SEA-PHAGES | D29 listed as temperate phage

Link to this post \| posted 06 Nov, 2019 22:13
afreise	My students did a journal club on Rebekah Dedrick's D29 paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712189/), and noticed when they looked D29 up on PhagesDB.org that it was listed as a temperate phage. Our understanding based on this paper and others is that D29 is lytic due to deletion of key lysogeny genes including a portion of the repressor. Could you clarify why it is designated as a temperate phage? Thank you!

Link to this post | posted 06 Nov, 2019 22:13

My students did a journal club on Rebekah Dedrick's D29 paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712189/), and noticed when they looked D29 up on PhagesDB.org that it was listed as a temperate phage. Our understanding based on this paper and others is that D29 is lytic due to deletion of key lysogeny genes including a portion of the repressor. Could you clarify why it is designated as a temperate phage? Thank you!

Link to this post \| posted 07 Nov, 2019 18:17
DanRussell	Hi Amanda, Awesome that 1) your students are reading papers like this and 2) that they noticed that obvious discrepancy! You'll notice that the label on D29's phage page actually says "Cluster Life Cycle" (rather than "Phage Life Cycle" or something like that). When deciding how to list life cycle information on the site, we had to choose between listing each phage's life cycle (which we wouldn't really know for the vast majority except for bioinformatic predictions, and would be much more onerous to maintain) or each cluster's typical life cycle. We chose the latter as a quick way to classify typical behavior, but with the caveat that not all phages in a cluster will fit with the norm. So D29 has the "Cluster Life Cycle" as "Temperate" because almost all Cluster A phages are, in fact, temperate. But it's one of the atypical Cluster As as you described. In fact, when Graham wrote the original D29 paper, he hypothesized that it had recently lost its lysogeny machinery and there were phages that would look very similar but with that machinery still intact. So when StarStuff was sequenced years later, it was a great confirmation! If you go to the Cluster A page, there's some language that summarizes this in the "Lysogeny Notes" section, mentioning that caveat. Hope that all makes sense! –Dan Edited 07 Nov, 2019 18:19

Link to this post | posted 07 Nov, 2019 18:17

DanRussell

Hi Amanda,

Awesome that 1) your students are reading papers like this and 2) that they noticed that obvious discrepancy!

You'll notice that the label on D29's phage page actually says "Cluster Life Cycle" (rather than "Phage Life Cycle" or something like that). When deciding how to list life cycle information on the site, we had to choose between listing each phage's life cycle (which we wouldn't really know for the vast majority except for bioinformatic predictions, and would be much more onerous to maintain) or each cluster's typical life cycle. We chose the latter as a quick way to classify typical behavior, but with the caveat that not all phages in a cluster will fit with the norm.

So D29 has the "Cluster Life Cycle" as "Temperate" because almost all Cluster A phages are, in fact, temperate. But it's one of the atypical Cluster As as you described. In fact, when Graham wrote the original D29 paper, he hypothesized that it had recently lost its lysogeny machinery and there were phages that would look very similar but with that machinery still intact. So when StarStuff was sequenced years later, it was a great confirmation!

If you go to the Cluster A page, there's some language that summarizes this in the "Lysogeny Notes" section, mentioning that caveat.

Hope that all makes sense!
–Dan

Edited 07 Nov, 2019 18:19

Link to this post \| posted 07 Nov, 2019 18:44
afreise	Hi Dan, Thank you so much for your reply! This clears everything up. Best, Amanda

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D29 listed as temperate phage