Disorders in dinitroaniline site opening as the factor, predetermining herbicide resistance of wild carrot

  • O. H. Melnyk Institute of Food Biotechnology and Genomics of Natl. Acad. Sci. of Ukraine, Ukraine, 04123, Kyiv, Baida Vyshnevetsky str., 2/А1; Educational and Scientific Center “Institute of Biology and Medicine”, Ukraine, 01601, Kyiv, Volodymyrska str., 64/13 https://orcid.org/0000-0002-4249-9175
  • P. A. Karpov Institute of Food Biotechnology and Genomics, Natl. Acad. Sci. Ukraine, Ukraine, 04123, Kyiv, Baidy-Vyshnevetskoho str., 2А https://orcid.org/0000-0002-6876-642X
DOI: https://doi.org/10.7124/FEEO.v36.1725
Keywords: α-tubulin, dinitroaniline, resistance, oryzalin, herbicides, binding site volume

Abstract

Aim. To investigate the structural basis of carrot's natural resistance to dinitroaniline herbicides based on analysis of binding site volume and sequence variations in α-tubulin isotypes. Methods. AI-assisted molecular modeling (Protenix, based on AlphaFold3) for protein-ligand complexes reconstruction. Binding site volume and shape analysis applying CavitOmiX. Bioinformatics comparisons including sequence alignment (ClustalX), phylogenetic analysis (MEGA11) and 3D-visualization (PyMOL, Discovery Studio). Results. Structural and computational analysis of 8 α-tubulin isotypes from Daucus carota L. revealed significant structural and functional heterogeneity in dinitroaniline-binding regions (DBR). The binding site analysis, using Protenix demonstrated variability among carrot α-tubulin isotypes. Although TBA1, TBA5 and TBA8 showed a partially shaped binding pockets of reduced volume, the remaining isotypes (TBA2-TBA4, TBA6-TBA7) revealed its complete disruption. It suggests mechanism where some isotypes retain reduced binding potential, while others completely lack of it. Conclusions. In the frame of studies of the native resistance of carrot plants to dinitroaniline herbicides, current study indicates critical collapse in binding site pocket formation. Considering the ligand-induced nature of the dinitroaniline binding site, the disruption of the site pocket formation mechanism may be one of the main reasons for such natural resistance, making interaction with the ligand initially impossible.

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