Resurrection of a global, metagenomically defined gokushovirus
- Department of Integrative Biology University of Texas, United States
Figures
Figure 1 with 1 supplement
Gokushovirus prophages of Enterobacteria.
(A) Genome organization and average pairwise nucleotide identities of the gokushovirus prophages detected in Escherichia. Integrated prophage genomes range from 4316 to 4692 bp in length, with genes …
Figure 1—figure supplement 1
Sequence similarities among gokushoviral prophages.
Average nucleotide identity values calculated from pairwise comparisons of whole prophage genomes indicated on a yellow-blue scale, with identical prophages indicated in black. Colors of individual …
Figure 2
Phylogeny and sources of Gokushovirinae.
Maximum likelihood tree built from concatenated alignments of VP1 and VP4 protein sequences of 855 gokushovirus genomes. Tree is midpoint rooted, and branch support estimated with 100 bootstrap …
Figure 3 with 1 supplement
In vitro assembly and revival of enterobacterial gokushoviruses.
(A) Scheme used to produce viable phage from prophage inserts. The prophage region, with genes colored in grey, is amplified from the bacterial genome (black) using primers that incorporate the …
Figure 3—figure supplement 1
Synthesis of gokushoviruses in Escherichia coli DH5α and natural host strains.
(A) Transformation and growth of four synthesized gokushovirus genomes (EC2703, EC5150, EC6098, EC6163) in E. coli DH5α. Gel image shows assay for circularized phage genomes in liquid cultures grown …
Figure 4
Integration of gokushoviruses into E. coli host genome.
(A) Schematic representation of phage integration process, and detection of circularized EC6098 phage genome and integrated prophages in E. coli BW25113. Upon infection, phage EC6098 releases ssDNA, …
Figure 5
Quantifying the effects of gokushovirus carriage.
(A) Superinfection immunity offered by integrated or non-integrated phages. Unimpeded growth in the presence of infecting EC6098 phage is shown for host cultures carrying lysogenic or …
Tables
Table 1
Percentage of lysogenic colonies after phage infection*.
| Strain | Phage | Plasmid | % Lysogens |
|---|---|---|---|
| BW25113 | EC6098 | - | 17.71 |
| BW25113ΔxerC | EC6098 | - | 0 |
| BW25113ΔxerC | EC6098 | pJN105::xerC (induced†) | 14.58 |
| BW25113ΔxerC | EC6098 | pJN105::xerC (uninduced) | 0 |
| BW25113ΔxerD | EC6098 | - | 0 |
| BW25113ΔxerD | EC6098 | pJN105::xerD (induced†) | 0 |
| BW25113ΔxerD | EC6098 | pJN105::xerD (uninduced) | 0 |
| BW25113 | EC6098ΔdifC | - | 0 |
| BW25113 | EC6098ΔdifD | - | 0 |
| BW25113 | EC6098ΔdifCD | - | 0 |
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*Assessed from screening 96 colonies for each strain.
†Expression induced by addition of 0.1% arabinose.
Additional files
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Supplementary file 1
Enterobacteria harboring gokushovirus prophages.
- https://cdn.elifesciences.org/articles/51599/elife-51599-supp1-v2.xlsx
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Supplementary file 2
Enterogokushoviral gene order and conservation within Gokushovirinae.
- https://cdn.elifesciences.org/articles/51599/elife-51599-supp2-v2.xlsx
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Supplementary file 3
Reference strains used for host-phylogeny.
- https://cdn.elifesciences.org/articles/51599/elife-51599-supp3-v2.xlsx
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Supplementary file 4
Gokushovirus genomes.
- https://cdn.elifesciences.org/articles/51599/elife-51599-supp4-v2.xlsx
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Supplementary file 5
Primers used in this study.
- https://cdn.elifesciences.org/articles/51599/elife-51599-supp5-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/51599/elife-51599-transrepform-v2.docx
