Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate
Abstract
:1. Introduction
2. Results
2.1. Analysis of Resistance to Glyphosate
2.2. EPSPS Kinetics Associated with Specific Mutations
2.3. Fitness Traits of E. indica with Different EPSPS Mutations
2.4. Metabolite Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Whole-Plant Assay
4.2. Shikimate Accumulation Assays
4.3. Sequencing and Expression of EPSPS
4.4. EPSPS Protein Expression and Purification
4.5. Biotinylation for EPSPS with Different Mutations
4.6. Kinetic Characterisation Assay
4.7. Fitness Traits Assay without Competition
4.8. Metabolite Analysis
4.9. Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Steinrücken, H.; Amrhein, N. The herbicide glyphosate is a potent inhibitor of 5-enolpyruvylshikimic acid-3-phosphate synthase. Biochem. Biophys. Res. Commun. 1980, 94, 1207–1212. [Google Scholar] [CrossRef] [PubMed]
- Duke, S.O.; Powles, S.B. Glyphosate: A once-in-a-century herbicide. Pest Manag. Sci. 2008, 64, 319–325. [Google Scholar] [CrossRef] [PubMed]
- The International Survey of Herbicide Resistant Weeds. Available online: www.weedscience.org (accessed on 18 November 2022).
- Baek, Y.; Bobadilla, L.K.; Giacomini, D.A.; Montgomery, J.S.; Murphy, B.P.; Tranel, P.J. Evolution of glyphosate-resistant weeds. Rev. Environ. Contam. Toxicol. 2021, 255, 93–128. [Google Scholar] [PubMed]
- Sammons, R.D.; Gaines, T.A. Glyphosate resistance: State of knowledge. Pest Manag. Sci. 2014, 70, 1367–1377. [Google Scholar] [CrossRef] [PubMed]
- Beres, Z.T.; Giese, L.A.; Mackey, D.M.; Owen, M.D.; Page, E.R.; Snow, A.A. Target-site EPSPS Pro-106-Ser mutation in Conyza canadensis biotypes with extreme resistance to glyphosate in Ohio and Iowa, USA. Sci. Rep. 2020, 10, 7577. [Google Scholar] [CrossRef]
- Yanniccari, M.; Vázquez-García, J.G.; Gigón, R.; Palma-Bautista, C.; Vila-Aiub, M.; De Prado, R. A novel EPSPS Pro-106-His mutation confers the first case of glyphosate resistance in Digitaria sanguinalis. Pest Manag. Sci. 2022, 78, 3135–3143. [Google Scholar] [CrossRef]
- Healy-Fried, M.L.; Funke, T.; Priestman, M.A.; Han, H.; Schönbrunn, E. Structural basis of glyphosate tolerance resulting from mutations of Pro101 in Escherichia coli 5-enolpyruvylshikimate-3-phosphate synthase. J. Biol. Chem. 2007, 282, 32949–32955. [Google Scholar] [CrossRef]
- Funke, T.; Yang, Y.; Han, H.; Healy-Fried, M.; Olesen, S.; Becker, A.; Schönbrunn, E. Structural Basis of Glyphosate Resistance Resulting from the Double Mutation Thr97→ Ile and Pro101→ Ser in 5-Enolpyruvylshikimate-3-phosphate Synthase from Escherichia coli. J. Biol. Chem. 2009, 284, 9854–9860. [Google Scholar] [CrossRef]
- Sammons, R.D.; You, J.; Qi, Y.; Flasinski, S.; Kavanaugh, C.; Washam, J.; Ostrander, E.; Wang, D.; Heck, G. Evaluation of glyphosate resistance in Arabidopsis thaliana expressing an altered target site EPSPS. Pest Manag. Sci. 2018, 74, 1174–1183. [Google Scholar] [CrossRef]
- Vila-Aiub, M.M.; Yu, Q.; Powles, S.B. Do plants pay a fitness cost to be resistant to glyphosate? New Phytol. 2019, 223, 532–547. [Google Scholar] [CrossRef]
