |
Phage (GenBank Accession No.) | Propagation Strain (Phage Titer; PFU mL−1) | Genome Length (bp) | GC Content (%) | Orf Count |
---|---|---|---|---|
14 (MH779519) | 738 (2.4 × 1010) | 21,710 | 36 | 37 |
27 (MH779520) | 738 (8 × 108) | 21,713 | 36.1 | 37 |
94p4 (MH779521) | 753 (1.1 × 1010) | 21,834 | 36.1 | 38 |
L81 (MH779526) | MG1363 (8.4 × 109) | 21,915 | 36.0 | 38 |
p6/4 (MH779527) | 739 (1.3 × 109) | 22,220 | 36.0 | 39 |
12 (MH779418) | 1787 (6.1 × 109) | 21,458 | 36.2 | 36 |
E1 (MH779525) | 1283 (1.3 × 1010) | 21,749 | 36.1 | 37 |
D4 (MH779524) | 1280 (1.4 × 1010) | 21,907 | 36.0 | 38 |
Am4 (MH779523) | 1219 (2.4 × 109) | 22,703 | 35.9 | 38 |
A3 (MH779522) | 1267 (7.2 × 109) | 21,906 | 36.2 | 39 |
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Chmielewska-Jeznach, M.; Bardowski, J.K.; Szczepankowska, A.K. Lactococcus Ceduovirus Phages Isolated from Industrial Dairy Plants—From Physiological to Genomic Analyses. Viruses 2020, 12, 280. https://doi.org/10.3390/v12030280
Chmielewska-Jeznach M, Bardowski JK, Szczepankowska AK. Lactococcus Ceduovirus Phages Isolated from Industrial Dairy Plants—From Physiological to Genomic Analyses. Viruses. 2020; 12(3):280. https://doi.org/10.3390/v12030280
Chicago/Turabian StyleChmielewska-Jeznach, Magdalena, Jacek K. Bardowski, and Agnieszka K. Szczepankowska. 2020. "Lactococcus Ceduovirus Phages Isolated from Industrial Dairy Plants—From Physiological to Genomic Analyses" Viruses 12, no. 3: 280. https://doi.org/10.3390/v12030280
APA StyleChmielewska-Jeznach, M., Bardowski, J. K., & Szczepankowska, A. K. (2020). Lactococcus Ceduovirus Phages Isolated from Industrial Dairy Plants—From Physiological to Genomic Analyses. Viruses, 12(3), 280. https://doi.org/10.3390/v12030280