Acod1(Irg1) gen is missing

[SlowinskiPiotr]

The mouse-GEM model is missing the Acod1(Irg1) gen and associated reaction. https://www.uniprot.org/uniprotkb/P54987/entry

I hereby confirm that I have:

• Done this analysis in the main branch of the repository
• Checked that a similar issue does not exist already

[haowang-bioinfo]

@SlowinskiPiotr thanks for reporting this

The cis-aconitate decarboxylase Acod1(Irg1) gene appears to be shared across eukaryotic model organisms, will thus be incorporated into Human-GEM, which serves as the template of all the other model animal GEMs.

[haowang-bioinfo]

@SlowinskiPiotr do you think there are more reactions (and genes) that should be added to metabolize itaconate, the product synthesized by Acod1?

[SlowinskiPiotr]

Just asked collaborators about it. Will get back asap. Thanks!

[haowang-bioinfo]

@SlowinskiPiotr a PR was made in Human-GEM to add the reaction proposed by you, please take a look this table and let me know:

1. now it was assigned to C5-branched dibasic acid metabolism subsystem according to the product itaconate, and if you come up with a better subsystem name?
2. will there be more reactions that you want to add?

[SlowinskiPiotr]

@haowang-bioinfo could you please also revise the reactions that are assigned to CLYBL (I think some of the reactions are in the model but without the gene and some might be missing) https://www.genecards.org/cgi-bin/carddisp.pl?gene=CLYBL
https://www.sciencedirect.com/science/article/pii/S0092867417311820
acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA + H(+)
glyoxylate + H2O + propanoyl-CoA = 3-methylmalate + CoA + H(+)
(3S)-citramalyl-CoA = acetyl-CoA + pyruvate (MAR08666?)
(S)-malyl-CoA + H2O = (S)-malate + CoA + H(+)

Many thanks!

[haowang-bioinfo]

@SlowinskiPiotr to implement the changes, can you please specify what reactions are expected to be added, and preferably with the supporting evidence.

[haowang-bioinfo]

@SlowinskiPiotr shall we focus on resolving this claimed issue add Acod1(Irg1) gene first.

Then we can come back the reactions/pathway incorporation of CLYBL gene, after you and your collaborators have a more specific plan

[SlowinskiPiotr]

Hi sorry for the late reply. I was busy with other projects. Let's resolve the Acod1 first. And I'll get back about the CLYBL gene.

[haowang-bioinfo]

@SlowinskiPiotr please review this PR #429 of adding Acod1

[haowang-bioinfo]

fixed in #429 of Human-GEM