Strategies and future trends to identify the mode of action of phytotoxic compounds

Plant Science

Volumn 212, Issue , 2013, Pages 60-71

  Tresch, Stefan ^a  

^a BASF SE   (Germany)

Author keywords

Chemical genetics; Herbicide; Mechanism of action; Mode of action; Phytotoxic compound

Indexed keywords

HERBICIDE;

CHEMICAL GENETICS; CHEMISTRY; DRUG DEVELOPMENT; DRUG EFFECT; EVALUATION STUDY; GENETICS; MECHANISM OF ACTION; METABOLISM; METHODOLOGY; MODE OF ACTION; PHENOTYPE; PHYTOTOXIC COMPOUND; PLANT; REVIEW;

CHEMICAL GENETICS; HERBICIDE; MECHANISM OF ACTION; MODE OF ACTION; PHYTOTOXIC COMPOUND;

DRUG DISCOVERY; HERBICIDES; PHENOTYPE; PLANTS;

EID: 84883675157     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2013.08.005     Document Type: Review

References (127)

1. Dayan F.E., Duke S.O., Grossmann K. Herbicides as probes in plant biology. Weed Sci. 2010, 58:340-350.
2. Rosellini D. Selectable marker genes from plants: reliability and potential. In vitro Cell. Dev. Biol. Plant 2011, 47:222-233.
3. Min Y.K., et al. New lead compounds for brassinosteroid biosynthesis inhibitors. Bioorg. Med. Chem. Lett. 1999, 9:425-430.
4. Grozinger C.M., Chao E.D., Blackwell H.E., Moazed D., Schreiber S.L. Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J. Biol. Chem. 2001, 276:38837-38843.
5. Armstrong J.I., Yuan S., Dale J.M., Tanner V.N., Theologis A. Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:14978-14983.
6. Weigel D., Ahn J.H., Blazquez M.A., Borevitz J.O., Lamb C.J. Activation tagging in Arabidopsis. Plant Physiol. 2000, 122:1003-1013.
7. Waterhouse P.M., Helliwell C.A. Exploring plant genomes by RNA-induced gene silencing. Nat. Rev. Genet. 2003, 4:29-38.
8. Cutler S., McCourt P. Dude, where's my phenotype? Dealing with redundancy in signaling networks. Plant Physiol. 2005, 138:558-559.
9. Blackwell H.E., Zhao Y. Chemical genetic approaches to plant biology. Plant Physiol. 2003, 133:448-455.
10. Walsh T.A. The emerging field of chemical genetics: potential applications for pesticide discovery. Pest. Manage. Sci. 2007, 63:1165-1171.
11. Toth R., van der Hoorn R.A.L. Emerging principles in plant chemical genetics. Trends Plant Sci. 2010, 15:81-88.
12. Hicks G.R., Raikhel N.V. Small molecules present large opportunities in plant biology. Annu. Rev. Plant Biol. 2012, 63:261-282.
13. Wielopolska A., Townley H., Moore I., Waterhouse P., Helliwell C. A high-throughput inducible RNAi vector for plants. Plant Biotechnol. 2005, 3:583-590.
14. Dharmasiri N., Dharmasiri S., Estelle M. The F-box protein TIR1 is an auxin receptor. Nature 2005, 435:441-445.
15. Kepinski S., Leyser O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 2005, 435:446-451.
16. Walsh T.A., et al. Mutations in an auxin receptor homolog AFB5 and in SGT1b confer resistance to synthetic picolinate auxin and not to 2,4-dichlorphenoxyacetic acid or indole-3-acetic acid in Arabidopsis. Plant Physiol. 2006, 142:542-552.
17. Lein W., et al. Target-based discovery of novel herbicides. Curr. Opin. Plant Biol. 2004, 7:219-225.
18. Duff S.M.G., et al. The carboxyterminal processing protease of D1 protein: herbicidal activity of novel inhibitors of the recombinant and native spinach enzymes. Pestic. Biochem. Physiol. 2007, 88:1-13.
19. Congreve M., Murray C.W., Blundell T.L. Keynote review: structural biology and drug discovery. Drug Discov. Today 2005, 10:895-907.
20. Occhipinti A., et al. Effectiveness and mode of action of phosphonate inhibitors of plant glutamine synthetase. Pest. Manage. Sci. 2010, 66:51-58.
21. Witschel M., et al. Inhibitors of the herbicidal target IspD: allosteric site binding. Angew. Chem. 2011, 50:7931-7935.
22. Duke S.O. Why have no new herbicide modes of action appeared in recent years?. Pest. Manage. Sci. 2012, 68:505-512.
23. Rüegg W.T., Quadranti M., Zoschke A. Herbicide research and development: challenges and opportunities. Weed Res. 2007, 47:271-275.
