Table 12 False gene essentiality predictions caused by technical issues in MetaFlux and EcoCyc

Lipoate biosynthesis and the final step of biotin biosynthesis are not operational in EcoCyc–18.0–GEM due

to reaction mass imbalances in EcoCyc 18.0. This leads to the presence of dethiobiotin instead of biotin in

the objective function, and prevents biotinylation of biotin carboxyl carrier protein.

EntDEFG activity is active in EcoCyc–18.0–GEM without EntD because of the presence of individual EntE, EntF, and EntG activity in EcoCyc in addition to an activity describing the overall EntDEFG complex, which leads to entD knockouts being ineffective.

EntDEFG activity is active in EcoCyc–18.0–GEM without EntD because of the presence of individual EntE, EntF, and EntG activity in EcoCyc in addition to an activity describing the overall EntDEFG complex, which leads to entD knockouts being ineffective.

The IspG reaction in the EcoCyc MEP pathway incorrectly requires ferredoxin (encoded by fdx) instead of flavodoxin I [137].

The IscS cysteine desulfurase lacks chemical structure in EcoCyc, preventing its participation in thiazole

biosynthesis and iron-sulfur cluster synthesis. This affects thiL essentiality by blocking thiazole synthesis and rendering EcoCyc–18.0–GEM unable to synthesize thiamin. Due to exogenous thiamin contamination in the experiments of [32] (see [73]; note that thiL is apparently mislabeled as thiI therein) this omission manifests itself only as an incorrect prediction of thiL nonessentiality, since endogenous and exogenous thiamin pathways can substitute for knockouts in each other until the final thiamin monophosphate kinase activity of ThiL.

MetaFlux does not correctly model polymerization reactions, which prevents the synthesis of 5-methyltetrahydropteroyl tri-L-glutamate by folate polyglutamylation. This in turn prevents MetE’s cob(I)alamin-independent methionine synthase reaction from operating properly.

MetH’s cob(I)alamin-dependent methionine synthase activity does not currently require cob(I)alamin cofactor in EcoCyc–18.0–GEM because cofactor requirements are not accounted for in enzymatic reactions. Because MetE is inoperational as a result of a lack of folate polyglutamylation (see above), the incorrectly operational MetH methionine synthase reaction becomes essential. This ambiguity will be remedied in future versions of MetaFlux.

ndk is falsely predicted as essential because its UDP kinase and dTDP kinase activities provide the only routes in EcoCyc to UTP and dTTP, respectively. In vivo, ndk null mutants are rescued by broad substrate specificity of adk[36, 138].

The catalytic subunit PyrB of the aspartate transcarbamylase PyrBI is active by itself in vitro [139]. The PyrBI complex catalyzes the physiologically regulated reaction, and the reaction is assigned to the PyrBI complex in EcoCyc. This causes the pyrI gene KO simulation to block PyrBI aspartate transcarbamylation activity entirely.

The activity of the glutaredoxin pathway can substitute for the thioredoxin pathway in E. coli, and vice versa. This ability is not properly modeled in EcoCyc–18.0–GEM as a result of the pathways’ structure in EcoCyc.