SEA-PHAGES | tRNA within clusterP integration-dependent immunity system

Link to this post \| posted 30 Mar, 2022 04:10
aahowel3@asu.edu	Hello, We are annotating cluster P phage Phegasus and trying to decide if we should call a tRNA at 26972-27076. Cluster P phages are known to have integration-dependent immunity systems, where one of the features is a tRNA. Our tRNA is immediately adjacent to the putative integrase and immunity repressor genes, but had a low infernal score in tRNAscan-SE (Infernal Score 12.6) and is in a region of high coding potential. Thank you for any advice! From Broussard et al., 2012 Integration-dependent bacteriophage immunity provides insights into the evolution of genetic switches: For example, we have identified at least five other examples of prophages that we predict have integration-dependent immunity systems, with all or most of the five characteristic features: 1) a putative repressor gene encoding a product of ~100 residues, 2) an adjacent tRNA gene transcribed towards the repressor gene, 3) direct repeats of 30–40 bp in the 3’ end of the adjacent tRNA gene and 40–70 kbp away (defining the size of the prophage), 4) an int gene near to the second repeat which both lacks an N-terminal domain, and contains a putative degradation tag at its C-terminus, and 5) a predicted viral form of the repressor that also contains a degradation tag (Table S2).

Link to this post | posted 30 Mar, 2022 04:10

Hello,

We are annotating cluster P phage Phegasus and trying to decide if we should call a tRNA at 26972-27076. Cluster P phages are known to have integration-dependent immunity systems, where one of the features is a tRNA. Our tRNA is immediately adjacent to the putative integrase and immunity repressor genes, but had a low infernal score in tRNAscan-SE (Infernal Score 12.6) and is in a region of high coding potential. Thank you for any advice!

From Broussard et al., 2012 Integration-dependent bacteriophage immunity provides insights into the evolution of genetic switches:
For example, we have identified at least five other examples of prophages that we predict have integration-dependent immunity systems, with all or most of the five characteristic features: 1) a putative repressor gene encoding a product of ~100 residues, 2) an adjacent tRNA gene transcribed towards the repressor gene, 3) direct repeats of 30–40 bp in the 3’ end of the adjacent tRNA gene and 40–70 kbp away (defining the size of the prophage), 4) an int gene near to the second repeat which both lacks an N-terminal domain, and contains a putative degradation tag at its C-terminus, and 5) a predicted viral form of the repressor that also contains a degradation tag (Table S2).

Link to this post \| posted 30 Mar, 2022 17:50
debbie	Hi Ann, No, I don't believe that sequence is a tRNA in the phage, but if you integrate it into smeg (you will find that it completes a tRNA gene in M. smegmatis (tRNA Thr (Msmeg_6152)). It is picked up by tRNAScanSE because it is likely half of a tRNA that is made when the phage is integrated as a prophage. There is nothing to call in the phage annotation for this. Make sense? debbie

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tRNA within clusterP integration-dependent immunity system