24. Shaner D.L. Herbicide safety relative to common targets in plants and mammals. Pest. Manage. Sci. 2003, 60:17-24.
25. Mulwa R.M.S., Mwanza L.M. Biotechnology approaches to developing herbicide tolerance/selectivity in crops. Afr. J. Biotechnol. 2006, 5:396-404.
26. Scott B.A., Vangessel M.J., White-Hansen S. Herbicide-resistant weeds in the United States and their impact on extension. Weed Technol. 2009, 23:599-603.
27. Beckie H.J., Tardif F.J. Herbicide cross resistance in weeds. Crop Prot. 2012, 35:15-28.
28. Zhao Y., et al. Chemical genetic interrogation of natural variation uncovers a molecule that is glycoactivated. Nat. Chem. Biol. 2007, 3:716-721.
29. Park S.Y., et al. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 2009, 324:1068-1071.
30. Frye S.V. The art of the chemical probe. Nat. Chem. Biol. 2010, 6:159-161.
31. Grossmann K., Tresch S., Plath P. Triaziflam and diaminotriazine affect enantioselectively multiple herbicide target sites. Z. Naturforsch. 2001, 56:559-569.
32. Dai X., Hayashi K., Nozaki H., Cheng Y., Zhao Y. Genetic and chemical analyses of the action mechanisms of sirtinol in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:3129-3134.
33. Grossmann K. Auxin herbicides: current status of mechanism and mode of action. Pest. Manage. Sci. 2010, 66:113-120.
34. Steinbrücken H.C., Amrhein N. The herbicide glyphosate is a potent inhibitor of 5-enolpyruvylshikimic acid-3-phosphate synthase. Biochem. Biophys. Res. Commun. 1980, 94:1207-1212.
35. Shaner D.L., Anderson P.C., Stidham M.A. Imidazolinones - potent inhibitors of acetohydroxyacid synthase. Plant. Physiol. 1984, 76:545-546.
36. LaRossa R.A., Schloss J.V. The sulfonylurea herbicide sulfometuron methyl is an extremely potent and selective inhibitor of acetolactate synthase in Salmonella typhimurium. J. Biol. Chem. 1984, 259:8753-8757.
37. Wessels J.S.C., Vanderveen R. The action of some derivatives of phenylurethan and of 3-phenyl-1,1-dimethylurea on the Hill reaction. Biochim. Biophys. Acta 1956, 19:548-549.
38. Pfister K., Steinback K.E., Gardner G., Arntzen C.J. Photoaffinity-labeling of an herbicide receptor protein in chloroplast membranes. Proc. Natl. Acad. Sci. U.S.A. 1981, 78:981-985.
39. Yamamoto E., Zeng L., Baird W. Alpha-tubulin missense mutations correlate with antimicrotubule drug resistance in Eleusine indica. Plant Cell 1998, 10:297-308.
40. Berg D., Tietjen K., Wollweber D., Hein R. From genes to targets: impact of functional genomics in herbicide discovery. Weeds 1999, 2:491-500.
41. The Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
42. Walsh T.A., et al. Chemical genetic identification of glutamine phosphoribosylpyrophosphate amidotransferase as the target for a novel bleaching herbicide in Arabidopsis. Plant Physiol. 2007, 144:1292-1304.
43. Williams M. Enabling technologies in drug discovery: the technical and cultural integration of the new with the old. Comprehensive Medicinal Chemistry 2007, vol. II:265-287. Elsevier Ltd., Oxford.
44. He W., et al. A small-molecule screen identifies L-kynurenine as a competitive inhibitor of TAA1/TAR activity in ethylene-directed auxin biosynthesis and root growth in Arabidopsis. Plant Cell 2011, 23:3944-3960.
45. Cottier S., et al. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: potential and limitations. Front. Plant Sci. 2011, 2:1-12.
46. Tice C.M. Selecting the right compounds for screening: does Lipinski's Rule of 5 for pharmaceuticals apply to agrochemicals?. Pest. Manage. Sci. 2001, 57:3-16.
47. Hopkins A.L., Groom C.R. The druggable genome. Nat. Rev. Cancer 2002, 1:727-730.
48. Perola E., Herman L., Weiss J. Development of a rule-based method for the assessment of protein druggability. J. Chem. Inf. Model. 2012, 52:1027-1038.
49. Sasaki Y., Nagano Y. Plant acetyl-coA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding. Biosci. Biotechnol. Biochem. 2004, 68:1175-1184.
50. Incledon B.J., Hall J.C. Acetyl-coenzyme A carboxylase: quaternary structure and inhibition by graminicidal herbicides. Pestic. Biochem. Physiol. 1997, 57:255-271.
