SEA-PHAGES | Truncated Immunity Repressor

Link to this post \| posted 17 Oct, 2018 21:10
ClaireRinehart	I have a question on what to list as the function for Kalb97 gene 76, which has good matches to the Immunity Repressor genes in other phages. An alignment of Kalb97 with one of it's closest relatives, Marius, show that Kalb97 has suffered a 630 bp deletion at base 44554. This deletion removes about 266 bp from the 5' end of gene 79 of Marius (Kalb97 gene 76), which is the immunity repressor, and about 10 bp from the 3' end of gene 80 in Marius (Kalb97 gene 77). Therefore the termination site is deleted in Kalb97 gene 77, thus allowing the reading frame to continue. The space for a promoter/regulation and the translation start site for Kalb97 gene 76 as well as about half the N-termal end of the immunity repressor coding region is missing and therefore it is doubtful if this phage has any immunity regulation. The Phagesdb entry for Kalb97 lists it as a Temperate phage but the plaque pictures look to be clear plaques. The deletion is also evident in the NCBI BLAST results where the T:Q From is 90:1 for Marius. My question is, what do I list as the function? Do I still put Immunity repressor and then try to put a note in the gene that indicates that this gene carries a clear plaque deletion? Or do I simply label it as NKF and ignore the discovery of the deletion?

Link to this post | posted 17 Oct, 2018 21:10

I have a question on what to list as the function for Kalb97 gene 76, which has good matches to the Immunity Repressor genes in other phages. An alignment of Kalb97 with one of it's closest relatives, Marius, show that Kalb97 has suffered a 630 bp deletion at base 44554. This deletion removes about 266 bp from the 5' end of gene 79 of Marius (Kalb97 gene 76), which is the immunity repressor, and about 10 bp from the 3' end of gene 80 in Marius (Kalb97 gene 77). Therefore the termination site is deleted in Kalb97 gene 77, thus allowing the reading frame to continue. The space for a promoter/regulation and the translation start site for Kalb97 gene 76 as well as about half the N-termal end of the immunity repressor coding region is missing and therefore it is doubtful if this phage has any immunity regulation. The Phagesdb entry for Kalb97 lists it as a Temperate phage but the plaque pictures look to be clear plaques. The deletion is also evident in the NCBI BLAST results where the T:Q From is 90:1 for Marius.

My question is, what do I list as the function? Do I still put Immunity repressor and then try to put a note in the gene that indicates that this gene carries a clear plaque deletion? Or do I simply label it as NKF and ignore the discovery of the deletion?

Link to this post \| posted 19 Oct, 2018 19:05
debbie	Claire, Good find! I would label it as Hypothetical Protein. Then I would write this note in the notes section of the DNA Master file and in the "Discovery Notes" of the phage page. We don't have an annotation field on the page page, so that is why I would put it there. debbie

Link to this post \| posted 19 Oct, 2018 19:11
welkin	yep– totally agree with Debbie— there isn't enough of it left to warrant "immunity repressor, truncated".

Link to this post \| posted 29 Jan, 2019 15:13
c.sunnen	Related question. I'm QC-ing the A3 phage Noella. There are two genes, largely overlapping, both with hits to immunity repressor, but both clearly truncated (the result of either a deletion or an insertion). This is consistent with the clear plaque morphology of the phage, as noted by the annotators. But I hesitate to call both genes "immunity repressor, truncated" since they're so overlapping. Should I call the first one (gp 74, that gets 1:1 alignments for the first 54 amino acids), but delete the second one (gp 73, aligning amino acids 57-169)? Or should I keep them both, but label the second, overlapping gene as "hypothetical protein" and add info to the Discovery Notes? The overlap is HUGE at ~280bp. I've included a DNAMaster screenshot. Thanks for all your input! Nikki 225Kb

Link to this post | posted 29 Jan, 2019 15:13

c.sunnen

Related question. I'm QC-ing the A3 phage Noella. There are two genes, largely overlapping, both with hits to immunity repressor, but both clearly truncated (the result of either a deletion or an insertion). This is consistent with the clear plaque morphology of the phage, as noted by the annotators. But I hesitate to call both genes "immunity repressor, truncated" since they're so overlapping. Should I call the first one (gp 74, that gets 1:1 alignments for the first 54 amino acids), but delete the second one (gp 73, aligning amino acids 57-169)? Or should I keep them both, but label the second, overlapping gene as "hypothetical protein" and add info to the Discovery Notes? The overlap is HUGE at ~280bp. I've included a DNAMaster screenshot.

Thanks for all your input!
Nikki

Link to this post \| posted 30 Jan, 2019 18:16
c.sunnen	Update. I looked into this a little further, and took Claire's lead. I included both genes, but the one with the most homology (gp 73, from aa 57-169) was declared "immunity repressor, truncated" and gp 74 (only matching aa 1-54) got called "Hypothetical Protein." I figured the immunity repressor part of it was too small to give it that function, but that it still should be called as a gene. This should look similar to Kalb97 and Pistacio, now. It will keep both genes, including the overlap, but only the one that still belongs to the immunity repressor pham will get the "truncated" label, whereas the other is NKF.

Link to this post | posted 30 Jan, 2019 18:16

c.sunnen

Update. I looked into this a little further, and took Claire's lead. I included both genes, but the one with the most homology (gp 73, from aa 57-169) was declared "immunity repressor, truncated" and gp 74 (only matching aa 1-54) got called "Hypothetical Protein." I figured the immunity repressor part of it was too small to give it that function, but that it still should be called as a gene. This should look similar to Kalb97 and Pistacio, now. It will keep both genes, including the overlap, but only the one that still belongs to the immunity repressor pham will get the "truncated" label, whereas the other is NKF.

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Truncated Immunity Repressor