Abstract

Weeds are becoming increasingly resistant to our current herbicides, posing a significant threat to agricultural production. Therefore, new herbicides with novel modes of action are urgently needed. In this study, we exploited a novel herbicide target, dihydrodipicolinate synthase (DHDPS), which catalyses the first and rate-limiting step in lysine biosynthesis. The first class of plant DHDPS inhibitors with micromolar potency against Arabidopsis thaliana DHDPS were identified using a high throughput chemical screen. We determined that this class of inhibitors binds to a novel and unexplored pocket within DHDPS, which is highly conserved across plant species. The inhibitors also attenuated the germination and growth of A. thaliana seedlings and confirmed their pre-emergence herbicidal activity in soil-grown plants. These results provide proof-of-concept that lysine biosynthesis represents a promising target for the development of herbicides with a novel mode of action to tackle the global rise of herbicide resistant weeds.

Data availability

Diffraction data have been deposited in PDB under the accession code 7MDS. The validation report has been uploaded as a 'Related Manuscript File'.Other data sets have been uploaded as 'Source Data' files.

Article and author information

Author details

  1. Tatiana P Soares da Costa

    La Trobe University, Melbourne, Australia
    For correspondence
    t.soaresdacosta@latrobe.edu.au
    Competing interests
    Tatiana P Soares da Costa, is listed as an inventor on a patent pertaining to inhibitors described in the manuscript. Patent Title: Heterocyclic inhibitors of lysine biosynthesis via the diaminopimelate pathway; International patent (PCT) No.: WO2018187845A1; Granted: 18/10/2018..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6275-7485
  2. Cody J Hall

    La Trobe University, Melbourne, Australia
    Competing interests
    No competing interests declared.
  3. Santosh Panjikar

    MX, Australian Synchrotron, Monash University, Melbourne, Australia
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7429-3879
  4. Jessica A Wyllie

    La Trobe University, Melbourne, Australia
    Competing interests
    No competing interests declared.
  5. Rebecca M Christoff

    La Trobe University, Melbourne, Australia
    Competing interests
    No competing interests declared.
  6. Saadi Bayat

    La Trobe University, Melbourne, Australia
    Competing interests
    No competing interests declared.
  7. Mark D Hulett

    La Trobe University, Melbourne, Australia
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2072-5968
  8. Belinda M Abbott

    La Trobe University, Melbourne, Australia
    Competing interests
    Belinda M Abbott, is listed as an inventor on a patent pertaining to inhibitors described in the manuscript. Patent Title: Heterocyclic inhibitors of lysine biosynthesis via the diaminopimelate pathway; International patent (PCT) No.: WO2018187845A1; Granted: 18/10/2018..
  9. Anthony R Gendall

    La Trobe University, Melbourne, Australia
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2255-3939
  10. Matthew A Perugini

    La Trobe University, Melbourne, Australia
    For correspondence
    Matt.Perugini@gmail.com
    Competing interests
    Matthew A Perugini, is listed as an inventor on a patent pertaining to inhibitors described in the manuscript. Patent Title: Heterocyclic inhibitors of lysine biosynthesis via the diaminopimelate pathway; International patent (PCT) No.: WO2018187845A1; Granted: 18/10/2018..

Funding

National Health and Medical Research Council (APP1091976)

  • Tatiana P Soares da Costa

Australian Research Council (DE190100806)

  • Tatiana P Soares da Costa

Australian Research Council (DP150103313)

  • Santosh Panjikar
  • Matthew A Perugini

Australian Research Council Research Hub for Medicinal Agriculture (IH180100006)

  • Anthony R Gendall

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, Soares da Costa et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,770
    views
  • 464
    downloads
  • 17
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Tatiana P Soares da Costa
  2. Cody J Hall
  3. Santosh Panjikar
  4. Jessica A Wyllie
  5. Rebecca M Christoff
  6. Saadi Bayat
  7. Mark D Hulett
  8. Belinda M Abbott
  9. Anthony R Gendall
  10. Matthew A Perugini
(2021)
Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
eLife 10:e69444.
https://doi.org/10.7554/eLife.69444

Share this article

https://doi.org/10.7554/eLife.69444

Further reading

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology
    A Sofia F Oliveira, Fiona L Kearns ... Adrian J Mulholland
    Short Report

    The spike protein is essential to the SARS-CoV-2 virus life cycle, facilitating virus entry and mediating viral-host membrane fusion. The spike contains a fatty acid (FA) binding site between every two neighbouring receptor-binding domains. This site is coupled to key regions in the protein, but the impact of glycans on these allosteric effects has not been investigated. Using dynamical nonequilibrium molecular dynamics (D-NEMD) simulations, we explore the allosteric effects of the FA site in the fully glycosylated spike of the SARS-CoV-2 ancestral variant. Our results identify the allosteric networks connecting the FA site to functionally important regions in the protein, including the receptor-binding motif, an antigenic supersite in the N-terminal domain, the fusion peptide region, and another allosteric site known to bind heme and biliverdin. The networks identified here highlight the complexity of the allosteric modulation in this protein and reveal a striking and unexpected link between different allosteric sites. Comparison of the FA site connections from D-NEMD in the glycosylated and non-glycosylated spike revealed that glycans do not qualitatively change the internal allosteric pathways but can facilitate the transmission of the structural changes within and between subunits.

    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics
    Conor J Howard, Nathan S Abell ... Nathan B Lubock
    Research Article

    Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands of sequence changes to a protein target in a single experiment. Because of its utility in interpreting both human variant effects and protein structure-function relationships, it holds substantial promise to improve drug discovery and clinical development. However, applications in this domain require improved experimental and analytical methods. To address this need, we report novel DMS methods to precisely and quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, and assess predicted response to drug treatment. Using these methods, we performed a DMS of the melanocortin-4 receptor (MC4R), a G-protein-coupled receptor (GPCR) implicated in obesity and an active target of drug development efforts. We assessed the effects of >6600 single amino acid substitutions on MC4R’s function across 18 distinct experimental conditions, resulting in >20 million unique measurements. From this, we identified variants that have unique effects on MC4R-mediated Gαs- and Gαq-signaling pathways, which could be used to design drugs that selectively bias MC4R’s activity. We also identified pathogenic variants that are likely amenable to a corrector therapy. Finally, we functionally characterized structural relationships that distinguish the binding of peptide versus small molecule ligands, which could guide compound optimization. Collectively, these results demonstrate that DMS is a powerful method to empower drug discovery and development.