51. Schmalfuß J., Matthes B., Mayer P., Böger P. Chloracetamide mode of action. I: Inhibition of very long chain fatty acid synthesis in Scenedesmus acutus. Z. Naturforsch. 1998, 53:995-1003.
52. Matthes B., Schmalfuß J., Böger P. Chloracetamide mode of action. II: Inhibition of very long chain fatty acid synthesis in higher plants. Z. Naturforsch. 1998, 53:1004-1011.
53. Couderchet M., Schmalfuß J., Böger P. Incorporation of oleic acid into sporopollenin and its inhibition by the chloroacetamide herbicide metazachlor. Pestic. Biochem. Physiol. 1996, 55:189-199.
54. Trenkamp S., Eckes P., Busch M., Fernie A.R. Temporally resolved GC-MS-based metabolic profiling of herbicide treated plants treated reveals that changes in polar primary metabolites alone can distinguish herbicides of differing mode of action. Metabolomics 2009, 5:277-291.
55. Grossmann K., et al. Physionomics and metabolomics - two key approaches in herbicidal mode of action discovery. Pest. Manage. Sci. 2012, 68:494-504.
56. Bouvier F., Harlingue A., Camara B. Molecular analysis of carotenoid cyclase inhibition. Arch. Biochem. Biophys. 1997, 346:53-64.
57. Sandmann G., Bramley P.M., Böger P. New herbicidal inhibitors of carotene biosynthesis. J. Pest. Sci. 1985, 10:19-24.
58. Mayer M.P., Bartlett D.L., Beyer P., Kleinig H. The in vitro mode of action of bleaching herbicides on the desaturation of 15-cis-phytoene and cis-ζ-carotene in isolated daffodil chromoplasts. Pestic. Biochem. Physiol. 1989, 34:111-117.
59. Scheible W., Eshed R., Richmond T., Delmer D., Somerville C. Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in Arabidopsis Ixr1 mutants. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:10079-10084.
60. Rojas-Pierce M., et al. Arabidopsis P-glycoprotein19 participates in the inhibition of gravitropism by gravacin. Chem. Biol. 2007, 14:1366-1376.
61. Sheard L.B., et al. Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor. Nature 2010, 468:400-405.
62. Tan X., et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 2007, 446:640-645.
63. Mur L.A., et al. Exploiting the Brachypodium tool box in cereal and grass research. New Phytol. 2011, 191:334-347.
64. Brkljacic J., et al. Brachypodium as a model for the grasses: today and the future. Plant Physiol. 2011, 157:3-13.
65. Gardner G. Azidoatrazine: photoaffinity label for the site of triazine herbicide action in chloroplasts. Science 1981, 211:937-940.
66. Kaschani F. Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using 'click chemistry'. Plant J. 2009, 57:373-385.
67. Serrano M., et al. Chemical interference of pathogen-associated molecular pattern-triggered immune responses in Arabidopsis reveals a potential role for fatty-acid synthase type II complex-derived lipid signals. J. Biol. Chem. 2007, 282:6803-6811.
68. Dayan F.E., et al. A pathogenic fungi diphenyl ether phytotoxin targets plant enoyl (acyl carrier protein) reductase. Plant Physiol. 2008, 147:1062-1071.
69. McMurry L.M., Oethinger M., Levy S.B. Triclosan targets lipid synthesis. Nature 1998, 394:531-532.
70. Guerineau F., et al. Sulfonamide resistance gene for plant transformation. Plant Mol. Biol. 1990, 15:127-136.
71. Mishima H., Kurihara H., Kobayashi K., Miyazawa S. Gabaculine: γ-aminobutyrate aminotransferase inhibitor of microbial origin. Tetrahedron Lett. 1976, 17:537-540.
72. Anderson C., Gray J.C. Effect of gabaculin on the synthesis of heme and cytochrome f in etiolated wheat seedlings. Plant Physiol. 1991, 96:584-587.
73. Ghannoum M.A., Rice L.B. Antifungal agents: mode of action, mechanisms of resistance, and correlation of these mechanisms with bacterial resistance. Clin. Microbiol. Rev. 1999, 12:501-517.
74. Hedden P., Graebe J.E. Inhibition of gibberellin biosynthesis by paclobutrazol in cell-free homogenates of Cucurbita maxima endosperm and Malus pumila embryos. J. Plant Growth Regul. 1985, 4:111-122.
