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

Mitchell G Thompson; Jacquelyn M Blake-Hedges; Jose Henrique Pereira; John A Hangasky; Michael S Belcher; William M Moore; Jesus F Barajas; Pablo Cruz-Morales; Lorenzo J Washington; Robert W Haushalter; Christopher B Eiben; Yuzhong Liu; Will Skyrud; Veronica T Benites; Tyler P Barnum; Edward E K Baidoo; Henrik V Scheller; Michael A Marletta; Patrick M Shih; Paul D Adams; Jay D Keasling

doi:10.1038/s41467-020-16815-3

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

Nat Commun. 2020 Jun 10;11(1):2931. doi: 10.1038/s41467-020-16815-3.

Authors

Mitchell G Thompson^#^{1

2

3}, Jacquelyn M Blake-Hedges^#^{1

2

4}, Jose Henrique Pereira^#^{1

5}, John A Hangasky⁴, Michael S Belcher^{1

2

3}, William M Moore^{1

2

3}, Jesus F Barajas^{1

2

6}, Pablo Cruz-Morales^{1

2}, Lorenzo J Washington^{1

2

3}, Robert W Haushalter^{1

2}, Christopher B Eiben^{1

2

7}, Yuzhong Liu^{1

2}, Will Skyrud⁴, Veronica T Benites^{1

2}, Tyler P Barnum³, Edward E K Baidoo^{1

2}, Henrik V Scheller^{1

2

3}, Michael A Marletta^{4

8}, Patrick M Shih^{1

2

9

10

11}, Paul D Adams^{1

5

7}, Jay D Keasling^{12

13

14

15

16

17}

Affiliations

¹ Joint BioEnergy Institute, Emeryville, CA, USA.
² Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³ Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA.
⁴ Department of Chemistry, University of California-Berkeley, Berkeley, CA, USA.
⁵ Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁶ Department of Energy Agile BioFoundry, Emeryville, CA, USA.
⁷ Department of Bioengineering, University of California-Berkeley, Berkeley, CA, 94720, USA.
⁸ Department of Molecular and Cellular Biology, University of California-Berkeley, Berkeley, CA, USA.
⁹ Department of Plant Biology, University of California-Davis, Davis, CA, USA.
¹⁰ Genome Center, University of California-Davis, Davis, CA, USA.
¹¹ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹² Joint BioEnergy Institute, Emeryville, CA, USA. jdkeasling@lbl.gov.
¹³ Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jdkeasling@lbl.gov.
¹⁴ Department of Bioengineering, University of California-Berkeley, Berkeley, CA, 94720, USA. jdkeasling@lbl.gov.
¹⁵ Department of Chemical and Biomolecular Engineering, University of California-Berkeley, Berkeley, CA, USA. jdkeasling@lbl.gov.
¹⁶ The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark. jdkeasling@lbl.gov.
¹⁷ Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China. jdkeasling@lbl.gov.

^# Contributed equally.

Abstract

Despite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 Å resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O₂-dependent manner. Specificity is mediated by a single arginine, highly conserved across most DUF1338 proteins. An Arabidopsis thaliana HglS homolog coexpresses with known lysine catabolism enzymes, and mutants show phenotypes consistent with disrupted lysine catabolism. Structural and biochemical analysis of Oryza sativa homolog FLO7 reveals identical activity to HglS despite low sequence identity. Our results suggest DUF1338-containing enzymes catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Arabidopsis / metabolism
Iron / metabolism*
Lysine / metabolism*
Oryza / metabolism
Oxygenases / metabolism*
Pseudomonas putida / metabolism

Substances

Iron
Oxygenases
Lysine

Abstract

Publication types

MeSH terms

Substances

Grants and funding