Figure 1 - uploaded by Freddy Castillo Alfonso
Content may be subject to copyright.
Graphical overview of FROG analysis encompassing (1) Flux variability, (2) Reaction deletion, (3) Objective function, and (4) Gene deletion analyses enable the generation of numerically reproducible reference datasets to assess the reproducibility of GEMs.
Source publication
Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the re...
Citations
Treponema pallidum , the causative agent of syphilis, poses a significant global health threat. Its strict reliance on host-derived nutrients and difficulties in in vitro cultivation have impeded detailed metabolic characterization. In this study, we present iTP251, the first genome-scale metabolic model of T. pallidum , reconstructed and extensively curated to capture its unique metabolic features. These refinements included the curation of key reactions such as pyrophosphate-dependent phosphorylation and pathways for nucleotide synthesis, amino acid synthesis, and cofactor metabolism. The model demonstrated high predictive accuracy, validated by a MEMOTE score of 92%. To further enhance its predictive capabilities, we developed ec-iTP251, an enzyme-constrained version of iTP251, incorporating enzyme turnover rate and molecular weight information for all reactions having gene-protein-reaction associations. Ec-iTP251 provides detailed insights into protein allocation across carbon sources, showing strong agreement with proteomics data (Pearson’s correlation of 0.88) in the central carbon pathway. Moreover, the thermodynamic analysis revealed that lactate uptake serves as an additional ATP-generating strategy to utilize unused proteomes, albeit at the cost of reducing the driving force of the central carbon pathway by 27%. Subsequent analysis identified glycerol-3-phosphate dehydrogenase as an alternative electron sink, compensating for the absence of a conventional electron transport chain while maintaining cellular redox balance. These findings highlight T. pallidum ’s metabolic adaptations for survival and redox balance in nutrient-limited, extracellular host environments, providing a foundation for future research into its unique bioenergetics.
IMPORTANCE
This study advances our understanding of Treponema pallidum , the syphilis-causing pathogen, through the reconstruction of iTP251, the first genome-scale metabolic model for this organism, and its enzyme-constrained version, ec-iTP251. The work addresses the challenges of studying T. pallidum , an extracellular, host-adapted pathogen, due to its strict dependence on host-derived nutrients and challenges in in vitro cultivation. Validated with strong agreement to proteomics data, the model demonstrates high predictive reliability. Key insights include unique metabolic adaptations such as lactate uptake for ATP production and alternative redox-balancing mechanisms. These findings provide a robust framework for future studies aimed at unraveling the pathogen's survival strategies and identifying potential metabolic vulnerabilities.
A comprehensive mechanistic analysis of emerging pharmaceutical pollutants’ stress response in plants is needed to understand its chronic impact on food-chain contamination and agricultural productivity. To unravel this at systems-level, the current study employs insights from green-liver concept and establishes the utility of constraint-based modelling approach for elucidating perturbations in a plant’s metabolism due to pharmaceutical stress.
In this study, the stress response of an emerging recalcitrant anticonvulsant pollutant, carbamazepine (CBZ), was simulated in tomato crop under phototrophic conditions. For this, an updated genome-scale metabolic model of tomato leaf (CBZ_ i SL3433) was developed and augmented with CBZ transformation reactions based on the green-liver concept. The model was able to capture energy and co-factor competition-induced biomass reduction in presence of CBZ stress. Further, the study provides an in silico mechanistic proof for abiotic stress response induced by CBZ in tomato with altered flux states in nutrient assimilation, synthesis of key precursors of leaf biomass and secondary metabolites. Additionally, to extend the applicability of model, potential ameliorative effects of biostimulants such as proline, spermine, glycerol, and ethanol were investigated through model predictions. Through systematic computational analysis, 154 significantly altered reactions were identified in the presence of CBZ stress, of which 92 % of reactions were ameliorated with biostimulants. Amino acid biosynthesis was found to be the most significantly altered pathway under CBZ stress in the presence of biostimulants.
Overall, the proposed framework can aid in screening and developing rational strategies to maintain agricultural yields amid rising plant stress due to such anthropogenic pollutants.
