SEA-PHAGES | All posts created by aahowel3@asu.edu

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).

Posted in: tRNAs → tRNA within clusterP integration-dependent immunity system

Link to this post \| posted 11 Feb, 2022 21:39
aahowel3@asu.edu	Thank you so much for clarifying we appreciate it!

Posted in: Gene or not a Gene → Overlapping Forward and Reverse Genes

Link to this post \| posted 11 Feb, 2022 18:40
aahowel3@asu.edu	Hello, we are looking at genes 70 (F) and 71 (R) in BiggityBass and they appear way too overlapping for genes going opposite directions. Looking at Yago84, AnClar, and Sour (the other cluster DRs most similar to BB in this region) it looks like we could either remove 70 entirely as it seems is done with Yago84 and AnClar or keep it as is the case with Sour. However we don't see any other frame that would accommodate 70 and no coding potential in other frames to support keeping it either, though there is plenty of coding potential in the frame its currently in. The large gap between 69 and 71 is still supported by Yago84 and AnClar. Its odd that the blast result returns a hit in BB 71 to the AnClar 71, and BB 70 to AnClar 70 when looking at the phamerator alignment BB 71 is AnClar's 70 and BB's 70 does not seem to exist in AnClar. Any guidance would be much appreciated! Supporting images in attached document. 831Kb

Link to this post | posted 11 Feb, 2022 18:40

aahowel3@asu.edu

Hello, we are looking at genes 70 (F) and 71 (R) in BiggityBass and they appear way too overlapping for genes going opposite directions. Looking at Yago84, AnClar, and Sour (the other cluster DRs most similar to BB in this region) it looks like we could either remove 70 entirely as it seems is done with Yago84 and AnClar or keep it as is the case with Sour. However we don't see any other frame that would accommodate 70 and no coding potential in other frames to support keeping it either, though there is plenty of coding potential in the frame its currently in. The large gap between 69 and 71 is still supported by Yago84 and AnClar. Its odd that the blast result returns a hit in BB 71 to the AnClar 71, and BB 70 to AnClar 70 when looking at the phamerator alignment BB 71 is AnClar's 70 and BB's 70 does not seem to exist in AnClar. Any guidance would be much appreciated! Supporting images in attached document.

Posted in: Gene or not a Gene → Overlapping Forward and Reverse Genes

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