SEA-PHAGES | TAC in FM cluster

Link to this post \| posted 08 Apr, 2022 18:18
uOttawaPHAGE	We are annotating Kharcho and Ottawa, which form a new FM cluster. gp40 (Kharcho) and gp44 (Ottawa) are tail assembly chaperones. We have found a slippery sequence and the extension would go up to gp41 and 45, respectively, but the extension has homology to a minor tail protein, not a TAC. Should we call the frameshift? None of the other pham members do (not sure we actually checked them all). We may have some experimental evidence that the frameshift occurs, but not yet conclusive. And weird because in E. coli it looks like the ratio of long:short is ~10-20, the opposite of what has been shown for previously tested TACs.

Link to this post | posted 08 Apr, 2022 18:18

We are annotating Kharcho and Ottawa, which form a new FM cluster. gp40 (Kharcho) and gp44 (Ottawa) are tail assembly chaperones. We have found a slippery sequence and the extension would go up to gp41 and 45, respectively, but the extension has homology to a minor tail protein, not a TAC. Should we call the frameshift? None of the other pham members do (not sure we actually checked them all).

We may have some experimental evidence that the frameshift occurs, but not yet conclusive. And weird because in E. coli it looks like the ratio of long:short is ~10-20, the opposite of what has been shown for previously tested TACs.

Link to this post \| posted 08 Apr, 2022 20:07
debbie	I am going to use the gene numbers on phamerator - and I used phage Ottawa to look a bit closer. I think that the two genes i the same pham - 42 and 42 are major tail proteins. The the next one -gene 44 is the "G" of the TAC. There is an opening reading frame with coding potential (stop is at 17367) that is likely the reading frame that "G" slips into, BUT I could not find the slippage. I would call thought the hit is weak, I would call it a TAC. debbie

Link to this post | posted 08 Apr, 2022 20:07

debbie

I am going to use the gene numbers on phamerator - and I used phage Ottawa to look a bit closer. I think that the two genes i the same pham - 42 and 42 are major tail proteins. The the next one -gene 44 is the "G" of the TAC. There is an opening reading frame with coding potential (stop is at 17367) that is likely the reading frame that "G" slips into, BUT I could not find the slippage. I would call thought the hit is weak, I would call it a TAC.
debbie

Link to this post \| posted 08 Apr, 2022 20:49
uOttawaPHAGE	We think it is GGGAAA at 17164, which would yield this sequence: MSTVTEQFIEGATADSYAADGSKTAEFSPVGAEPIAAETEGYKAPGGGLRESIRDRIAKRRPYASREVFVPAWEETIEVRSISLGLRNEMLTSVMDEETKEADIKKLYPELIIRTSYDPQTGERVFSNDDLAFINGLDAGSADLLAKPALELSGMTDDAKDKEAGKILRDGNLRLAFEVAERTGRTLDELFHGGPSCQPMSSREFTQWRALIEIVEPYEREQAEAKSKTSR The extra C-terminal bit doesn't bring up anything on Blastp (because it has never been called), but on Hhpred there is homology to minor tail protein T, though is this the gpT from lambda? In which case it does match a TAC (I had that wrong above). Edited 08 Apr, 2022 20:50 2.50Mb

Link to this post | posted 08 Apr, 2022 20:49

uOttawaPHAGE

We think it is GGGAAA at 17164, which would yield this sequence: MSTVTEQFIEGATADSYAADGSKTAEFSPVGAEPIAAETEGYKAPGGGLRESIRDRIAKRRPYASREVFVPAWEETIEVRSISLGLRNEMLTSVMDEETKEADIKKLYPELIIRTSYDPQTGERVFSNDDLAFINGLDAGSADLLAKPALELSGMTDDAKDKEAGKILRDGNLRLAFEVAERTGRTLDELFHGGPSCQPMSSREFTQWRALIEIVEPYEREQAEAKSKTSR

The extra C-terminal bit doesn't bring up anything on Blastp (because it has never been called), but on Hhpred there is homology to minor tail protein T, though is this the gpT from lambda? In which case it does match a TAC (I had that wrong above).

Edited 08 Apr, 2022 20:50

Link to this post \| posted 08 Apr, 2022 21:31
debbie	We are in Ottawa, right, so the nucleotide both regions share is 17167 and not 17164. sorry, i must have been looking elsewhere before. cool. debbie

Link to this post \| posted 10 Apr, 2022 13:19
uOttawaPHAGE	yes, 17167. I was referring to the G at the start of the slippery sequence. We will call this frameshift for both Ottawa and Kharcho. The 54457 Pham has 22 members. 2 have called the frameshift (phiSASD1 and Dubu), the rest have not. Should we investigate and make those calls too? Also, any opinion about the very small extension? Is homology to lambda unsual for Actino TACs?

Link to this post \| posted 10 Apr, 2022 19:29
debbie	We have a systematic approach to revising genomes. Just call what you have well and eventually we can work out the rest. Some phages are not ours to change. Nope, no opinion. I think that all TAC homology stems back to lambda and lambda-like phages.

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TAC in FM cluster