SEA-PHAGES | 2 Repressors in some Cluster F phages

Link to this post \| posted 08 Aug, 2023 13:22
debbie	The immunity repressor (pham 99175) from cluster A is present in other cluster genomes along with their own cluster specific immunity repressor– specifically C1 (LittleE) , K (, and F1(DLane), CA (Phrankenstein), J(Courthouse), and K (SamScheppers). Graham described this “immunity theft” in Pope et al 2011 in PLoS One https://pubmed.ncbi.nlm.nih.gov/21298013/ From Rick Pollenz: Some of the cluster F1 (and the others Debbie mentioned) have TWO “immunity repressors”, one that is grouped to those mostly from cluster A (Pham 99175) and a second one that is specific to the cluster phage. These rogue one is typically found in a set of 2-3 reverse genes upstream of the integrase. The 2nd repressor is found downstream of the integrase in a 2nd set of reverse genes and groups to a different PHAM. Both sets of reverse genes are on during lysogeny and this is nicely illustrated in the RNA seq figure 4 for phage Fruitloop in the gp52 Wag paper (https://onlinelibrary.wiley.com/doi/10.1111/mmi.13946) where gp37 is the “rogue” hetroimmunity repressor and gp44 is the putative immunity repressor.

Link to this post | posted 08 Aug, 2023 13:22

The immunity repressor (pham 99175) from cluster A is present in other cluster genomes along with their own cluster specific immunity repressor– specifically C1 (LittleE) , K (, and F1(DLane), CA (Phrankenstein), J(Courthouse), and K (SamScheppers).

Graham described this “immunity theft” in Pope et al 2011 in PLoS One
https://pubmed.ncbi.nlm.nih.gov/21298013/

From Rick Pollenz:
Some of the cluster F1 (and the others Debbie mentioned) have TWO “immunity repressors”, one that is grouped to those mostly from cluster A (Pham 99175) and a second one that is specific to the cluster phage. These rogue one is typically found in a set of 2-3 reverse genes upstream of the integrase. The 2nd repressor is found downstream of the integrase in a 2nd set of reverse genes and groups to a different PHAM. Both sets of reverse genes are on during lysogeny and this is nicely illustrated in the RNA seq figure 4 for phage Fruitloop in the gp52 Wag paper (https://onlinelibrary.wiley.com/doi/10.1111/mmi.13946) where gp37 is the “rogue” hetroimmunity repressor and gp44 is the putative immunity repressor.

Link to this post \| posted 07 Nov, 2023 06:25
anders	In the other thread about immunty repressors (https://seaphages.org/forums/topic/4952/), Debbie invited folks to post wet bench data. My students and I have some preliminary evidence that the A1-like immunity repressor in the F1 phages Coco12 and Phanphagia is sufficient to defend against the A1 phage Bxb1. Briefly, –they made lysogens of five F1 phages, and found that lysogens of Coco12 and Phanphagia reduced plaque formation of superinfecting A1 phage Bxb1 (EOP ~10^-3). The other three lysogens (carrying GUmbie, Gandalph, and Veteran) had no effect on Bxb1 superinfection. –They observed that Coco12 and Phanphagia carry the A1-like immunity repressor gene, wereas the other F1 phages in their tests do not. Perhaps this A1 repressor gene is causing the defense against Bxb1. –They cloned the A1-like repressor ORF into the expression plasmid pLAM12, and they cloned the two gene operon including the A1-like repressor and its upstream gene into the integration plasmid pMH94. They transformed M.smeg with the plasmids and tested for Bxb1 plaque formation. –Both plasmid clones appear to be sufficient for defense against Bxb1 infection, compared to strains carrying empty plasmids. I'm attaching a summary of the experiments. 2.10Mb

Link to this post | posted 07 Nov, 2023 06:25

anders

In the other thread about immunty repressors (https://seaphages.org/forums/topic/4952/), Debbie invited folks to post wet bench data.

My students and I have some preliminary evidence that the A1-like immunity repressor in the F1 phages Coco12 and Phanphagia is sufficient to defend against the A1 phage Bxb1.

Briefly,
–they made lysogens of five F1 phages, and found that lysogens of Coco12 and Phanphagia reduced plaque formation of superinfecting A1 phage Bxb1 (EOP ~10^-3). The other three lysogens (carrying GUmbie, Gandalph, and Veteran) had no effect on Bxb1 superinfection.

–They observed that Coco12 and Phanphagia carry the A1-like immunity repressor gene, wereas the other F1 phages in their tests do not. Perhaps this A1 repressor gene is causing the defense against Bxb1.

–They cloned the A1-like repressor ORF into the expression plasmid pLAM12, and they cloned the two gene operon including the A1-like repressor and its upstream gene into the integration plasmid pMH94. They transformed M.smeg with the plasmids and tested for Bxb1 plaque formation.

–Both plasmid clones appear to be sufficient for defense against Bxb1 infection, compared to strains carrying empty plasmids.

I'm attaching a summary of the experiments.

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2 Repressors in some Cluster F phages