Molecular Binding of Cycloxydim to Acetyl-CoA Carboxylase in Cultivated Soybeans and Weed Plants

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Abstract

Acetyl-CoA carboxylase (ACC) is one of the main enzymes that play a regulatory role in the biosynthesis of fatty acids in plants. Cyclodime is one of the herbicides that is an inhibitor of this enzyme. Some weedy cereal plants, such as common hedgehog (Echinochloa crus-galli L.) and annual bluegrass (Poa annua L.), are resistant to cycloxyme. Other types of grass weeds – blood-red dewdrop (Digitaria sanguinalis (L.) Scop.) and green bristle (Setaria viridis (L.) P. Beauv.), on the contrary, are susceptible to the herbicide. The molecular mechanisms underlying ACC resistance are poorly understood. The explanation of the mechanism of resistance probably lies in the structure of ACC in different species. The use of bioinformatics methods will help to understand the mechanisms of adaptation based on the molecular properties of the enzyme, which will contribute to the creation of new herbicides. The purpose of this work was to study the specifics of the binding of cycloxydime to the ACC enzyme for each of these weed species, including soy (Glycine max (L.) Merr.). For weeds E. crus-galli and P. annua revealed from 6 to 7 possible complexes with different ligand positions relative to the receptor, which could potentially explain the mechanism of resistance. At the same time, a low binding energy was determined for the cycloxydime complex with G. max (up to –7.31 kcal/mol), which demonstrates the presence of other resistance mechanisms in the culture.

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About the authors

P. D. Timkin

Federal Scientific Center All-Russian Scientific Research Institute of Soybean

Email: penzin9898@mail.ru
Russian Federation, Ignatievskoye shosse 19, Amur region, Blagoveshchensk 675028

A. A. Ivaniy

Federal Scientific Center All-Russian Scientific Research Institute of Soybean

Email: penzin9898@mail.ru
Russian Federation, Ignatievskoye shosse 19, Amur region, Blagoveshchensk 675028

M. P. Mikhaylova

Federal Scientific Center All-Russian Scientific Research Institute of Soybean

Email: penzin9898@mail.ru
Russian Federation, Ignatievskoye shosse 19, Amur region, Blagoveshchensk 675028

U. E. Shtabnaya

Federal Scientific Center All-Russian Scientific Research Institute of Soybean

Email: penzin9898@mail.ru
Russian Federation, Ignatievskoye shosse 19, Amur region, Blagoveshchensk 675028

A. E. Gretchenko

Federal Scientific Center All-Russian Scientific Research Institute of Soybean

Email: penzin9898@mail.ru
Russian Federation, Ignatievskoye shosse 19, Amur region, Blagoveshchensk 675028

Yu. O. Serebrennikova

Federal Scientific Center All-Russian Scientific Research Institute of Soybean

Email: penzin9898@mail.ru
Russian Federation, Ignatievskoye shosse 19, Amur region, Blagoveshchensk 675028

A. A. Penzin

Federal Scientific Center All-Russian Scientific Research Institute of Soybean

Author for correspondence.
Email: penzin9898@mail.ru
Russian Federation, Ignatievskoye shosse 19, Amur region, Blagoveshchensk 675028