75. Asami T., et al. Selective interaction of triazole derivatives with DWF4, a cytochrome P450 monooxygenase of the brassinosteroid biosynthetic pathway, correlates with brassinosteroid deficiency in planta. J. Biol. Chem. 2001, 276:25687-25691.
76. Stoller A., Kreuz K., Haake M., Wenger J. Lambda(4),2,4,6-thiatriazines with herbicidal activity. Chimia 2003, 57:725-730.
77. Tresch S., Niggeweg R., Grossmann K. The herbicide flamprop-M-methyl has a new antimicrotubule mechanism of action. Pest. Manage. Sci. 2008, 64:1195-1203.
78. Anthony R.G., Waldin T.R., Ray J.A. Herbicide resistance caused by spontaneous mutation of the cytoskeletal protein tubulin. Nature 1998, 393:260-263.
79. Tresch S., Plath P., Grossmann K. Herbicidal cyanoacrylates with antimicrotubule mechanism of action. Pest. Manage. Sci. 2005, 61:1052-1059.
80. Hayashi K., Ogino K., Oono Y., Uchimiya H., Nozaki H., Yokonolide A. a new inhibitor of auxin signal transduction, from Streptomyces diastatochromogenes B59. J. Antibiot. 2001, 54:573-581.
81. Yamazoe A., Hayashi K., Kuboki A., Ohira S., Nozaki H. The isolation, structural determination, and total synthesis of terfestatin A, a novel auxin signaling inhibitor from Streptomyces sp. Tetrahedron Lett. 2004, 45:8359-8362.
82. Gendron J.M., et al. Chemical genetic dissection of brassinosteroid-ethylene interaction. Mol. Plant 2008, 1:368-379.
83. Hayashi K., et al. Active core structure of terfestatin A, a new specific inhibitor of auxin signaling. Bioorgan. Med. Chem. 2008, 16:5331-5344.
84. Ulmanov T., Murfett J., Hagen G., Guilfoyle T.J. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 1997, 9:1963-1971.
85. Oono Y., Chen Q.C., Overvoorde P.J., Köhler C., Theologis A. Age mutants of Arabidopsis exhibit altered auxin-regulated gene expression. Plant Cell 1998, 10:1649-1662.
86. Hayashi K., Kamio S., Oono Y., Townsend L.B., Nozaki H. Toyocamycin specifically inhibits auxin signaling mediated by SCFTIR1 pathway. Phytochemistry 2009, 70:190-197.
87. Sverak L., Bonar R.A., Langlois A.J., Beard J.W. Inhibition by toyocamycin of RNA synthesis in mammalian cells and in normal and avian tumor virus-infected chick embryo cells. Biochim. Biophys. Acta 1970, 224:441-450.
88. Hatzios K.K. Metabolism and elimination of toxicants. Plant toxicology 2005, 469-518. Marcel Dekker, NY, USA. B. Hock, E.F. Elstner (Eds.).
89. Cseke C., et al. 2 α-phosphohydantocid. The in vivo adenylosuccinate synthetase inhibitor responsible for hydantocidin phytotoxicity. Pest. Biochem. Physiol. 1996, 55:210-217.
90. Fonne-Pfister R., et al. The mode of action and the structure of a herbicide in complex with its target: binding of activated hydantocidin to the feedback regulation site of adenylosuccinate synthetase. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:9431-9436.
91. Grossmann K. What it takes to get a herbicide's mode of action. Physionomics, a classical approach in a new complexion. Pest. Manage. Sci. 2005, 61:423-431.
92. Eckes P., van Almsick C., Weidler M. Gene expression profiling, a revolutionary tool in Bayer CropScience herbicide discovery. Pflanzensch.-Nachrich. Bayer 2004, 57:62-77.
93. Trenkamp S., Martin W., Tietjen K. Specific and differential inhibition of very-long-chain fatty acid elongases from Arabidopsis thaliana by different herbicides. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:11903-11908.
94. Aliferis K.A., Jabaji S. Metabolomics - a robust bioanalytical approach for the discovery of the modes-of-action of pesticides: a review. Pestic. Biochem. Physiol. 2011, 100:105-117.
95. Eckes P., Busch M. Fast identification of the mode of action of herbicides by DNA chips. Modern Methods in Crop Protection Research 2012, 161-174. Wiley-VCH, Weinheim, Germany. P. Jeschke, W. Krämer, U. Schirmer, M. Witschel (Eds.).
96. Xie D.X., Feys B.F., James S., Nieto-Rostro M., Turner J.G. COI1: an Arabidopsis gene required for jasmonate-regulated defense and fertility. Science 1998, 280:1091-1094.
