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Reed KB, Kim W, Lu H, Larue CT, Guo S, Brooks SM, Montez MR, Wagner JW, Zhang YJ, Alper HS. Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system. Proc Natl Acad Sci U S A 2024; 121:e2317027121. [PMID: 39159366 PMCID: PMC11363307 DOI: 10.1073/pnas.2317027121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 07/13/2024] [Indexed: 08/21/2024] Open
Abstract
The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) functions in the shikimate pathway which is responsible for the production of aromatic amino acids and precursors of other essential secondary metabolites in all plant species. EPSPS is also the molecular target of the herbicide glyphosate. While some plant EPSPS variants have been characterized with reduced glyphosate sensitivity and have been used in biotechnology, the glyphosate insensitivity typically comes with a cost to catalytic efficiency. Thus, there exists a need to generate additional EPSPS variants that maintain both high catalytic efficiency and high glyphosate tolerance. Here, we create a synthetic yeast system to rapidly study and evolve heterologous EPSP synthases for these dual traits. Using known EPSPS variants, we first validate that our synthetic yeast system is capable of recapitulating growth characteristics observed in plants grown in varying levels of glyphosate. Next, we demonstrate that variants from mutagenesis libraries with distinct phenotypic traits can be isolated depending on the selection criteria applied. By applying strong dual-trait selection pressure, we identify a notable EPSPS mutant after just a single round of evolution that displays robust glyphosate tolerance (Ki of nearly 1 mM) and improved enzymatic efficiency over the starting point (~2.5 fold). Finally, we show the crystal structure of corn EPSPS and the top resulting mutants and demonstrate that certain mutants have the potential to outperform previously reported glyphosate-resistant EPSPS mutants, such as T102I and P106S (denoted as TIPS), in whole-plant testing. Altogether, this platform helps explore the trade-off between glyphosate resistance and enzymatic efficiency.
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Affiliation(s)
- Kevin B. Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Wantae Kim
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Hongyuan Lu
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | | | - Shirley Guo
- Crop Science Division, Bayer, Chesterfield, MO63017
| | - Sierra M. Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Michael R. Montez
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - James W. Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Y. Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX78712
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX78712
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Bharti J, Verma R, Gupta I, Chakraborty P, Eashwaran M, Sony SK, Nehra M, Thangraj A, Kaul R, Fathy K, Kaul T. Functional characterization of novel mutations in the conserved region of EPSPS for herbicide resistance in pigeonpea: structure-based coherent design. J Biomol Struct Dyn 2024; 42:6065-6080. [PMID: 37652402 DOI: 10.1080/07391102.2023.2243522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/21/2023] [Indexed: 09/02/2023]
Abstract
Prospectively, agroecosystems for the growth of crops provide the potential fertile, productive, and tropical environment which attracts infestation by weedy plant species that compete with the primary crop plants. Infestation by weed is a major biotic stress factor faced by pigeonpea that hampers the productivity of the crop. In the modern era with the development of chemicals the problem of weed infestation is dealt with armours called herbicides. The most widely utilized, post-emergent, broad-spectrum herbicide has an essential active ingredient called glyphosate. Glyphosate mechanistically inhibits a chloroplastic enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) by competitively interacting with the PEP binding site which hinders the shikimate pathway and the production of essential aromatic amino acids (Phe, Tyr, Trp) and other secondary metabolites in plants. Moreover, herbicide spray for weed management is lethal to both the primary crop and the weeds. Therefore, it is critical to develop herbicide-resistant crops for field purposes to reduce the associated yield and economic losses. In this study, the in-silico analysis drove the selection and validation of the point mutations in the conserved region of the EPSPS gene, which confers efficient herbicide resistance to mutated-CcEPSPS enzyme along with the retention of the normal enzyme function. An optimized in-silico validation of the target mutation before the development of the genome-edited resistant plant lines is a prerequisite for testing their efficacy as a proof of concept. We validated the combination of GATIPS mutation for its no-cost effect at the enzyme level via molecular dynamic (MD) simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jyotsna Bharti
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Rachana Verma
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Isha Gupta
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Puja Chakraborty
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Murugesh Eashwaran
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sonia Khan Sony
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Mamta Nehra
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Arulprakash Thangraj
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Rashmi Kaul
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Khaled Fathy
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Tanushri Kaul
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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A Highly Glyphosate-Resistant EPSPS Mutant from Laboratory Evolution. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
EPSP synthase is the target enzyme of glyphosate herbicides. Due to the extensive use of glyphosate, it is very important to obtain EPSPS genes with high glyphosate resistance for the development of transgenic crops. GR79-EPSPS is a class I EPSP synthase with certain glyphosate resistance isolated from glyphosate-contaminated soil. After more than 1000 generations, a Y40I substitution was identified, and the enzyme had a nearly 1.8-fold decrease in Km [PEP] and a 1.7-fold increase in Ki[glyphosate] compared to the wild-type enzyme. Enzyme dynamics and molecular dynamics analysis showed that the substitution was near the hinge region of EPSPS, and the affinity of glyphosate binding to amino acid residues of the active site decreased due to Y40I substitution, resulting in an increase in glyphosate resistance. These results provide more evidence for the combination of directed evolution and rational design of protein engineering.
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