- Fernández-Moreno, P.T.; Alcántara-de la Cruz, R.; Smeda, R.J.; De Prado, R. Differential resistance mechanisms to glyphosate result in fitness cost for Lolium perenne and L. multiflorum. Front. Plant Sci. 2017, 8, 1796. [Google Scholar] [CrossRef]
- Han, H.; Vila-Aiub, M.M.; Jalaludin, A.; Yu, Q.; Powles, S.B. A double EPSPS gene mutation endowing glyphosate resistance shows a remarkably high resistance cost. Plant Cell Environ. 2017, 40, 3031–3042. [Google Scholar] [CrossRef]
- Holm, L.G.; Plucknett, D.L.; Pancho, J.V.; Herberger, J.P. The World’s Worst Weeds: Distribution and Biology; University Press of Hawaii: Honolulu, HI, USA, 1977; pp. 47–53. [Google Scholar]
- Ma, X.; Wu, H.; Jiang, W.; Ma, Y. Goosegrass (Eleusine indica) density effects on cotton (Gossypium hirsutum). J. Integr. Agr. 2015, 14, 1778–1785. [Google Scholar] [CrossRef]
- Song, W.; Qi, N.; Liang, C.; Duan, F.; Zhao, H.H. First report of the southern root-knot nematode meloidogyne incognita on goosegrass (Eleusine indica) in China. Plant Dis. 2019, 103, 1045. [Google Scholar] [CrossRef]
- Baerson, S.R.; Rodriguez, D.J.; Tran, M.; Feng, Y.; Biest, N.A.; Dill, G.M. Glyphosate-resistant goosegrass. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase. Plant Physiol. 2002, 129, 1265–1275. [Google Scholar] [CrossRef]
- Chen, J.; Huang, H.; Wei, S.; Cui, H.; Li, X.; Zhang, C. Glyphosate resistance in Eleusine indica: EPSPS overexpression and P106A mutation evolved in the same individuals. Pestic. Biochem. Phys. 2020, 164, 203–208. [Google Scholar] [CrossRef]
- Franci, J.; Lam, K.W.; Chuah, T.S.; San Cha, T. Genetic diversity and in silico evidence of target-site mutation in the EPSPS gene in endowing glyphosate resistance in Eleusine indica (L.) from Malaysia. Pestic. Biochem. Phys. 2020, 165, 104556. [Google Scholar] [CrossRef]
- Yu, Q.; Jalaludin, A.; Han, H.; Chen, M.; Sammons, R.D.; Powles, S.B. Evolution of a double amino acid substitution in the EPSP synthase in Eleusine indica conferring high level glyphosate resistance. Plant Physiol. 2015, 167, 1440–1447. [Google Scholar] [CrossRef]
- Chen, J.; Huang, H.; Zhang, C.; Wei, S.; Huang, Z.; Chen, J.; Wang, X. Mutations and amplification of EPSPS gene confer resistance to glyphosate in goosegrass (Eleusine indica). Planta 2015, 242, 859–868. [Google Scholar] [CrossRef]
- Morran, S.; Moretti, M.L.; Brunharo, C.A.; Fischer, A.J.; Hanson, B.D. Multiple target site resistance to glyphosate in junglerice (Echinochloa colona) lines from California orchards. Pest Manag. Sci. 2018, 74, 2747–2753. [Google Scholar] [CrossRef]
- Malik, J.; Barry, G.; Kishore, G. The herbicide glyphosate. BioFactors 1989, 2, 17–25. [Google Scholar] [PubMed]
- Boocock, M.R.; Coggins, J.R. Kinetics of 5-enolpyruvylshikimate-3-phosphate synthase inhibition by glyphosate. FEBS Lett. 1983, 154, 127–133. [Google Scholar] [CrossRef] [PubMed]
- Funke, T.; Han, H.; Healy-Fried, M.L.; Fischer, M.; Schönbrunn, E. Molecular basis for the herbicide resistance of Roundup Ready crops. Proc. Natl. Acad. Sci. USA 2006, 103, 13010–13015. [Google Scholar] [CrossRef] [PubMed]
- Zhou, M.; Xu, H.; Wei, X.; Ye, Z.; Wei, L.; Gong, W.; Wang, Y.; Zhu, Z. Identification of a glyphosate-resistant mutant of rice 5-enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol. 2006, 140, 184–195. [Google Scholar] [CrossRef]
