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Yan Y, Chen Y, Hu H, Jiang Y, Kang Z, Wu J. Discovery of a New Class of Lipophilic Pyrimidine-Biphenyl Herbicides Using an Integrated Experimental-Computational Approach. Molecules 2024; 29:2409. [PMID: 38893290 PMCID: PMC11173721 DOI: 10.3390/molecules29112409] [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: 04/22/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Herbicides are useful tools for managing weeds and promoting food production and sustainable agriculture. In this study, we report on the development of a novel class of lipophilic pyrimidine-biphenyl (PMB) herbicides. Firstly, three PMBs, Ia, IIa, and IIIa, were rationally designed via a scaffold hopping strategy and were determined to inhibit acetohydroxyacid synthase (AHAS). Computational simulation was carried out to investigate the molecular basis for the efficiency of PMBs against AHAS. With a rational binding mode, and the highest in vitro as well as in vivo potency, Ia was identified as a preferable hit. Furthermore, these integrated analyses guided the design of eighteen new PMBs, which were synthesized via a one-step Suzuki-Miyaura cross-coupling reaction. These new PMBs, Iba-ic, were more effective in post-emergence control of grass weeds compared with Ia. Interestingly, six of the PMBs displayed 98-100% inhibition in the control of grass weeds at 750 g ai/ha. Remarkably, Ica exhibited ≥ 80% control against grass weeds at 187.5 g ai/ha. Overall, our comprehensive and systematic investigation revealed that a structurally distinct class of lipophilic PMB herbicides, which pair excellent herbicidal activities with new interactions with AHAS, represent a noteworthy development in the pursuit of sustainable weed control solutions.
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Affiliation(s)
- Yitao Yan
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yinglu Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Hanxian Hu
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Youwei Jiang
- Hangzhou Jingyinkang Biological Technology Co., Ltd., Hangzhou 311110, China
| | | | - Jun Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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2
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Tian T, Song D, Zhang L, Huang H, Li Y. Facile and selective recognition of sulfonylurea pesticides based on the multienzyme-like activities enhancement of nanozymes combining sensor array. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133847. [PMID: 38422731 DOI: 10.1016/j.jhazmat.2024.133847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
Traditional identification methods based on cholinesterase inhibition are limited to recognizing organic phosphorus and carbamate esters, and their response to sulfonylurea pesticides is weak. Residual sulfonylurea pesticides can pose a threat to human health. So, it is very important to develop an effective, rapid and portable method for sulfonylurea pesticides detection. Herein, we first found that sulfonylurea pesticides have activity-enhancing effects on copper-based nanozymes, and then combined them with the array technology to construct a six-channel sensing array method for selectively identifying sulfonylurea pesticides and detecting total concentration of sulfonylurea pesticides (the limit of detection was 0.03 µg/mL). This method has good selectivity towards sulfonylurea pesticides. In addition, a smartphone-based colorimetric paper sensor analysis method was developed to achieve the on-site detection of the total concentration of sulfonylurea pesticides. And this array can also be used for individual differentiation (1-100 µg/mL). Our work not only investigates the specific responses of copper-based nanozymes to sulfonylurea pesticides, but also develops a simple method that contributes to directly detect sulfonylurea pesticides at the source of pollution, providing insights for further research on sulfonylurea pesticides detection and filling the gap in pesticide residue studies.
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Affiliation(s)
- Tian Tian
- College of Food Science and Engineering, Jilin University, Changchun 130025, PR China
| | - Donghui Song
- College of Food Science and Engineering, Jilin University, Changchun 130025, PR China
| | - Ling Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130025, PR China
| | - Hui Huang
- College of Food Science and Engineering, Jilin University, Changchun 130025, PR China
| | - Yongxin Li
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Water Environment, College of New Energy and Environment, Jilin University, Changchun 130021, PR China.
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3
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Wang HL, Sun HP, Zheng PR, Cheng RT, Liu ZW, Yuan H, Gao WY, Li H. Re-investigation of in vitro activity of acetohydroxyacid synthase I holoenzyme from Escherichia coli. Arch Biochem Biophys 2024; 754:109962. [PMID: 38499055 DOI: 10.1016/j.abb.2024.109962] [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: 02/14/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Acetohydroxyacid synthase (AHAS) is one of the key enzymes of the biosynthesis of branched-chain amino acids, it is also an effective target for the screening of herbicides and antibiotics. In this study we present a method for preparing Escherichia coli AHAS I holoenzyme (EcAHAS I) with exceptional stability, which provides a solid ground for us to re-investigate the in vitro catalytic properties of the protein. The results show EcAHAS I synthesized in this way exhibits similar function to Bacillus subtilis acetolactate synthase in its catalysis with pyruvate and 2-ketobutyrate (2-KB) as dual-substrate, producing four 2-hydroxy-3-ketoacids including (S)-2-acetolactate, (S)-2-aceto-2-hydroxybutyrate, (S)-2-propionyllactate, and (S)-2-propionyl-2-hydroxybutyrate. Quantification of the reaction indicates that the two substrates almost totally consume, and compound (S)-2-aceto-2- hydroxybutyrate forms in the highest yield among the four major products. Moreover, the protein also condenses two molecules of 2-KB to furnish (S)-2-propionyl-2-hydroxybutyrate. Further exploration manifests that EcAHAS I ligates pyruvate/2-KB and nitrosobenzene to generate two arylhydroxamic acids N-hydroxy-N-phenylacetamide and N-hydroxy-N-phenyl- propionamide. These findings enhance our comprehension of the catalytic characteristics of EcAHAS I. Furthermore, the application of this enzyme as a catalyst in construction of C-N bonds displays promising potential.
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Affiliation(s)
- Hai-Ling Wang
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Hui-Peng Sun
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Pei-Rong Zheng
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Rui-Tong Cheng
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Zhi-Wen Liu
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Heng Yuan
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Heng Li
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
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Flores F, Stapp LS, van Dam J, Fisher R, Kaserzon S, Negri AP. Toxicity of herbicides to the marine microalgae Tisochrysis lutea and Tetraselmis sp. Sci Rep 2024; 14:1727. [PMID: 38242962 PMCID: PMC10798944 DOI: 10.1038/s41598-024-51401-3] [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: 01/04/2024] [Indexed: 01/21/2024] Open
Abstract
Pesticides are ubiquitous in the catchments of the Great Barrier Reef (GBR) and regularly discharge into the nearshore waters. Effective management of pesticides requires suitable water quality guideline values (WQGVs), and further ecotoxicological data for many pesticides are needed to improve the reliability of environmental risk assessments. To help address this issue, toxicity thresholds were determined to two species of tropical marine microalgae Tisochrysis lutea and Tetraselmis sp. for a suite of herbicides detected in the GBR. Photosystem II (PSII) herbicides significantly reduced growth with no effect concentration (NEC) and 10% effect concentration (EC10) values spanning two orders of magnitude from 0.60 µg L-1 for diuron to 60 µg L-1 for simazine across both species. However, growth was insensitive to the non-PSII herbicides. The NEC/EC10 thresholds for most herbicide-microalgae combinations were greater than recent WQGVs intended to protect 99% of species (PC99); however, metribuzin was toxic to T. lutea at concentrations lower than the current PC99 value, which may have to be revisited. The toxicity thresholds for alternative herbicides derived here further inform the development of national and GBR-specific WQGVs, but more toxicity data is needed to develop WQGVs for the > 50 additional pesticides detected in catchments of the GBR.
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Affiliation(s)
- Florita Flores
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, Townsville, QLD, 4810, Australia.
- AIMS@JCU Division of Research and Innovation, Townsville, QLD, 4810, Australia.
| | - Laura S Stapp
- Australian Institute of Marine Science, Casuarina, NT, 0811, Australia
| | - Joost van Dam
- Australian Institute of Marine Science, Casuarina, NT, 0811, Australia
| | - Rebecca Fisher
- Indian Ocean Marine Research Centre, Australian Institute of Marine Science, University of Western Australia, Crawley, WA, 6009, Australia
| | - Sarit Kaserzon
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, Townsville, QLD, 4810, Australia
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Zhao K, Tang H, Zhang B, Zou S, Liu Z, Zheng Y. Microbial production of vitamin B5: current status and prospects. Crit Rev Biotechnol 2023; 43:1172-1192. [PMID: 36210178 DOI: 10.1080/07388551.2022.2104690] [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: 11/21/2021] [Accepted: 07/01/2022] [Indexed: 11/03/2022]
Abstract
Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.
