Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition
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Notice bibliographique
Résumé
BACKGROUND: Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and triacylglycerols (TAG). Under nitrogen-limited (N-limited) condition, the level of storage increases as is commonly observed for other bacteria. The proportion of each storage compound changes with substrate, but it remains unclear what modelling approach should be adopted to predict the relative composition of the mixture of the storage compounds. We analyzed the growth of R. jostii RHA1 under N-limited conditions using a genome-scale metabolic modelling approach to determine which global metabolic objective function could be used for the prediction. RESULTS: The R. jostii RHA1 model (iMT1174) produced during this study contains 1,243 balanced metabolites, 1,935 unique reactions, and 1,174 open reading frames (ORFs). Seven objective functions used with flux balance analysis (FBA) were compared for their capacity to predict the mixture of storage compounds accumulated after the sudden onset of N-limitation. Predictive abilities were determined using a Bayesian approach. Experimental data on storage accumulation mixture (glycogen, polyhydroxyalkanoates, and triacylglycerols) were obtained for batch cultures grown on glucose or acetate. The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA). The FBA solutions for the non-limited growth conditions were simply constrained by the objective function of growth rate maximization. Measurement of central metabolic fluxes by (13)C-labelling experiments of amino acids further supported the application of the environmental MOMA principle in the context of changing environment. Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected. CONCLUSIONS: The genome-scale metabolic model analysis of R. jostii RHA1 cultures suggested that the intracellular reaction flux profile immediately after the onset of N-limited condition are impacted by the values of the same fluxes during the period of non-limited growth. PHA turned out to be the main storage pool of the mixture in R. jostii RHA1.
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Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,001 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découle