Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase)

Abstract

Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the widespread use of glyphosate may have unsuspected impacts on the diversity and composition of microbial communities, including the human gut microbiome. Here, we introduce the first bioinformatics method to assess the potential sensitivity of organisms to glyphosate based on the type of EPSPS enzyme. We have precomputed a dataset of EPSPS sequences from thousands of species that will be an invaluable resource to advancing the research field. This novel methodology can classify sequences from >90% of eukaryotes and >80% of prokaryotes. A conservative estimate from our results shows that 54% of species in the core human gut microbiome are sensitive to glyphosate.

Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase

“…We analyzed 663 microbial genomes distributed across 32 alignable tight genomic clusters (ATGCs) 14 , with the EPSPSClass server 15 to identify changes in sensitivity to glyphosate. The algorithm classifies EPSPS proteins based on the presence and absence of amino acid markers in the active site 15…”

“…Glyphosate inhibits the shikimate pathway by inhibiting the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) 3,24 . The EPSPS class has been classified with the EPSPSClass server ( http://ppuigbo.me/programs/EPSPSClass ), which assesses the type of potential sensitivity of the EPSPS enzyme to the herbicide glyphosate 15 . PSPS enzymes can be classified as class I (alpha or beta) 25,26 , class II 27,28 , III 29 or IV 30 based on the presence of amino acid markers (class I, class II and class IV) and motifs (class III).…”

“…PSPS enzymes can be classified as class I (alpha or beta) 25,26 , class II 27,28 , III 29 or IV 30 based on the presence of amino acid markers (class I, class II and class IV) and motifs (class III). In addition, a large portion of microbial species are yet unclassified, and their potential sensitivities to glyphosate are unknown 15 . Different uses of amino acid markers distinguish the EPSPS enzymes into four classes using the reference EPSPS enzymes from Vibrio cholerae serotype O1 (vcEPSPS, class I), Coxiella burnetii (cbEPSPS, class II), Brevundimonas vesicularis (bvEPSPS, class III) and Streptomyces davawensis (sdEPSPS, class IV).…”

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

“…As the enzyme is not found in animals, the use of glyphosate is supposed to be safe for human health. Even if this is the case, the herbicide may still affect the biodiversity of free-living and host-associated microorganisms [6][7][8][9][10]. Thus, the study of the glyphosate target enzyme will provide clues about the potential effect of the herbicide.…”

“…Thus, the study of the glyphosate target enzyme will provide clues about the potential effect of the herbicide. In recent studies, we analyzed the distribution of the EPSPS protein in organisms and we estimated the differential sensitivity of organisms to the herbicide [7,8].…”