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Affiliation(s)
- Kuo Zhao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Heng Tang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Shuping Zou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Zhiqiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
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Guan Y, Cao S, Zou Y, Liu L, Yang C, Ji M. Enhanced metabolic ability enabled wild panicgrass (Panicum miliaceum L. var. ruderale kit.) resistance to ALS inhibitor herbicide. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 194:105510. [PMID: 37532326 DOI: 10.1016/j.pestbp.2023.105510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023]
Abstract
Wild panicgrass (Panicum miliaceum L. var. ruderale kit.) is an annual grass weed that primarily occurs in maize fields. Nicosulfuron is a widely used selective herbicide that effectively controls gramineous weeds in maize fields. However, owing to its long-term and extensive application, the control of P. miliaceum has been substantially reduced. The objective of this study was to determine the resistance pattern to ALS inhibitors in P. miliaceum and investigate the underlying resistance mechanisms. These are important for guiding the prevention and eradication of resistant weeds. Whole plant bioassays showed P. miliaceum had evolved high levels of resistance to nicosulfuron and multiple resistance to atrazine and mesotrione. The ALS gene sequence results indicated the absence of mutations in the resistant population. Additionally, there was no significant difference found in the inhibition rate of the ALS enzyme activity (I50) between the resistant and sensitive populations. Following the application of malathion the resistant P. miliaceum population became more sensitive to nicosulfuron. At 96 h after application of nicosulfuron, glutathione-S-transferase activity in the resistant population was significantly higher than that in the susceptible population. The study reveals that the main cause of resistance to ALS inhibitor herbicide in P. miliaceum is likely increased metabolism of herbicides. These findings may assist in devising effective strategies for preventing and eliminating resistant P. miliaceum.
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Affiliation(s)
- Yidi Guan
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang City 110866, People's Republic of China
| | - Shihan Cao
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang City 110866, People's Republic of China
| | - Yize Zou
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang City 110866, People's Republic of China
| | - Liru Liu
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang City 110866, People's Republic of China
| | - Changbi Yang
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang City 110866, People's Republic of China
| | - Mingshan Ji
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang City 110866, People's Republic of China.
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Ustun R, Chalmers G, Tehrani D, Uzun B. Computational molecular explanation of Soybean AHAS resistance from P197S mutation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107782. [PMID: 37315349 DOI: 10.1016/j.plaphy.2023.107782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
The first enzyme in the pathway involving branched-chain amino is acetohydroxyacid synthase (AHAS, E.C. 2.2.1.6), which is inhibited by five commercial herbicide families. In this work a computational study of a point mutation of Proline-197-Serine of the Soybean AHAS enzyme, which was obtained by mutagenesis, explains the latter's S197 resistance to the commonly used Chlorsulfuron. Using protein-ligand docking and large-scale sampling and distributions from AlphaFold-generated the resistant and susceptible soybean AHAS protein structure. The computational approach here is scaled to screen for mutation probabilities of protein binding sites, similar to screening compounds for potential hits in therapeutic design using the docking software. P197 and S197 AHAS structures were found to be different even if only one amino acid was changed. The non-specific distribution of bindings in the S197 cavity after the P197S change has been rigorously calculated by RMSD analysis that it would require x20 more concentrations to fill the P197 site by the same amount. There is no previously performed detailed chlorsulfuron soybean P197S AHAS binding calculation. In the herbicide site of AHAS, several amino acids interact - a computational study could elucidate the optimal choice of point mutations for herbicidal resistance either individually or collectively by mutations one at a time and analyzing the effects with a set of herbicides individually. With a computational approach, enzymes involved in crop research and development could be analyzed more quickly, enabling faster discovery and development of herbicides.
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Affiliation(s)
- Rustem Ustun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye.
| | - Gordon Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Daniel Tehrani
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
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Bown L, Hirota R, Goettge MN, Cui J, Krist DT, Zhu L, Giurgiu C, van der Donk WA, Ju KS, Metcalf WW. A Novel Pathway for Biosynthesis of the Herbicidal Phosphonate Natural Product Phosphonothrixin Is Widespread in Actinobacteria. J Bacteriol 2023; 205:e0048522. [PMID: 37074199 PMCID: PMC10210982 DOI: 10.1128/jb.00485-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
Phosphonothrixin is an herbicidal phosphonate natural product with an unusual, branched carbon skeleton. Bioinformatic analyses of the ftx gene cluster, which is responsible for synthesis of the compound, suggest that early steps of the biosynthetic pathway, up to production of the intermediate 2,3-dihydroxypropylphosphonic acid (DHPPA) are identical to those of the unrelated phosphonate natural product valinophos. This conclusion was strongly supported by the observation of biosynthetic intermediates from the shared pathway in spent media from two phosphonothrixin producing strains. Biochemical characterization of ftx-encoded proteins confirmed these early steps, as well as subsequent steps involving the oxidation of DHPPA to 3-hydroxy-2-oxopropylphosphonate and its conversion to phosphonothrixin by the combined action of an unusual heterodimeric, thiamine-pyrophosphate (TPP)-dependent ketotransferase and a TPP-dependent acetolactate synthase. The frequent observation of ftx-like gene clusters within actinobacteria suggests that production of compounds related to phosphonothrixin is common within these bacteria. IMPORTANCE Phosphonic acid natural products, such as phosphonothrixin, have great potential for biomedical and agricultural applications; however, discovery and development of these compounds requires detailed knowledge of the metabolism involved in their biosynthesis. The studies reported here reveal the biochemical pathway phosphonothrixin production, which enhances our ability to design strains that overproduce this potentially useful herbicide. This knowledge also improves our ability to predict the products of related biosynthetic gene clusters and the functions of homologous enzymes.
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Affiliation(s)
- Luke Bown
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ryuichi Hirota
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Michelle N. Goettge
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jerry Cui
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - David T. Krist
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lingyang Zhu
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Constantin Giurgiu
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wilfred A. van der Donk
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
| | - William W. Metcalf
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Kato T, Kano M, Yokomori A, Azegami J, El Enshasy HA, Park EY. Involvement of a flavoprotein, acetohydroxyacid synthase, in growth and riboflavin production in riboflavin-overproducing Ashbya gossypii mutant. Microb Cell Fact 2023; 22:105. [PMID: 37217979 PMCID: PMC10201721 DOI: 10.1186/s12934-023-02114-1] [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: 04/06/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Previously, we isolated a riboflavin-overproducing Ashbya gossypii mutant (MT strain) and discovered some mutations in genes encoding flavoproteins. Here, we analyzed the riboflavin production in the MT strain, in view of flavoproteins, which are localized in the mitochondria. RESULTS In the MT strain, mitochondrial membrane potential was decreased compared with that in the wild type (WT) strain, resulting in increased reactive oxygen species. Additionally, diphenyleneiodonium (DPI), a universal flavoprotein inhibitor, inhibited riboflavin production in the WT and MT strains at 50 µM, indicating that some flavoproteins may be involved in riboflavin production. The specific activities of NADH and succinate dehydrogenases were significantly reduced in the MT strain, but those of glutathione reductase and acetohydroxyacid synthase were increased by 4.9- and 25-fold, respectively. By contrast, the expression of AgGLR1 gene encoding glutathione reductase was increased by 32-fold in the MT strain. However, that of AgILV2 gene encoding the catalytic subunit of acetohydroxyacid synthase was increased by only 2.1-fold. These results suggest that in the MT strain, acetohydroxyacid synthase, which catalyzes the first reaction of branched-chain amino acid biosynthesis, is vital for riboflavin production. The addition of valine, which is a feedback inhibitor of acetohydroxyacid synthase, to a minimal medium inhibited the growth of the MT strain and its riboflavin production. In addition, the addition of branched-chain amino acids enhanced the growth and riboflavin production in the MT strain. CONCLUSION The significance of branched-chain amino acids for riboflavin production in A. gossypii is reported and this study opens a novel approach for the effective production of riboflavin in A. gossypii.
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Affiliation(s)
- Tatsuya Kato
- Molecular and Biological Function Research Core, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan.
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan.
- Department of Applied Life Science, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan.
| | - Mai Kano
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan
| | - Ami Yokomori
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan
| | - Junya Azegami
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan
| | - Hesham A El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81310 UTM, Johor Bahru, Malaysia
- City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, Egypt
| | - Enoch Y Park
- Molecular and Biological Function Research Core, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan
- Department of Applied Life Science, Shizuoka University, Ohya 836, Suruga-Ku, Shizuoka, Japan
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Zafar K, Khan MZ, Amin I, Mukhtar Z, Zafar M, Mansoor S. Employing template-directed CRISPR-based editing of the OsALS gene to create herbicide tolerance in Basmati rice. AOB PLANTS 2023; 15:plac059. [PMID: 36873055 PMCID: PMC9977225 DOI: 10.1093/aobpla/plac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Rice (Oryza sativa) is one of the primary food crops which contributes major portion of daily calorie intake. It is used as model crop for various genome editing studies. Basmati rice was also explored for establishing non-homologous end joining-based genome editing. But it was not clear whether homology-directed repair (HDR)-based genome editing can be done in Basmati rice. The current study was designed to establish HDR-based genome editing in Basmati rice to develop herbicide tolerance. There is severe weed spread when rice is grown via direct planted rice method in various countries to save labour and water resources. Therefore, the use of herbicides is necessary to control weeds. These herbicides can also affect cultivated rice which creates the need to develop herbicide-tolerant rice. In current study, we introduced a point mutation in Acetolactate Synthase gene to convert tryptophan to leucine at position 548. For this purpose, different constructs for HDR were tested with different RNA scaffold and orientation of repair templates. Out of four different architectures, the one having repair template identical to the target DNA strand precisely edited the target site. We successfully established template-directed CRISPR-Cas9 system in Super Basmati rice by detecting desired substitutions at the target site in Acetolactate Synthase locus. Moreover, this editing of Acetolactate Synthase gene resulted in the production of herbicide tolerance in Super Basmati rice. This study suggests that such type of HDR system can be used to precisely edit other genes for crop improvement.
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Affiliation(s)
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Mehak Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
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11
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Hui X, Tian JM, Wang X, Zhang ZQ, Zhao YM, Gao WY, Li H. Overall analyses of the reactions catalyzed by acetohydroxyacid synthase/acetolactate synthase using a precolumn derivatization-HPLC method. Anal Biochem 2023; 660:114980. [PMID: 36368345 DOI: 10.1016/j.ab.2022.114980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
A precolumn derivatization-HPLC method using 2,4-dinitrophenylhydrazine and 4-nitro-o-phenylenediamine as respective labeling reagents for comprehensive analyses of the reactions catalyzed by acetohydroxyacid synthase (AHAS)/acetolactate synthase (ALS) is developed and evaluated in this research. Comparison with the classic Bauerle' UV assay which can analyze the enzymes only through measurement of acetoin production, the HPLC method shows advantages because it can analyze the enzymes not only via determination of consumption of the substrate pyruvate, but also via measurement of formation of the products including acetoin, 2,3-butanedione, and acetaldehyde in the enzymatic reactions. Thus the results deduced from the HPLC method can reflect the trait of each enzyme in a more precise manner. As far as we know, this is the first time that the reactions mediated by AHAS/ALS using pyruvate as a single substrate are globally analyzed and the features of the enzymes are properly discussed.
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Affiliation(s)
- Xian Hui
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Jin-Meng Tian
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Xin Wang
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Zhen-Qian Zhang
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Ya-Mei Zhao
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Wen-Yun Gao
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Heng Li
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
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12
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Sheremetieva M, Anufriev K, Khlebodarova T, Kolchanov N, Yanenko A. Rational metabolic engineering of Corynebacterium glutamicum to create a producer of L-valine. Vavilovskii Zhurnal Genet Selektsii 2022; 26:743-757. [PMID: 36694718 PMCID: PMC9834717 DOI: 10.18699/vjgb-22-90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 01/06/2023] Open
Abstract
L-Valine is one of the nine amino acids that cannot be synthesized de novo by higher organisms and must come from food. This amino acid not only serves as a building block for proteins, but also regulates protein and energy metabolism and participates in neurotransmission. L-Valine is used in the food and pharmaceutical industries, medicine and cosmetics, but primarily as an animal feed additive. Adding L-valine to feed, alone or mixed with other essential amino acids, allows for feeds with lower crude protein content, increases the quality and quantity of pig meat and broiler chicken meat, as well as improves reproductive functions of farm animals. Despite the fact that the market for L-valine is constantly growing, this amino acid is not yet produced in our country. In modern conditions, the creation of strains-producers and organization of L-valine production are especially relevant for Russia. One of the basic microorganisms most commonly used for the creation of amino acid producers, along with Escherichia coli, is the soil bacterium Corynebacterium glutamicum. This review is devoted to the analysis of the main strategies for the development of L- valine producers based on C. glutamicum. Various aspects of L-valine biosynthesis in C. glutamicum are reviewed: process biochemistry, stoichiometry and regulation, enzymes and their corresponding genes, export and import systems, and the relationship of L-valine biosynthesis with central cell metabolism. Key genetic elements for the creation of C. glutamicum-based strains-producers are identified. The use of metabolic engineering to enhance L-valine biosynthesis reactions and to reduce the formation of byproducts is described. The prospects for improving strains in terms of their productivity and technological characteristics are shown. The information presented in the review can be used in the production of producers of other amino acids with a branched side chain, namely L-leucine and L-isoleucine, as well as D-pantothenate.
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Affiliation(s)
| | - K.E. Anufriev
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
| | - T.M. Khlebodarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N.A. Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.S. Yanenko
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
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13
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Golubyatnikov V, Akinshin A, Ayupova N, Minushkina L. Stratifications and foliations in phase portraits of gene network models. Vavilovskii Zhurnal Genet Selektsii 2022; 26:758-764. [PMID: 36694713 PMCID: PMC9837163 DOI: 10.18699/vjgb-22-91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Periodic processes of gene network functioning are described with good precision by periodic trajectories (limit cycles) of multidimensional systems of kinetic-type differential equations. In the literature, such systems are often called dynamical, they are composed according to schemes of positive and negative feedback between components of these networks. The variables in these equations describe concentrations of these components as functions of time. In the preparation of numerical experiments with such mathematical models, it is useful to start with studies of qualitative behavior of ensembles of trajectories of the corresponding dynamical systems, in particular, to estimate the highest likelihood domain of the initial data, to solve inverse problems of parameter identification, to list the equilibrium points and their characteristics, to localize cycles in the phase portraits, to construct stratification of the phase portraits to subdomains with different qualities of trajectory behavior, etc. Such an à priori geometric analysis of the dynamical systems is quite analogous to the basic section "Investigation of functions and plot of their graphs" of Calculus, where the methods of qualitative studies of shapes of curves determined by equations are exposed. In the present paper, we construct ensembles of trajectories in phase portraits of some dynamical systems. These ensembles are 2-dimensional surfaces invariant with respect to shifts along the trajectories. This is analogous to classical construction in analytic mechanics, i. e. the level surfaces of motion integrals (energy, kinetic moment, etc.). Such surfaces compose foliations in phase portraits of dynamical systems of Hamiltonian mechanics. In contrast with this classical mechanical case, the foliations considered in this paper have singularities: all their leaves have a non-empty intersection, they contain limit cycles on their boundaries. Description of the phase portraits of these systems at the level of their stratifications, and that of ensembles of trajectories allows one to construct more realistic gene network models on the basis of methods of statistical physics and the theory of stochastic differential equations.
