d-2-Hydroxyglutarate dehydrogenase plays a dual role in l-serine biosynthesis and d-malate utilization in the bacterium Pseudomonas stutzeri

Abstract

is a very large bacterial genus in which several species can use d-malate for growth. However, the enzymes that can metabolize d-malate, such as d-malate dehydrogenase, appear to be absent in most species. d-3-Phosphoglycerate dehydrogenase (SerA) can catalyze the production of d-2-hydroxyglutarate (d-2-HG) from 2-ketoglutarate to support d-3-phosphoglycerate dehydrogenation, which is the initial reaction in bacterial l-serine biosynthesis. In this study, we show that SerA of the strain A1501 reduces oxaloacetate to d-malate and that d-2-HG dehydrogenase (D2HGDH) from displays d-malate-oxidizing activity. Of note, D2HGDH participates in converting a trace amount of d-malate to oxaloacetate during bacterial l-serine biosynthesis. Moreover, D2HGDH is crucial for the utilization of d-malate as the sole carbon source for growth of A1501. We also found that the D2HGDH expression is induced by the exogenously added d-2-HG or d-malate and that a flavoprotein functions as a soluble electron carrier between D2HGDH and electron transport chains to support d-malate utilization by These results support the idea that D2HGDH evolves as an enzyme for both d-malate and d-2-HG dehydrogenation in In summary, D2HGDH from A1501 participates in both a core metabolic pathway for l-serine biosynthesis and utilization of extracellular d-malate.

Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations

“…Although D-2-HGDH exhibits also a slightly weaker binding ( K m ) with D-LAC (1.3-fold), it has a significantly low k cat for D-LAC (13.5-fold) (Supplementary Table S1 ). Similar results were also observed for P. stutzeri D-2-HGDH 39 . Consistently, SPR analyses show that D-2-HGDH has a tighter binding with D-2-HG ( K d of 149 μM) than D-MAL ( K d of 799 μM) and D-LAC ( K d of 1.62 mM) (Fig.…”

“…Previous biochemical data showed that D-2-HGDH exhibits high activity towards D-2-HG, moderate activity towards D-LAC and D-MAL, but no activity towards L-2-HG 17,38,39 . Our biochemical data show that D-2-HGDH exhibits high specific activities towards both D-2-HG (2.02 ± 0.04 μmol/min/mg) and D-MAL (2.52 ± 0.05 μmol/ min/mg), a very weak activity towards D-LAC (0.16 ± 0.01 μmol/min/mg), and a negligible activity towards L-2-HG (0.06 ± 0.01 μmol/min/mg) ( Fig.…”

Fermentative Production of l-2-Hydroxyglutarate by Engineered Corynebacterium glutamicum via Pathway Extension of l-Lysine Biosynthesis

“…To this end, the glutarate pathway described here has to be extended with enzymes for conversion of glutarate to d -2HG. These enzymes may be sourced from lysine degrading bacteria as d -2HG occurs as intermediate in some of these pathways, e.g., in E. coli (Zhao and Winkler, 1996 ) and different Pseudomonaceace (Zhang et al, 2017 ; Guo et al, 2018 ; Thompson et al, 2019 ). Future work will reveal if this approach is suitable for fermentative production of d -2HG.…”

A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR

“…Further, genetically encoded fluorescent probes based on DhdR might also be developed to detect D-2-HG in vivo . Beyond reducing 2-KG to D-2-HG, in many organisms, SerA can also reduce oxalacetate to D-malate 13 . Given the importance of L-serine in metabolism, D2HGDH in these organisms has evolved to be a versatile enzyme capable of dehydrogenating both D-malate and D-2-HG to eliminate these two metabolites 40 .…”

“…D-2-HG dehydrogenase (D2HGDH) catalyzes the conversion of D-2-HG to 2-ketoglutarate (2-KG) and is the key enzyme involved in D-2-HG catabolism 7 . D-2-HG is harmful to cells and is present at rather low levels under physiological conditions, suggesting that organisms may have evolved specific mechanisms to recognize D-2-HG accumulation and enhance D2HGDH expression to catabolize D-2-HG 10–13 . However, the regulation of D2HGDH expression is not fully understood and how organisms respond to the presence of D-2-HG has not yet been elucidated.…”