Genes and enzymes involved in the biodegradation of the quaternary carbon compound pivalate in the denitrifying Thauera humireducens strain PIV‐1

• Published in: Environmental microbiology 2022-07, Vol.24 (7), p.3181-3194
• Main Authors: Jacoby, Christian, Ebenau‐Jehle, Christa, Saum, Katharina, Jehmlich, Nico, Bergen, Martin, Brüls, Thomas, Boll, Matthias
• Format: Article
• Language: English
• Subjects: Adenosylcobalamin; Bacteriology; Biochemistry; Biochemistry, Molecular Biology; Biodegradation; Carbon; Carbon compounds; Carboxylation; Carboxylic acids; Fossils; Gene clusters; Genes; Genomes; Leucine; Life Sciences; Microbiology and Parasitology; Propionic acid; Proteomics; Quaternary; Skeleton; Thauera
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.16021

Summary Quaternary carbon‐containing compounds exist in natural and fossil oil‐derived products and are used in chemical and pharmaceutical applications up to industrial scale. Due to the inaccessibility of the quaternary carbon atom for a direct oxidative or reductive attack, they are considered as persistent in the environment. Here, we investigated the unknown degradation of the quaternary carbon‐containing model compound pivalate (2,2‐dimethyl‐propionate) in the denitrifying bacterium Thauera humireducens strain PIV‐1 (formerly Thauera pivalivorans). We provide multiple evidence for a pathway comprising the activation to pivalyl‐CoA and the carbon skeleton rearrangement to isovaleryl‐CoA. Subsequent reactions proceed similar to the catabolic leucine degradation pathway such as the carboxylation to 3‐methylglutaconyl‐CoA and the cleavage of 3‐methyl‐3‐hydroxyglutaryl‐CoA to acetyl‐CoA and acetoacetate. The completed genome of Thauera humireducens strain PIV‐1 together with proteomic data was used to identify pivalate‐upregulated gene clusters including genes putatively encoding pivalate CoA ligase and adenosylcobalamin‐dependent pivalyl‐CoA mutase. A pivalate‐induced gene encoding a putative carboxylic acid CoA ligase was heterologously expressed, and its highly enriched product exhibited pivalate CoA ligase activity. The results provide the first experimental insights into the biodegradation pathway of a quaternary carbon‐containing model compound that serves as a blueprint for the degradation of related quaternary carbon‐containing compounds.