Serine hydroxymethyl transferase is a binding target of caprylic acid: Uncovering a novel molecular target for a herbicide and for producing caprylic acid-tolerant crops
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Curated by eLife
eLife assessment
This study presents a valuable contribution towards understanding the protein target and mechanism of action of an herbicide, which could be applied to the development of herbicide-based technologies to improve crop yields. Evidence is gathered using a variety of technical approaches that enrich and support the findings, but the methodology and the presentation of the results are incomplete.
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- Plant Biology (eLife)
Abstract
Identification of new binding targets is essential for the development of herbicides and phytotoxin-tolerant crops. Caprylic acid (CAP) is a safe and non-selective bio-herbicide in uncultivated areas. However, the herbicidal action of CAP remains unclear. Herein, metabolomic and proteomic profiling indicated that a serine hydroxymethyl transferase in Conyza canadensis ( Cc SHMT1) is a promising candidate binding targeted for CAP. The protein abundance and activity of Cc SHMT1 were decreased in a time- and dosage-dependent manners after CAP treatment. CAP competes with phenyl-serine at the binding sites, decreasing the enzymatic activity of Cc SHMT1. Overexpression of CcSHMT1, AtSHMT1 and OsSHMT1 in Arabidopsis or rice endowed plants with high tolerance to CAP treatment, whereas the knockout of osshmt1 led to death of plants under normal atmospheric conditions. Furthermore, T194A, T194A/ M195V and D209N Osshmt1 mutant plants derived from base editing exhibited tolerance to CAP. CAP bound to Cc SHMT1 with high affinity, and Ala191 in the key domains of N-terminus was identified to be critical for the binding site of CAP. Collectively, our findings demonstrate that Cc SHMT1 is a binding target for herbicidal activity of CAP. This study marks a key step in the druggability of SHMT inhibitors and represents an attractive target for phytotoxin-tolerant crops.
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eLife assessment
This study presents a valuable contribution towards understanding the protein target and mechanism of action of an herbicide, which could be applied to the development of herbicide-based technologies to improve crop yields. Evidence is gathered using a variety of technical approaches that enrich and support the findings, but the methodology and the presentation of the results are incomplete.
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Reviewer #1 (Public Review):
Caprylic acid (CAP), i.e., octanoic acid, is a saturated fatty acid. CAP is commonly used as a food contact surface sanitizer. In mammals, caprylic acid is related to hunger sensation (i.e., food consumption). serine hydroxymethyl transferase (SHMT) has been previously known as a potential herbicidal target. The present study involves a huge amount of work. The results are useful and contribute well to the literature. The data does support the conclusion. It does not seem that SHMT is the only target of CAP though (CAP may act on other proteins as well). A major deficiency of this manuscript is that there are many unclear, inaccurate, or unconcise descriptions.
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Reviewer #2 (Public Review):
Summary:
Li et al. investigated the mechanism of action of an important herbicide, caprylic acid (CAP). The authors used untargeted metabolomics to find out differently expressed metabolites (DEM). It led to the identification of metabolites involved in amino acid metabolism, carbon fixation, carbon, glyoxylate, and dicarboxylate metabolism. Using previously published proteomics data and the newly conducted metabolomics data, the authors identified a serine hydroxymethyl transferase in Conyza canadensis (CcSHMT1) to be a likely candidate for CAP inhibition.
The authors conducted a series of in vitro and in vivo tests to elucidate the effect of CAP on SHMT1 inhibition. Plants overexpressing SHMT1 were used to analyze the effect of SHMT1 expression, activity, and inhibition, among others. Purified SHMT1 was …
Reviewer #2 (Public Review):
Summary:
Li et al. investigated the mechanism of action of an important herbicide, caprylic acid (CAP). The authors used untargeted metabolomics to find out differently expressed metabolites (DEM). It led to the identification of metabolites involved in amino acid metabolism, carbon fixation, carbon, glyoxylate, and dicarboxylate metabolism. Using previously published proteomics data and the newly conducted metabolomics data, the authors identified a serine hydroxymethyl transferase in Conyza canadensis (CcSHMT1) to be a likely candidate for CAP inhibition.
