PXD039574-2

PXD039574 is an original dataset announced via ProteomeXchange.

Title	An integrated systems-biology platform for power-to-gas technology
Description	Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance of three wild-type strains and one genetically engineered strain in two independent chemostat bioreactor experiments, first, with molecular hydrogen and carbon dioxide, and second, with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. Transcriptomics and proteomics data sets from these steady-state bioreactors, in combination with the implementation of a pan-model that contains combined reactions from all three microbes, allowed us to perform an interspecies comparison. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach combining fermentation and omics data with genome-scale modeling to reveal knowledge gaps of archaeal metabolisms and the biotechnological potential of Methanothermobacter spp. as production platform hosts.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:09:38.803.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Isabella Casini
SpeciesList	scientific name: Methanothermobacter thermautotrophicus str. Delta H; NCBI TaxID: 187420; scientific name: Methanothermobacter thermautotrophicus; NCBI TaxID: 145262; scientific name: Methanothermobacter marburgensis; NCBI TaxID: 145263;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-20 02:30:37	ID requested
1	2023-10-24 12:39:36	announced
⏵ 2	2023-11-14 09:09:39	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:09:58	announced	2024-10-22: Updated project metadata.

Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dr, ä, ger A, Ley RE, Marcellin E, Angenent LT, Molitor B, . iScience, 26(10):108016(2023) [pubmed]

submitter keyword: Formate, Gas Fermentation,Archaea, Genome Sequencing, Genetic Engineering, Methanothermobacter, Genome-Scale Metabolic Modeling, Transcriptomics, Proteomics

Bastian Molitor
contact affiliation	University of Tübingen Center for Applied Geosciences Environmental Biotechnology Group
contact email	bastian.molitor@uni-tuebingen.de
lab head
Isabella Casini
contact affiliation	University of Tübingen
contact email	isacasini@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD039574

PRIDE project URI

• PRIDE
  1. PXD039574
     1. Label: PRIDE project
     2. Name: An integrated systems-biology platform for power-to-gas technology