dlp1 and dps1 involved in isoprenoid biosynthetic process?

[ValWood]

Are pombe dlp1 and dps1 involved in isoprenoid biosynthetic process? they don’t seem to be to me? but I’m not sure. all the pathway maps are a bit confusing there was once a discussion about this https://github.com/geneontology/go-annotation/issues/1461 but I never filtered the mappings and I’m not sure if I should but it seems to be in the dolichol part of the pathway?

• [ ] if no filter mapping (manually annotate correct ones)
• [ ] if no report error

[Antonialock]

I think it is involved in isoprenoid biosynthesis? It is needed for ubiquinone biosynthesis... Eg. coenzyme Q10 has a benzoquinone ring + 10 isoprene units in its sidechain (decaprenyl)

The a benzoquinone ring comes from phenylalanine or tyrosine, and the isoprene units come from the mevalonate pathway

To make some isoprenes:

Now you have made some IPP... dlp1 and dps1 ( decaprenyl diphosphate synthase) make the decaprenyl-PP by adding isopentenyl diphosphate (IPP) molecules to farnesyl diphosphate or geranylgeranyl diphosphate (also derived from mevalonate pathway) in multiple steps catalyzed by

https://www.google.com/patents/US8367395

I say "to farnesyl diphosphate or geranylgeranyl diphosphate" because I also found this image so maybe different eukaryotes have a different preference (or one of the images are the wrong way around)

[Antonialock]

I think by definition you need >2 isoprene units to form an isoprenoid? Therefore, because dlp1 and dps1 add on the isoprene units I think by definition they are involved in isoprenoid biosynthesis?

[Antonialock]

So similarily, what metabolic steps does ubiquinone biosynthesis encompass?

tyrosine -> benzoate ring + IPP -> decaprenyl + combining them into ubiquinone?

[ValWood]

Ubiqunone isn't an isoprenoid This step is downstream of isoprenoid biosynthesis.

so its isoprenoid metabolism, but not isoprenoid biosynthesis?

Correct?

re ubiquninone biosynthesis, I think there are other steps downstream of dlp1/dps1 coq3-9

If the steps from tyrosine to 4-OH benzoate are only used to synthesize ubiquinone they should be included to. But I can't locate any of these intermediates in GO, so I'm not sure which GPs they are? Seems odd. I wonder if that is the eukaryotic way to ubiquinone?

[ValWood]

might be a bit of proposed engineering -link to a patent;)

FIG. 3 depicts the mevalonate isoprenoid biosynthesis pathway, which typically operates in eukaryotes, including fungi; as well as the mevalonate-independent isoprenoid biosynthesis pathway, also known as the DXP pathway, which typically operates in bacteria and in the plastids of plants and production of isoprenoid precursors.

[Antonialock]

I think it is involved in isoprenoid biosynthesis "The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues."

it catalyses the last step in isoprenoid biosynthesis, see here (terpenoid=isoprenoid) http://www.genome.jp/kegg-bin/show_pathway?map00900

[Antonialock]

ubiquinone contains 10 isoprene subunits

dps1/dlp1 condense 10 isoprene subunits + farnesyl diphosphate into an isoprenoid

I'll add isoprenoid biosynthesis to the publication where you added ubiquinone biosynthesis (I'm not sure if I should remove that one....maybe it is considered upstream?

http://www.genome.jp/kegg-bin/show_pathway?map00130

[Antonialock]

ah thought it was my session..

[ValWood]

I'll close this and leave the mapping as is... Its not far wrong int he whole scheme of things