Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate

Abstract

Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an α-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate. CsiD is found widespread in bacteria. We present crystal structures of CsiD in complex with glutarate, succinate, and the inhibitor N-oxalyl-glycine, demonstrating strong discrimination between the structurally related ligands. We show that L-2-hydroxyglutarate is converted to α-ketoglutarate by LhgO acting as a membrane-bound, ubiquinone-linked dehydrogenase. Lysine enters the pathway via 5-aminovalerate by the promiscuous enzymes GabT and GabD. We demonstrate that repression of the pathway by CsiR is relieved upon glutarate binding. In conclusion, lysine degradation provides an important link in central metabolism. Our results imply the gut microbiome as a potential source of glutarate and L-2-hydroxyglutarate associated with human diseases such as cancer and organic acidurias.

Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors

“…The assay showed multiple binding sites in this intergenic region, as four distinct bands appeared. These results appear to confirm the finding in E. coli where four binding sites of the E. coli CsiR homolog were observed 18 . CsiR had a high affinity for the DNA probe, with a calculated K d of approximately 30 nM (Figure 3a), which is similar to the 10 nM CsiR/DNA K d of the E. coli CsiR homolog 18 .…”

“…Genomic contexts of csiR and gcdR homologs and prediction of P. putida binding sites Work in Pseudomonas aeruginosa has characterized the GcdR regulation of ketogenic glutarate metabolism, and shown that the binding site is conserved across multiple bacterial species 17 . While binding sites for CsiR in E. coli have been identified, whether there is a conserved binding site for homologs across bacterial species has yet to be investigated 18 . In order to identify conserved binding sites of CsiR homologs, we compared the syntenic genomic contexts of 12 selected genomes that contained neighboring csiD and csiR homologs.…”

“…coli, though only in E. coli has the CsiR homolog been characterized 14,18 . Our bioinformatic approach to predict the conserved binding site of CsiR largely agrees with the empirically determined binding site identified in E. coli (Figure 2), and our EMSA results also confirm the existence of four distinct CsiR binding sites (Figure 3).…”

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

“…Unfortunately, almost no fungal catabolic lysine pathways are fully characterized genetically or biochemically. 28 34,35 E. coli also possesses a HglS homolog, YdcJ, which we showed has identical activity to HglS.…”

A fluorescent l-2-hydroxyglutarate biosensor

“…In mammals and plants, it is produced by lactate dehydrogenase (LDH) and malate dehydrogenase (MDH)-mediated 2-ketoglutarate (2-KG) reduction under hypoxic conditions [1][2][3][4][5] . In microorganisms, it is a metabolic intermediate of glutarate catabolism produced by a glutarate hydroxylase, CsiD [6][7][8] . L-2-HG dehydrogenase (L2HGDH) or L-2-HG oxidase (LhgO), an FAD-containing oxidoreductase that converts L-2-HG to 2-KG, plays an indispensable role in the catabolism of L-2-HG 9 .…”