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Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development

Herbicides are commonly deployed as the front-line treatment to control infestations of weeds in native ecosystems and among crop plants in agriculture. However, the prevalence of herbicide resistance in many species is a major global challenge. The specificity and effectiveness of herbicides acting...

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Autores principales: Shah, Sarah, Lonhienne, Thierry, Murray, Cody-Ellen, Chen, Yibi, Dougan, Katherine E., Low, Yu Shang, Williams, Craig M., Schenk, Gerhard, Walter, Gimme H., Guddat, Luke W., Chan, Cheong Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9277346/
https://www.ncbi.nlm.nih.gov/pubmed/35845697
http://dx.doi.org/10.3389/fpls.2022.909073
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author Shah, Sarah
Lonhienne, Thierry
Murray, Cody-Ellen
Chen, Yibi
Dougan, Katherine E.
Low, Yu Shang
Williams, Craig M.
Schenk, Gerhard
Walter, Gimme H.
Guddat, Luke W.
Chan, Cheong Xin
author_facet Shah, Sarah
Lonhienne, Thierry
Murray, Cody-Ellen
Chen, Yibi
Dougan, Katherine E.
Low, Yu Shang
Williams, Craig M.
Schenk, Gerhard
Walter, Gimme H.
Guddat, Luke W.
Chan, Cheong Xin
author_sort Shah, Sarah
collection PubMed
description Herbicides are commonly deployed as the front-line treatment to control infestations of weeds in native ecosystems and among crop plants in agriculture. However, the prevalence of herbicide resistance in many species is a major global challenge. The specificity and effectiveness of herbicides acting on diverse weed species are tightly linked to targeted proteins. The conservation and variance at these sites among different weed species remain largely unexplored. Using novel genome data in a genome-guided approach, 12 common herbicide-target genes and their coded proteins were identified from seven species of Weeds of National Significance in Australia: Alternanthera philoxeroides (alligator weed), Lycium ferocissimum (African boxthorn), Senecio madagascariensis (fireweed), Lantana camara (lantana), Parthenium hysterophorus (parthenium), Cryptostegia grandiflora (rubber vine), and Eichhornia crassipes (water hyacinth). Gene and protein sequences targeted by the acetolactate synthase (ALS) inhibitors and glyphosate were recovered. Compared to structurally resolved homologous proteins as reference, high sequence conservation was observed at the herbicide-target sites in the ALS (target for ALS inhibitors), and in 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (target for glyphosate). Although the sequences are largely conserved in the seven phylogenetically diverse species, mutations observed in the ALS proteins of fireweed and parthenium suggest resistance of these weeds to ALS-inhibiting and other herbicides. These protein sites remain as attractive targets for the development of novel inhibitors and herbicides. This notion is reinforced by the results from the phylogenetic analysis of the 12 proteins, which reveal a largely consistent vertical inheritance in their evolutionary histories. These results demonstrate the utility of high-throughput genome sequencing to rapidly identify and characterize gene targets by computational methods, bypassing the experimental characterization of individual genes. Data generated from this study provide a useful reference for future investigations in herbicide discovery and development.
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spelling pubmed-92773462022-07-14 Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development Shah, Sarah Lonhienne, Thierry Murray, Cody-Ellen Chen, Yibi Dougan, Katherine E. Low, Yu Shang Williams, Craig M. Schenk, Gerhard Walter, Gimme H. Guddat, Luke W. Chan, Cheong Xin Front Plant Sci Plant Science Herbicides are commonly deployed as the front-line treatment to control infestations of weeds in native ecosystems and among crop plants in agriculture. However, the prevalence of herbicide resistance in many species is a major global challenge. The specificity and effectiveness of herbicides acting on diverse weed species are tightly linked to targeted proteins. The conservation and variance at these sites among different weed species remain largely unexplored. Using novel genome data in a genome-guided approach, 12 common herbicide-target genes and their coded proteins were identified from seven species of Weeds of National Significance in Australia: Alternanthera philoxeroides (alligator weed), Lycium ferocissimum (African boxthorn), Senecio madagascariensis (fireweed), Lantana camara (lantana), Parthenium hysterophorus (parthenium), Cryptostegia grandiflora (rubber vine), and Eichhornia crassipes (water hyacinth). Gene and protein sequences targeted by the acetolactate synthase (ALS) inhibitors and glyphosate were recovered. Compared to structurally resolved homologous proteins as reference, high sequence conservation was observed at the herbicide-target sites in the ALS (target for ALS inhibitors), and in 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (target for glyphosate). Although the sequences are largely conserved in the seven phylogenetically diverse species, mutations observed in the ALS proteins of fireweed and parthenium suggest resistance of these weeds to ALS-inhibiting and other herbicides. These protein sites remain as attractive targets for the development of novel inhibitors and herbicides. This notion is reinforced by the results from the phylogenetic analysis of the 12 proteins, which reveal a largely consistent vertical inheritance in their evolutionary histories. These results demonstrate the utility of high-throughput genome sequencing to rapidly identify and characterize gene targets by computational methods, bypassing the experimental characterization of individual genes. Data generated from this study provide a useful reference for future investigations in herbicide discovery and development. Frontiers Media S.A. 2022-06-29 /pmc/articles/PMC9277346/ /pubmed/35845697 http://dx.doi.org/10.3389/fpls.2022.909073 Text en Copyright © 2022 Shah, Lonhienne, Murray, Chen, Dougan, Low, Williams, Schenk, Walter, Guddat and Chan. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Shah, Sarah
Lonhienne, Thierry
Murray, Cody-Ellen
Chen, Yibi
Dougan, Katherine E.
Low, Yu Shang
Williams, Craig M.
Schenk, Gerhard
Walter, Gimme H.
Guddat, Luke W.
Chan, Cheong Xin
Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development
title Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development
title_full Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development
title_fullStr Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development
title_full_unstemmed Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development
title_short Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development
title_sort genome-guided analysis of seven weed species reveals conserved sequence and structural features of key gene targets for herbicide development
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9277346/
https://www.ncbi.nlm.nih.gov/pubmed/35845697
http://dx.doi.org/10.3389/fpls.2022.909073
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