PXD062027-1

PXD062027 is an original dataset announced via ProteomeXchange.

Title	Reverse-engineered gas-fermenting acetogen strains recover enhanced phenotypes from autotrophic adaptive laboratory evolution
Description	Gas-fermenting acetogens, such as Clostridium autoethanogenum, have emerged as promising biocatalysts capable of converting CO and CO2-containing gases into fuels and chemicals relevant for a circular economy. However, functionalities of the majority of genes in acetogens remain uncharacterised, hindering the development of acetogen cell factories through targeted genetic engineering. We previously identified gene targets through adaptive laboratory evolution (ALE) that potentially realise enhanced autotrophic phenotypes in C. autoethanogenum. In this study, we deleted one of the targets – CLAU_0471 (proposed amino acid permease) – with high mutation occurrence in ALE isolates and extensively characterised autotrophic growth of strain RE3 in batch bottle and bioreactor continuous cultures. In addition, we characterized two previously reverse-engineered strains RE1 (deletion of CLAU_3129; putative sporulation transcriptional activator Spo0A) and RE2 (SNP in CLAU_1957; proposed two component transcriptional regulator winged helix family). Strikingly, the strains recovered the superior phenotypes of ALE isolates, including faster autotrophic growth, no need for yeast extract, and robustness in bioreactor operation (e.g. low sensitivity to gas ramping, high biomass, and dilution rates). Notably, RE3 exhibited elevated 2,3-butanediol production while RE1 performed similar to the best-performing previously characterised ALE isolate LAbrini. The three reverse-engineered strains showed similarities in proteome expression and bioinformatic analyses suggest that the targeted genes may be involved in overlapping regulatory networks. Our work provides insights into genotype-phenotype relationships for a better understanding of the metabolism of an industrially-relevant acetogen.
HostingRepository	PRIDE
AnnounceDate	2025-08-12
AnnouncementXML	Submission_2025-08-12_05:16:10.469.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	2025-03-19 04:36:23	ID requested
⏵ 1	2025-08-12 05:16:10	announced

10.1111/1751-7915.70208;

submitter keyword: microbial proteomics, gas fermentation, acetogen,DIA

Kaspar Valgepea
contact affiliation	ValgepeaLab, Institute of Bioengineering, University of Tartu
contact email	kaspar.valgepea@ut.ee
lab head
Kaspar Valgepea
contact affiliation	Institute of Bioengineering, University of Tartu
contact email	kaspar.valgepea@ut.ee
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062027
     1. Label: PRIDE project
     2. Name: Reverse-engineered gas-fermenting acetogen strains recover enhanced phenotypes from autotrophic adaptive laboratory evolution