SEA-PHAGES | GG cluster DNA primse/helicase

Link to this post \| posted 06 Apr, 2023 22:49
engstrom	I could use some thoughts on an interesting gene in Huwbert, called stop codon is 58,402. This is syntenic to a Pham called as RecA-like DNA recombinase in Triscuit. But I am not so sure. Nucleotides 335-568/9 find homology to RecA-like recombinases, but only to the AAA-ATPase domain (HHPred). Likewise HHPred picks up other proteins that have an AAA-ATPase in the same stretch. From nt 1-312, there is strong predicted structural homology to Replication Protein B Primase, a function not in the approved function list. Not completely sure where to go with this thing. I could call a DNA primase/helicase, but do I actually have evidence for the helicase function, or just for an AAA-ATPase. A primase would not need an ATPase, so I rather suspect the helicase is there. Anyway, I'd love some feedback. Thanks.

Link to this post | posted 06 Apr, 2023 22:49

I could use some thoughts on an interesting gene in Huwbert, called stop codon is 58,402. This is syntenic to a Pham called as RecA-like DNA recombinase in Triscuit. But I am not so sure. Nucleotides 335-568/9 find homology to RecA-like recombinases, but only to the AAA-ATPase domain (HHPred). Likewise HHPred picks up other proteins that have an AAA-ATPase in the same stretch. From nt 1-312, there is strong predicted structural homology to Replication Protein B Primase, a function not in the approved function list. Not completely sure where to go with this thing. I could call a DNA primase/helicase, but do I actually have evidence for the helicase function, or just for an AAA-ATPase. A primase would not need an ATPase, so I rather suspect the helicase is there. Anyway, I'd love some feedback. Thanks.

Link to this post \| posted 07 Apr, 2023 17:35
cdshaffer	TL;DR: I see on Pecaan that your current annotation is "DNA Primase/helicase" and I would also annotate that way as well. Long story: I ran a full HHPRED result and looked at the overall general structure of this protein. See attached annotated imare. I noted in the results 3 regions each with a unique set of hits. In looking at the N terminal region the consensus of the 4 hits in the green box strongly suggest some kind of primase or polymerase. Since primases are a specialized type of polymerases cannot really tell from just those 4 hits what would be the best annotation. However the middle section has over 100 hits and I cut off the image with the top 15 or so. The general consensus of all those hits in the blue box are (as you said) some kind of helicase which is also supported by the AAA-ATPase hits. The really curious part is all the hits in the region of the orange box, the general consensus of all those hits is a DNA binding domain. I don't ever remember seeing a DNA binding domain attached to a helicase domain. I did look through the pfam architectures to see if this combination has been seen before but my 10 minutes of poking did not reveal any examples like this. So taken together we have a DNA binding domain, a helicase domain, and a primase/polymerase domain. It looks to me like maybe a polymerase specifically designed to start replication at a single location "maybe?". It would take a really deep dive to know for sure this combination of domains is truly novel but with just my 30 minutes poking around I could not find anything quite like this, hence I have no good annotation because there is nothing else like this I could find in the published literature to link to. So the practical solution in my mind is to pick the best of the approved terms, which in this case is to highlight the presence of both the primase domain and the helicase domain. Hence I would annotate as you did: DNA primase/helicase As with many annotations, not ideal, one might say "not even good" but in the end it is the best term we have. 206Kb

Link to this post | posted 07 Apr, 2023 17:35

cdshaffer

TL;DR: I see on Pecaan that your current annotation is "DNA Primase/helicase" and I would also annotate that way as well.

Long story:
I ran a full HHPRED result and looked at the overall general structure of this protein. See attached annotated imare. I noted in the results 3 regions each with a unique set of hits. In looking at the N terminal region the consensus of the 4 hits in the green box strongly suggest some kind of primase or polymerase. Since primases are a specialized type of polymerases cannot really tell from just those 4 hits what would be the best annotation. However the middle section has over 100 hits and I cut off the image with the top 15 or so. The general consensus of all those hits in the blue box are (as you said) some kind of helicase which is also supported by the AAA-ATPase hits. The really curious part is all the hits in the region of the orange box, the general consensus of all those hits is a DNA binding domain. I don't ever remember seeing a DNA binding domain attached to a helicase domain. I did look through the pfam architectures to see if this combination has been seen before but my 10 minutes of poking did not reveal any examples like this. So taken together we have a DNA binding domain, a helicase domain, and a primase/polymerase domain. It looks to me like maybe a polymerase specifically designed to start replication at a single location "maybe?". It would take a really deep dive to know for sure this combination of domains is truly novel but with just my 30 minutes poking around I could not find anything quite like this, hence I have no good annotation because there is nothing else like this I could find in the published literature to link to. So the practical solution in my mind is to pick the best of the approved terms, which in this case is to highlight the presence of both the primase domain and the helicase domain. Hence I would annotate as you did: DNA primase/helicase

As with many annotations, not ideal, one might say "not even good" but in the end it is the best term we have.

Link to this post \| posted 09 Apr, 2023 14:57
engstrom	Thanks–that is really quite helpful. We'll leave it a primase/helicase and move along, but I do think that this gene warrants a deep-dive. I'll put it on my list of potential student projects.

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GG cluster DNA primse/helicase