SEA-PHAGES | Annotation advise: Frameshift in EA1

Link to this post \| posted 20 Feb, 2018 11:28
MSMC	Bringing back an old thread here: We are annotating a phage from the host Microbacterium foliorum. When we get to the tail assembly chaperone genes (15 and 16 in Schnapsidee), we see what could be a programmed frame shift (two genes, both coding for tail assembly chaperone, of the same Pham, with overlapping open reading frames). However, in Phamerator, all of the EA1 subcluster Microbacteriophages do not indicate a programmed frame shift. I have not had an opportunity to look at the specific sequences yet, but have programmed frame shifts been observed in phages from hosts other than Mycobacterium? If this is not a programmed frame shift, is it strange for the two genes to have the same Pham number?

Link to this post | posted 20 Feb, 2018 11:28

Bringing back an old thread here:

We are annotating a phage from the host Microbacterium foliorum. When we get to the tail assembly chaperone genes (15 and 16 in Schnapsidee), we see what could be a programmed frame shift (two genes, both coding for tail assembly chaperone, of the same Pham, with overlapping open reading frames). However, in Phamerator, all of the EA1 subcluster Microbacteriophages do not indicate a programmed frame shift. I have not had an opportunity to look at the specific sequences yet, but have programmed frame shifts been observed in phages from hosts other than Mycobacterium? If this is not a programmed frame shift, is it strange for the two genes to have the same Pham number?

Link to this post \| posted 20 Feb, 2018 12:16
debbie	Evan, I think these are the tail assembly chaperone genes, but I could not locate the slippery sequence. If you have a suggestion, let me know.

Link to this post \| posted 05 Apr, 2018 14:29
MSMC	Debbie Jacobs-Sera Evan, I think these are the tail assembly chaperone genes, but I could not locate the slippery sequence. If you have a suggestion, let me know. I'm going to have my students look a little closer at this. If there is no programmed frameshift, is there a reason they two different genes would have the same pham #?

Link to this post \| posted 26 Apr, 2018 17:11
meckardt21	Debbie Jacobs-Sera Evan, I think these are the tail assembly chaperone genes, but I could not locate the slippery sequence. If you have a suggestion, let me know. Hi Debbie et al., I am checking our annotation of an EA2 phage and have encountered the same issue. My phage is Andromedas and this is in re genes 13/14 on phamerator. By comparing to an EA4 phage I believe I have found the location of where the frameshift should occur, but there is a stop codon at this location. I did not find any other slippery sequences in this region. I have attached some documentation that I assembled while searching. I would love some advice on how to document in my final file. Given the fact that we cannot pinpoint the location of the frameshift, should I leave them as is in the final annotation? Thanks in advance. Edited 26 Apr, 2018 17:22 514Kb

Link to this post | posted 26 Apr, 2018 17:11

meckardt21

Debbie Jacobs-Sera
Evan,
I think these are the tail assembly chaperone genes, but I could not locate the slippery sequence. If you have a suggestion, let me know.

Hi Debbie et al., I am checking our annotation of an EA2 phage and have encountered the same issue. My phage is Andromedas and this is in re genes 13/14 on phamerator. By comparing to an EA4 phage I believe I have found the location of where the frameshift should occur, but there is a stop codon at this location. I did not find any other slippery sequences in this region.

I have attached some documentation that I assembled while searching. I would love some advice on how to document in my final file. Given the fact that we cannot pinpoint the location of the frameshift, should I leave them as is in the final annotation?

Thanks in advance.

Edited 26 Apr, 2018 17:22

Link to this post \| posted 27 Apr, 2018 02:28
debbie	Megan, I agree in your assessment. If I am right in the Golden annotation of the slippery sequence, then Adromedas shows a point mutation obliterating the slippage with a stop codon. While I believe that is where the slippage occurs, it is unclear how that works or what the slippage is. So I am confident calling both genes the TAC genes, but no slippage should be annotated.

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Annotation advise: Frameshift in EA1