PXD040151

PXD040151 is an original dataset announced via ProteomeXchange.

Title	Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum
Description	Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C1) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO2) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C1-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions – hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950) – directly adjacent and expressed at similar levels to the C1-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO2 and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C1-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:00:22.929.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

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-16 07:57:19	ID requested
1	2023-05-10 10:47:09	announced
⏵ 2	2023-11-14 09:00:23	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: gas fermentation

acetogen

CRISPR/nCas9

genetic engineering

metabolomics

proteomics

chemostat

continuous cultivation

syngas

Kaspar Valgepea
contact affiliation	ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu
contact email	kaspar.valgepea@ut.ee
lab head
Kaspar Valgepea
contact affiliation	ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu
contact email	kaspar.valgepea@ut.ee
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040151
     1. Label: PRIDE project
     2. Name: Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum