1
|
Figueroa NE, Hernandez-Sanchez IE, Maruri-Lopez I, Chodasiewicz M. Affinity Purification Protocol Starting with a Small Molecule as Bait. Methods Mol Biol 2023; 2554:11-19. [PMID: 36178617 DOI: 10.1007/978-1-0716-2624-5_2] [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] [Indexed: 06/16/2023]
Abstract
Protein-metabolite interactions (PMIs) are fundamental for several biological processes. Even though PMI studies have increased in recent years, our knowledge is still limited. The screening of PMIs using small molecules as bait will broaden our ability to uncover novel PMIs, setting the basis for establishing their biological relevance. Here, we describe a protocol that allows the identification of multiple protein partners for one ligand. This protocol describes a straightforward methodology that can be adapted to a wide variety of organisms.
Collapse
Affiliation(s)
- Nicolás E Figueroa
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Itzell E Hernandez-Sanchez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| |
Collapse
|
2
|
Bloch I, Haviv H, Rapoport I, Cohen E, Shushan RSB, Dotan N, Sher I, Hacham Y, Amir R, Gal M. Discovery and characterization of small molecule inhibitors of cystathionine gamma-synthase with in planta activity. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1785-1797. [PMID: 33773037 PMCID: PMC8428831 DOI: 10.1111/pbi.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
The synthesis of essential amino acids in plants is pivotal for their viability and growth, and these cellular pathways are therefore targeted for the discovery of new molecules for weed control. Herein, we describe the discovery and design of small molecule inhibitors of cystathionine gamma-synthase, a key enzyme in the biosynthesis of methionine. Based on in silico screening and filtering of a large molecular database followed by the in vitro selection of molecules, we identified small molecules capable of binding the target enzyme. Molecular modelling of the interaction and direct biophysical binding enabled us to explore a focussed chemical expansion set of molecules characterized by an active phenyl-benzamide chemical group. These molecules are bio-active and efficiently inhibit the viability of BY-2 tobacco cells and seedlings growth of Arabidopsis thaliana on agar plates.
Collapse
Affiliation(s)
- Itai Bloch
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | - Hadar Haviv
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | | | - Elad Cohen
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | | | - Nesly Dotan
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | - Inbal Sher
- Department of Oral BiologyThe Goldschleger School of Dental MedicineSackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Yael Hacham
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
- Tel‐Hai CollegeUpper GalileeIsrael
| | - Rachel Amir
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
- Tel‐Hai CollegeUpper GalileeIsrael
| | - Maayan Gal
- Department of Oral BiologyThe Goldschleger School of Dental MedicineSackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| |
Collapse
|
3
|
Omeprazole Promotes Chloride Exclusion and Induces Salt Tolerance in Greenhouse Basil. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9070355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The role of small bioactive molecules (<500 Da) in mechanisms improving resource use efficiency in plants under stress conditions draws increasing interest. One such molecule is omeprazole (OMP), a benzimidazole derivative and inhibitor of animal proton pumps shown to improve nitrate uptake and exclusion of toxic ions, especially of chloride from the cytosol of salt-stressed leaves. Currently, OMP was applied as substrate drench at two rates (0 or 10 μM) on hydroponic basil (Ocimum basilicum L. cv. Genovese) grown under decreasing NO3−:Cl− ratio (80:20, 60:40, 40:60, or 20:80). Chloride concentration and stomatal resistance increased while transpiration, net CO2 assimilation rate and beneficial ions (NO3−, PO43−, and SO42−) decreased with reduced NO3−:Cl− ratio under the 0 μM OMP treatment. The negative effects of chloride were not only mitigated by the 10 μM OMP application in all treatments, with the exception of 20:80 NO3−:Cl−, but plant growth at 80:20, 60:40, and 40:60 NO3−:Cl− ratios receiving OMP application showed maximum fresh yield (+13%, 24%, and 22%, respectively), shoot (+10%, 25%, and 21%, respectively) and root (+32%, 76%, and 75%, respectively) biomass compared to the corresponding untreated treatments. OMP was not directly involved in ion homeostasis and compartmentalization of vacuolar or apoplastic chloride. However, it was active in limiting chloride loading into the shoot, as manifested by the lower chloride concentration in the 80:20, 60:40, and 40:60 NO3−:Cl− treatments compared to the respective controls (−41%, −37%, and −24%), favoring instead that of nitrate and potassium while also boosting photosynthetic activity. Despite its unequivocally beneficial effect on plants, the large-scale application of OMP is currently limited by the molecule’s high cost. However, further studies are warranted to unravel the molecular mechanisms of OMP-induced reduction of chloride loading to shoot and improved salt tolerance.
Collapse
|
4
|
Jørgensen FP, Madsen D, Meldal M, Olsen JV, Petersen M, Granhøj J, Bols M. Synthesis of Shld Derivatives, Their Binding to the Destabilizing Domain, and Influence on Protein Accumulation in Transgenic Plants. J Med Chem 2019; 62:5191-5216. [PMID: 31059249 DOI: 10.1021/acs.jmedchem.9b00497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 35 analogues of Shld with modifications in the A-residue and the C-residues were prepared and investigated for binding to FKBP and GFP accumulation in transgenic plants. The modifications investigated explored variations that were supposedly inside or outside the receptor binding site with the latter being important by influencing the overall polarity of the compounds in order to improve the absorption in plants. The binding of the new compounds to the destabilizing domain was determined using a fluorescence polarization competition assay, and the GFP expression in engineered Arabidopsis thaliana was studied. The results showed that modifications of the C-building block phenol with acidic, basic, and neutral groups led to better ligands with some being better than Shld in the plant. Generally small, polar substituents showed the best GFP accumulation.
Collapse
Affiliation(s)
- Frederik Præstholm Jørgensen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Daniel Madsen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Morten Meldal
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Jacob Valdbjørn Olsen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Morten Petersen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Jeppe Granhøj
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Mikael Bols
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| |
Collapse
|
5
|
Farkas E, Oláh M, Földi A, Kóti J, Éles J, Nagy J, Gal CA, Paizs C, Hornyánszky G, Poppe L. Chemoenzymatic Dynamic Kinetic Resolution of Amines in Fully Continuous-Flow Mode. Org Lett 2018; 20:8052-8056. [DOI: 10.1021/acs.orglett.8b03676] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emese Farkas
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Márk Oláh
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Attila Földi
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - János Kóti
- Gedeon Richter Plc., P.O. Box 27, H-1475 Budapest, Hungary
| | - János Éles
- Gedeon Richter Plc., P.O. Box 27, H-1475 Budapest, Hungary
| | - József Nagy
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Cristian Andrei Gal
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, Arany János str. 11, RO-400028 Cluj-Napoca, Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, Arany János str. 11, RO-400028 Cluj-Napoca, Romania
| | - Gábor Hornyánszky
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- SynBiocat LLC., Szilasliget u. 3, H-1172 Budapest, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, Arany János str. 11, RO-400028 Cluj-Napoca, Romania
- SynBiocat LLC., Szilasliget u. 3, H-1172 Budapest, Hungary
| |
Collapse
|
6
|
Rugen MD, Vernet MMJL, Hantouti L, Soenens A, Andriotis VME, Rejzek M, Brett P, van den Berg RJBHN, Aerts JMFG, Overkleeft HS, Field RA. A chemical genetic screen reveals that iminosugar inhibitors of plant glucosylceramide synthase inhibit root growth in Arabidopsis and cereals. Sci Rep 2018; 8:16421. [PMID: 30401902 PMCID: PMC6219604 DOI: 10.1038/s41598-018-34749-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/19/2018] [Indexed: 01/11/2023] Open
Abstract
Iminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- L-ido-deoxynojirimycin (L-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of L-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. L-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species.
Collapse
Affiliation(s)
- Michael D Rugen
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mathieu M J L Vernet
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Laila Hantouti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amalia Soenens
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Vasilios M E Andriotis
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Richard J B H N van den Berg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Hermen S Overkleeft
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| |
Collapse
|
7
|
Joglekar S, Suliman M, Bartsch M, Halder V, Maintz J, Bautor J, Zeier J, Parker JE, Kombrink E. Chemical Activation of EDS1/PAD4 Signaling Leading to Pathogen Resistance in Arabidopsis. PLANT & CELL PHYSIOLOGY 2018; 59:1592-1607. [PMID: 29931201 DOI: 10.1093/pcp/pcy106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Indexed: 05/20/2023]
Abstract
In a chemical screen we identified thaxtomin A (TXA), a phytotoxin from plant pathogenic Streptomyces scabies, as a selective and potent activator of FLAVIN-DEPENDENT MONOOXYGENASE1 (FMO1) expression in Arabidopsis (Arabidopsis thaliana). TXA induction of FMO1 was unrelated to the production of reactive oxygen species (ROS), plant cell death or its known inhibition of cellulose synthesis. TXA-stimulated FMO1 expression was strictly dependent on ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) but independent of salicylic acid (SA) synthesis via ISOCHORISMATE SYNTHASE1 (ICS1). TXA induced the expression of several EDS1/PAD4-regulated genes, including EDS1, PAD4, SENESCENCE ASSOCIATED GENE101 (SAG101), ICS1, AGD2-LIKE DEFENSE RESPONSE PROTEIN1 (ALD1) and PATHOGENESIS-RELATED PROTEIN1 (PR1), and accumulation of SA. Notably, enhanced ALD1 expression did not result in accumulation of the product pipecolic acid (PIP), which promotes FMO1 expression during biologically induced systemic acquired resistance. TXA treatment preferentially stimulated expression of PAD4 compared with EDS1, which was mirrored by PAD4 protein accumulation, suggesting that TXA leads to increased PAD4 availability to form EDS1-PAD4 signaling complexes. Also, TXA treatment of Arabidopsis plants led to enhanced disease resistance to bacterial and oomycete infection, which was dependent on EDS1 and PAD4, as well as on FMO1 and ICS1. Collectively, the data identify TXA as a potentially useful chemical tool to conditionally activate and interrogate EDS1- and PAD4-controlled pathways in plant immunity.
Collapse
Affiliation(s)
- Shachi Joglekar
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Mohamed Suliman
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Michael Bartsch
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Vivek Halder
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jens Maintz
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jürgen Zeier
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| |
Collapse
|
8
|
Rouphael Y, Raimondi G, Lucini L, Carillo P, Kyriacou MC, Colla G, Cirillo V, Pannico A, El-Nakhel C, De Pascale S. Physiological and Metabolic Responses Triggered by Omeprazole Improve Tomato Plant Tolerance to NaCl Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:249. [PMID: 29535755 PMCID: PMC5835327 DOI: 10.3389/fpls.2018.00249] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/12/2018] [Indexed: 05/09/2023]
Abstract
Interest in the role of small bioactive molecules (< 500 Da) in plants is on the rise, compelled by plant scientists' attempt to unravel their mode of action implicated in stimulating growth and enhancing tolerance to environmental stressors. The current study aimed at elucidating the morphological, physiological and metabolomic changes occurring in greenhouse tomato (cv. Seny) treated with omeprazole (OMP), a benzimidazole inhibitor of animal proton pumps. The OMP was applied at three rates (0, 10, or 100 μM) as substrate drench for tomato plants grown under nonsaline (control) or saline conditions sustained by nutrient solutions of 1 or 75 mM NaCl, respectively. Increasing NaCl concentration from 1 to 75 mM decreased the tomato shoot dry weight by 49% in the 0 μM OMP treatment, whereas the reduction was not significant at 10 or 100 μM of OMP. Treatment of salinized (75 mM NaCl) tomato plants with 10 and especially 100 μM OMP decreased Na+ and Cl- while it increased Ca2+ concentration in the leaves. However, OMP was not strictly involved in ion homeostasis since the K+ to Na+ ratio did not increase under combined salinity and OMP treatment. OMP increased root dry weight, root morphological characteristics (total length and surface), transpiration, and net photosynthetic rate independently of salinity. Metabolic profiling of leaves through UHPLC liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry facilitated identification of the reprogramming of a wide range of metabolites in response to OMP treatment. Hormonal changes involved an increase in ABA, decrease in auxins and cytokinin, and a tendency for GA down accumulation. Cutin biosynthesis, alteration of membrane lipids and heightened radical scavenging ability related to the accumulation of phenolics and carotenoids were observed. Several other stress-related compounds, such as polyamine conjugates, alkaloids and sesquiterpene lactones, were altered in response to OMP. Although a specific and well-defined mechanism could not be posited, the metabolic processes involved in OMP action suggest that this small bioactive molecule might have a hormone-like activity that ultimately elicits an improved tolerance to NaCl salinity stress.
Collapse
Affiliation(s)
- Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Giampaolo Raimondi
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Petronia Carillo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Marios C. Kyriacou
- Department of Vegetable Crops, Agricultural Research Institute, Nicosia, Cyprus
| | - Giuseppe Colla
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Valerio Cirillo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Antonio Pannico
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Christophe El-Nakhel
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Stefania De Pascale
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| |
Collapse
|
9
|
Ma Q, Grones P, Robert S. Auxin signaling: a big question to be addressed by small molecules. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:313-328. [PMID: 29237069 PMCID: PMC5853230 DOI: 10.1093/jxb/erx375] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/16/2017] [Indexed: 05/20/2023]
Abstract
Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.
Collapse
Affiliation(s)
- Qian Ma
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
| | - Peter Grones
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
| | | |
Collapse
|
10
|
Oláh M, Boros Z, Hornyánszky G, Poppe L. Isopropyl 2-ethoxyacetate—an efficient acylating agent for lipase-catalyzed kinetic resolution of amines in batch and continuous-flow modes. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
11
|
Serra AA, Couée I, Heijnen D, Michon-Coudouel S, Sulmon C, Gouesbet G. Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress. FRONTIERS IN PLANT SCIENCE 2015; 6:1124. [PMID: 26734031 PMCID: PMC4681785 DOI: 10.3389/fpls.2015.01124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/27/2015] [Indexed: 05/26/2023]
Abstract
Lolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling.
Collapse
Affiliation(s)
- Anne-Antonella Serra
- Centre National de la Recherche Scientifique, Université de Rennes 1, UMR 6553 ECOBIORennes, France
| | - Ivan Couée
- Centre National de la Recherche Scientifique, Université de Rennes 1, UMR 6553 ECOBIORennes, France
| | - David Heijnen
- Centre National de la Recherche Scientifique, Université de Rennes 1, UMR 6553 ECOBIORennes, France
| | - Sophie Michon-Coudouel
- Centre National de la Recherche Scientifique, Université de Rennes 1, UMS 3343 OSURRennes, France
| | - Cécile Sulmon
- Centre National de la Recherche Scientifique, Université de Rennes 1, UMR 6553 ECOBIORennes, France
| | - Gwenola Gouesbet
- Centre National de la Recherche Scientifique, Université de Rennes 1, UMR 6553 ECOBIORennes, France
| |
Collapse
|
12
|
Lahaye M, Falourd X, Limami AM, Foucat L. Water mobility and microstructure evolution in the germinating Medicago truncatula seed studied by NMR relaxometry. A revisited interpretation of multicomponent relaxation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:1698-710. [PMID: 25619228 DOI: 10.1021/jf505515n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The water status of Medicago truncatula Gaertn. seed was followed by low-field NMR relaxometry during germination with and without oryzalin or fusicoccin used as growth modulators. T1 and T2 relaxation times and proportions P1 and P2 were determined on fresh, frozen, and freeze-thawed samples to characterize changes in water dynamics and compartmentation and in the nonfreezing water fraction. The results demonstrate that low-field NMR relaxometry allowed differentiating germination phases and events occurring during them as well as perturbations related to the presence of growth modulators. The results provide clear evidence that the classical multicomponent relaxation interpretation cannot directly relate T2 components and morphological compartments in biological tissue.
Collapse
Affiliation(s)
- Marc Lahaye
- INRA, UR1268 Biopolymers, Interactions and Assemblies, rue de la Géraudière, F-44316 Nantes, France
| | | | | | | |
Collapse
|
13
|
Halder V, Kombrink E. Facile high-throughput forward chemical genetic screening by in situ monitoring of glucuronidase-based reporter gene expression in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2015; 6:13. [PMID: 25688251 PMCID: PMC4310277 DOI: 10.3389/fpls.2015.00013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/07/2015] [Indexed: 05/20/2023]
Abstract
The use of biologically active small molecules to perturb biological functions holds enormous potential for investigating complex signaling networks. However, in contrast to animal systems, the search for and application of chemical tools for basic discovery in the plant sciences, generally referred to as "chemical genetics," has only recently gained momentum. In addition to cultured cells, the well-characterized, small-sized model plant Arabidopsis thaliana is suitable for cultivation in microplates, which allows employing diverse cell- or phenotype-based chemical screens. In such screens, a chemical's bioactivity is typically assessed either through scoring its impact on morphological traits or quantifying molecular attributes such as enzyme or reporter activities. Here, we describe a facile forward chemical screening methodology for intact Arabidopsis seedlings harboring the β-glucuronidase (GUS) reporter by directly quantifying GUS activity in situ with 4-methylumbelliferyl-β-D-glucuronide (4-MUG) as substrate. The quantitative nature of this screening assay has an obvious advantage over the also convenient histochemical GUS staining method, as it allows application of statistical procedures and unbiased hit selection based on threshold values as well as distinction between compounds with strong or weak bioactivity. At the same time, the in situ bioassay is very convenient requiring less effort and time for sample handling in comparison to the conventional quantitative in vitro GUS assay using 4-MUG, as validated with several Arabidopsis lines harboring different GUS reporter constructs. To demonstrate that the developed assays is particularly suitable for large-scale screening projects, we performed a pilot screen for chemical activators or inhibitors of salicylic acid-mediated defense signaling using the Arabidopsis PR1p::GUS line. Importantly, the screening methodology provided here can be adopted for any inducible GUS reporter line.
Collapse
Affiliation(s)
| | - Erich Kombrink
- *Correspondence: Erich Kombrink, Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany e-mail:
| |
Collapse
|
14
|
Walsh TA. Early stage hit triage for plant chemical genetic screens and target site identification. Methods Mol Biol 2014; 1056:191-199. [PMID: 24306874 DOI: 10.1007/978-1-62703-592-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The increasing use of plant biological screens of large compound libraries to discover informative chemical probes for plant chemical genetics requires efficient methods for hit selection and advancement. Downstream target identification and validation studies with selected chemistries can also be resource-intensive and have a significant failure rate. Several steps and considerations for early stage hit triage are outlined to increase the probability of success that downstream studies with the chemical probe will be robust and productive, especially for target site discovery. Conversely, problematic compounds can be shelved or avoided entirely, saving time and resources. These steps include assessment of compound availability, purity, stability and solubility; determination of the biological dose-response; early and iterative evaluation of analogs; avoidance of promiscuous "frequent-hitters"; consideration of physicochemical parameters affecting compound bioavailability and mobility, use of "low-barrier" biological testing systems; and assessing the potential for compound metabolism or bioconversion.
Collapse
Affiliation(s)
- Terence A Walsh
- Discovery Research, Dow AgroSciences LLC, Indianapolis, IN, USA
| |
Collapse
|
15
|
Hicks GR, Raikhel NV. Plant chemical biology: are we meeting the promise? FRONTIERS IN PLANT SCIENCE 2014; 5:455. [PMID: 25250041 PMCID: PMC4157539 DOI: 10.3389/fpls.2014.00455] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/22/2014] [Indexed: 05/04/2023]
Abstract
As an early adopter of plant chemical genetics to the study of endomembrane trafficking, we have observed the growth of small molecule approaches. Within the field, we often describe the strengths of the approach in a broad, generic manner, such as the ability to address redundancy and lethality. But, we are now in a much better position to evaluate the demonstrated value of the approach based on examples. In this perspective, we offer an assessment of chemical genetics in plants and where its applications may be of particular utility from the perspective of the cell biologist. Beyond this, we suggest areas to be addressed to provide broader access and enhance the effectiveness of small molecule approaches in plant biology.
Collapse
Affiliation(s)
- Glenn R. Hicks
- *Correspondence: Glenn R. Hicks, Center for Plant Cell Biology, Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California, Riverside,CA 92521, USA e-mail:
| | | |
Collapse
|
16
|
Couée I, Serra AA, Ramel F, Gouesbet G, Sulmon C. Physiology and toxicology of hormone-disrupting chemicals in higher plants. PLANT CELL REPORTS 2013; 32:933-41. [PMID: 23553555 DOI: 10.1007/s00299-013-1428-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/15/2013] [Accepted: 03/19/2013] [Indexed: 05/13/2023]
Abstract
Higher plants are exposed to natural environmental organic chemicals, associated with plant-environment interactions, and xenobiotic environmental organic chemicals, associated with anthropogenic activities. The effects of these chemicals result not only from interaction with metabolic targets, but also from interaction with the complex regulatory networks of hormone signaling. Purpose-designed plant hormone analogues thus show extensive signaling effects on gene regulation and are as such important for understanding plant hormone mechanisms and for manipulating plant growth and development. Some natural environmental chemicals also act on plants through interference with the perception and transduction of endogenous hormone signals. In a number of cases, bioactive xenobiotics, including herbicides that have been designed to affect specific metabolic targets, show extensive gene regulation effects, which are more in accordance with signaling effects than with consequences of metabolic effects. Some of these effects could be due to structural analogies with plant hormones or to interference with hormone metabolism, thus resulting in situations of hormone disruption similar to animal cell endocrine disruption by xenobiotics. These hormone-disrupting effects can be superimposed on parallel metabolic effects, thus indicating that toxicological characterisation of xenobiotics must take into consideration the whole range of signaling and metabolic effects. Hormone-disruptive signaling effects probably predominate when xenobiotic concentrations are low, as occurs in situations of residual low-level pollutions. These hormone-disruptive effects in plants may thus be of importance for understanding cryptic effects of low-dosage xenobiotics, as well as the interactive effects of mixtures of xenobiotic pollutants.
Collapse
Affiliation(s)
- Ivan Couée
- Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Université de Rennes 1, Campus de Beaulieu, bâtiment 14A, 35042 Rennes Cedex, France.
| | | | | | | | | |
Collapse
|
17
|
Mishev K, Dejonghe W, Russinova E. Small Molecules for Dissecting Endomembrane Trafficking: A Cross-Systems View. ACTA ACUST UNITED AC 2013; 20:475-86. [DOI: 10.1016/j.chembiol.2013.03.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 01/31/2023]
|
18
|
Gouws LM, Botes E, Wiese AJ, Trenkamp S, Torres-Jerez I, Tang Y, Hills PN, Usadel B, Lloyd JR, Fernie AR, Kossmann J, van der Merwe MJ. The plant growth promoting substance, lumichrome, mimics starch, and ethylene-associated symbiotic responses in lotus and tomato roots. FRONTIERS IN PLANT SCIENCE 2012; 3:120. [PMID: 22701462 PMCID: PMC3371600 DOI: 10.3389/fpls.2012.00120] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/18/2012] [Indexed: 05/08/2023]
Abstract
Symbiosis involves responses that maintain the plant host and symbiotic partner's genetic program; yet these cues are far from elucidated. Here we describe the effects of lumichrome, a flavin identified from Rhizobium spp., applied to lotus (Lotus japonicus) and tomato (Solanum lycopersicum). Combined transcriptional and metabolite analyses suggest that both species shared common pathways that were altered in response to this application under replete, sterile conditions. These included genes involved in symbiosis, as well as transcriptional and metabolic responses related to enhanced starch accumulation and altered ethylene metabolism. Lumichrome priming also resulted in altered colonization with either Mesorhizobium loti (for lotus) or Glomus intraradices/G. mossea (for tomato). It enhanced nodule number but not nodule formation in lotus; while leading to enhanced hyphae initiation and delayed arbuscule maturation in tomato.
Collapse
Affiliation(s)
- Liezel M. Gouws
- Institute of Plant Biotechnology, Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Eileen Botes
- Institute of Plant Biotechnology, Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Anna J. Wiese
- Institute of Plant Biotechnology, Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Sandra Trenkamp
- Max-Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | | | - Yuhong Tang
- The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Paul N. Hills
- Institute of Plant Biotechnology, Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Björn Usadel
- Max-Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - James R. Lloyd
- Institute of Plant Biotechnology, Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | | | - Jens Kossmann
- Institute of Plant Biotechnology, Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Margaretha J. van der Merwe
- Institute of Plant Biotechnology, Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
- Max-Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| |
Collapse
|
19
|
Hicks GR, Raikhel NV. Small molecules present large opportunities in plant biology. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:261-82. [PMID: 22404475 DOI: 10.1146/annurev-arplant-042811-105456] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Since the introduction of chemical genomics to plant biology as a tool for basic research, the field has advanced significantly. There are now examples of important basic discoveries that demonstrate the power and untapped potential of this approach. Given the combination of protein and small-molecule complexity, new phenotypes can be described through the perturbation of cellular functions that can be linked to growth and developmental phenotypes. There are now clear examples of overcoming functional redundancy in plants to dissect molecular mechanisms or critical pathways such as hormone signaling and dynamic intracellular processes. Owing to ongoing advances, including more sophisticated high-content screening and rapid approaches for target identification, the field is beginning to move forward. However, there are also challenges to improve automation, imaging, and analysis and provide chemical biology resources to the broader plant biology community.
Collapse
Affiliation(s)
- Glenn R Hicks
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
| | | |
Collapse
|
20
|
Rosado A, Hicks GR, Norambuena L, Rogachev I, Meir S, Pourcel L, Zouhar J, Brown MQ, Boirsdore MP, Puckrin RS, Cutler SR, Rojo E, Aharoni A, Raikhel NV. Sortin1-hypersensitive mutants link vacuolar-trafficking defects and flavonoid metabolism in Arabidopsis vegetative tissues. ACTA ACUST UNITED AC 2011; 18:187-97. [PMID: 21338917 DOI: 10.1016/j.chembiol.2010.11.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Revised: 11/23/2010] [Accepted: 11/29/2010] [Indexed: 01/08/2023]
Abstract
Sortin1 is a chemical genetic-hit molecule that causes specific mislocalization of plant and yeast-soluble and membrane vacuolar markers. To better understand its mode of action, we designed a Sortin1-hypersensitive screen and identified several Sortin1-hypersensitive and flavonoid-defective mutants. Mechanistically, Sortin1 mimics the effect of the glutathione inhibitor buthionine sulfoximine and alters the vacuolar accumulation of flavonoids, likely blocking their transport through vacuole-localized ABC transporters. Structure-activity relationship studies conducted in Arabidopsis revealed the structural requirements for Sortin1 bioactivity and demonstrated that overlapping Sortin1 substructures can be used to discriminate between vacuolar-flavonoid accumulations and vacuolar-biogenesis defects. We conclude that Sortin1 is a valuable probe for dissecting novel links among flavonoid transport, vacuolar integrity, and the trafficking of vacuolar targeted cargoes in Arabidopsis.
Collapse
Affiliation(s)
- Abel Rosado
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California-Riverside, CA 92521, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Brown LA, O'Leary-Steele C, Brookes P, Armitage L, Kepinski S, Warriner SL, Baker A. A small molecule with differential effects on the PTS1 and PTS2 peroxisome matrix import pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:980-90. [PMID: 21323771 DOI: 10.1111/j.1365-313x.2010.04473.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The use of small molecules has great power to dissect biological processes. This study presents the identification and characterisation of an inhibitor of peroxisome matrix protein import. A mini-screen was carried out to identify molecules that cause alteration in peroxisome morphology, or mislocalization of a peroxisome targeted fluorescent reporter protein. A benzimidazole lead compound (LDS-003655) was identified that resulted in reduced GFP fluorescence in peroxisomes and cytosolic GFP accumulation. The effect of the compound was specific to peroxisomes as Golgi bodies, endoplasmic reticulum and the actin cytoskeleton were unaffected even at 25 μM, whereas peroxisome import via the PTS1 pathway was compromised at 100 nM. When seedlings were grown on 25 μM LDS-003655 they displayed morphology typical of seedlings grown in the presence of auxin, and expression of the auxin reporter DR5::GFP was induced. Analysis of a focussed library of LDS-003655 derivatives in comparison with known auxins led to the conclusion that the auxin-like activity of LDS-003655 is attributable to its in situ hydrolysis giving rise to 2,5-dichlorobenzoic acid, whereas the import inhibiting activity of LDS-003655 requires the whole molecule. None of the auxins tested had any effect on peroxisome protein import. Matrix import by the PTS2 import pathway was relatively insensitive to LDS-003655 and its active analogues, with effects only seen after prolonged incubation on high concentrations. Steady-state protein levels of PEX5, the PTS1 import pathway receptor, were reduced in the presence of 100 nM LDS-003655, suggesting a possible mechanism for the import inhibition.
Collapse
Affiliation(s)
- Laura-Anne Brown
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS29JT, UK
| | | | | | | | | | | | | |
Collapse
|
22
|
van der Hoorn RAL, Colby T, Nickel S, Richau KH, Schmidt J, Kaiser M. Mining the Active Proteome of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2011; 2:89. [PMID: 22639616 PMCID: PMC3355598 DOI: 10.3389/fpls.2011.00089] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/08/2011] [Indexed: 05/20/2023]
Abstract
Assigning functions to the >30,000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied activity-based protein profiling (ABPP). ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed activities of 76 Arabidopsis proteins. These proteins represent over 10 different protein classes that contain over 250 Arabidopsis proteins, including cysteine, serine, and metalloproteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed additional protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities, e.g., of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry, and proteomics.
