PXD046638-1

PXD046638 is an original dataset announced via ProteomeXchange.

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	2024-02-01
AnnouncementXML	Submission_2024-02-01_03:28:43.505.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

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.

Dataset with its publication pending

submitter keyword: Desulfovibrio vulgaris Hildenborough, formate metabolism, sulfate respiration, proteomic, metabolic flexibility, hydrogen metabolism, flux balance analysis,metabolic model

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

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PRIDE project URI

• PRIDE
  1. PXD046638
     1. Label: PRIDE project
     2. Name: Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough