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

Jinyu Yin, Yifeng Wei, Dazhi Liu, Yiling Hu, Qiang Lu, Ee Lui Ang, Huimin Zhao, Yan Zhang

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)15662-15671
Number of pages10
JournalJournal of Biological Chemistry
Volume294
Issue number43
DOIs
StatePublished - Jan 1 2019

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Alanine
Nitrogen
Degradation
Bacteria
Uracil
Bacilli
Bacillus
Genes
Waste Products
Atoms
Clostridium
Uridine
Gram-Positive Bacteria
Enzymes
Bioinformatics
Multigene Family
pyrimidine
Computational Biology
Alanine Transaminase
NAD

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine. / Yin, Jinyu; Wei, Yifeng; Liu, Dazhi; Hu, Yiling; Lu, Qiang; Lui Ang, Ee; Zhao, Huimin; Zhang, Yan.

In: Journal of Biological Chemistry, Vol. 294, No. 43, 01.01.2019, p. 15662-15671.

Research output: Contribution to journalArticle

Yin, Jinyu ; Wei, Yifeng ; Liu, Dazhi ; Hu, Yiling ; Lu, Qiang ; Lui Ang, Ee ; Zhao, Huimin ; Zhang, Yan. / An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine. In: Journal of Biological Chemistry. 2019 ; Vol. 294, No. 43. pp. 15662-15671.
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