TABLE 1.
Reactions present in the current P. gingivalis model but not in the H. pylori model iIT341
| Reaction namea | Enzyme | Reaction details | Pathway(s) | Reference | EC no. | Protein ID | GenBank accession no. | E value | BLAST result (top hit) | BLAST accession no. |
|---|---|---|---|---|---|---|---|---|---|---|
| R00654 | l-Methionine methanethiol-lyase (deaminating) | Methionine + water ↔ methylmercaptan + ammonia + 2-oxobutanoate | Methionine metabolism | 100 | 4.4.1.11 | PG0343 | NP_904655 | 3.00E-175 | Methionine gamma-lyase (Treponema denticola ATCC 35405) | NP_972801 |
| R00357 | l-Aspartic acid:oxygen oxidoreductase (deaminating) | Aspartate + water + oxygen ↔ oxaloacetate + ammonia + hydrogen peroxide | Alanine and aspartate metabolism | 11 | 1.4.3.16 | PG1576 | NP_905707 | 7.00E-119 | l-Aspartate oxidase (Geobacillus sp. strain Y412MC10) | ZP_03038236 |
| R00764 | Pyrophosphate:d-fructose-6-phosphate 1-phosphotransferase | Diphosphate + d-fructose-6-phosphate ↔ phosphate + d-fructose-1,6-bisphosphate | Glycolysis | 5 | 2.7.1.90 | PG0163 | NP_904504 | 0 | Diphosphate-fructose-6-phosphate 1-phosphotransferase (Parabacteroides distasonis ATCC 8503) | YP_001302896 |
| CTT | Butyryl-CoA oxireductase | Crotonoyl-CoA + menaquinol ↔ butanoyl-CoA + menaquinone | Glutamine metabolism | 90 | 1.3.99.2 | |||||
| 4HB2COA | 4-Hydroxy butyrate to crotonoyl-CoA | Acetyl-CoA + 4-hydroxybutyrate ↔ acetate + butanoyl-CoA + water | Glutamine metabolism | 90 |
R00654 (METase) is a part of the methionine metabolism and is instrumental in methyl-mercaptan production directly from methionine and water. Methyl mercaptan is a toxic volatile sulfur compound known to be a predominant source of oral malodor. In addition, volatile sulfur compounds are able to increase the permeability of the oral mucosa, making them candidate mediators of periodontal disease. This is backed up by the fact that METase mutants have a reduced level of pathogenicity compared with the wild type (100). The reaction R00357 is part of a more generic response to the presence of molecular oxygen. The organism uses an amino acid oxidase to convert molecular oxygen into hydrogen peroxide, which prevents the formation of highly damaging superoxide ions (11). R00764 is a prominent reaction in the glycolytic and gluconeogenic pathway. This reaction is part of a functioning gluconeogenesis pathway that can produce intermediates for pathways such as LPS synthesis (5). Reactions CTT and 4HB2COA are both important reactions required for butyrate production in P. gingivalis. These reactions are extracted directly from the literature (90) and hence do not have associated ORFs or corroborating BLAST evidence. CoA, coenzyme A.