Collapse
Affiliation(s)
- Renier A. L. van der Hoorn
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- *Correspondence: Renier A. L. van der Hoorn, Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. e-mail:
| | - Tom Colby
- Proteomics Service Unit, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Sabrina Nickel
- Fakultät für Biologie, Chemische Biologie, Zentrum für Medizinische Biotechnologie, University of Duisburg-EssenEssen, Germany
| | - Kerstin H. Richau
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jürgen Schmidt
- Proteomics Service Unit, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Markus Kaiser
- Fakultät für Biologie, Chemische Biologie, Zentrum für Medizinische Biotechnologie, University of Duisburg-EssenEssen, Germany
| |
Collapse
|
23
|
Rejzek M, Stevenson CE, Southard AM, Stanley D, Denyer K, Smith AM, Naldrett MJ, Lawson DM, Field RA. Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley β-amylase. MOLECULAR BIOSYSTEMS 2010; 7:718-30. [PMID: 21085740 DOI: 10.1039/c0mb00204f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There are major issues regarding the proposed pathway for starch degradation in germinating cereal grain. Given the commercial importance but genetic intractability of the problem, we have embarked on a program of chemical genetics studies to identify and dissect the pathway and regulation of starch degradation in germinating barley grains. As a precursor to in vivo studies, here we report systematic analysis of the reversible and irreversible inhibition of the major β-amylase of the grain endosperm (BMY1). The molecular basis of inhibitor action was defined through high resolution X-ray crystallography studies of unliganded barley β-amylase, as well as its complexes with glycone site binder disaccharide iminosugar G1M, irreversible inhibitors α-epoxypropyl and α-epoxybutyl glucosides, which target the enzyme's catalytic residues, and the aglycone site binders acarbose and α-cyclodextrin.
Collapse
Affiliation(s)
- Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Serrano M, Hubert DA, Dangl JL, Schulze-Lefert P, Kombrink E. A chemical screen for suppressors of the avrRpm1-RPM1-dependent hypersensitive cell death response in Arabidopsis thaliana. PLANTA 2010; 231:1013-23. [PMID: 20140739 PMCID: PMC2840663 DOI: 10.1007/s00425-010-1105-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 01/18/2010] [Indexed: 05/20/2023]
Abstract
Arabidopsis thaliana RPM1 encodes an intracellular immune sensor that conditions disease resistance to Pseudomonas syringae expressing the type III effector protein AvrRpm1. Conditional expression of this type III effector in a transgenic line carrying avrRpm1 under the control of a steroid-inducible promoter results in RPM1-dependent cell death that resembles the cell death response of the incompatible RPM1-avrRpm1 plant-bacterium interaction. This line was previously used in a genetic screen, which revealed two genes that likely function in the folding of pre-activation RPM1. We established a chemical screen for small molecules that suppress steroid-inducible and RPM1-avrRpm1-dependent cell death in Arabidopsis seedlings. Screening of a library comprising 6,800 compounds of natural origin identified two trichothecene-type mycotoxins, 4,15-diacetoxyscirpenol (DAS) and neosolaniol (NEO), which are synthesized by Fusarium and other fungal species. However, protein blot analysis revealed that DAS and NEO inhibit AvrRpm1 synthesis rather than suppress RPM1-mediated responses. This inhibition of translational activity likely explains the survival of the seedlings under screening conditions. Likewise, flg22-induced defense responses are also impaired at the translational, but not the transcriptional, level by DAS or NEO. Unexpectedly, both compounds not only prevented AvrRpm1 synthesis, but rather caused an apparent hyper-accumulation of RPM1 and HSP70. The hyper-accumulation phenotype is likely unrelated to the ribotoxic function of DAS and NEO and could be due to an inhibitory activity on the proteolytic machinery of Arabidopsis or elicitor-like activities of type A trichothecenes.
Collapse
Affiliation(s)
- Mario Serrano
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Present Address: Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - David A. Hubert
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280 USA
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280 USA
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Erich Kombrink
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| |
Collapse
|
25
|
Tóth R, van der Hoorn RAL. Emerging principles in plant chemical genetics. TRENDS IN PLANT SCIENCE 2010; 15:81-8. [PMID: 20036182 DOI: 10.1016/j.tplants.2009.11.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/19/2009] [Accepted: 11/22/2009] [Indexed: 05/04/2023]
Abstract
Chemical genetics is a powerful new discipline in plant science. Bioactive small molecules can be used to identify novel signalling nodes and unravel redundant networks. Observations made so far have revealed a series of principles in plant chemical genetics. These principles concern compound properties, such as bioactivation and bioavailability; and valuable approaches, like the use of derivatives and transcriptomics and successful ways of target identification. Together, these principles explain why the choice of the chemical library is important and instruct the design of future chemical genetic screens.
