PXD026569

PXD026569 is an original dataset announced via ProteomeXchange.

Title	A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction
Description	Cheap and renewable feedstocks such as the one carbon substrate formate are emerging for sustainable production in a growing chemical industry. By quantitatively analyzing physiology, transcriptome, proteome in chemostat cultivations in combination with computational analyses, we investigated the acetogen Acetobacterium woodii as a potential host for bioproduction from formate alone and together with autotrophic and heterotrophic co-substrates. Continuous cultivations with a specific growth rate of 0.05 h-1 on formate showed high specific substrate uptake rates (47 mmol g‑1 h‑1). Co-utilization of formate with H2, CO, CO2 or fructose was achieved without catabolite repression and with acetate as the sole metabolic product. A transcriptomic comparison of all growth conditions revealed a distinct adaptation of A. woodii to growth on formate as 570 genes were changed in their transcription. Transcriptome and proteome showed higher expression of the Wood-Ljungdahl pathway during growth on formate and gaseous substrates, underlining its function during utilization of one carbon substrates. Flux balance analysis showed varying flux levels for the WLP (0.7-16.4 mmol/g/h) and major differences in redox and energy metabolism. Growth on formate, H2/CO2, and formate+H2/CO2 resulted in low energy availability (0.20-0.22 ATP/acetate) which was increased during co-utilization with CO or fructose (0.31 ATP/acetate for formate+H2/CO/CO2, 0.75 ATP/acetate for formate+fructose). Unitrophic and mixotrophic conversion of all substrates was further characterized by high energetic efficiencies. In silico analysis of bioproduction of ethanol and lactate from formate and autotrophic and heterotrophic co-substrates showed promising energetic efficiencies (70-92%). Collectively, our findings reveal A. woodii as a promising host for flexible and simultaneous bioconversion of multiple substrates, underline the potential of substrate co-utilization to improve the energy availability of acetogens and encourage metabolic engineering of acetogenic bacteria for the efficient synthesis of bulk chemicals and fuels from sustainable one carbon substrates.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:48:34.459.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tamara Tomin
SpeciesList	scientific name: Acetobacterium woodii; NCBI TaxID: 33952;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-08 09:04:21	ID requested
1	2023-03-08 06:28:44	announced
⏵ 2	2023-11-14 07:48:36	announced	2023-11-14: Updated project metadata.

Neuendorf CS, Vignolle GA, Derntl C, Tomin T, Novak K, Mach RL, Birner-Gr, ü, nberger R, Pfl, ü, gl S, A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction. Metab Eng, 68():68-85(2021) [pubmed]

submitter keyword: mixed gas fermentation, continuous fermentation, metabolic modelling, substrate co-utilization, acetogens, omics analysis,Formate bioeconomy

Ruth Birner-Gruenberger
contact affiliation	Full Professor for Analytical Chemistry Institute of Chemical Technologies and Analytics TU Wien Getreidemarkt 9/E164 A-1060 Vienna Austria
contact email	ruth.birner-gruenberger@tuwien.ac.at
lab head
Tamara Tomin
contact affiliation	Senior Scientist at Institute of Chemical Technologies and Analytics Faculty of Technical Chemistry, TU Wien Getreidemarkt 9/164, 1060 Vienna
contact email	tamara.tomin@tuwien.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026569
     1. Label: PRIDE project
     2. Name: A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction