fix: corrections to curation since v2.0.1 from an evidence review by edkerk · Pull Request #1105 · SysBioChalmers/Human-GEM

edkerk · 2026-09-26T21:08:36Z

Main improvements in this PR:

Corrections to the curation merged since v2.0.1. Every decision of #1028–#1103 was reviewed twice against literature and curated databases (UniProt, Rhea, ChEBI), with source models (Recon3D, HMR) used only to explain where something came from. Only corrections to that curation are included; problems that already existed in v2.0.1 follow in a separate PR.

Biology

MAR20193: MCT1 exports succinate with 2 H+, SLC16A1 only (UniProt P53985, RHEA:29303).
Vesicular secretion back to 2 ATP per 3 amines/acetylcholine and 1 ATP per 3 GABA/glycine/beta-alanine; BGT1 3 Na+ : 2 Cl-.
Peroxisome-to-extracellular bile salt exports without gene removed.
Genes that the fix: one base id per metabolite, and correct cytochrome c and water MetaNetX ids #1090 GPR unions put on the wrong reactions removed (CH25H, CYP2E1, CYP27A1, and others without evidence); LDHD off NADH reactions; LDH-family GPRs made consistent.
H2O2 through peroxiporins (AQP3/8/9/11) instead of free diffusion; histone import by IPO4; ammonia also by RHBG/RHCG; Ca2+ entry also by TRPV5/TRPV6.
One-way prostacyclin and thromboxane hydrolysis; more non-enzymatic reactions and diffusion transports flagged spontaneous; acetone diffusion; Pictet-Spengler condensations in their direction.
5,6-dihydroxyindole and aminochrome separated; thiosulfate hydrolysis removed, H2S2O3 merged into thiosulfate, and the mitochondrial TST step GSSH + sulfite <=> thiosulfate + GSH added.

Annotations

Cross-references that fix: add and correct reaction and metabolite cross-references #1087/feat: add ModelSEED reaction and compound cross-references #1086 took from wrong structures or that describe other reactions removed or corrected; four respiratory-chain BiGG ids and 14 KEGG ids restored; deprecated MetaNetX ids updated.
Structures, names and ids of merged, peptide, lipid and carnitine-ester metabolites corrected; renamed and merged ids recorded in metRetired/rxnRetired; incomplete deprecated rows completed.

No reaction becomes mass- or charge-imbalanced; all essential and verification tasks pass; growth is unchanged. Two new genes each for H2O2/histone (AQP11, IPO4) and Ca2+ (TRPV5, TRPV6) transport, and one new reaction (MAR20203); none existed in the deprecated lists.

Reasoning and evidence: corrections to recent curation are documented where that curation was made: comments on #347, #348, #424, #528, #618, #626, #837, #964, #967, #968, #1001, #1015 and #1074, and on PRs #1100, #1101 and #1103. Changes to content that was already in v2.0.1 are in #1111, #1112 and #1115.

The PRs merged after #1103 (#1043, #1044, #1047, #1088, #1089, #1093-#1096) were reviewed in the same way; their corrections are here too and are documented as comments on those PRs.

I hereby confirm that I have:

Tested my code on my own computer for running the model
Selected develop as a target branch
Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

…from the curation review - MAR20193: MCT1 carries succinate with 2 H+ (UniProt P53985, RHEA:29303, PMID:32946811); MCT4 has no succinate evidence, so the GPR is SLC16A1. - Vesicular secretion goes back to the HMR stoichiometries (2 ATP per 3 amines or acetylcholine, 1 ATP per 3 GABA, glycine or beta-alanine): VMAT exchanges 2 H+ per amine and the V-ATPase pumps about 10 H+ per 3 ATP (PMID:32165585), so 1 ATP per molecule overestimates the cost. - BGT1 (SLC6A12) couples 3 Na+ and 2 Cl- (human BGT-1, PMID:7589472). - MAR01857/MAR01861 exported bile salts straight from the peroxisome with 2 ATP and no gene; ABCB11 uses 1 ATP (RHEA:50052/50064), as in MAR01870/MAR01872. - Kept reactions record the reactions #1040 and #1041 deprecated into them. - #1090 GPR unions: MAR01762 and MAR01605 are CYP27A1 only, MAR01765 is CYP7B1 (CH25H only 25-hydroxylates, CYP2E1 and CYP27A1 do not 7alpha-hydroxylate); duplicate genes removed from joined GPRs. - MAR08607 has the cross-references and EC of glutamine transaminase K (RHEA:30391, EC 2.6.1.117); HCl keeps MNXM735978; MAM03543 has the (2E,4Z) structure its name and DECR1 require; renamed ids are recorded in metRetired; MAR00751 is merged into MAR06346 with its gene; MAR00036 uses one 15-deoxy-PGD2. - MAR00483 and MAR03838 carry the ids of their quinone reactions, and no deprecated reaction lists them as retired any more. - MAR08433/MAR08434 carry the BiGG/MetaNetX ids of their glycine cleavage steps. - LDHD, a mitochondrial FAD (R)-2-hydroxyacid dehydrogenase (UniProt Q86WU2), is removed from the NADH reactions MAR11476/MAR11479.

…ation review - H2O2 crosses the plasma, ER and inner mitochondrial membranes through peroxiporins, as water does through aquaporins in the model: MAR08408 AQP3/AQP8/AQP9, MAR13002 AQP11/AQP8, MAR03946 AQP8 (PMID:20724658, PMID:31546170, PMID:22910329); no longer flagged spontaneous. AQP11 is added as a gene. - Histone import (MAR08024) is by importin-4 (PMID:36103578): GPR IPO4 (new gene), cytosol to nucleus only, not spontaneous. - Prostacyclin and thromboxane A2 hydrolysis are one-way (PMID:29320, PMID:1059088); MAR06877 is written as the spontaneous addition of cysteine to dopaquinone. - Leu-Gly-type errors of #1084: palmitoleoylcarnitine and selenohomocysteine get their own structures back. - ModelSEED ids of a different reaction (proton-pumping variants on plain hydrolases, 18:2 on 18:3 elongation, degenerate or plant reactions) or compound are removed or corrected. - #1087: unrelated ids on the NH4+/NH3 and xanthurenate protonation reactions removed; the respiratory chain BiGG ids NADH2_u10mi, CYOR_u10mi, CYOOm2i and CYOOm3i restored; the carnitine-shuttle MetaNetX ids it added use (R)-carnitine; ids inherited from misannotated metabolites removed; D-ribulose 1-phosphate ids removed from the D-xylulose 1-phosphate aldolase; RHEA:10160 restored on MAR09470. - PubChem ids that #1087 took from wrong model structures (a different compound, D-peptides, all-trans lipids) are replaced by the correct one where verified, otherwise removed; 14,15-DiHETE has CHEBI:133916 and 13(S)-HODE loses the 13R LIPID MAPS id.

…1099 ids, LDH GPRs, notes) - Deprecated rows of MAR00449, MAR08610 and MAM01690m are complete copies of their last model rows. - MAR08441 (choline to ubiquinone) loses the ids of the FAD reaction and cites the evidence for the quinone route (PMID:1218095, PMID:9630673, PMID:34428349). - #1099: the apo H protein is named as such (CHEBI:29969); the aminomethyl H protein has CHEBI:83143 and KEGG C01242 and records MAM02878m as retired; S-propanoyldihydrolipoamide loses the protein-bound ids; MAR20168 is named after LIPT1 and filed under lipoic acid metabolism. - TPO iodination (MAR06793/MAR06794) is tyrosine metabolism. - The 40 PXMP2 pore reactions note that Pxmp2 loss only partly restricts peroxisomal permeability (PMID:19352492). - MAR11476, MAR11479 and MAR05351 get every LDH with demonstrated activity (LDHA, LDHB, LDHC, LDHAL6A): LDH reduces the branched-chain 2-oxo acid (PMID:26014429) and 2-oxobutyrate (PMID:26059096); LDHAL6B has no demonstrated activity.