97. Michel H., et al. The 'light' and 'medium' subunits of the photosynthetic reaction center from Rhodopseudomonas viridis: isolation of the genes, nucleotide and amino acid sequence. EMBO J. 1986, 5:1149-1158.
98. Reina-Pinto J.J., Yephremov A. Lipid determinants of cell death. Plant Signal. Behav. 2009, 4:625-628.
99. La R.N., Rascio N., Oster U., Rüdiger W. Inhibition of lycopene cyclase results in accumulation of chlorophyll precursors. Planta 2007, 225:1019-1029.
100. Laule O., et al. Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:6866-6871.
101. Montezinos D., Delmer D.P. Characterization of inhibitors of cellulose synthesis in cotton fibers. Planta 1980, 305:305-311.
102. Rosado A., et al. Sortin1-hypersensitive mutants link vacuolar-trafficking defects and flavonoid metabolism in Arabidopsis vegetative tissues. Chem. Biol. 2011, 18:187-197.
103. Wheelock C.E., Miyagawa H. The omicization of agrochemical research. J. Pest. Sci. 2006, 31:240-244.
104. Seaver S.M.D., Henry C.S., Hanson A.D. Frontiers in metabolic reconstruction and modeling of plant genomes. J. Exp. Bot. 2012, 63:2247-2258.
105. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
106. Huang B., Bates M., Zhuang X. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 2009, 78:993-1016.
107. Gutierrez R., Grossmann G., Frommer W.B., Ehrhardt D.W. Opportunities to explore plant membrane organization with super-resolution microscopy. Plant Physiol. 2010, 154:463-466.
108. Horn P.J., et al. Spatial mapping of lipids at cellular resolution in embryos of cotton. Plant Cell 2012, 24:622-636.
109. Haynes P.A., Roberts T.H. Subcellular shotgun proteomics in plants: looking beyond the unusual suspects. Proteomics 2007, 7:2963-2975.
110. Metzker M.L. Sequencing technologies - the next generation. Nat. Rev. Genet. 2010, 11:31-46.
111. Trapnell C., et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28:511-515.
112. Wang Y., Shyy J.Y., Chien S. Fluorescence proteins, live-cell imaging, and mechanobiology: seeing is believing, Annu. Rev. Biom. Eng. 2008, 10:1-38.
113. Choi W., Swanson S.J., Gilroy S. High-resolution imaging of Ca2+, redox status, ROS and pH using GFP biosensors. Plant J. 2012, 70:118-128.
114. Lee Y.J., Perdian D.C., Song Z., Yeung E.S., Nikolau J. Use of mass spectrometry for imaging metabolites in plants. Plant J. 2012, 70:81-95.
115. Schneeberger K., Weigel D. Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci. 2011, 16:282-288.
116. Austin R.S., et al. Next-generation mapping of Arabidopsis genes. Plant J. 2011, 67:715-725.
117. Hamilton J.P., Buell C.R. Advances in plant genome sequencing. Plant J. 2012, 70:177-190.
118. Cravatt B.F., Wright A.T., Kozarich J.W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 2008, 77:383-414.
119. Böger P., Matthes B., Schmalfuß J. Towards the primary target of chloroacetamides - new findings pave the way. Pest. Manage. Sci. 2000, 56:497-508.
120. Eckermann C., et al. Covalent binding of chloroacetamide herbicides to the active site cysteine of plant type III polyketide syntheses. Phytochemistry 2003, 64:1045-1054.
121. Chidley C., et al. Searching for the protein targets of bioactive molecules. Chimia 2011, 65:720-724.
122. Keiser M.J., et al. Predicting new molecular targets for known drugs. Nature 2009, 462:175-182.
123. Koutsoukas A., et al. From in silico target prediction to multi-target drug design: current databases, methods and applications. Proteomics 2011, 74:2554-2574.
124. Tresch S. Methods and strategies to identify the mode of action of phytoactive compounds 2012, University of Mainz, (Ph.D. Thesis).
125. Cobb A.H., Reade J.P.H. Herbicides and Plant Physiology 2010, Wiley-Blackwell, Chichester. second ed.
126. Heath R.J., et al. Mechanism of triclosan inhibition of bacterial fatty acid synthesis. J. Biol. Chem. 1999, 274:11110-11114.
127. Trebst A. Inhibitors in the functional dissection of the photosynthetic electron transport system. Photosynth. Res. 2007, 92:217-224.