Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Australia
- Australian Synchrotron, ANSTO, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Australia
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, Australia
Figures
Figure 1
Lysine biosynthesis in plants.
Plants utilise the diaminopimelate (DAP) pathway, a branch of the aspartate-derived super-pathway, to synthesise l-lysine. Firstly, l-aspartate semialdehyde (ASA) and pyruvate are converted to (4S)−4…
Figure 2 with 1 supplement
Structure and sequence conservation of plant DHDPS enzymes.
(A) Cartoon structure of Arabidopsis thaliana (At) DHDPS1 (PDB: 6VVI) in the unliganded form illustrating the ‘back-to-back’ homotetramer conformation. (B) Cartoon structure of AtDHDPS1, with …
Figure 2—figure supplement 1
Sequence alignment of plant DHDPS enzymes.
Arabidopsis thaliana DHDPS1 (UNIPROT ID: Q9LZX6) and DHDPS2 (UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (UNIPROT ID: D7LRV3) and DHDPS2 (UNIPROT ID: D7LCJ3), Nicotiana tabacum DHDPS (UNIPROT ID: …
Figure 3
Structure of DHDPS inhibitors.
Chemical structures of the hit compound, (Z)−2-(5-(4-fluorobenzylidene)−2,4-dioxothiazolidin-3-yl)acetic acid (FBDTA), and two analogues, (Z)−2-(5-(2-methoxybenzylidene)−2,4-dioxothiazolidin-3-yl)ace…
Figure 4
In vitro potency of DHDPS inhibitors.
Dose responses of MBDTA-1 (● or ■) and MBDTA-2 (○ or □) against recombinant (A) AtDHDPS1 and (B) AtDHDPS2. Initial enzyme rates were normalised against a vehicle control (1% [v/v] DMSO). Normalised …
-
Figure 4—source data 1
In vitropotency of DHDPS inhibitors.
- https://cdn.elifesciences.org/articles/69444/elife-69444-fig4-data1-v2.xlsx
Figure 5 with 1 supplement
Crystal structure of AtDHDPS1 bound to MBDTA-2.
(A) Cartoon view of overall AtDHDPS1 quaternary (tetrameric) structure, illustrating the binding sites for MBDTA-2 at the centre of the tetramer. (B) Overlay of the lysine-bound (PDB: 6VVH) and …
Figure 5—figure supplement 1
Non-specific binding of MBDTA-2 between symmetry mates.
(A) Surface view of symmetry mates of MBDTA-2 bound toAtDHDPS1, highlighting chains A (blue), B (purple), C (cyan), and D (turquoise). (B) Close up of MBDTA-2 molecules bound to the surface of the …
Figure 6
Effect of compounds on the viability of human cell lines.
Toxicity of MBDTA-1 (black) and MBDTA-2 (grey), compared to the positive control defensin (white), assessed against (A) HepG2 and (B) HEK293 human cell lines using the MTT assay. Data were …
-
Figure 6—source data 1
Minimum inhibitory concentration(MIC) values for MBDTA-1 and MBDTA-2 against several bacterial strains.
- https://cdn.elifesciences.org/articles/69444/elife-69444-fig6-data1-v2.xlsx
Figure 7
Effect of MBDTA compounds on agar-grown A. thaliana.
A thaliana root lengths after treatment with increasing concentrations of either (A) MBDTA-1 or (B) MBDTA-2. Root lengths were determined using ImageJ v 1.53b and normalised against a vehicle …
-
Figure 7—source data 1
Effect of MBDTA compounds on agar-grown A. thaliana.
- https://cdn.elifesciences.org/articles/69444/elife-69444-fig7-data1-v2.xlsx
Figure 8
Pre-emergence efficacy of inhibitors on A. thaliana grown in soil.
Treatments of (A) vehicle control (1% [v/v] DMSO), (B) 300 mg·L−1 MBDTA-1, and (C) 300 mg·L−1 MBDTA-2 given at day 0 (first day under controlled environment room conditions). A representative in …
-
Figure 8—source data 1
Pre-emergence efficacy of inhibitors on A. thaliana grown in soil.
- https://cdn.elifesciences.org/articles/69444/elife-69444-fig8-data1-v2.xlsx
Tables
Table 1
Summary of MBDTA-2-bound AtDHDPS1 crystallographic data collection, processing, and refinement statistics.
| Data collection | AtDHDPS1 + MBDTA-2 |
|---|---|
| Space group | P41212 |
| Unit-cell parameters (Å) | 94.47, 94.47, 181.41 |
| Resolution (Å) | 20–2.29 (2.43–2.29) |
| No. of observations | 491,320 (74,297) |
| No. of unique reflections | 37,390 (5768) |
| Completeness (%) | 99.4 (96.6) |
| Redundancy | 13.1 (12.8) |
| Rmerge (%) | 9.9 (39.1) |
| Rmeas (%) | 10.0 (40.7) |
| CC1/2 | 99.9 (97.8) |
| Average I/σ(I) | 27.9 (7.9) |
| Refinement | |
| R (%) | 18.3 |
| Rfree (%) | 22.6 |
| No. (%) of reflections in test set | 1071 |
| No. of protein molecules per asu | 2 |
| r.m.s.d bond length (Å) | 0.007 |
| r.m.s.d bond angle (°) | 1.415 |
| Average B-factors (Å2)* | |
| Protein molecules | 44.52 |
| Ligand molecules | 60.01 |
| Water molecules | 40.33 |
| Ramachandran plot† | |
| Residues other than Gly and Pro in: | |
| Most favored regions (%) | 98.0 |
| Additionally allowed regions (%) | 2.0 |
| Disallowed regions (%) | 0.0 |
| PDB code | 7MDS |
-
Values in parentheses are for the highest-resolution shell.
*Calculated by BAVERAGE in CCP4 Suite (Winn et al., 2011).
-
†Calculated using MolProbity (Chen et al., 2010).
Table 2
Minimum inhibitory concentration (MIC) values for MBDTA-1 and MBDTA-2 against several bacterial strains.
| MBDTA-1 MIC (µg·mL−1) | MBDTA-2 MIC (µg·mL−1) | |
|---|---|---|
| Human flora | ||
| Enterococcus spp. | >128 | >128 |
| Staphylococcus aureus | >128 | >128 |
| Escherichia coli | >128 | >128 |
| Soil bacteria | ||
| Enterobacter ludwigii | >128 | >128 |
| Arthrobacter sp. | >128 | >128 |
| Enterobacter cancerogenus | >128 | >128 |
| Cedecea davisae | >128 | >128 |
| Rhodococcus erthropolis | >128 | >128 |
-
Table 2—source data 1
Minimum inhibitory concentration(MIC) values for MBDTA-1 and MBDTA-2 against several bacterial strains.
- https://cdn.elifesciences.org/articles/69444/elife-69444-table2-data1-v2.xlsx
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Arabidopsis thaliana) | DHDPS1 | TAIR | At3G60880 | |
| Gene (Arabidopsis thaliana) | DHDPS2 | TAIR | At2G45440 | |
| Cell line (Homo sapiens) | HepG2 | ATCC | ATCC: HB-8065 RRID:CVCL_0027 | |
| Cell line (Homo sapiens) | HEK293 | ATCC | ATCC:ACS-4500 RRID:CVCL_0063 |
Additional files
-
Supplementary file 1
Physicochemical properties of MBDTA-1/2.
- https://cdn.elifesciences.org/articles/69444/elife-69444-supp1-v2.docx
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/69444/elife-69444-transrepform-v2.docx