- Dong, Y.; Ng, E.; Lu, J.; Fenwick, T.; Tao, Y.; Bertain, S.; Sandoval, M.; Bermudez, E.; Hou, Z.; Patten, P. Desensitizing plant EPSP synthase to glyphosate: Optimized global sequence context accommodates a glycine-to-alanine change in the active site. J. Biol. Chem. 2019, 294, 716–725. [Google Scholar] [CrossRef]
- Li, J.; Peng, Q.; Han, H.; Nyporko, A.; Kulynych, T.; Yu, Q.; Powles, S. Glyphosate resistance in Tridax procumbens via a novel EPSPS Thr-102-Ser substitution. J. Agr. Food Chem. 2018, 66, 7880–7888. [Google Scholar] [CrossRef]
- Weaver, L.M.; Herrmann, K.M. Dynamics of the shikimate pathway in plants. Trends Plant Sci. 1997, 2, 346–351. [Google Scholar] [CrossRef]
- Orcaray, L.; Igal, M.; Marino, D.; Zabalza, A.; Royuela, M. The possible role of quinate in the mode of action of glyphosate and acetolactate synthase inhibitors. Pest Manag. Sci. 2010, 66, 262–269. [Google Scholar] [CrossRef]
- Li, Z.; Li, X.; Cui, H.; Zhao, G.; Zhai, D.; Chen, J. Vegetative and fecundity fitness benefit found in a glyphosate-resistant Eleusine indica population caused by 5-enolpyruvylshikimate-3-phosphate synthase overexpression. Front. Plant Sci. 2021, 12, 776990. [Google Scholar] [CrossRef]
- Ren, Y.; Miao, M.; Meng, Y.; Cao, J.; Fan, T.; Yue, J.; Xiao, F.; Liu, Y.; Cao, S. DFR1-mediated inhibition of proline degradation pathway regulates drought and freezing tolerance in Arabidopsis. Cell Rep. 2018, 23, 3960–3974. [Google Scholar] [CrossRef]
- Chen, J.; Huang, H.; Wei, S.; Zhang, C.; Huang, Z. Characterization of glyphosate-resistant goosegrass (Eleusine indica) populations in China. J. Integr. Agr. 2015, 14, 919–925. [Google Scholar] [CrossRef]
- Chen, J.; Wei, S.; Huang, H.; Cui, H.; Zhang, C.; Li, X. Characterization of glyphosate and quizalofop-p-ethyl multiple resistance in Eleusine indica. Pestic. Biochem. Phys. 2021, 176, 104862. [Google Scholar] [CrossRef]
- Chen, J.; Huang, Z.; Huang, H.; Wei, S.; Yan, L.; Jiang, C.; Jie, Z.; Zhang, C. Selection of relatively exact reference genes for gene expression studies in goosegrass (Eleusine indica) under herbicide stress. Sci. Rep. 2017, 7, 46494. [Google Scholar] [CrossRef]
- Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25, 402–408. [Google Scholar] [CrossRef]
- Kumar, S.; Sharife, H.; Kreisel, T.; Mogilevsky, M.; Bar-Lev, L.; Grunewald, M.; Aizenshtein, E.; Karni, R.; Paldor, I.; Shlomi, T. Intra-tumoral metabolic zonation and resultant phenotypic diversification are dictated by blood vessel proximity. Cell Metab. 2019, 30, 201–211.e6. [Google Scholar] [CrossRef]
- Abdiche, Y.; Malashock, D.; Pinkerton, A.; Pons, J. Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet. Anal. Biochem. 2008, 377, 209–217. [Google Scholar] [CrossRef]
- Ghanizadeh, H.; Harrington, K.C. Fitness costs associated with multiple resistance to dicamba and atrazine in Chenopodium album. Planta 2019, 249, 787–797. [Google Scholar] [CrossRef]
- Matzrafi, M.; Gerson, O.; Rubin, B.; Peleg, Z. Different mutations endowing resistance to Acetyl-CoA Carboxylase inhibitors results in changes in ecological fitness of Lolium rigidum populations. Front. Plant Sci. 2017, 8, 1078. [Google Scholar] [CrossRef]
