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Yin F, Wang Z, Jiang M, Liao M, Cao H, Zhao N. Two Cytochrome P450s, CYP709B1 and CYP704C1, Play Essential Roles in Metabolism-Based Multiple Herbicide Resistance in American Sloughgrass ( Beckmannia syzigachne (Steud.) Fernald). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38861684 DOI: 10.1021/acs.jafc.4c02674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
This study confirmed a field population of American sloughgrass (Beckmannia syzigachne (Steud.) Fernald) that developed simultaneously high levels of resistance (resistance index >10) to three divergent modes of action herbicides: fenoxaprop-P-ethyl, mesosulfuron-methyl, and isoproturon. The resistance phenotype observed in this population was not attributed to target-site alterations; rather, the resistant plants exhibited a significant increase in the activity of cytochrome P450s (P450s) and enhanced metabolism rates for all three herbicides. RNA sequencing revealed significant upregulation of two P450s, CYP709B1 and CYP704C1, in the resistant plants both before and after herbicide treatments. Molecular docking predicted that the homology models of these P450s should exhibit a binding affinity for a range of herbicides. The heterologous expression of the identified P450s in yeast cells indicated improved growth in the presence of all three of the aforementioned herbicides. Collectively, the increased expression of CYP709B1 and CYP704C1 likely contributed to the P450s-mediated enhanced metabolism, thereby conferring multiple herbicide resistance in B. syzigachne.
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Affiliation(s)
- Fan Yin
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agri-Products Quality and Biosafety, Anhui Agricultural University, Ministry of Education, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Zilu Wang
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agri-Products Quality and Biosafety, Anhui Agricultural University, Ministry of Education, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Minghao Jiang
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agri-Products Quality and Biosafety, Anhui Agricultural University, Ministry of Education, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Min Liao
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agri-Products Quality and Biosafety, Anhui Agricultural University, Ministry of Education, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Haiqun Cao
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agri-Products Quality and Biosafety, Anhui Agricultural University, Ministry of Education, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Ning Zhao
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agri-Products Quality and Biosafety, Anhui Agricultural University, Ministry of Education, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
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Yamaguchi T, Asano Y. Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review. J Biotechnol 2024; 384:20-28. [PMID: 38395363 DOI: 10.1016/j.jbiotec.2024.02.007] [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: 12/24/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.
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Affiliation(s)
- Takuya Yamaguchi
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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Bobadilla LK, Tranel PJ. Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance. PEST MANAGEMENT SCIENCE 2024; 80:235-244. [PMID: 37595061 DOI: 10.1002/ps.7728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023]
Abstract
The emergence of herbicide-resistant weeds is a significant threat to modern agriculture. Cross resistance, a phenomenon where resistance to one herbicide confers resistance to another, is a particular concern owing to its unpredictability. Nontarget-site (NTS) cross resistance is especially challenging to predict, as it arises from genes that encode enzymes that do not directly involve the herbicide target site and can affect multiple herbicides. Recent advancements in genomic and structural biology techniques could provide new venues for predicting NTS resistance in weed species. In this review, we present an overview of the latest approaches that could be used. We discuss the use of genomic and epigenomics techniques such as ATAC-seq and DAP-seq to identify transcription factors and cis-regulatory elements associated with resistance traits. Enzyme/protein structure prediction and docking analysis are discussed as an initial step for predicting herbicide binding affinities with key enzymes to identify candidates for subsequent in vitro validation. We also provide example analyses that can be deployed toward elucidating cross resistance and its regulatory patterns. Ultimately, our review provides important insights into the latest scientific advancements and potential directions for predicting and managing herbicide cross resistance in weeds. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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Iwakami S, Ishizawa H, Sugiura K, Kashiwagi K, Oga T, Niwayama S, Uchino A. Syntenic analysis of ACCase loci and target-site-resistance mutations in cyhalofop-butyl resistant Echinochloa crus-galli var. crus-galli in Japan. PEST MANAGEMENT SCIENCE 2024; 80:627-636. [PMID: 37743410 DOI: 10.1002/ps.7789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/07/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Recently, suspected cyhalofop-butyl-resistant populations of allohexaploid weed Echinochloa crus-galli var. crus-galli were discovered in rice fields in Aichi Prefecture, Japan. Analyzing the target-site ACCase genes of cyhalofop-butyl helps understand the resistance mechanism. However, in E. crus-galli, the presence of multiple ACCase genes and the lack of detailed gene investigations have complicated the analysis of target-site genes. Therefore, in this study, we characterized the herbicide response of E. crus-galli lines and thoroughly characterized the ACCase genes, including the evaluation of gene mutations in the ACCase genes of each line. RESULT Four suspected resistant lines collected from Aichi Prefecture showed varying degrees of resistance to cyhalofop-butyl and other FOP-class ACCase inhibitors but were sensitive to herbicides with other modes of action. Through genomic analysis, six ACCase loci were identified in the E. crus-galli genome. We renamed each gene based on its syntenic relationship with other ACCase genes in the Poaceae species. RNA-sequencing analysis revealed that all ACCase genes, except the pseudogenized copy ACCase2A, were transcribed at a similar level in the shoots of E. crus-galli. Mutations known to confer resistance to FOP-class herbicides, that is W1999C, W2027C/S and I2041N, were found in all resistant lines in either ACCase1A, ACCase1B or ACCase2C. CONCLUSION In this study, we found that the E. crus-galli lines were resistant exclusively to ACCase-inhibiting herbicides, with a target-site resistance mutation in the ACCase gene. Characterization of ACCase loci in E. crus-galli provides a basis for further research on ACCase herbicide resistance in Echinochloa spp. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Satoshi Iwakami
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Kyoto, Japan
| | - Hinata Ishizawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Kyoto, Japan
| | - Kai Sugiura
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Kyoto, Japan
| | | | - Toshiya Oga
- Aichi Agricultural Research Center, Nagakute, Japan
| | | | - Akira Uchino
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsu, Japan
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Sato MP, Iwakami S, Fukunishi K, Sugiura K, Yasuda K, Isobe S, Shirasawa K. Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon. DNA Res 2023; 30:dsad023. [PMID: 37943179 PMCID: PMC10634394 DOI: 10.1093/dnares/dsad023] [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: 08/24/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023] Open
Abstract
Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.
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Affiliation(s)
- Mitsuhiko P Sato
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Satoshi Iwakami
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kanade Fukunishi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kai Sugiura
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kentaro Yasuda
- Agri-Innovation Education and Research Center, Akita Prefectural University, Akita 010-0451, Japan
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
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