Diversity of NADH dehydrogenases in acetic acid bacteria: adaptation to modify their phenotype through gene expansions and losses and neo-functionalization

NADH dehydrogenase plays an important role in the central metabolism of almost all organisms, including acetic acid bacteria (AAB). In this study, the gene diversity of the NADH dehydrogenases in AAB was investigated. The distribution of the genes of the type I and type II NADH dehydrogenases in AAB was mostly congruent with their phylogenetic relationships. There are two phylogenetically distinct type I NADH dehydrogenase complexes, complex IA and complex IE. Complex IA', which lacks the nuoM gene from complex IA, was only conserved in the genera Acetobacter, Gluconacetobacter and Komagataeibacter, which all have the ability to perform acetic acid fermentation, whereas the complex IE gene cluster was found randomly in several species of AAB. Almost all AAB, excluding the early-diverged species, had the type II NADH dehydrogenase, while some of the species also had the homologue with an amino acid replacement at the residue responsible for NADPH oxidation ability. Thus, the gene repertoire of NADH dehydrogenases shows a history of adaptation towards their habitats through gene expansions and losses and neo-functionalization in AAB.