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Affiliation(s)
- V.P. Golubyatnikov
- Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - A.A. Akinshin
- Huawei Russian Research Institute, St. Petersburg, Russia
| | - N.B. Ayupova
- Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
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14
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Cai T, Wen S, Yang X, Yu X, Chen J, Wu J, Zhang L, Zhan L, Luo K, Yi J, Zhu X, Nie Y. Subacute dermal toxicity study of bensulfuron-methyl in Sprague-Dawley rats. Cutan Ocul Toxicol 2022; 41:162-167. [DOI: 10.1080/15569527.2022.2077750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Tuo Cai
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Sihui Wen
- Key Laboratory of Molecular Epidemiology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, P. R. China
| | - Xiuhong Yang
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Xiaowei Yu
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Jianfeng Chen
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Jun Wu
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Lina Zhang
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Lichao Zhan
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Kaiwen Luo
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Jiping Yi
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Xiaochuan Zhu
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
| | - Yunfeng Nie
- Department of Occupational Disease, Hunan Prevention and Treatment Institute for Occupational Disease, Changsha, P. R. China
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15
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Ohtsuka H, Shimasaki T, Aiba H. Response to leucine in Schizosaccharomyces pombe (fission yeast). FEMS Yeast Res 2022; 22:6553821. [PMID: 35325114 PMCID: PMC9041340 DOI: 10.1093/femsyr/foac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Leucine (Leu) is a branched-chain, essential amino acid in animals, including humans. Fungi, including the fission yeast Schizosaccharomyces pombe, can biosynthesize Leu, but deletion of any of the genes in this biosynthesis leads to Leu auxotrophy. In this yeast, although a mutation in the Leu biosynthetic pathway, leu1-32, is clearly inconvenient for this species, it has increased its usefulness as a model organism in laboratories worldwide. Leu auxotrophy produces intracellular responses and phenotypes different from those of the prototrophic strains, depending on the growing environment, which necessitates a certain degree of caution in the analysis and interpretation of the experimental results. Under amino acid starvation, the amino acid-auxotrophic yeast induces cellular responses, which are conserved in higher organisms without the ability of synthesizing amino acids. This mini-review focuses on the roles of Leu in S. pombe and discusses biosynthetic pathways, contribution to experimental convenience using a plasmid specific for Leu auxotrophic yeast, signaling pathways, and phenotypes caused by Leu starvation. An accurate understanding of the intracellular responses brought about by Leu auxotrophy can contribute to research in various fields using this model organism and to the understanding of intracellular responses in higher organisms that cannot synthesize Leu.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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16
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Palmieri F, Monné M, Fiermonte G, Palmieri L. Mitochondrial transport and metabolism of the vitamin B-derived cofactors thiamine pyrophosphate, coenzyme A, FAD and NAD + , and related diseases: A review. IUBMB Life 2022; 74:592-617. [PMID: 35304818 PMCID: PMC9311062 DOI: 10.1002/iub.2612] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 01/19/2023]
Abstract
Multiple mitochondrial matrix enzymes playing key roles in metabolism require cofactors for their action. Due to the high impermeability of the mitochondrial inner membrane, these cofactors need to be synthesized within the mitochondria or be imported, themselves or one of their precursors, into the organelles. Transporters belonging to the protein family of mitochondrial carriers have been identified to transport the coenzymes: thiamine pyrophosphate, coenzyme A, FAD and NAD+ , which are all structurally similar to nucleotides and derived from different B-vitamins. These mitochondrial cofactors bind more or less tightly to their enzymes and, after having been involved in a specific reaction step, are regenerated, spontaneously or by other enzymes, to return to their active form, ready for the next catalysis round. Disease-causing mutations in the mitochondrial cofactor carrier genes compromise not only the transport reaction but also the activity of all mitochondrial enzymes using that particular cofactor and the metabolic pathways in which the cofactor-dependent enzymes are involved. The mitochondrial transport, metabolism and diseases of the cofactors thiamine pyrophosphate, coenzyme A, FAD and NAD+ are the focus of this review.
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Affiliation(s)
- Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,Department of Sciences, University of Basilicata, Potenza, Italy
| | - Giuseppe Fiermonte
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
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17
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Yu S, Zheng B, Chen Z, Huo YX. Metabolic engineering of Corynebacterium glutamicum for producing branched chain amino acids. Microb Cell Fact 2021; 20:230. [PMID: 34952576 PMCID: PMC8709942 DOI: 10.1186/s12934-021-01721-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background Branched chain amino acids (BCAAs) are widely applied in the food, pharmaceutical, and animal feed industries. Traditional chemical synthetic and enzymatic BCAAs production in vitro has been hampered by expensive raw materials, harsh reaction conditions, and environmental pollution. Microbial metabolic engineering has attracted considerable attention as an alternative method for BCAAs biosynthesis because it is environmentally friendly and delivers high yield. Main text Corynebacterium glutamicum (C. glutamicum) possesses clear genetic background and mature gene manipulation toolbox, and has been utilized as industrial host for producing BCAAs. Acetohydroxy acid synthase (AHAS) is a crucial enzyme in the BCAAs biosynthetic pathway of C. glutamicum, but feedback inhibition is a disadvantage. We therefore reviewed AHAS modifications that relieve feedback inhibition and then investigated the importance of AHAS modifications in regulating production ratios of three BCAAs. We have comprehensively summarized and discussed metabolic engineering strategies to promote BCAAs synthesis in C. glutamicum and offer solutions to the barriers associated with BCAAs biosynthesis. We also considered the future applications of strains that could produce abundant amounts of BCAAs. Conclusions Branched chain amino acids have been synthesized by engineering the metabolism of C. glutamicum. Future investigations should focus on the feedback inhibition and/or transcription attenuation mechanisms of crucial enzymes. Enzymes with substrate specificity should be developed and applied to the production of individual BCAAs. The strategies used to construct strains producing BCAAs provide guidance for the biosynthesis of other high value-added compounds.
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Affiliation(s)
- Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
| | - Bo Zheng
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
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18
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Peng M, Siebert DL, Engqvist MKM, Niemeyer CM, Rabe KS. Modeling-Assisted Design of Thermostable Benzaldehyde Lyases from Rhodococcus erythropolis for Continuous Production of α-Hydroxy Ketones. Chembiochem 2021; 23:e202100468. [PMID: 34558792 PMCID: PMC9293332 DOI: 10.1002/cbic.202100468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Indexed: 12/18/2022]
Abstract
Enantiopure α-hydroxy ketones are important building blocks of active pharmaceutical ingredients (APIs), which can be produced by thiamine-diphosphate-dependent lyases, such as benzaldehyde lyase. Here we report the discovery of a novel thermostable benzaldehyde lyase from Rhodococcus erythropolis R138 (ReBAL). While the overall sequence identity to the only experimentally confirmed benzaldehyde lyase from Pseudomonas fluorescens Biovar I (PfBAL) was only 65 %, comparison of a structural model of ReBAL with the crystal structure of PfBAL revealed only four divergent amino acids in the substrate binding cavity. Based on rational design, we generated two ReBAL variants, which were characterized along with the wild-type enzyme in terms of their substrate spectrum, thermostability and biocatalytic performance in the presence of different co-solvents. We found that the new enzyme variants have a significantly higher thermostability (up to 22 °C increase in T50 ) and a different co-solvent-dependent activity. Using the most stable variant immobilized in packed-bed reactors via the SpyCatcher/SpyTag system, (R)-benzoin was synthesized from benzaldehyde over a period of seven days with a stable space-time-yield of 9.3 mmol ⋅ L-1 ⋅ d-1 . Our work expands the important class of benzaldehyde lyases and therefore contributes to the development of continuous biocatalytic processes for the production of α-hydroxy ketones and APIs.
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Affiliation(s)
- Martin Peng
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Dominik L Siebert
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin K M Engqvist
- Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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19
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Gao H, Tuyishime P, Zhang X, Yang T, Xu M, Rao Z. Engineering of microbial cells for L-valine production: challenges and opportunities. Microb Cell Fact 2021; 20:172. [PMID: 34461907 PMCID: PMC8406616 DOI: 10.1186/s12934-021-01665-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
L-valine is an essential amino acid that has wide and expanding applications with a suspected growing market demand. Its applicability ranges from animal feed additive, ingredient in cosmetic and special nutrients in pharmaceutical and agriculture fields. Currently, fermentation with the aid of model organisms, is a major method for the production of L-valine. However, achieving the optimal production has often been limited because of the metabolic imbalance in recombinant strains. In this review, the constrains in L-valine biosynthesis are discussed first. Then, we summarize the current advances in engineering of microbial cell factories that have been developed to address and overcome major challenges in the L-valine production process. Future prospects for enhancing the current L-valine production strategies are also discussed.
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Affiliation(s)
- Hui Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Philibert Tuyishime
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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20
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L-valine production in Corynebacterium glutamicum based on systematic metabolic engineering: progress and prospects. Amino Acids 2021; 53:1301-1312. [PMID: 34401958 DOI: 10.1007/s00726-021-03066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
L-valine is an essential branched-chain amino acid that cannot be synthesized by the human body and has a wide range of applications in food, medicine and feed. Market demand has stimulated people's interest in the industrial production of L-valine. At present, the mutagenized or engineered Corynebacterium glutamicum is an effective microbial cell factory for producing L-valine. Because the biosynthetic pathway and metabolic network of L-valine are intricate and strictly regulated by a variety of key enzymes and genes, highly targeted metabolic engineering can no longer meet the demand for efficient biosynthesis of L-valine. In recent years, the development of omics technology has promoted the upgrading of traditional metabolic engineering to systematic metabolic engineering. This whole-cell-scale transformation strategy has become a productive method for developing L-valine producing strains. This review provides an overview of the biosynthesis and regulation mechanism of L-valine, and summarizes the current metabolic engineering techniques and strategies for constructing L-valine high-producing strains. Finally, the opinion of constructing a cell factory for efficiently biosynthesizing L-valine was proposed.