The authors conducted a series of in vitro and in vivo tests to elucidate the effect of CAP on SHMT1 inhibition. Plants overexpressing SHMT1 were used to analyze the effect of SHMT1 expression, activity, and inhibition, among others. Purified SHMT1 was used to elucidate enzyme kinetics in the presence or absence of inhibitors. CRISPR-based editing was a powerful method of investigating the effect of SHMT1 mutants on CAP application and complements the overexpression and in vitro studies. Finally, computational docking of CAP on SHMT1 was conducted to identify key interacting residues. The results are overall consistent with one another and present a unified framework for CAP activity as an herbicide. Unexpected variations in SHMT1 expression and activity levels upon CAP treatment suggest complex biological compensatory mechanisms in response to SHMT1 deficiency. Further studies are needed to understand the effect of these perturbations that will be required to successfully develop and deploy CAP-resistant crops for widespread use in agriculture. In conclusion, the authors did a commendable job of elucidating SHMT1 as a biologically relevant target for CAP.
Strengths:
- Combines computational docking, enzyme kinetics using purified proteins, and several different model plant species and two different methods of testing (overexpression and base editing) to establish plant response and survival.
- Sound experimental designs and the presence of controls validate the results and provide additional confidence in the authors' conclusions.
Weaknesses:
- Relied too heavily on the study of plants overexpressing SHMT1, which do not have native gene regulation, and this might limit the generalizability of their conclusions.
-The authors did not leverage computational docking analysis to validate or seek corroboration of the performance of plant alleles obtained from the base editing experiments.
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Reviewer #3 (Public Review):
Summary:
Li et al investigated the initial target of the herbicidal caprilic acid (CAP). Using a combination of proteomic and metabolomic approaches, they generated a list of candidate targets for CAP and identified a Serine hydroxymethyl transferase (SHMT) as the best candidate.
CAP application to Conyza canadensis induces an early and brief increase in SHMT1 protein and transcript. Studies with purified recombinant CcSHMT1 indicate that enzymatic activity is inhibited by CAP. The authors suggest a kinetic mechanism of CAP inhibition but more data should be collected to reach a firm conclusion on this point.
Transgenic Arabidopsis and rice plants expressing CcSHMT1 show increased tolerance to CAP, as measured by biomass reduction 7 days after treatment with CAP. Similar results were obtained with …
Reviewer #3 (Public Review):
Summary:
Li et al investigated the initial target of the herbicidal caprilic acid (CAP). Using a combination of proteomic and metabolomic approaches, they generated a list of candidate targets for CAP and identified a Serine hydroxymethyl transferase (SHMT) as the best candidate.
CAP application to Conyza canadensis induces an early and brief increase in SHMT1 protein and transcript. Studies with purified recombinant CcSHMT1 indicate that enzymatic activity is inhibited by CAP. The authors suggest a kinetic mechanism of CAP inhibition but more data should be collected to reach a firm conclusion on this point.
Transgenic Arabidopsis and rice plants expressing CcSHMT1 show increased tolerance to CAP, as measured by biomass reduction 7 days after treatment with CAP. Similar results were obtained with Arabidopsis and rice plants overexpressing AtSHMT2 and OsSHMT1, respectively. OsSHMT1 single and double mutant rice plants showed increased tolerance to CAP. These results strongly link CAP tolerance to the level of SHMT, which can be manipulated by transgenesis, and suggest that engineered SHMT can also lead to higher CAP tolerance.
Finally, structural analysis allowed the identification of three residues close to the active site involved in the binding of CAP. Arabidopsis plants containing AtSHMT2 modified in these three residues are more sensitive to CAP.
Strengths:
The work of Li et al. includes a large number of assays using different methodologies. The evidence suggests that SHMT inhibition by CAP is effective in inhibiting plant growth. In addition, new technologies that manipulate SHMT levels or activity may improve crop yield by controlling weeds. Structural analysis can be the starting point for the design of more complex molecules that exceed the herbicidal activity of CAP.
Weaknesses:
The methods are rather incomplete, lacking many details necessary to fully understand the author's reasoning. It is not possible to reproduce the experiments on the basis of the information provided.
Although the conclusions are generally well supported, the results are presented in an incorrect or confusing manner. In the comparison of wild-type and transgenic plants, the control condition is missing in some experiments (Figures 4A and 5A). In some plots, the scales are not logical, making them difficult to interpret and fit into an equation (Figures 4B, 4C, 4E, 5E, 6E, 6F).
A final concern is the finding that some point mutations in the SHMT1 gene lead to more tolerant plants (Figures 6D, 6E, 6F). The authors could then explain whether this means that resistance to CAP could be easily acquired by weeds.
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