Diffusion and non-enzymatic reactions (#1101, #1103): - 14 missed diffusion transports (CO, ethanol, methanol, acetaldehyde, formaldehyde) flagged spontaneous; acetone diffuses mitochondria <=> cytosol <=> extracellular (MAR02222, MAR08364) and is not an MCT1 substrate (MAR08365 deprecated). - Plasma-membrane NH3 transport also by RHBG and RHCG (PMID:24077989); the NH4+ Rhea id is removed from NH3 transports. - Lipid nuclear transports named for what they move, with a note on lateral diffusion in the ER/nuclear envelope; flagged nuclear diffusions reversible. - MAM01739 is 5,6-dihydroxyindole (its ChEBI, KEGG and structure); the reactions that used it as aminochrome now use aminochrome (MAM02160); the two resulting duplicates are merged into the NQO1 and GSTM2 reactions, and the two glutathionyl-aminochrome ids into MAM01136. - MAR04840 (thiosulfate hydrolysis) has no chemical or enzymatic basis and is deprecated; H2S2O3 is merged into thiosulfate; mitochondrial TST transfers sulfur from GSSH to sulfite (MAR20203, RHEA:55976, PMID:25225291). - Further non-enzymatic reactions flagged (statin lactonisation, 1-pyrroline, aminochrome tautomerisation, mevalonolactone, PAH diols); Pictet-Spengler condensations are written as condensations. Annotations (#1084, #1086, #1087, #1090, #1033): - Deprecated MetaNetX reaction ids replaced by their matching successor or removed; R_-prefixed BiGG ids removed; KEGG ids of the lipoamide half-reactions and chloro-compound hydrolyses restored; ModelSEED ids that differ in proton coupling removed. - L-form PubChem/ChEBI ids for stereo-less amino-acid derivatives; iodide, ammonium and ascorbate ids of the ionic forms. - Chemically sensible protonation sites in 11 re-protonated SMILES; synaptamide structure; more precise names for kept ids of #1090 merges; (11Z)- and (7Z)-octadecenoylcarnitine and cis-vaccenoyl-CoA structures. - Gene rows of the Ca2+ channels, IPO4 and AQP11 completed; TRPV5 and TRPV6 added to MAR11311 (UniProt RHEA:29671, PMIDs 11097838, 19261737). - Genes without evidence removed from #1090 unions: CYP2J2 (MAR06700), ALDH3A1/ALDH9A1 (MAR01611); MAR04049 keeps CYP1A1 and CYP1B1.

github-actions · 2026-09-26T21:08:46Z

Model quality report

⚠️ 3 pre-existing finding(s), no regressions vs develop. Non-blocking. Gates: duplicate keys 0 ✅, growth 1.9 ✅.

Section	Status
Model & network checks (19)	⚠️ 3 pre-existing
Model file & metabolic tasks (5)	✅ all pass
MEMOTE	✅ 63.8% (core subset)
Full report	model_qc_summary.md

Improved:

Reactions flagged by MACAW dead-end test: 1100
Charge-imbalanced reactions: 179
Structure vs formula/charge inconsistencies: 58

Pre-existing:

Reactions split across compartments: 26
Reactions flagged as MACAW duplicates: 342
Mass-imbalanced reactions: 69

✅ unchanged · ✨ improved vs develop · ⚠️ pre-existing, non-blocking · ❌ regression

Full workflow run · this comment is edited as results come in

UniProt Q6V0L0 gives human CYP26C1 the all-trans and 9-cis 4-hydroxylations and 4-oxo steps (RHEA:51984, 75851, 75847, 75855; PMID:14532297); it also 4-hydroxylates 13-cis-retinoate (PMID:29476041).

# Conflicts: # data/deprecatedIdentifiers/deprecatedMetabolites.tsv # data/deprecatedIdentifiers/deprecatedReactions.tsv # data/testResults/README.md # data/testResults/balance_results.csv # data/testResults/memote_score.md # data/testResults/model_qc_comment.md # data/testResults/model_qc_summary.md # data/testResults/qc_structure_consistency.csv # model/metabolites.tsv # model/reactions.tsv

edkerk · 2026-09-28T13:32:58Z

About the gene-essentiality run:

ACAA2 (knockout now blocks growth in 5/5 lines, wrong vs Hart 2015) is an effect of the biomass definition, not of the curation. This PR adds ACAA2 as the thiolase of the vitamin E side-chain beta-oxidation rounds, and the cofactor and vitamin pool MAR10065 requires two end products of that pathway, 3-carboxy-alpha-chromanol and gamma-CEHC-glucuronide. In the full model, the ACAA2 knockout blocks growth, and removing these two metabolites from MAR10065 makes it dispensable again (the same holds for CYP4F2). Same mechanism as on fix: vitamin E beta-oxidation GPRs and electron acceptor, CYP4F2 for omega-hydroxylation #1096; redefining the biomass is described in Redefine the biomass reactions MAR13082 and MAR00021 (and review the tasks that depend on them) #1118.
CYP3A4 (no longer blocks growth in 3/5 lines, now correct vs Hart 2015) was growth-essential because it was the only expressed enzyme on the 13-cis-retinoate route that the same pool requires (fix: MAM01026 is 4-oxo-13-cis-retinoate; merge duplicate and correct CYP26 stoichiometry #1044, Questions about MAR10065. Is it essential to include 4-oxo-9-cis-retinal? #1072). The GPRs added here (isoforms with human data, and CYP26C1) remove that dependency.
AKR1A1 and GNPAT (no longer block growth in 3/5 lines) appear among the likely-noise genes in almost every run, and their knockouts do not affect growth in the full model, so this is most likely run-to-run variation of ftINIT.

edkerk · 2026-09-28T13:33:06Z

/run gene-essentiality

github-actions · 2026-09-28T13:33:16Z

Gene essentiality was run on this pull request via GH Actions.

Gene essentiality: effect of this change

Checked 110 gene(s) directly affected plus 2340 more that share a metabolite with one of them.

A gene counts as changed below only if the flip agrees in direction across at least 3 of the 5 cell-line models; fewer than that is grouped as likely noise from ftINIT's run-to-run variability instead.

Category	Status
Growth effect changed (vs Hart 2015)	❌ 1 wrong · ✨ 3 correct
Other role changed (not Hart-comparable)	✅ 0
Likely noise (<3/5 lines)	ℹ️ 20
No change	✅ 2426

Full detail: gene-essential_summary.md.

✅ unchanged · ✨ correct vs Hart 2015 · ❌ wrong vs Hart 2015 · ℹ️ not comparable to Hart 2015

The unscoped, every-gene matrix behind the table above is committed to gene-essential.csv.

Note: each run posts its results in place of its own start notice; earlier results link here.

edkerk · 2026-10-20T20:48:32Z

This pull request added five genes: AQP11, IPO4, TRPV5, TRPV6 and CYP26C1. The description names the first four. CYP26C1 (ENSG00000187553) is an alternative gene of the retinoate hydroxylations (MAR06664, MAR06665, MAR06681, MAR06682, MAR06700–MAR06703, MAR20199, MAR20200). The 2.1.0 release notes list all five.

edkerk added 4 commits September 26, 2026 21:34

chore: update model QC results [skip ci]

3f534a3

edkerk added this to the 2.1.0 milestone Sep 26, 2026

This was referenced Sep 28, 2026

fix: QC check for reactions split across compartments, and curation of those found #1095

Merged

fix: vitamin E beta-oxidation GPRs and electron acceptor, CYP4F2 for omega-hydroxylation #1096

Merged

edkerk and others added 3 commits September 28, 2026 10:42

chore: update model QC results [skip ci]

e2e4956

feat: add CYP26C1 to the retinoate 4-hydroxylation and 4-oxo reactions

5d8a854

UniProt Q6V0L0 gives human CYP26C1 the all-trans and 9-cis 4-hydroxylations and 4-oxo steps (RHEA:51984, 75851, 75847, 75855; PMID:14532297); it also 4-hydroxylates 13-cis-retinoate (PMID:29476041).

edkerk and others added 2 commits September 28, 2026 11:12

chore: update model QC results [skip ci]

e9617ab

chore: add gene essentiality test result [skip ci]

29a05ef

chore: add gene essentiality test result [skip ci]

e03cdd7

SysBioChalmers deleted a comment from github-actions Bot Sep 28, 2026

edkerk merged commit 76e27b9 into develop Sep 28, 2026

edkerk deleted the fix/review-v2.0.1-curation branch September 28, 2026 15:33

edkerk mentioned this pull request Sep 29, 2026

chore: version 2.1.0 #1123

Merged

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fix: corrections to curation since v2.0.1 from an evidence review - #1105

fix: corrections to curation since v2.0.1 from an evidence review#1105
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