Collapse
Affiliation(s)
- Réka Tóth
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany.
| | | |
Collapse
|
26
|
Abstract
The success of the genomics revolution to construct a genetic architecture of a variety of model organisms has placed functional biologists under pressure to show what each individual gene does in vivo. Traditionally, this task has fallen on geneticists who systematically perturb gene function and study the consequences. With the advent of large, easily accessible, small-molecule libraries and new methods of chemical synthesis, biologists now have new ways to probe gene function. Often called chemical genetics, this approach involves the screening of compounds that perturb a process of interest. In this scenario, each perturbing chemical is analogous to a specific mutation. Here, we summarize, with specific examples, how chemical genetics is being used in combination with traditional genetics to address problems in plant biology. Because chemical genetics is rooted in genetic analysis, we focus on how chemicals used in combination with genetics can be very powerful in dissecting a process of interest.
Collapse
Affiliation(s)
- Peter McCourt
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, ON, Canada.
| | | |
Collapse
|
27
|
Kaschani F, Verhelst SHL, van Swieten PF, Verdoes M, Wong CS, Wang Z, Kaiser M, Overkleeft HS, Bogyo M, van der Hoorn RAL. Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using 'click chemistry'. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:373-85. [PMID: 18786180 DOI: 10.1111/j.1365-313x.2008.03683.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Small molecules offer unprecedented opportunities for plant research since plants respond to, metabolize, and react with a diverse range of endogenous and exogenous small molecules. Many of these small molecules become covalently attached to proteins. To display these small molecule targets in plants, we introduce a two-step labelling method for minitagged small molecules. Minitags are small chemical moieties (azide or alkyne) that are inert under biological conditions and have little influence on the membrane permeability and specificity of the small molecule. After labelling, proteomes are extracted under denaturing conditions and minitagged proteins are coupled to reporter tags through a 'click chemistry' reaction. We introduce this two-step labelling procedure in plants by studying the well-characterized targets of E-64, a small molecule cysteine protease inhibitor. In contrast to biotinylated E-64, minitagged E-64 efficiently labels vacuolar proteases in vivo. We displayed, purified and identified targets of a minitagged inhibitor that targets the proteasome and cysteine proteases in living plant cells. Chemical interference assays with inhibitors showed that MG132, a frequently used proteasome inhibitor, preferentially inhibits cysteine proteases in vivo. The two-step labelling procedure can be applied on detached leaves, cell cultures, seedlings and other living plant tissues and, when combined with photoreactive groups, can be used to identify targets of herbicides, phytohormones and reactive small molecules selected from chemical genetic screens.
Collapse
Affiliation(s)
- Farnusch Kaschani
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Sergeant MJ, Li JJ, Fox C, Brookbank N, Rea D, Bugg TDH, Thompson AJ. Selective inhibition of carotenoid cleavage dioxygenases: phenotypic effects on shoot branching. J Biol Chem 2008; 284:5257-64. [PMID: 19098002 PMCID: PMC2643498 DOI: 10.1074/jbc.m805453200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Members of the carotenoid cleavage dioxygenase family catalyze the
oxidative cleavage of carotenoids at various chain positions, leading to the
formation of a wide range of apocarotenoid signaling molecules. To explore the
functions of this diverse enzyme family, we have used a chemical genetic
approach to design selective inhibitors for different classes of carotenoid
cleavage dioxygenase. A set of 18 arylalkyl-hydroxamic acids was synthesized
in which the distance between an iron-chelating hydroxamic acid and an
aromatic ring was varied; these compounds were screened as inhibitors of four
different enzyme classes, either in vitro or in vivo. Potent
inhibitors were found that selectively inhibited enzymes that cleave
carotenoids at the 9,10 position; 50% inhibition was achieved at submicromolar
concentrations. Application of certain inhibitors at 100 μm to
Arabidopsis node explants or whole plants led to increased shoot
branching, consistent with inhibition of 9,10-cleavage.
Collapse
Affiliation(s)
- Martin J Sergeant
- Warwick HRI, University of Warwick, Wellesbourne CV35, 9EF, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
29
|
Walsh TA. The emerging field of chemical genetics: potential applications for pesticide discovery. PEST MANAGEMENT SCIENCE 2007; 63:1165-71. [PMID: 17912687 DOI: 10.1002/ps.1452] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The use of small molecules to probe biological systems, generally described as 'chemical genetics', has grown considerably in the past 7 years, especially in areas related to human biology and therapeutics. This review describes some aspects of chemical genetics technologies that can be usefully applied to pesticide target discovery and lead generation. The chemical genetics approach (consisting of a phenotype screen, a chemical library and a robust target identification methodology) is compared with conventional and target-based screening. The outcomes of a chemical genetics approach are novel protein targets coupled with in vivo-active chemical ligands. The 'chemistry-first' paradigm of the chemical genetics approach can circumvent some of the obstacles that have emerged for the exploitation of novel but chemically unvalidated targets identified from genetic or genomic screens. Some of the advantages and challenges in using chemical genetics approaches are reviewed.
Collapse
Affiliation(s)
- Terence A Walsh
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, USA.
| |
Collapse
|