Link to this post | posted 13 Apr, 2018 22:26
welkin	We do not know where the frameshift is in the DH tail assembly chaperones.

Link to this post | posted 24 Jun, 2020 13:54
debbie	In fact, there are no hits to tail assembly chaperones proteins in DH, so for now, we are not going to call them at all.

Link to this post | posted 19 Apr, 2022 15:44

balish

I'd like to suggest that: 1) By BLAST homology, especially with cluster DN phages and proximity to the tape measure protein gene, the tail assembly chaperone genes in DH are the two genes that are the next ones upstream from the tape measure protein gene on the same strand (there is an intervening gene on the opposite strand); and 2) the frameshift position is in the same position as it is in the similar DN phage genes, at a GGGGGAA site near the 3' end of the upstream ORF. Best, Mitch

Link to this post | posted 19 Apr, 2022 18:10

debbie

Mitch, I started to look at this and found what you did and it is believable. But before we go forward. There are 2 caveats that I find troubling: 1. There is no homology to tail assembly chaperones other than what we called. And we called those because of their position. So is there any evidence that these proteins have homology to anything else called a tail assembly chaperone? 2. Would you take a look at Whitney and reconcile our predictions there? very interesting! debbie

Link to this post | posted 19 Apr, 2022 19:58

balish

Debbie, There's dissimilarity in that region between cluster DN phages Whitney and Kuwabara, the phage that I found to have tail assembly chaperone homology with cluster DH phages. It appears that subclusters DN3 and DN4 are entirely different from the other DNs in this region, and are similar to DH here and in a few other places. So there may not be an all-encompassing rule for DN, but I'd say that for DN3, DN4, and DH, this is the way to go. -Mitch

Link to this post | posted 19 Apr, 2022 21:22

debbie

Mitch, I agree. I would call the tail assembly chaperones in Morkie (that is the phage you are annotating, right?) The tail assembly chaperones are in the 'right place' and the slippage is cannonical. However, not all slippages in the DNs are cannonical and I would shy away from calling them. Cool! PS I consulted Dr. Hatfull about this and he agreed that the slippage is the compelling piece of data. debbie

Link to this post | posted 20 Apr, 2022 14:02
balish	Debbie, Thank you (and the big boss). Yes, Morkie is the one that brought this to my attention. I suppose as more DH's are found we'll be able to see whether this is universally applicable to cluster DH, as it clearly isn't for DN. -Mitch

Link to this post | posted 20 Apr, 2022 17:17

cdshaffer

I would be curious to know how strong the synteny evidence is here. Are there are any phage where we have good evidence from HHPRED/BLAST and a good quality slippery sequence for the G/T Tail assembly chaperones (TASs) but where synteny places them outside the region upstream and very close to the tape measure? Said another way, if we have never found TASs outside this region, then synteny is another pretty strong piece of evidence that support the conclusion that these are indeed TASs. I can't think of any TAS's outside this region, but my own experience is restricted to only two hosts. I don't have time to look into the question of TAS synteny right now, but can get to it later if no one knows off the top of their head that thare are a large number of counter examples. Edited 20 Apr, 2022 17:27

Link to this post | posted 20 Apr, 2022 20:46
debbie	But as the 2022 Davidson paper shows, T4's TAC were finally elucidated and they go in opposite directions. Check it out. https://pubmed.ncbi.nlm.nih.gov/34826709/