“Candidatus Galacturonibacter soehngenii” Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex

“Candidatus Galacturonibacter soehngenii” Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex

Valk, L.C. (TU Delft BT/Industriele Microbiologie)
Diender, Martijn (Wageningen University & Research)
Stouten, G.R. (TU Delft BT/Environmental Biotechnology)
Petersen, Jette F. (Aalborg University)
Nielsen, Per H. (Aalborg University)
Dueholm, Morten S. (Aalborg University)
Pronk, J.T. (TU Delft BT/Biotechnologie)
van Loosdrecht, Mark C.M. (TU Delft BT/Environmental Biotechnology)

BT/Biotechnologie

2020

Acetogens have the ability to fixate carbon during fermentation by employing the Wood-Ljungdahl pathway (WLP), which is highly conserved across Bacteria and Archaea. In a previous study, product stoichometries in galacturonate-limited, anaerobic enrichment cultures of “Candidatus Galacturonibacter soehngenii,” from a novel genus within the Lachnospiraceae, suggested the simultaneous operation of a modified Entner-Doudoroff pathway for galacturonate fermentation and a WLP for acetogenesis. However, a draft metagenome-assembled genome (MAG) based on short reads did not reveal homologs of genes encoding a canonical WLP carbon-monoxide-dehydrogenase/acetyl-Coenzyme A synthase (CODH/ACS) complex. In this study, NaH¹³CO₃ fed to chemostat-grown, galacturonate-limited enrichment cultures of “Ca. G. soehngenii” was shown to be incorporated into acetate. Preferential labeling of the carboxyl group of acetate was consistent with acetogenesis via a WLP in which the methyl group of acetate was predominately derived from formate. This interpretation was further supported by high transcript levels of a putative pyruvate-formate lyase gene and very low transcript levels of a candidate gene for formate dehydrogenase. Reassembly of the “Ca. G. soehngenii” MAG with support from long-read nanopore sequencing data produced a single-scaffold MAG, which confirmed the absence of canonical CODH/ACS-complex genes homologs. However, high CO-dehydrogenase activities were measured in cell extracts of “Ca. G. soehngenii” enrichment cultures, contradicting the absence of corresponding homologs in the MAG. Based on the highly conserved amino-acid motif associated with anaerobic Ni-CO dehydrogenase proteins, a novel candidate was identified which could be responsible for the observed activities. These results demonstrate operation of an acetogenic pathway, most probably as a yet unresolved variant of the Wood-Ljungdahl pathway, in anaerobic, galacturonate-limited cultures of “Ca. G. soehngenii.”

C-labeling
acetogenesis
chemostat enrichment culture
meta-transcriptomics
Wood-Ljungdahl pathway

http://resolver.tudelft.nl/uuid:7b60aae1-f2b7-4731-a1d6-a21b0460f3ce

https://doi.org/10.3389/fmicb.2020.00063

1664-302X

Frontiers in Microbiology, 11

Institutional Repository

journal article

© 2020 L.C. Valk, Martijn Diender, G.R. Stouten, Jette F. Petersen, Per H. Nielsen, Morten S. Dueholm, J.T. Pronk, Mark C.M. van Loosdrecht