SEA-PHAGES | Apparent structural proteins from EK2 phage

Link to this post \| posted 07 Mar, 2023 15:14
balish	While annotating our new phage Moleficent, we see that the product of gene 45, which is highly conserved among related phages, has significant HHpred hits to a variety of types of capsid proteins: major capsid protein, needle protein, tailspike protein, tail tubular protein, etc. It's located amid other capsid protein genes. Relatedly, gene 44's best HHpred hit is a phage adaptor protein, though it's below the 90% probability mark. Both these genes are given as NKFs in all other phages. But it seems like their actual functions are potentially discernable. Can someone take a look and see if they think there are any functions we should be calling for these genes? We haven't looked at the neighboring genes yet, but it wouldn't surprise me if they also had some clues among hits. Best, Mitch Edited 07 Mar, 2023 16:21

Link to this post | posted 07 Mar, 2023 15:14

While annotating our new phage Moleficent, we see that the product of gene 45, which is highly conserved among related phages, has significant HHpred hits to a variety of types of capsid proteins: major capsid protein, needle protein, tailspike protein, tail tubular protein, etc. It's located amid other capsid protein genes.

Relatedly, gene 44's best HHpred hit is a phage adaptor protein, though it's below the 90% probability mark.

Both these genes are given as NKFs in all other phages. But it seems like their actual functions are potentially discernable.

Can someone take a look and see if they think there are any functions we should be calling for these genes? We haven't looked at the neighboring genes yet, but it wouldn't surprise me if they also had some clues among hits.

Best,
Mitch

Edited 07 Mar, 2023 16:21

Link to this post \| posted 07 Mar, 2023 16:15
debbie	Hi Mitch and students, I would refer to the structures of phi29 and P68, both of which are prototypes for podoviruses. https://pubmed.ncbi.nlm.nih.gov/31147544/ https://pubmed.ncbi.nlm.nih.gov/31663016/ Last year, I took a close look at the podovirus PineapplePizza and thought I could apply the terminology of those papers to the gene hits. I quickly looked at the whole lot of genes in the vicinity and the only one that has a significant hit is 45. BUT, I couldn't quickly discern if it is a tail needle, tail knob, or collar protein. So i would want to think about this. Looking forward to what you come up with! Rick Pollenz (U of South Florida) and Simon White (U Conn) have worked out some of the structural proteins, finding the major capsid. Check with them to see if they have further identified any other genes. debbie

Link to this post | posted 07 Mar, 2023 16:15

debbie

Hi Mitch and students,
I would refer to the structures of phi29 and P68, both of which are prototypes for podoviruses.
https://pubmed.ncbi.nlm.nih.gov/31147544/
https://pubmed.ncbi.nlm.nih.gov/31663016/

Last year, I took a close look at the podovirus PineapplePizza and thought I could apply the terminology of those papers to the gene hits.

I quickly looked at the whole lot of genes in the vicinity and the only one that has a significant hit is 45. BUT, I couldn't quickly discern if it is a tail needle, tail knob, or collar protein. So i would want to think about this. Looking forward to what you come up with!

Rick Pollenz (U of South Florida) and Simon White (U Conn) have worked out some of the structural proteins, finding the major capsid. Check with them to see if they have further identified any other genes.

debbie

Link to this post \| posted 07 Mar, 2023 16:26
balish	Debbie, Thanks for the response. It's indicated on the cluster-specific page that the major capsid protein is #33. Looking forward to figuring out the rest! -Mitch

Link to this post \| posted 30 Mar, 2023 16:54
balish	I think we might have an answer! I believe this gene encodes a baseplate protein, and if so, I also believe it's the first one identified in one of the SEA's podoviruses. Its top hits on HHpred are very strong but partial hits, mostly to "DNA stabilization" proteins, etc. But the fourth hit (probability >99%) is across almost the entire protein for both the query and target proteins, albeit with a large gap in the target protein. When we follow the links, they lead us to gp10 from Salmonella's famous phage P22, which is also a podovirus. P22's gp10 is a baseplate protein, which links the capsid head to the tail needle. This is different structurally from the baseplates of myoviruses like in clusters C and AR, for which baseplate wedge proteins and baseplate J-proteins are annotated as two separate things. (And I think all those top hits on HHpred are also probably baseplate proteins, for what it's worth.) This is what we'll be presenting as our big idea in our SEA-PHAGES presentation. So I'd love for someone to evaluate this idea and see if I'm just a hopeful nut. -Mitch

Link to this post | posted 30 Mar, 2023 16:54

balish

I think we might have an answer! I believe this gene encodes a baseplate protein, and if so, I also believe it's the first one identified in one of the SEA's podoviruses. Its top hits on HHpred are very strong but partial hits, mostly to "DNA stabilization" proteins, etc. But the fourth hit (probability >99%) is across almost the entire protein for both the query and target proteins, albeit with a large gap in the target protein. When we follow the links, they lead us to gp10 from Salmonella's famous phage P22, which is also a podovirus.

P22's gp10 is a baseplate protein, which links the capsid head to the tail needle. This is different structurally from the baseplates of myoviruses like in clusters C and AR, for which baseplate wedge proteins and baseplate J-proteins are annotated as two separate things. (And I think all those top hits on HHpred are also probably baseplate proteins, for what it's worth.)

This is what we'll be presenting as our big idea in our SEA-PHAGES presentation. So I'd love for someone to evaluate this idea and see if I'm just a hopeful nut.

-Mitch

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Apparent structural proteins from EK2 phage