The Glyphosate Target Enzyme 5-Enolpyruvyl Shikimate 3-Phosphate Synthase (EPSPS) Contains Several EPSPS-Associated Domains in Fungi

Tall, Tuomas; Puigbò, Pere

doi:10.3390/iecge-07146

Cited by 6 publications

(3 citation statements)

References 20 publications

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“…A survey of bacteria in the human gut microbiome showed that around 30% of them were unclassified (i.e., EPSPS proteins from these species do not belong to any of the known classes), and additional studies are needed to identify other EPSPS classes. Also, it should be noticed that the EPSPS protein sequence in bacteria and plants is unidomain, whereas fungal EPSPS proteins contain several domains 59 . Thus, a protein folding in fungi may lead to a different response of the EPSPS enzyme to glyphosate.…”

Section: Discussionmentioning

confidence: 99%

Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes

Mathew¹,

Muola²,

Saikkonen³

et al. 2022

JoVE

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Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. The target of glyphosate is the enzyme 5-enolpyruvylshikimate-3phosphate synthase (EPSPS) in the shikimate pathway, which is virtually universal in plants. The inhibition of the enzyme stops the production of three essential amino acids: phenylalanine, tyrosine, and tryptophan. EPSPS is also present in fungi and prokaryotes, such as archaea and bacteria; thus, the use of GBP may have an impact on the microbiome composition of soils, plants, herbivores, and secondary consumers. This article aims to present general guidelines to assess the effect of GBP on microbiomes from field experiments to bioinformatics analyses and provide a few testable hypotheses. Two field experiments are presented to test the GBP on non-target organisms. First, plant-associated microbes from 10 replicated control and GBP treatment plots simulating no-till cropping are sampled and analyzed. In the second experiment, samples from experimental plots fertilized by either poultry manure containing glyphosate residues or non-treated control manure were obtained.Bioinformatics analysis of EPSPS protein sequences is utilized to determine the potential sensitivity of microbes to glyphosate. The first step in estimating the effect of GBP on microbiomes is to determine their potential sensitivity to the target enzyme (EPSPS). Microbial sequences can be obtained either from public repositories or by means of PCR amplification. However, in the majority of field studies, microbiome composition has been determined based on universal DNA markers such as the 16S rRNA and the internal transcribed spacer (ITS). In these cases, sensitivity to glyphosate can only be estimated through a probabilistic analysis of EPSPS sequences using closely related species. The quantification of the potential sensitivity of organisms to glyphosate, based on the EPSPS enzyme, provides a robust approach for further experiments to study target and non-target resistant mechanisms.

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Section: Discussionmentioning

confidence: 99%

Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes

Mathew¹,

Muola²,

Saikkonen³

et al. 2022

JoVE

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“… Domains: domain names; Freq: frequency of the domain in the subset of proteins with more than one domain; Sp: number of species in the pfam database (on May 2022) with at least one copy of the domain; D: number of domain architectures in pfam database (on May 2022); and Function: description of the product. This table has been modified with permission by authors from [ 26 ]. …”

Section: Figurementioning

confidence: 99%

Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate

Tall

Puigbò

2022

BioTech

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The 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize the three aromatic amino acids in fungi, plants, and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain family, the EPSP synthase (PF00275) domain, whereas in fungi, the protein is formed by a multi-domain structure from combinations of 22 EPSPS-associated domains. The most common multi-domain EPSPS structure in fungi involves five EPSPS-associated domains of the shikimate pathway. In this article, we analyze 390 EPSPS proteins of fungi to determine the extent of the EPSPS-associated domains. Based on the current classification of the EPSPS protein, most fungal species are intrinsically sensitive to glyphosate. However, complex domain architectures may have multiple responses to the herbicide. Further empirical studies are needed to determine the effect of glyphosate on fungi, taking into account the diversity of multi-domain architectures of the EPSPS. This research opens the door to novel biotechnological applications for microbial degradation of glyphosate.

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“…Glyphosate (Monsanto, Belgium) is the world's most widely used non-selective systemic 1 herbicide used to control weeds or suppress cover crops (Woodburn 2000;Duke 2021). It kills plants by inhibiting the 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase), a key enzyme in the shikimate biosynthetic pathway (Tzin et al 2012;Helander et al 2012;Tall and Puigbò 2020). Over 30% of the C fixed by the plants passes through this pathway (Shaner 2006;Tzin et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Glyphosate affects the sporulation dynamics of Rhizophagus species more severely than mechanical defoliation or the contact herbicide diquat

Bastogne,

Buysens,

Schtickzelle

et al. 2024

Preprint

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Arbuscular mycorrhizal fungi (AMF) are totally dependent on a suitable host plant for their carbon resources. Here, we investigated under in vitro conditions, the impact of defoliation practices, i.e. mechanical defoliation or chemical defoliation with a contact (Reglone®, containing the active ingredient diquat) or systemic (RoundUp®, containing the active ingredient glyphosate) herbicide, on the dynamics of spore production of Rhizophagus irregularis and Rhizophagus intraradices associated to Solanum tuberosum and/or Medicago truncatula. Glyphosate affected the spore production rate more rapidly and severely than diquat or mechanical defoliation. We hypothesize that this effect was related to the disruption of the C metabolism in the whole plant combined with a possible direct effect of glyphosate on the fungus within the roots and/or in the soil via the release of this active ingredient from decaying roots. No glyphosate could be detected in the roots due to technical constraints, while its release from the roots in the medium corresponded to 0.11% of the active ingredient applied to the leaves. The three defoliation practices strongly affected root colonization, compared to the non-defoliated plants. However, the amount of glyphosate released into the medium did not affect spore germination and germ tube growth. These results suggest that the effects of defoliation on the dynamics of spore production are mainly indirect via an impact on the plant, and that the effect is faster and more marked with the glyphosate-formulation, possibly via a direct effect on the fungus in the roots and more hypothetically on spore germination in the environment.

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The Glyphosate Target Enzyme 5-Enolpyruvyl Shikimate 3-Phosphate Synthase (EPSPS) Contains Several EPSPS-Associated Domains in Fungi

Cited by 6 publications

References 20 publications

Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes

Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes

Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate

Glyphosate affects the sporulation dynamics of Rhizophagus species more severely than mechanical defoliation or the contact herbicide diquat

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