PXD016381

PXD016381 is an original dataset announced via ProteomeXchange.

Title	Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum
Description	Living biological systems display a fascinating ability to self-organise their metabolism. This ability ultimately determines metabolic robustness that is fundamental to control cellular behaviour. However, fluctuations in metabolism can affect cellular homeostasis through transient oscillations. For example, yeast cultures exhibit rhythmic oscillatory behaviour in high-cell density continuous cultures. Oscillatory behaviour provides a unique opportunity for quantitating the robustness of metabolism, as cells respond to changes by inherently compromising metabolic efficiency. Here, we quantify the limits of metabolic robustness in self-oscillating autotrophic continuous cultures of the gas-fermenting acetogen Clostridium autoethanogenum. On-line gas analysis and high-resolution temporal metabolomics showed oscillations in gas uptake rates and extracellular by-products synchronised with biomass levels. Loss of H2 uptake makes CO the sole carbon and energy source until cells recover uptake of H2 in synchrony with increasing biomass levels. Intriguingly, oscillations are not linked to translational control as no differences were observed in protein expression during oscillations. However, intracellular metabolomics analysis revealed decreasing levels of redox ratios in perfect synchrony with the cycles. Therefore, we developed a thermodynamic metabolic flux analysis (tMFA) model to investigate if regulation in acetogens is controlled at the thermodynamic level. The data shows that the feasible range for the thermodynamic driving force of the Nfn transhydrogenase complex (i.e. NADH/NAD+×NADP+/NADPH) closely matched the experimentally observed range. The data indicate that metabolic oscillations in gas fermentation acetogens are controlled at the thermodynamic level. Our work suggests thermodynamic control of metabolism, potentially contributing to metabolic efficiency and working as a mean of energy conservation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:24.368.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kaspar Valgepea
SpeciesList	scientific name: Clostridium autoethanogenum; NCBI TaxID: 84023;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-21 05:56:37	ID requested
1	2020-05-17 23:49:43	announced
2	2020-06-01 06:15:07	announced	2020-06-01: Updated publication reference for DOI(s): 10.1073/pnas.1919531117.
3	2020-08-11 05:25:25	announced	2020-06-01: Updated publication reference for DOI(s): 10.1073/pnas.1919531117. 2020-08-11: Updated publication reference for PubMed record(s): 32471945. 2020-08-11: Updated publication reference for DOI(s): 10.1073/pnas.1919531117.
⏵ 4	2023-11-14 08:50:25	announced	2023-11-14: Updated project metadata.

Mahamkali V, Valgepea K, de Souza Pinto Lemgruber R, Plan M, Tappel R, K, ö, pke M, Simpson SD, Nielsen LK, Marcellin E, . Proc Natl Acad Sci U S A, 117(23):13168-13175(2020) [pubmed]

submitter keyword: metabolic robustness

oscillations

acetogen

gas fermentation

Wood-Ljungdahl pathway

metabolism

data-independent acquisition

Esteban Marcellin
contact affiliation	Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Australia
contact email	e.marcellin@uq.edu.au
lab head
Kaspar Valgepea
contact affiliation	Australian Institute for Bioengineering and Nanotechnology,The University of Queensland
contact email	k.valgepea@uq.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016381
     1. Label: PRIDE project
     2. Name: Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum