SEA-PHAGES | Immunity Repressor and CRO starts

Link to this post \| posted 25 Sep, 2019 18:40
debbie	If one looks at the immunity repressor of Cluster F1s like Mycobacteriophage Strokeseat, the coding potential data is confusing. The Starterator data clearly shows only 1 start that is found in all pham members. The start in Strokeseat is at position 34251 (stop is at 33682).(gene length is 570bp). This then provides adequate (just barely) space for promoters for this gene (CRO) and the next one (because they are transcribed in opposite directions). The start of this gene is at 34358 (stop is at 34651). Hope you find this helpful! Unfortunately, as is the nature of Cluster F1s, not all F1s have these phams. Edited 08 Aug, 2023 13:20 152Kb

Link to this post | posted 25 Sep, 2019 18:40

If one looks at the immunity repressor of Cluster F1s like Mycobacteriophage Strokeseat, the coding potential data is confusing. The Starterator data clearly shows only 1 start that is found in all pham members.
The start in Strokeseat is at position 34251 (stop is at 33682).(gene length is 570bp).

This then provides adequate (just barely) space for promoters for this gene (CRO) and the next one (because they are transcribed in opposite directions). The start of this gene is at 34358 (stop is at 34651).
Hope you find this helpful!

Unfortunately, as is the nature of Cluster F1s, not all F1s have these phams.

Edited 08 Aug, 2023 13:20

Link to this post \| posted 15 Jun, 2023 02:50
debbie	The F2 phage Soul22 was annotated with a single immunity repressor but at the time we were annotating the genome, we did find another gp that we could have called an immunity repressor, but it more resembled that in A1 phages. So we did not identify the function as an immunity repressor. But it may very well be an immunity repressor but NOT to the F2 phages but to A1 phages (I have some prelim lab data indicating it is functional as one against A1 phages; we will be following up on this in the fall). The A1 repressor is also found in at least some C1 phages. Bottom line – how do we annotate a second immunity repressor that is specific for a different cluster than the phage it is found in? This post and question was constructed at 2023 Faculty Meeting: Cluster Specific Annotation Tips. Hi all, This is definitely worth the post, but more data is needed to annotated this. When wet bench data is available, post here. We are looking forward to those experiments! debbie

Link to this post | posted 15 Jun, 2023 02:50

debbie

The F2 phage Soul22 was annotated with a single immunity repressor but at the time we were annotating the genome, we did find another gp that we could have called an immunity repressor, but it more resembled that in A1 phages. So we did not identify the function as an immunity repressor. But it may very well be an immunity repressor but NOT to the F2 phages but to A1 phages (I have some prelim lab data indicating it is functional as one against A1 phages; we will be following up on this in the fall). The A1 repressor is also found in at least some C1 phages. Bottom line – how do we annotate a second immunity repressor that is specific for a different cluster than the phage it is found in?
This post and question was constructed at 2023 Faculty Meeting: Cluster Specific Annotation Tips.

Hi all,
This is definitely worth the post, but more data is needed to annotated this. When wet bench data is available, post here. We are looking forward to those experiments!
debbie

Link to this post \| posted 04 Aug, 2023 20:36
jawsWPI	I'm QCing an F1 phage (Rialto) that also seems to have two immunity repressors: the first at 32973-33485 (rev) current pham 96090 is found primarily in A phages and a few others (including a handful of C1), and 36289-36855 (Rev) that is clearly the cluster F repressor. My question is this: do we assign hypothetical to the first (A phage immunity repressor) until wet bench data is available?

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Immunity Repressor and CRO starts