SEA-PHAGES | DPS protein for Yaboi

Link to this post \| posted 13 Jul, 2018 16:00
cdshaffer	Getting quite a few HHPRED hits to a large collection of related crystal structures for Yaboi_draft 37 (15,584 to 15183 Rev) results are available on PECAAN as gene 36. Gene is member of pham 3874. The top 50 or so HHPpred hits are all 99.9% probability and >99% coverage with titles that include the term DPS or DPS-like. There are then a large number of 99.8% probability >99% coverage hits to ferratin from various species from Humans to M tuberculosis. Looking into the literature a bit DPS is short for "DNA protection during starvation protein", these proteins are a family of proteins that have a ferritin-fold, show DNA binding activity, and whose expression is induced during starvation or other sources of oxidative stress, see this paper for more info on the original e coli protein and this on a M smegmatis DPS. The issue is what term to use for these protein. "DPS protein" seems too simplistic and uninformative. On the other hand, it would make it really easy for annotators to match hhpred hits to the proper annotation term. About 1 in 10 hhpred descriptions do include the full "DNA protection during starvation protein" so we could use this longer term. A few descriptions have "ferritin DPS family protein" which I like didactically as it links ferritin an important protein conserved across all kingdoms. So maybe following the recent trend in approved terms, would the best term be "ferritin-like DPS protein"?

Link to this post | posted 13 Jul, 2018 16:00

Getting quite a few HHPRED hits to a large collection of related crystal structures for Yaboi_draft 37 (15,584 to 15183 Rev) results are available on PECAAN as gene 36. Gene is member of pham 3874. The top 50 or so HHPpred hits are all 99.9% probability and >99% coverage with titles that include the term DPS or DPS-like. There are then a large number of 99.8% probability >99% coverage hits to ferratin from various species from Humans to M tuberculosis.

Looking into the literature a bit DPS is short for "DNA protection during starvation protein", these proteins are a family of proteins that have a ferritin-fold, show DNA binding activity, and whose expression is induced during starvation or other sources of oxidative stress, see this paper for more info on the original e coli protein and this on a M smegmatis DPS.

The issue is what term to use for these protein. "DPS protein" seems too simplistic and uninformative. On the other hand, it would make it really easy for annotators to match hhpred hits to the proper annotation term. About 1 in 10 hhpred descriptions do include the full "DNA protection during starvation protein" so we could use this longer term.

A few descriptions have "ferritin DPS family protein" which I like didactically as it links ferritin an important protein conserved across all kingdoms. So maybe following the recent trend in approved terms, would the best term be "ferritin-like DPS protein"?

Link to this post \| posted 17 Jul, 2018 16:01
welkin	This one has me stumped– it hits the trifecta of things I don't like to put in official function names: a TLA, a structural motif, and a phenotype. I really dislike TLAs in the functional annotations, unless it is one like "DNA" which is totally unambiguous and everyone knows. You are right that DPS is simplistic and uninformative. re the ferritin component— is it actually binding iron? I dislike naming functions after the structural fold of something that does something completely different— And DNA protection during starvation could be accomplished by a number of proteins with different shapes. Thoughts?

Link to this post | posted 17 Jul, 2018 16:01

welkin

This one has me stumped– it hits the trifecta of things I don't like to put in official function names: a TLA, a structural motif, and a phenotype.

I really dislike TLAs in the functional annotations, unless it is one like "DNA" which is totally unambiguous and everyone knows. You are right that DPS is simplistic and uninformative.

re the ferritin component— is it actually binding iron? I dislike naming functions after the structural fold of something that does something completely different—

And DNA protection during starvation could be accomplished by a number of proteins with different shapes.
Thoughts?

Link to this post \| posted 20 Jul, 2018 19:17
cdshaffer	To answer your question on Fe+2 binding, I could not find any in vivo studies but this result is a crystal of an "iron soaked" version of the protein complete with Iron bound as expected and a discussion of the conserved Asp channels that could allow ions to flow into the cavity. I agree on every single point you made. I really don't think there is a good annotation here. I think maybe the best option here is "do no harm" so we will proceed with Yaboi and annotate this gene NKF. We can always change it later.

Link to this post | posted 20 Jul, 2018 19:17

cdshaffer

To answer your question on Fe+2 binding, I could not find any in vivo studies but this result is a crystal of an "iron soaked" version of the protein complete with Iron bound as expected and a discussion of the conserved Asp channels that could allow ions to flow into the cavity.

I agree on every single point you made. I really don't think there is a good annotation here.
I think maybe the best option here is "do no harm" so we will proceed with Yaboi and annotate this gene NKF. We can always change it later.

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DPS protein for Yaboi_draft 37