Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification

Abstract

Abstract Pyruvic oxime dioxygenase (POD) is the enzyme that is involved in the heterotrophic nitrification process in Alcaligenes faecalis. Genes encoding POD were found in bacteria of the phyla Proteobacteria and Actinobacteria, and in fungi of the phylum Ascomycota, and their gene products were found to be active in recombinant experiments. No pod genes were found in the well-known heterotrophic nitrifying species such as Paracoccus and Bacillus, suggesting that heterotrophic nitrification in these bacteria proceeds without the involvement of POD. Phylogenetic analysis of amino acid sequences classified POD into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compound, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.