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21
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Lowes DJ, Miao J, Al-waqfi RA, Avad KA, Hevener KE, Peters BM. Identification of Dual-Target Compounds with Antifungal and Anti-NLRP3 Inflammasome Activity. ACS Infect Dis 2021; 7:2522-2535. [PMID: 34260210 DOI: 10.1021/acsinfecdis.1c00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Invasive and superficial infections caused by the Candida species result in significant global morbidity and mortality. As the pathogenicity of these organisms is intimately intertwined with host immune response, therapies to target both the fungus and host inflammation may be warranted. Structural similarities exist between established inhibitors of the NLRP3 inflammasome and those of fungal acetohydroxyacid synthase (AHAS). Therefore, we leveraged this information to conduct an in silico molecular docking screen to find novel polypharmacologic inhibitors of these targets that resulted in the identification of 12 candidate molecules. Of these, compound 10 significantly attenuated activation of the NLPR3 inflammasome by LPS + ATP, while also demonstrating growth inhibitory activity against C. albicans that was alleviated in the presence of exogenous branched chain amino acids, consistent with targeting of fungal AHAS. SAR studies delineated an essential molecular scaffold required for dual activity. Ultimately, 10 and its analog 10a resulted in IC50 (IL-1β release) and MIC50 (fungal growth) values with low μM potency against several Candida species. Collectively, this work demonstrates promising potential of dual-target approaches for improved management of fungal infections.
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Affiliation(s)
- David J Lowes
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Jian Miao
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Rand A Al-waqfi
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Kristiana A. Avad
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Doctor of Pharmacy Program, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Brian M Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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22
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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 707:108849. [PMID: 33832752 DOI: 10.1016/j.abb.2021.108849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4 kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9 kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, UK; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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Liang YF, Long ZX, Zhang YJ, Luo CY, Yan LT, Gao WY, Li H. The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications. Biochimie 2021; 184:72-87. [PMID: 33607240 DOI: 10.1016/j.biochi.2021.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/27/2022]
Abstract
l-Valine, l-isoleucine, and l-leucine are three key proteinogenic amino acids, and they are also the essential amino acids required for mammalian growth, possessing important and to some extent, special physiological and biological functions. Because of the branched structures in their carbon chains, they are also named as branched-chain amino acids (BCAAs). This review will highlight the advance in studies of the enzymes involved in the biosynthetic pathway of BCAAs, concentrating on their chemical mechanisms and applications in screening herbicides and antibacterial agents. The uses of some of these enzymes in lab scale organic synthesis are also discussed.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Zi-Xian Long
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Ya-Jian Zhang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Cai-Yun Luo
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Le-Tian Yan
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
| | - Heng Li
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 701:108807. [PMID: 33587902 DOI: 10.1016/j.abb.2021.108807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, United Kingdom; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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Fang Y, Zhang S, Wang J, Yin L, Zhang H, Wang Z, Song J, Hu X, Wang X. Metabolic Detoxification of 2-Oxobutyrate by Remodeling Escherichia coli Acetate Bypass. Metabolites 2021; 11:metabo11010030. [PMID: 33406667 PMCID: PMC7824062 DOI: 10.3390/metabo11010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/03/2022] Open
Abstract
2-Oxobutyrate (2-OBA), as a toxic metabolic intermediate, generally arrests the cell growth of most microorganisms and blocks the biosynthesis of target metabolites. In this study, we demonstrated that using the acetate bypass to replace the pyruvate dehydrogenase complex (PDHc) in Escherichia coli could recharge the intracellular acetyl-CoA pool to alleviate the metabolic toxicity of 2-OBA. Furthermore, based on the crystal structure of pyruvate oxidase (PoxB), two candidate residues in the substrate-binding pocket of PoxB were predicted by computational simulation. Site-directed saturation mutagenesis was performed to attenuate 2-OBA-binding affinity, and one of the variants, PoxBF112W, exhibited a 20-fold activity ratio of pyruvate/2-OBA in substrate selectivity. PoxBF112W was employed to remodel the acetate bypass in E. coli, resulting in l-threonine (a precursor of 2-OBA) biosynthesis with minimal inhibition from 2-OBA. After metabolic detoxification of 2-OBA, the supplies of intracellular acetyl-CoA and NADPH (nicotinamide adenine dinucleotide phosphate) used for l-threonine biosynthesis were restored. Therefore, 2-OBA is the substitute for pyruvate to engage in enzymatic reactions and disturbs pyruvate metabolism. Our study makes a straightforward explanation of the 2-OBA toxicity mechanism and gives an effective approach for its metabolic detoxification.
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Affiliation(s)
- Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Lianghong Yin
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China;
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai 264005, China;
| | - Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Jie Song
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel./Fax: +86-510-85329239
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Hong Y, Arbter P, Wang W, Rojas LN, Zeng AP. Introduction of glycine synthase enables uptake of exogenous formate and strongly impacts the metabolism in Clostridium pasteurianum. Biotechnol Bioeng 2020; 118:1366-1380. [PMID: 33331660 DOI: 10.1002/bit.27658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 11/11/2022]
Abstract
Autotrophic or mixotrophic use of one-carbon (C1) compounds is gaining importance for sustainable bioproduction. In an effort to integrate the reductive glycine pathway (rGP) as a highly promising pathway for the assimilation of CO2 and formate, genes coding for glycine synthase system from Gottschalkia acidurici were successfully introduced into Clostridium pasteurianum, a non-model host microorganism with industrial interests. The mutant harboring glycine synthase exhibited assimilation of exogenous formate and reduced CO2 formation. Further metabolic data clearly showed large impacts of expression of glycine synthase on the product metabolism of C. pasteurianum. In particular, 2-oxobutyrate (2-OB) was observed for the first time as a metabolic intermediate of C. pasteurianum and its secretion was solely triggered by the expression of glycine synthase. The perturbation of C1 metabolism is discussed regarding its interactions with pathways of the central metabolism, acidogenesis, solventogenesis, and amino acid metabolism. The secretion of 2-OB is considered as a consequence of metabolic and redox instabilities due to the activity of glycine synthase and may represent a common metabolic response of Clostridia in enhanced use of C1 compounds.
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Affiliation(s)
- Yaeseong Hong
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Philipp Arbter
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Wei Wang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Lilian N Rojas
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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Guo M, Liu J, Xu Z, Wang J, Li T, Lei H, Duan X, Sun Y, Zhang X, Huang R. 2-Methoxy-1,4-naphthoquinone Induces Metabolic Shifts in Penicillium Digitatum Revealed by High-Dimensional Biological Data. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9697-9706. [PMID: 32803964 DOI: 10.1021/acs.jafc.0c03396] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Penicillium digitatum is the primary pathogen causing the green mold of citrus. The need for the development of higher effective and lower toxic natural antifungal agents is urgent, owing to the lack of antifungal agents that can successfully combat P. digitatum. Herein, the effects and mechanisms of 2-methoxy-1,4-naphthoquinone (MNQ) as a potential inhibitor of P. digitatumwere studied. First, MNQ showed a significant anti-P. digitatum effect with a minimum inhibitory concentration value of 5.0 μg/mL. Then, transcriptome, proteome, and metabolome profiling were performed on the MNQ-treated P. digitatum. A total of 910 genes, 297 proteins, and 174 metabolites changed significantly. The omics analysis indicated that it could be seen that MNQ mainly inhibits the growth of P. digitatum by affecting the synthesis of branched-chain amino acids and cell walls. These findings will be a great contribution to the further understanding of the possible molecular action of MNQ.
