SEA-PHAGES | Weird domain distribution over "cytosine methyltransferase" hits in an AS3 phage

Link to this post \| posted 16 Apr, 2025 17:55
nic.vega	Phage being annotated is Atlantica (AS3); gp's in question (gp42 stop 27,408; gp43 stop 27,967) are forward strand, right side of genome after the reverse block. Both have BLASTP @ PhagesDB hits to gps annotated as DNA methyltransferase. gp42 has pretty solid hits on HHPred and BLAST @NCBI to other phage and bacterial cytosine MTases. However, this gp is short (most targets are ~300 residues, vs 200 in our phage). Correspondingly, most of the expected conserved catalytic/functional domains are found (refs at bottom), but the expected C-terminal domain is not in this product. It is, however, at the C terminal of gp43. Hits to gp43 are to cytosine MTase C term ends and reliably contain the missing domain; the rest of the annotated gp43 (residues 1-178 with our current putative start) has no hits outside SEA-PHAGES, anywhere, for anything. (The start situation/coding potential for gp43 is also a mess. There is a nice, solid, wide peak of coding potential that overlaps 200+ bases into the gp42 ORF.) As of now, my plan is to call DNA methyltransferase function on gp42 and hypothetical on gp43 based on preponderance of domains, but I am wondering whether something is up with this region. https://pmc.ncbi.nlm.nih.gov/articles/PMC317633/pdf/nar00124-0054.pdf https://www.sciencedirect.com/science/article/pii/0022283689904804

Link to this post | posted 16 Apr, 2025 17:55

Phage being annotated is Atlantica (AS3); gp's in question (gp42 stop 27,408; gp43 stop 27,967) are forward strand, right side of genome after the reverse block. Both have BLASTP @ PhagesDB hits to gps annotated as DNA methyltransferase.

gp42 has pretty solid hits on HHPred and BLAST @NCBI to other phage and bacterial cytosine MTases. However, this gp is short (most targets are ~300 residues, vs 200 in our phage). Correspondingly, most of the expected conserved catalytic/functional domains are found (refs at bottom), but the expected C-terminal domain is not in this product.

It is, however, at the C terminal of gp43. Hits to gp43 are to cytosine MTase C term ends and reliably contain the missing domain; the rest of the annotated gp43 (residues 1-178 with our current putative start) has no hits outside SEA-PHAGES, anywhere, for anything. (The start situation/coding potential for gp43 is also a mess. There is a nice, solid, wide peak of coding potential that overlaps 200+ bases into the gp42 ORF.)

As of now, my plan is to call DNA methyltransferase function on gp42 and hypothetical on gp43 based on preponderance of domains, but I am wondering whether something is up with this region.

https://pmc.ncbi.nlm.nih.gov/articles/PMC317633/pdf/nar00124-0054.pdf
https://www.sciencedirect.com/science/article/pii/0022283689904804

Link to this post \| posted 16 Apr, 2025 19:17
debbie	Hi Nic, I think, but have little experimental evidence to support is that there is a frameshift between 42 and 43. So calling them both DNA methyltransferases is not a bad idea.Likely it is not functional without both parts. If 42 was not present, then I would not call a function for 43. Something to consider, debbie

Link to this post \| posted 16 Apr, 2025 19:23
nic.vega	Thanks Debbie! We thought it might be a frameshift as well, but without wet lab evidence we didn't want to merge the products. We'll annotate both genes with the DNA MTase function & put our observations in the notes.

Link to this post \| posted 16 Apr, 2025 19:28
debbie	We won't merge the products. But I think it is reasonable to say they are the parts of whole. Bench data to support this would be great! I don't always call this, but in this case, I think it is a reasonable call. debbie

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Weird domain distribution over "cytosine methyltransferase" hits in an AS3 phage