Alterations in EPSPS enzyme active site: Changes in position and reduced interaction energy contributing to glyphosate resistance in Amaranthus hybridus

Abstract

Glyphosate-resistant weeds are widespread in agricultural regions in the world, posing significant challenges to weed management and agricultural practices. Amaranthus hybridus, a common annual weed, has been detected in Argentina with a great glyphosate-resistant level. In Brazil, this species is also a prevalent weed, with glyphosate-resistant biotypes already identified in the southern region. Understanding the resistance mechanisms in these A. hybridus biotypes is essential to define effective management strategies and preventing further spread to other locations. This study aimed to characterize the resistance mechanisms related to the site of action of the EPSPS enzyme (5-enolpyruvylshikimate-3-phosphate synthase) in glyphosate-resistant A. hybridus biotypes from southern Brazil. Using molecular analysis and protein modeling techniques we characterized the resistance mechanisms in detail. Our results confirmed the presence of the triple mutation (TAP-IVS: T102I, A103V, and P106S) in the EPSPS enzyme, alongside an increase in copy number (2), elevated expression levels of the EPSPS gene in all resistant biotypes examined and the appearance of a new silent mutation. Additionally, the resistant biotypes were found to be heterozygous, indicating a recent mutation event. Theoretical studies of the enzyme structure revealed alterations in the position and interaction energy of amino acids with glyphosate, leading to a reduced active site cavity and destabilized interactions between glyphosate and the mutant EPSPS enzyme. These findings provide a deeper understanding of the molecular basis of glyphosate resistance in A. hybridus and highlight the need for adaptive management strategies.

Keywords: Amaranthaceae; Docking; EPSPS triple mutation; Number of EPSPS copies.