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Affiliation(s)
- Meixia Guo
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Jun Liu
- Laboratory of Pathogenic Biology, Guangdong Medical University, Zhanjiang 524023, China
| | - Zhenlin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Taotao Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yuanming Sun
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyong Zhang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Riming Huang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
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Isobutanol production freed from biological limits using synthetic biochemistry. Nat Commun 2020; 11:4292. [PMID: 32855421 PMCID: PMC7453195 DOI: 10.1038/s41467-020-18124-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/07/2020] [Indexed: 11/09/2022] Open
Abstract
Cost competitive conversion of biomass-derived sugars into biofuel will require high yields, high volumetric productivities and high titers. Suitable production parameters are hard to achieve in cell-based systems because of the need to maintain life processes. As a result, next-generation biofuel production in engineered microbes has yet to match the stringent cost targets set by petroleum fuels. Removing the constraints imposed by having to maintain cell viability might facilitate improved production metrics. Here, we report a cell-free system in a bioreactor with continuous product removal that produces isobutanol from glucose at a maximum productivity of 4 g L−1 h−1, a titer of 275 g L−1 and 95% yield over the course of nearly 5 days. These production metrics exceed even the highly developed ethanol fermentation process. Our results suggest that moving beyond cells has the potential to expand what is possible for bio-based chemical production. A cell free or synthetic biochemistry approach offers a way to circumvent the many constraints of living cells. Here, the authors demonstrate, via enzyme and process enhancements, the production of isobutanol with the metrics exceeding highly developed ethanol fermentation.
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Fang J, Wan C, Wang W, Ma L, Wang X, Cheng C, Zhou J, Qiao Y, Wang X. Engineering Herbicide-Tolerance Rice Expressing an Acetohydroxyacid Synthase with a Single Amino Acid Deletion. Int J Mol Sci 2020; 21:ijms21041265. [PMID: 32070060 PMCID: PMC7072996 DOI: 10.3390/ijms21041265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
The acetohydroxyacid synthase (AHAS) is an essential enzyme involved in branched amino acids. Several herbicides wither weeds via inhibiting AHAS activity, and the AHAS mutants show tolerance to these herbicides. However, most AHAS mutations are residue substitutions but not residue deletion. Here, residue deletion was used to engineering the AHAS gene and herbicide-tolerant rice. Molecular docking analysis predicted that the W548 of the AHAS was a residue deletion to generate herbicide tolerance. The AHAS-ΔW548 protein was generated in vitro to remove the W548 residue. Interestingly, the deletion led to the tetramer dissociation of the AHAS, while this dissociation did not reduce the activity of the AHAS. Moreover, the W548 deletion contributed to multi-family herbicides tolerance. Specially, it conferred more tolerance to sulfometuron-methyl and bispyribac-sodium than the W548L substitution. Further analysis revealed that AHAS-ΔW548 had the best performance on the sulfometuron-methyl tolerance compared to the wild-type control. Over-expression of the AHAS-ΔW548 gene into rice led to the tolerance of multiple herbicides in the transgenic line. The T-DNA insertion and the herbicide treatment did not affect the agronomic traits and yields, while more branched-chain amino acids were detected in transgenic rice seeds. Residue deletion of W548 in the AHAS could be a useful strategy for engineering herbicide tolerant rice. The increase of branched-chain amino acids might improve the umami tastes of the rice.
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Affiliation(s)
- Jun Fang
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Rd, Shanghai 201403, China; (C.W.); (X.W.); (C.C.); (J.Z.); (Y.Q.)
- Correspondence:
| | - Changzhao Wan
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Rd, Shanghai 201403, China; (C.W.); (X.W.); (C.C.); (J.Z.); (Y.Q.)
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 99 Haike Rd, Shanghai 201210, China;
| | - Liuyin Ma
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Xinqi Wang
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Rd, Shanghai 201403, China; (C.W.); (X.W.); (C.C.); (J.Z.); (Y.Q.)
| | - Can Cheng
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Rd, Shanghai 201403, China; (C.W.); (X.W.); (C.C.); (J.Z.); (Y.Q.)
| | - Jihua Zhou
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Rd, Shanghai 201403, China; (C.W.); (X.W.); (C.C.); (J.Z.); (Y.Q.)
| | - Yongjin Qiao
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Rd, Shanghai 201403, China; (C.W.); (X.W.); (C.C.); (J.Z.); (Y.Q.)
| | - Xiao Wang
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Rd, Shanghai 201403, China; (C.W.); (X.W.); (C.C.); (J.Z.); (Y.Q.)
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Seo PW, Jo HJ, Hwang IY, Jeong HY, Kim JH, Kim JW, Lee EY, Park JB, Kim JS. Understanding the molecular properties of the E1 subunit (SucA) of α-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin. Catal Sci Technol 2020. [DOI: 10.1039/c9cy01566c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Enantioselective ligation of acetaldehydes into (R)-acetoin by SucA from Vibrio vulnificus.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry
- Chonnam National University
- Gwangju 61186
- Republic of Korea
| | - Hye-Jin Jo
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - In Yeub Hwang
- Department of Chemical Engineering
- Kyung Hee University
- Republic of Korea
| | - Ha-Yeon Jeong
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry
- Chonnam National University
- Gwangju 61186
- Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry
- Chonnam National University
- Gwangju 61186
- Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering
- Kyung Hee University
- Republic of Korea
| | - Jin-Byung Park
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry
- Chonnam National University
- Gwangju 61186
- Republic of Korea
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Amemiya K, Dankmeyer JL, Biryukov SS, Treviño SR, Klimko CP, Mou SM, Fetterer DP, Garnes PG, Cote CK, Worsham PL, DeShazer D. Deletion of Two Genes in Burkholderia pseudomallei MSHR668 That Target Essential Amino Acids Protect Acutely Infected BALB/c Mice and Promote Long Term Survival. Vaccines (Basel) 2019; 7:vaccines7040196. [PMID: 31779073 PMCID: PMC6963190 DOI: 10.3390/vaccines7040196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/31/2019] [Accepted: 11/15/2019] [Indexed: 12/25/2022] Open
Abstract
Melioidosis is an emerging disease that is caused by the facultative intracellular pathogen Burkholderia pseudomallei. It is intrinsically resistant to many antibiotics and host risk factors play a major role in susceptibility to infection. Currently, there is no human or animal vaccine against melioidosis. In this study, multiple B. pseudomallei MSHR668 deletion mutants were evaluated as live attenuated vaccines in the sensitive BALB/c mouse model of melioidosis. The most efficacious vaccines after an intraperitoneal challenge with 50-fold over the 50% median lethal dose (MLD50) with B. pseudomallei K96243 were 668 ΔhisF and 668 ΔilvI. Both vaccines completely protected mice in the acute phase of infection and showed significant protection (50% survivors) during the chronic phase of infection. The spleens of the survivors that were examined were sterile. Splenocytes from mice vaccinated with 668 ΔhisF and 668 ΔilvI expressed higher amounts of IFN-γ after stimulation with B. pseudomallei antigens than splenocytes from mice vaccinated with less protective candidates. Finally, we demonstrate that 668 ΔhisF is nonlethal in immunocompromised NOD/SCID mice. Our results show that 668 ΔhisF and 668 ΔilvI provide protective cell-mediated immune responses in the acute phase of infection and promote long term survival in the sensitive BALB/c mouse model of melioidosis.
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Affiliation(s)
- Kei Amemiya
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - Jennifer L. Dankmeyer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - Sergei S. Biryukov
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - Sylvia R. Treviño
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - Christopher P. Klimko
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - Sherry M. Mou
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - David P. Fetterer
- Biostatistical Services, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (D.P.F.); (P.G.G.)
| | - Preston G. Garnes
- Biostatistical Services, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (D.P.F.); (P.G.G.)
| | - Christopher K. Cote
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - Patricia L. Worsham
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
| | - David DeShazer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; (K.A.); (J.L.D.); (S.S.B.); (S.R.T.); (C.P.K.); (S.M.M.); (C.K.C.); (P.L.W.)
