SEA-PHAGES | frame shift

Link to this post \| posted 02 Apr, 2019 15:40
welkin	As of April 2019, we do not know where the frameshift is in the tail assembly chaperones in the EA1 phages, and so therefore the tail assembly chaperones should be kept as two separate un-shifted genes.

Link to this post \| posted 22 Nov, 2019 13:54
westoverk	Hi Welkin, We are annotating one EA5 (Nebulous)phage and one EA11 (Ixel) phage. They are both very similar to Neferthena (EA5). Neferthena called a frameshift for the tail chaperones. We find the same slippery set of 6 guanines in both of our sequences. Other closely related phages did not call the shift and left the genes separate (MCubed, Finny, Sansa). Recommendations? Thanks for your help. Kristi Edited 22 Nov, 2019 16:50

Link to this post | posted 22 Nov, 2019 13:54

westoverk

Hi Welkin,
We are annotating one EA5 (Nebulous)phage and one EA11 (Ixel) phage. They are both very similar to Neferthena (EA5). Neferthena called a frameshift for the tail chaperones. We find the same slippery set of 6 guanines in both of our sequences. Other closely related phages did not call the shift and left the genes separate (MCubed, Finny, Sansa). Recommendations? Thanks for your help.
Kristi

Edited 22 Nov, 2019 16:50

Link to this post \| posted 22 Nov, 2019 17:16
debbie	Here is what I know so far. A slippery sequence could not be found in the original EA1 and EA2 annotations. We have looked at EA1 - EA8 annotations so far. Slippery sequences have been annotated in Subclusters EA3,EA4,EA5,and EA6, not in Subclusters EA1, EA2, EA7, and EA8. So if you can find a canonical sequence for the slippage, i would recommend calling it. if you can't, then don't. 212Kb

Link to this post \| posted 22 Nov, 2019 18:14
westoverk	Thanks Debbie!

Link to this post \| posted 07 Jun, 2023 20:26
Pollenz	Review of EA4 phages at the 2023 faculty meeting shows a sequence of CGGGGGAc that has been annotated many times as the slippery sequence. While this has the 5Gs, it does not match exactly to the sequences listed in the Guide as they have the sequence CGGGGGCG or GGGGGAA. While compelling, are we calling sequences that are "almost" identical? RS Pollenz

Link to this post \| posted 07 Jun, 2023 23:30
debbie	Rick, I think that this version of TAC matches L5's -1 frameshift. https://seaphagesbioinformatics.helpdocsonline.com/article-54 G_GG.G_GA. Wanna check? debbie

Link to this post \| posted 08 Jun, 2023 00:22
Pollenz	L5 is listed as GGGGGAA with two A's both in the paper and in the nice table. Its the same issue with using GGGAAA, that is formally listed as being GGGAAAA with 4 A's, not three. RS Pollenz

Link to this post \| posted 07 Apr, 2024 15:26
ombeline.rossier	Bonjour, Our team is annotating the tail assembly chaperones of phage BouleyBill (EA4). All 10 EA4 members have an annotated frameshit for gene 15. We are unable to identify the slippery sequence for BouleyBill using the Baranov 2016 table or the supplemental table S2 of Xu 2004. We understand that we cannot call a frameshift without identifying the slippery sequence. At least for phage Bustletown, gene 15 has only 3 nucleotides differing from BouleyBill gene 15 (549 nt). These differences are not located in the G-rich region at the 3'end: GGGGGAC. This sequence resembles but is not identical to the reference slippery sequences (GGGGGAA). We do not understand how the frameshift has been called for these phages. Are there additional slippery sequences in other publications? Thanks in advance for your help Ombeline Edited 07 Apr, 2024 20:30 177Kb

Link to this post | posted 07 Apr, 2024 15:26

ombeline.rossier

Bonjour,
Our team is annotating the tail assembly chaperones of phage BouleyBill (EA4). All 10 EA4 members have an annotated frameshit for gene 15. We are unable to identify the slippery sequence for BouleyBill using the Baranov 2016 table or the supplemental table S2 of Xu 2004.

We understand that we cannot call a frameshift without identifying the slippery sequence. At least for phage Bustletown, gene 15 has only 3 nucleotides differing from BouleyBill gene 15 (549 nt). These differences are not located in the G-rich region at the 3'end: GGGGGAC. This sequence resembles but is not identical to the reference slippery sequences (GGGGGAA). We do not understand how the frameshift has been called for these phages. Are there additional slippery sequences in other publications?

Thanks in advance for your help
Ombeline

Edited 07 Apr, 2024 20:30

Link to this post \| posted 08 Apr, 2024 02:06
debbie	Hi Ombeline, I am not one to say that close enough is good enough, but in this case, I think the resemblance will do. I would call this slippage. The explanation is that for many years we believed that all siphoviridae had to have a programmed frameshift. In 2022 Alan Davidson's group published this paper to counter that. https://www.sciencedirect.com/science/article/pii/S0042682221002221 The sequence identified for the programmed frameshift is just too believable to not annotate it! best, debbie

Link to this post | posted 08 Apr, 2024 02:06

debbie

Hi Ombeline,
I am not one to say that close enough is good enough, but in this case, I think the resemblance will do. I would call this slippage.

The explanation is that for many years we believed that all siphoviridae had to have a programmed frameshift.
In 2022 Alan Davidson's group published this paper to counter that.
https://www.sciencedirect.com/science/article/pii/S0042682221002221

The sequence identified for the programmed frameshift is just too believable to not annotate it!

best,
debbie

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