An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine

The reductive pyrimidine catabolic pathway is the most widespread pathway for pyrimidine degradation in bacteria, enabling assimilation of nitrogen for growth. This pathway, which has been studied in several bacteria including Escherichia coli B, releases only one utilizable nitrogen atom from each molecule of uracil, whereas the other nitrogen atom remains trapped in the end product β-alanine. Here, we report the biochemical characterization of a β-alanine:2-oxoglutarate aminotransferase (PydD) and an NAD(P)H-dependent malonic semialdehyde reductase (PydE) from a pyrimidine degradation gene cluster in the bacterium Lysinibacillus massiliensis. Together, these two enzymes converted β-alanine into 3-hydroxypropionate (3-HP) and generated glutamate, thereby making the second nitrogen from the pyrimidine ring available for assimilation. Using bioinformatics analyses, we found that PydDE homologs are associated with reductive pyrimidine pathway genes in many Gram-positive bacteria in the classes Bacilli and Clostridia. We demonstrate that Bacillus smithii grows in a defined medium with uracil or uridine as its sole nitrogen source and detected the accumulation of 3-HP as a waste product. Our findings extend the reductive pyrimidine catabolic pathway and expand the diversity of enzymes involved in bacterial pyrimidine degradation.