- Correspondence: ; Tel.: +1-301-619-4919
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Liu Y, Wang X, Zhan J, Hu J. The 138th residue of acetohydroxyacid synthase in Corynebacterium glutamicum is important for the substrate binding specificity. Enzyme Microb Technol 2019; 129:109357. [DOI: 10.1016/j.enzmictec.2019.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/12/2019] [Accepted: 06/01/2019] [Indexed: 11/28/2022]
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Han YJ, Kim JI. Application of CRISPR/Cas9-mediated gene editing for the development of herbicide-resistant plants. PLANT BIOTECHNOLOGY REPORTS 2019; 13:447-457. [PMID: 0 DOI: 10.1007/s11816-019-00575-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/26/2019] [Indexed: 05/27/2023]
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Thiour-Mauprivez C, Martin-Laurent F, Calvayrac C, Barthelmebs L. Effects of herbicide on non-target microorganisms: Towards a new class of biomarkers? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:314-325. [PMID: 31153078 DOI: 10.1016/j.scitotenv.2019.05.230] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 05/19/2023]
Abstract
Conventional agriculture still relies on the general use of agrochemicals (herbicides, fungicides and insecticides) to control various pests (weeds, fungal pathogens and insects), to ensure the yield of crop and to feed a constantly growing population. The generalized use of pesticides in agriculture leads to the contamination of soil and other connected environmental resources. The persistence of pesticide residues in soil is identified as a major threat for in-soil living organisms that are supporting an important number of ecosystem services. Although authorities released pesticides on the market only after their careful and thorough evaluation, the risk assessment for in-soil living organisms is unsatisfactory, particularly for microorganisms for which pesticide toxicity is solely considered by one global test measuring N mineralization. Recently, European Food Safety Authority (EFSA) underlined the lack of standardized methods to assess pesticide ecotoxicological effects on soil microorganisms. Within this context, there is an obvious need to develop innovative microbial markers sensitive to pesticide exposure. Biomarkers that reveal direct effects of pesticides on microorganisms are often viewed as the panacea. Such biomarkers can only be developed for pesticides having a mode of action inhibiting a specific enzyme not only found in the targeted organisms but also in microorganisms which are considered as "non-target organisms" by current regulations. This review explores possible ways of innovation to develop such biomarkers for herbicides. We scanned the herbicide classification by considering the mode of action, the targeted enzyme and the ecotoxicological effects of each class of active substance in order to identify those that can be tracked using sensitive microbial markers.
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Affiliation(s)
- Clémence Thiour-Mauprivez
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21065 Dijon, France
| | - Fabrice Martin-Laurent
- AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21065 Dijon, France
| | - Christophe Calvayrac
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Lise Barthelmebs
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650 Banyuls-sur-Mer, France.
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Buchholz PCF, Ferrario V, Pohl M, Gardossi L, Pleiss J. Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites. Proteins 2019; 87:774-785. [PMID: 31070804 DOI: 10.1002/prot.25706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/23/2019] [Accepted: 05/05/2019] [Indexed: 11/10/2022]
Abstract
Thiamine diphosphate-dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP-dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP-dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.,Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Martina Pohl
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Lucia Gardossi
- Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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Li Y, Netherland MD, Zhang C, Hong H, Gong P. In silico identification of genetic mutations conferring resistance to acetohydroxyacid synthase inhibitors: A case study of Kochia scoparia. PLoS One 2019; 14:e0216116. [PMID: 31063467 PMCID: PMC6504096 DOI: 10.1371/journal.pone.0216116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/14/2019] [Indexed: 12/17/2022] Open
Abstract
Mutations that confer herbicide resistance are a primary concern for herbicide-based chemical control of invasive plants and are often under-characterized structurally and functionally. As the outcome of selection pressure, resistance mutations usually result from repeated long-term applications of herbicides with the same mode of action and are discovered through extensive field trials. Here we used acetohydroxyacid synthase (AHAS) of Kochia scoparia (KsAHAS) as an example to demonstrate that, given the sequence of a target protein, the impact of genetic mutations on ligand binding could be evaluated and resistance mutations could be identified using a biophysics-based computational approach. Briefly, the 3D structures of wild-type (WT) and mutated KsAHAS-herbicide complexes were constructed by homology modeling, docking and molecular dynamics simulation. The resistance profile of two AHAS-inhibiting herbicides, tribenuron methyl and thifensulfuron methyl, was obtained by estimating their binding affinity with 29 KsAHAS (1 WT and 28 mutated) using 6 molecular mechanical (MM) and 18 hybrid quantum mechanical/molecular mechanical (QM/MM) methods in combination with three structure sampling strategies. By comparing predicted resistance with experimentally determined resistance in the 29 biotypes of K. scoparia field populations, we identified the best method (i.e., MM-PBSA with single structure) out of all tested methods for the herbicide-KsAHAS system, which exhibited the highest accuracy (up to 100%) in discerning mutations conferring resistance or susceptibility to the two AHAS inhibitors. Our results suggest that the in silico approach has the potential to be widely adopted for assessing mutation-endowed herbicide resistance on a case-by-case basis.
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Affiliation(s)
- Yan Li
- Bennett Aerospace, Inc., Cary, North Carolina, United States of America
| | - Michael D. Netherland
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Chaoyang Zhang
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Ping Gong
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
- * E-mail:
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Sélem-Mojica N, Aguilar C, Gutiérrez-García K, Martínez-Guerrero CE, Barona-Gómez F. EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microb Genom 2019; 5. [PMID: 30946645 PMCID: PMC6939163 DOI: 10.1099/mgen.0.000260] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Natural products (NPs), or specialized metabolites, are important for medicine and agriculture alike, and for the fitness of the organisms that produce them. NP genome-mining aims at extracting biosynthetic information from the genomes of microbes presumed to produce these compounds. Typically, canonical enzyme sequences from known biosynthetic systems are identified after sequence similarity searches. Despite this being an efficient process, the likelihood of identifying truly novel systems by this approach is low. To overcome this limitation, we previously introduced EvoMining, a genome-mining approach that incorporates evolutionary principles. Here, we release and use our latest EvoMining version, which includes novel visualization features and customizable databases, to analyse 42 central metabolic enzyme families (EFs) conserved throughout Actinobacteria, Cyanobacteria, Pseudomonas and Archaea. We found that expansion-and-recruitment profiles of these 42 families are lineage specific, opening the metabolic space related to ‘shell’ enzymes. These enzymes, which have been overlooked, are EFs with orthologues present in most of the genomes of a taxonomic group, but not in all. As a case study of canonical shell enzymes, we characterized the expansion and recruitment of glutamate dehydrogenase and acetolactate synthase into scytonemin biosynthesis, and into other central metabolic pathways driving Archaea and Bacteria adaptive evolution. By defining the origin and fate of enzymes, EvoMining complements traditional genome-mining approaches as an unbiased strategy and opens the door to gaining insights into the evolution of NP biosynthesis. We anticipate that EvoMining will be broadly used for evolutionary studies, and for generating predictions of unprecedented chemical scaffolds and new antibiotics. This article contains data hosted by Microreact.
