PXD046638 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough |
Description | Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria, a group of microbes that can perform dissimilatory sulfate reduction coupled to the oxidation of various substrates as carbon and energy sources. In the absence of sulfate, they can also ferment organic acids in syntrophy with methanogens. They exhibit high metabolic diversity switching from one energy mode to another depending on nutrients availability in the environments. Hence, they play a central role in shaping ecosystems. Despite, intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remains far from being fully understood. Alternatively, few metabolic models were also proposed to explain D. vulgaris bioenergetics. However, they appeared to be not easily adaptable to various environmental conditions. To lift off these limitations, here we constructed a new transparent and robust metabolic model of D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:28:14.500.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Regine Lebrun |
SpeciesList | scientific name: Desulfovibrio vulgaris str. Hildenborough; NCBI TaxID: 882; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-11-03 03:49:17 | ID requested | |
1 | 2024-02-01 03:28:43 | announced | |
⏵ 2 | 2024-10-22 06:28:14 | announced | 2024-10-22: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Desulfovibrio vulgaris Hildenborough, formate metabolism, sulfate respiration, proteomic, metabolic flexibility, hydrogen metabolism, flux balance analysis,metabolic model |
Contact List
Lebrun Regine |
contact affiliation | Proteomic Platform of Institut de Microbiologie de la Mediterranee CNRS FR 3479 Marseille Proteomique |
contact email | rlebrun@imm.cnrs.fr |
lab head | |
Regine Lebrun |
contact affiliation | CNRS |
contact email | rlebrun@imm.cnrs.fr |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD046638
- Label: PRIDE project
- Name: Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough