Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i>
In <i>E. coli</i> and <i>P. ananatis</i>, L-serine biosynthesis is initiated by the action of D-3-phosphoglycerate dehydrogenase (SerA), which converts D-3-phosphoglycerate into 3-phosphohydroxypyruvate. SerA can concomitantly catalyze the production of D-2-hydroxyglutarate (...
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MDPI AG
2022-08-01
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| Series: | Microorganisms |
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| author | Victor V. Samsonov Anna A. Kuznetsova Julia G. Rostova Svetlana A. Samsonova Mikhail K. Ziyatdinov Michael Y. Kiriukhin |
| author_facet | Victor V. Samsonov Anna A. Kuznetsova Julia G. Rostova Svetlana A. Samsonova Mikhail K. Ziyatdinov Michael Y. Kiriukhin |
| author_sort | Victor V. Samsonov |
| collection | DOAJ |
| description | In <i>E. coli</i> and <i>P. ananatis</i>, L-serine biosynthesis is initiated by the action of D-3-phosphoglycerate dehydrogenase (SerA), which converts D-3-phosphoglycerate into 3-phosphohydroxypyruvate. SerA can concomitantly catalyze the production of D-2-hydroxyglutarate (D-2-HGA) from 2-ketoglutarate by oxidizing NADH to NAD<sup>+</sup>. Several bacterial D-2-hydroxyglutarate dehydrogenases (D2HGDHs) have recently been identified, which convert D-2-HGA back to 2-ketoglutarate. However, knowledge about the enzymes that can metabolize D-2-HGA is lacking in bacteria belonging to the <i>Enterobacteriaceae</i> family. We found that <i>ydiJ</i> encodes novel D2HGDHs in <i>P. ananatis</i> and <i>E. coli</i>, which were assigned as D2HGDH<i>Pa</i> and D2HGDH<i>Ec</i>, respectively. Inactivation of <i>ydiJ</i> in <i>P. ananatis</i> and <i>E. coli</i> led to the significant accumulation of D-2-HGA. Recombinant D2HGDH<i>Ec</i> and D2HGDH<i>Pa</i> were purified to homogeneity and characterized. D2HGDH<i>Ec</i> and D2HGDH<i>Pa</i> are homotetrameric with a subunit molecular mass of 110 kDa. The pH optimum was 7.5 for D2HGDH<i>Pa</i> and 8.0 for D2HGDH<i>Ec</i>. The Km for D-2-HGA was 208 μM for D2HGDHPa and 83 μM for D2HGDH<i>Ec</i>. The enzymes have strict substrate specificity towards D-2-HGA and displayed maximal activity at 45 °C. Their activity was completely inhibited by 0.5 mM Mn<sup>2+</sup>, Ni<sup>2+</sup> or Co<sup>2+</sup>. The discovery of a novel family of D2HGDHs may provide fundamental information for the metabolic engineering of microbial chassis with desired properties. |
| first_indexed | 2024-03-09T23:05:35Z |
| format | Article |
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| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T23:05:35Z |
| publishDate | 2022-08-01 |
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| spelling | doaj.art-122cf707edfd44fe969e1ceff12668f12023-11-23T17:52:53ZengMDPI AGMicroorganisms2076-26072022-08-01109176610.3390/microorganisms10091766Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i>Victor V. Samsonov0Anna A. Kuznetsova1Julia G. Rostova2Svetlana A. Samsonova3Mikhail K. Ziyatdinov4Michael Y. Kiriukhin5Ajinomoto-Genetika Research Institute, 117545 Moscow, RussiaAjinomoto-Genetika Research Institute, 117545 Moscow, RussiaAjinomoto-Genetika Research Institute, 117545 Moscow, RussiaAjinomoto-Genetika Research Institute, 117545 Moscow, RussiaAjinomoto-Genetika Research Institute, 117545 Moscow, RussiaAjinomoto-Genetika Research Institute, 117545 Moscow, RussiaIn <i>E. coli</i> and <i>P. ananatis</i>, L-serine biosynthesis is initiated by the action of D-3-phosphoglycerate dehydrogenase (SerA), which converts D-3-phosphoglycerate into 3-phosphohydroxypyruvate. SerA can concomitantly catalyze the production of D-2-hydroxyglutarate (D-2-HGA) from 2-ketoglutarate by oxidizing NADH to NAD<sup>+</sup>. Several bacterial D-2-hydroxyglutarate dehydrogenases (D2HGDHs) have recently been identified, which convert D-2-HGA back to 2-ketoglutarate. However, knowledge about the enzymes that can metabolize D-2-HGA is lacking in bacteria belonging to the <i>Enterobacteriaceae</i> family. We found that <i>ydiJ</i> encodes novel D2HGDHs in <i>P. ananatis</i> and <i>E. coli</i>, which were assigned as D2HGDH<i>Pa</i> and D2HGDH<i>Ec</i>, respectively. Inactivation of <i>ydiJ</i> in <i>P. ananatis</i> and <i>E. coli</i> led to the significant accumulation of D-2-HGA. Recombinant D2HGDH<i>Ec</i> and D2HGDH<i>Pa</i> were purified to homogeneity and characterized. D2HGDH<i>Ec</i> and D2HGDH<i>Pa</i> are homotetrameric with a subunit molecular mass of 110 kDa. The pH optimum was 7.5 for D2HGDH<i>Pa</i> and 8.0 for D2HGDH<i>Ec</i>. The Km for D-2-HGA was 208 μM for D2HGDHPa and 83 μM for D2HGDH<i>Ec</i>. The enzymes have strict substrate specificity towards D-2-HGA and displayed maximal activity at 45 °C. Their activity was completely inhibited by 0.5 mM Mn<sup>2+</sup>, Ni<sup>2+</sup> or Co<sup>2+</sup>. The discovery of a novel family of D2HGDHs may provide fundamental information for the metabolic engineering of microbial chassis with desired properties.https://www.mdpi.com/2076-2607/10/9/1766L-serine biosynthesisD-3-phosphoglycerate dehydrogenaseD-2-hydroxyglutaric acidD-2-hydroxyglutarate dehydrogenase |
| spellingShingle | Victor V. Samsonov Anna A. Kuznetsova Julia G. Rostova Svetlana A. Samsonova Mikhail K. Ziyatdinov Michael Y. Kiriukhin Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i> Microorganisms L-serine biosynthesis D-3-phosphoglycerate dehydrogenase D-2-hydroxyglutaric acid D-2-hydroxyglutarate dehydrogenase |
| title | Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i> |
| title_full | Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i> |
| title_fullStr | Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i> |
| title_full_unstemmed | Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i> |
| title_short | Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in <i>Escherichia coli</i> and <i>Pantoea ananatis</i> Encoded by <i>ydiJ</i> |
| title_sort | revealing a new family of d 2 hydroxyglutarate dehydrogenases in i escherichia coli i and i pantoea ananatis i encoded by i ydij i |
| topic | L-serine biosynthesis D-3-phosphoglycerate dehydrogenase D-2-hydroxyglutaric acid D-2-hydroxyglutarate dehydrogenase |
| url | https://www.mdpi.com/2076-2607/10/9/1766 |
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