Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink
ABSTRACT 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 me...
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American Society for Microbiology
2025-05-01
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| Series: | mSystems |
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| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01555-24 |
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| author | Nabia Shahreen Niaz Bahar Chowdhury Edward Stone Elle Knobbe Rajib Saha |
| author_facet | Nabia Shahreen Niaz Bahar Chowdhury Edward Stone Elle Knobbe Rajib Saha |
| author_sort | Nabia Shahreen |
| collection | DOAJ |
| description | ABSTRACT 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.IMPORTANCEThis 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. |
| format | Article |
| id | doaj-art-d44a45a1befa40389f1aa5b2ba2a27b5 |
| institution | Kabale University |
| issn | 2379-5077 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | American Society for Microbiology |
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| series | mSystems |
| spelling | doaj-art-d44a45a1befa40389f1aa5b2ba2a27b52025-08-20T03:54:01ZengAmerican Society for MicrobiologymSystems2379-50772025-05-0110510.1128/msystems.01555-24Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sinkNabia Shahreen0Niaz Bahar Chowdhury1Edward Stone2Elle Knobbe3Rajib Saha4Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USADepartment of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USADepartment of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USADepartment of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USADepartment of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USAABSTRACT 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.IMPORTANCEThis 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.https://journals.asm.org/doi/10.1128/msystems.01555-24Treponema pallidumgenome-scale metabolic modelenzyme-constrained modelingalternative electron sinkglycerol-3-phosphate dehydrogenaseredox balance |
| spellingShingle | Nabia Shahreen Niaz Bahar Chowdhury Edward Stone Elle Knobbe Rajib Saha Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink mSystems Treponema pallidum genome-scale metabolic model enzyme-constrained modeling alternative electron sink glycerol-3-phosphate dehydrogenase redox balance |
| title | Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink |
| title_full | Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink |
| title_fullStr | Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink |
| title_full_unstemmed | Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink |
| title_short | Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink |
| title_sort | enzyme constrained metabolic model of treponema pallidum identified glycerol 3 phosphate dehydrogenase as an alternate electron sink |
| topic | Treponema pallidum genome-scale metabolic model enzyme-constrained modeling alternative electron sink glycerol-3-phosphate dehydrogenase redox balance |
| url | https://journals.asm.org/doi/10.1128/msystems.01555-24 |
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