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Affiliation(s)
- Nelly Sélem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
| | - César Aguilar
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
| | | | - Christian E Martínez-Guerrero
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México.,Present address: Nuclear-Mitochondrial Interaction and Paleogenomics Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
| | - Fancisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
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Breccia G, Gianotto L, Altieri E, Bulos M, Nestares G. Effect of Ahasl1-1 and Ahasl1-4 alleles on herbicide resistance and its associated dominance in sunflower. PEST MANAGEMENT SCIENCE 2019; 75:935-941. [PMID: 30187639 DOI: 10.1002/ps.5197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Acetohydroxyacid synthase large subunit 1 (Ahasl1) is a multiallelic locus involved in herbicide resistance in sunflower. Ahasl1-1 and Ahasl1-4 alleles harbor different point mutations that lead to different amino acid substitutions (Ala205Val and Trp574Leu, respectively). The objectives of this work were to evaluate the effect of these alleles at the enzymatic and whole-plant levels, and to determine the dominance relationships for imazapyr and metsulfuron-methyl herbicides. RESULTS Resistant near-isogenic lines showed significantly lower specific AHAS activity than susceptible near-isoline. However, kinetic studies indicated that mutations did not change AHAS pyruvate affinity. Dose-response for six near-isolines carrying different combinations of Ahasl1-1 and Ahasl1-4 alleles and two herbicides (imazapyr and metsulfuron-methyl) were evaluated at whole-plant and enzymatic levels. Ahasl1-1 allele conferred moderate resistance to imazapyr and low resistance to metsulfuron-methyl. Conversely, Ahasl1-4 allele endowed high levels of resistance for both herbicides. Dominance of resistance at whole-plant level showed a semi-dominant behavior among the alleles for both herbicides. CONCLUSION Ahasl1-4 allele confers higher resistance levels than Ahasl1-1 when evaluated with imazapyr and metsulfuron-methyl. Dominance estimations suggested that both parental lines should carry a resistance trait when developing hybrids. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Gabriela Breccia
- IICAR, UNR, CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Laura Gianotto
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
| | | | - Mariano Bulos
- Department of Biotechnology, Nidera S.A., Santa Fe, Argentina
| | - Graciela Nestares
- IICAR, UNR, CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
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Wang X, Zhang H, Quinn PJ. Production of l-valine from metabolically engineered Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:4319-4330. [DOI: 10.1007/s00253-018-8952-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 01/25/2023]
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Piao Z, Wang W, Wei Y, Zonta F, Wan C, Bai J, Wu S, Wang X, Fang J. Characterization of an acetohydroxy acid synthase mutant conferring tolerance to imidazolinone herbicides in rice (Oryza sativa). PLANTA 2018; 247:693-703. [PMID: 29170911 DOI: 10.1007/s00425-017-2817-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/18/2017] [Indexed: 06/07/2023]
Abstract
The acetohydroxy acid synthase S627N mutation confers herbicide tolerance in rice, and the rice variety containing this mutation produces good yields. This variety is commercially viable at Shanghai and Jiangsu regions in China. Weedy rice is a type of rice that produces lower yields and poorer quality grains than cultivated rice. It plagues commercial rice fields in many countries. One strategy to control its proliferation is to develop rice varieties that are tolerant to specific herbicides. Acetohydroxy acid synthase (AHAS) mutations have been found to confer herbicide tolerance to rice. Here, we identified a single mutation (S627N) in AHAS from an indica rice variety that conferred tolerance against imidazolinone herbicides, including imazethapyr and imazamox. A japonica rice variety (JD164) was developed to obtain herbicide tolerance by introducing the mutated indica ahas gene. Imidazolinone application was sufficient to efficiently control weedy rice in the JD164 field. Although the imazethapyr treatment caused dwarfing in the JD164 plants, it did not significantly reduce yields. To determine whether the decrease of the ahas mRNA expression caused the dwarfism of JD164 after imazethapyr application, we detected the ahas mRNA level in plants. The abundance of the ahas mRNA in JD164 increased after imidazolinone application, thus excluding the mRNA expression level as a possible cause of dwarfism. Activity assays showed that the mutated AHAS was tolerant to imidazolinone but the catalytic efficiency of the mutated AHAS decreased in its presence. Moreover, the activity of the mutated AHAS decreased more in the presence of imazethapyr than in the presence of imazamox. We observed no difference in the AHAS secondary structures, but homology modeling suggested that the S627N mutation enabled the substrate to access the active site channel in AHAS, resulting in imidazolinone tolerance. Our work combined herbicides with a rice variety to control weedy rice and showed the mechanism of herbicide tolerance in this rice variety.
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Affiliation(s)
- Zhongze Piao
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agriculture Sciences, 1000 Jingqi Rd, Shanghai, 201403, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 99 Haike Rd, Shanghai, 201210, China
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 99 Haike Rd, Shanghai, 201210, China
- Department of Biomedical Sciences, Institute of Cell Biology and Neurobiology, Italian National Research Council, 00015, Monterotondo, RM, Italy
| | - Changzhao Wan
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agriculture Sciences, 1000 Jingqi Rd, Shanghai, 201403, China
| | - Jianjiang Bai
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agriculture Sciences, 1000 Jingqi Rd, Shanghai, 201403, China
| | - Shujun Wu
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agriculture Sciences, 1000 Jingqi Rd, Shanghai, 201403, China
| | - Xinqi Wang
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agriculture Sciences, 1000 Jingqi Rd, Shanghai, 201403, China
| | - Jun Fang
- Crop Breeding and Cultivating Institute, Shanghai Academy of Agriculture Sciences, 1000 Jingqi Rd, Shanghai, 201403, China.
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Rehberg N, Akone HS, Ioerger TR, Erlenkamp G, Daletos G, Gohlke H, Proksch P, Kalscheuer R. Chlorflavonin Targets Acetohydroxyacid Synthase Catalytic Subunit IlvB1 for Synergistic Killing of Mycobacterium tuberculosis. ACS Infect Dis 2018; 4:123-134. [PMID: 29108416 DOI: 10.1021/acsinfecdis.7b00055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flavonoid natural compound chlorflavonin was isolated from the endophytic fungus Mucor irregularis, which was obtained from the Cameroonian medicinal plant Moringa stenopetala. Chlorflavonin exhibited strong growth inhibitory activity in vitro against Mycobacterium tuberculosis (MIC90 1.56 μM) while exhibiting no cytotoxicity toward the human cell lines MRC-5 and THP-1 up to concentrations of 100 μM. Mapping of resistance-mediating mutations employing whole-genome sequencing, chemical supplementation assays, and molecular docking studies as well as enzymatic characterization revealed that chlorflavonin specifically inhibits the acetohydroxyacid synthase catalytic subunit IlvB1, causing combined auxotrophies to branched-chain amino acids and to pantothenic acid. While exhibiting a bacteriostatic effect in monotreatment, chlorflavonin displayed synergistic effects with the first-line antibiotic isoniazid and particularly with delamanid, leading to a complete sterilization in liquid culture in combination treatment. Using a fluorescent reporter strain, intracellular activity of chlorflavonin against Mycobacterium tuberculosis inside infected macrophages was demonstrated and was superior to streptomycin treatment.
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Affiliation(s)
- Nidja Rehberg
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Herve Sergi Akone
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Faculty of Science, Department of Chemistry, University of Douala,
PO Box 24157, 2701 Douala, Cameroon
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, 710 Ross St., College Station, Texas 77843, United States
| | - German Erlenkamp
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Georgios Daletos
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Peter Proksch
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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42
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Liu Y, Li Y, Wang X. Molecular evolution of acetohydroxyacid synthase in bacteria. Microbiologyopen 2017; 6. [PMID: 28782269 PMCID: PMC5727371 DOI: 10.1002/mbo3.524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 11/16/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) is the key enzyme in the biosynthetic pathways of branched chain amino acids in bacteria. Since it does not exist in animal and plant cells, AHAS is an attractive target for developing antimicrobials and herbicides. In some bacteria, there is a single copy of AHAS, while in others there are multiple copies. Therefore, it is necessary to investigate the origin and evolutionary pathway of various AHASs in bacteria. In this study, all the available protein sequences of AHAS in bacteria were investigated, and an evolutionary model of AHAS in bacteria is proposed, according to gene structure, organization and phylogeny. Multiple copies of AHAS in some bacteria might be evolved from the single copy of AHAS, the ancestor. Gene duplication, domain deletion and horizontal gene transfer might occur during the evolution of this enzyme. The results show the biological significance of AHAS, help to understand the functions of various AHASs in bacteria, and would be useful for developing industrial production strains of branched chain amino acids or novel antimicrobials.
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Affiliation(s)
- Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yanyan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
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43
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Jia X, Liu Y, Han Y. A thermophilic cell-free cascade enzymatic reaction for acetoin synthesis from pyruvate. Sci Rep 2017; 7:4333. [PMID: 28659601 PMCID: PMC5489476 DOI: 10.1038/s41598-017-04684-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/18/2017] [Indexed: 11/09/2022] Open
Abstract
Acetoin (3-hydroxy-2-butanone) is an important bio-based platform chemical with wide applications. In vitro enzyme catalysed synthesis exhibits great feasibility in the production of chemicals with high purity. In the present work, a synthetic pathway involving a two-step continuous reaction was constructed in vitro for acetoin production from pyruvate at improved temperature. Thermostable candidates, acetolactate synthase (coAHASL1 and coAHASL2 from Caldicellulosiruptor owensensis OL) and α-acetolactate decarboxylase (bsALDC from Bacillus subtilis IPE5-4) were cloned, heterologously expressed, and characterized. All the enzymes showed maximum activities at 65–70 °C and pH of 6.5. Enzyme kinetics analysis showed that coAHASL1 had a higher activity but lower affinity against pyruvate than that of coAHASL2. In addition, the activities of coAHASL1 and bsALDC were promoted by Mn2+ and NADPH. The cascade enzymatic reaction was optimized by using coAHASL1 and bsALDC based on their kinetic properties. Under optimal conditions, a maximum concentration of 3.36 ± 0.26 mM acetoin was produced from 10 mM pyruvate after reaction for 24 h at 65 °C. The productivity of acetoin was 0.14 mM h−1, and the yield was 67.80% compared with the theoretical value. The results confirmed the feasibility of synthesis of acetoin from pyruvate with a cell-free enzyme catalysed system at improved temperature.
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Affiliation(s)
- Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ying Liu
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.
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