- Li, L.-X.; Liu, W.-Q.; Liao, Y.; Liu, Z.-Y.; Chen, Y.-R.; Luo, L.-M.; Chen, H.; Peng, Y.-M.; Zeng, Y.-Q.; Wu, Q.-N.; et al. Integrated analysis of microRNAs and metabolomics in rat’s serum reveals multi-action modes of qingfei paidu decoction for COVID-19 Treatment. Res. Sq. 2021; preprint. [Google Scholar] [CrossRef]
- Wen, B.; Mei, Z.; Zeng, C.; Liu, S. metaX: A flexible and comprehensive software for processing metabolomics data. BMC Bioinform. 2017, 18, 183. [Google Scholar] [CrossRef]
- Seefeldt, S.S.; Fuerst, E.P. Log-logistic analysis of herbicide dose-response relationships. Weed Technol. 1995, 9, 218–227. [Google Scholar] [CrossRef]
- Ritz, C.; Pipper, C.B.; Streibig, J.C. Analysis of germination data from agricultural experiments. Eur. J. Agron. 2013, 45, 1–6. [Google Scholar] [CrossRef]
Genotype | EPSPS Vmax | Km (PEP) | Kon (M−1 S−1) 1 | Koff (S−1) 2 | KD (M) 3 | ||||
---|---|---|---|---|---|---|---|---|---|
Glyphosate | PEP | Glyphosate | PEP | Glyphosate | PEP | Ratio | |||
Wild type | 1.6 | 24.6 | 417.6 | 8.0 | 2.4 × 10−2 | 2.5 × 10−2 | 5.8 × 10−5 | 3.1 × 10−3 | 53.8 |
(0.1) | (5.0) | (9.0) | (0.3) | (2.0 × 10−4) | (3.6 × 10−4) | (1.3 × 10−6) | (1.1 × 10−4) | ||
Pro106Ser | 1.5 | 18.2 | 1264.0 | 31.8 | 3.2 × 10−2 | 3.8 × 10−2 | 2.5 × 10−5 | 1.2 × 10−3 | 46.9 |
(0.1) | (2.8) | (31.1) | (0.7) | (4.2 × 10−4) | (4.8 × 10−4) | (7.1 × 10−7) | (3.0 × 10−5) | ||
Pro106Leu | 1.41 | 59.2 (13.8) | 1254.0 | 31.3 | 3.5 × 10−2 | 3.5 × 10−2 | 2.8 × 10−5 | 1.1 × 10−3 | 39.9 |
(0.1) | (30.3) | (0.7) | (4.6 × 10−4) | (4.3 × 10−4) | (7.2 × 10−7) | (2.8 × 10−5) | |||
Thr102Ile + Pro106Ser | 0.4 | 100.8 (18.1) | 1647.0 | 32.95 | 3.7 × 10−2 | 6.5 × 10−2 | 2.3 × 10−5 | 2.0 × 10−3 | 87.5 |
(0.3 × 10−1) | (52.8) | (1.3) | (6.7 × 10−4) | (1.5× 10−3) | (8.3 × 10−7) | (8.9× 10−5) |
Repeat | Population | Dry Weight (mg Plant−1) | Leaf Area (cm2 Plant−1) | ||||
---|---|---|---|---|---|---|---|
20 d | 40 d | 60 d | 20 d | 40 d | 60 d | ||
Experiment 1 | WT | 0.48 a * | 1.55 a | 3.28 a | 98.75 a | 263.63 a | 314.38 a |
LL | 0.32 b | 1.46 b | 2.37 bc | 64.60 b | 245.98 b | 250.29 b | |
SS | 0.27 b | 1.25 b | 2.67 b | 61.55 b | 233.66 b | 289.62 ab | |
IISS | 0.12 c | 0.84 b | 2.00 c | 28.80 c | 159.58 b | 256.83 b | |
Experiment 2 | WT | 0.08 a | 0.47 a | 1.92 a | 25.22 a | 130.44 a | 167.78 a |
LL | 0.03 c | 0.36 b | 1.65 a | 13.93 b | 92.78 c | 111.63 b | |
SS | 0.05 b | 0.42 ab | 1.72 a | 26.08 a | 109.17 b | 116.38 b | |
IISS | 0.03 c | 0.22 c | 1.32 b | 15.09 b | 62.85 d | 90.88 c |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Chen, J.; Cui, H.; Li, Z.; Yu, H.; Hou, Q.; Li, X. Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate. Int. J. Mol. Sci. 2023, 24, 8250. https://doi.org/10.3390/ijms24098250
Chen J, Cui H, Li Z, Yu H, Hou Q, Li X. Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate. International Journal of Molecular Sciences. 2023; 24(9):8250. https://doi.org/10.3390/ijms24098250
Chicago/Turabian StyleChen, Jingchao, Hailan Cui, Zhiling Li, Haiyan Yu, Qiang Hou, and Xiangju Li. 2023. "Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate" International Journal of Molecular Sciences 24, no. 9: 8250. https://doi.org/10.3390/ijms24098250