SEA-PHAGES | PineapplePizza_a Microbacterium podoviridae

Link to this post \| posted 18 May, 2022 00:53
debbie	This bacteriophage is very much like 2 well studied podoviridae, phi29 and P68 both with Cryo EM data. One of the genes described in these phages is a "DNA encapsidation protein". When reading about a DNA encapsidation protein , it functions like a terminase protein. Chris Shaffer (Washington University at St. Louis) answered the question of what to call this gene this way: "I always like gathering more data, so the question I had was: how is the term "Encapsidation" used in general. So I did a quick search of the term "Encapsidation" on swissprot (the manually annotated subset of uniprot), the results show a bit over 600 hits. Scrolling through, I am seeing about 95+% are hits to Eukaryotic RNA viruses. If you sort the data by taxonomy there are only 8 entries out of 615 where this term has been applied to Caudovirales. So it looks to me, (if you take the swissprot professional annotators as your source) that encapsidation is a term mostly used for single stranded RNA viruses but has been applied rarely to a few phage proteins. Interestingly, these including the SSP1 protein 2, more commonly known as "Terminase, large subunit". So when encapsidation was applied to this phage it has been used as a synonym for Terminase. So I too think we should avoid using this term, we could even put it on the approved list in the "do not use" column. Here is the link to all 615 entries." So I think we can easily call gene 15 of PineapplePizza "terminase".

Link to this post | posted 18 May, 2022 00:53

This bacteriophage is very much like 2 well studied podoviridae, phi29 and P68 both with Cryo EM data. One of the genes described in these phages is a "DNA encapsidation protein". When reading about a DNA encapsidation protein , it functions like a terminase protein.
Chris Shaffer (Washington University at St. Louis) answered the question of what to call this gene this way:
"I always like gathering more data, so the question I had was: how is the term "Encapsidation" used in general.
So I did a quick search of the term "Encapsidation" on swissprot (the manually annotated subset of uniprot), the results show a bit over 600 hits. Scrolling through, I am seeing about 95+% are hits to Eukaryotic RNA viruses. If you sort the data by taxonomy there are only 8 entries out of 615 where this term has been applied to Caudovirales. So it looks to me, (if you take the swissprot professional annotators as your source) that encapsidation is a term mostly used for single stranded RNA viruses but has been applied rarely to a few phage proteins. Interestingly, these including the SSP1 protein 2, more commonly known as "Terminase, large subunit". So when encapsidation was applied to this phage it has been used as a synonym for Terminase. So I too think we should avoid using this term, we could even put it on the approved list in the "do not use" column.
Here is the link to all 615 entries."

So I think we can easily call gene 15 of PineapplePizza "terminase".

Link to this post \| posted 01 Jun, 2022 18:30
debbie	PineapplePizza is the first Microbacterium phage that is like phi29 (a Bacillus phage) and P68 (a Staphylococcus phage). I have used a new set of structural gene names for its various parts that are unique to phages like this. See the attached map for specifics. Cool little phage! debbie 60Kb

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PineapplePizza_a Microbacterium podoviridae