References

  1. Burke I.C., Bell J.L. Plant health management: Herbicides, Encyclopedia of Agriculture and Food Systems. 2014. P. 425–440. doi: 10.1016/b978-0-444-52512-3.00181-9
  2. Jursík M., Hamouzová K., Hajšlová J. Dynamics of the degradation of acetyl-CoA carboxylase herbicides in vegetables // Foods. 2021. V. 10(2). P. 405. doi: 10.3390/foods10020405
  3. Ye F. Herbicidal activity and molecular docking study of novel ACCase inhibitors // Front. Plant Sci. 2018. V. 9. doi: 10.3389/fpls.2018.01850
  4. Rosculete C. Determination of the environmental pollution potential of some herbicides by the assessment of cytotoxic and genotoxic effects on Allium cepa // Inter. J. Environ. Res. Public Health. 2018. V. 16(1). P. 75. doi: 10.3390/ijerph16010075
  5. De Prado R., Osuna M.D., Fischer A.J. Resistance to accase inhibitor herbicides in a green foxtail (Setaria viridis) biotype in Europe // Weed Sci. 2004. V. 52(4). P. 506–512. doi: 10.1614/ws-03-097r
  6. Claerhout S., Reheul D., De Cauwer B. Sensitivity of echinochloa crus-galli populations to maize herbicides: A comparison between cropping systems // Weed Res. 2015. V. 55(5). P. 470–481. doi: 10.1111/wre.12160
  7. Grichar W.J. Control of Texas panicum (Panicum texanum) and southern crabgrass (Digitaria ciliaris) in peanuts (Arachis hypogaea) with postemergence herbicides // Peanut Sci. 1991. V. 18(1). P. 6–9. doi: 10.3146/i0095-3679-18-1-3
  8. Barua R., Boutsalis P., Kleemann S., Malone J., Gill G., Preston C. Alternative herbicides for controlling herbicide-resistant annual bluegrass (Poa annua L.) in Turf // Agronomy. 2021. V. 11. P. 2148. doi: 10.3390/agronomy11112148
  9. Clay D.V., Dixon F.L., Willoughby I. Efficacy of graminicides on grass weed species of Forestry // Crop Protect. 2006. V. 25(9). P. 1039–1050. doi: 10.1016/j.cropro.2006.01.015
  10. Захарова Е.Б., Немыкин A.A. Сорные растения Амурской области и меры борьбы с ними. Изд. 2-е, испр. и доп. Благовещенск: Дальневост. ГАУ, 2015. 153 с.
  11. Ye F. Herbicidal activity and molecular docking study of novel ACCase inhibitors // Front. Plant Sci. 2018. V. 9. doi: 10.3389/fpls.2018.01850
  12. Jumper J., Evans R., Pritzel A. Highly accurate protein structure prediction with AlphaFold // Nature. 2021. V. 596. P. 583–589. doi: 10.1038/s41586-021-03819-2
  13. Mirdita M., Schütze K., Moriwaki Y., Heo L., Ovchinnikov S., Steinegger M. ColabFold: Making protein folding accessible to all // Nature Methods. 2022.
  14. Jakubec D., Škoda P., Krivák R., Novotný M., Hoksza D. PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures // Nucl. Acid. Res. 2022. № 5.
  15. Jendele L., Krivák R., Škoda P., Novotný M., Hoksza D. PrankWeb: a web server for ligand binding site prediction and visualization // Nucl. Acid. Res. 2019. № 5.
  16. Krivák R., Hoksza D. P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure // J. Cheminformat. 2018 № 10(1). P. 39.
  17. Scripps Research. AutoDock. 2014. Available from: https://ccsb.scripps.edu/autodock/
  18. O'Boyle N.M., Banck M., James C.A. et al. Open Babel: An open chemical toolbox // J. Cheminform. 2011. V. 3. P. 33. doi: 10.1186/1758-2946-3-33
  19. BIOVIA, DassaultSystèmes, [Discovery studio], [ver. 4.5]. San Diego: Dassault Systèmes, 2021.

Supplementary files

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2. Fig. 1. Visualization of ACC complexes with cycloxydim for: (a) – D. sanguinalis, (b) – E. crus-galli, (c) – G. max, (d) – P. annua, (d) – S. viridis.

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3. Fig. 2. Visualization of ACC in complex with cycloxydim for D. sanguinalis: (a) – full scale, (b) – enlargement.

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4. Fig. 3. Visualization of ACC with cycloxydim in two-dimensional projection for: (a) – D. sanguinalis, (b) – E. crus-galli, (c) – G. max, (c) – P. annua, (d) – S. viridis.

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