Abstract
Chemical genetics is a scientific strategy that utilizes bioactive small molecules as experimental tools to dissect biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that potentially can be used as activators or inhibitors of biochemical pathways, transport processes, regulatory networks, or developmental programs. Screening methods to identify bioactive small molecules can vary greatly, ranging from visual evaluation of phenotypic alterations to quantifying biometric traits such as enzyme activities. Here, we describe a general methodology that permits identification of compounds modulating the expression of reporter genes in Arabidopsis thaliana seedlings. The selection of luciferase-based reporter systems has the advantage that it allows in vivo imaging of reporter gene activity in a semiquantitative manner without affecting plant viability. We chose an Arabidopsis line harboring the luciferase reporter under the control of the jasmonate-inducible LOX2 promoter to screen for either activators or inhibitors of gene expression. The outlined assay conditions can readily be applied to Arabidopsis lines containing other reporter genes. Thereby screening for small molecules affecting different signaling pathways and/or phenotypic responses is possible.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hicks GR, Raikhel NV (2012) Small molecules present large opportunities in plant biology. Annu Rev Plant Biol 63:261–282
Smukste I, Stockwell BR (2005) Advances in chemical genetics. Annu Rev Genom Human Genet 6:261–286
Schreiber SL (1998) Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg Med Chem 6:1127–1152
Stockwell BR (2000) Chemical genetics: ligand-based discovery of gene function. Nat Rev Genet 1:116–125
Mayer TU (2003) Chemical genetics: tailoring tools for cell biology. Trends Cell Biol 13:270–277
Gangadhar NM, Stockwell BR (2007) Chemical genetic approaches to probing cell death. Curr Opin Chem Biol 11:83–87
Blackwell HE, Zhao Y (2003) Chemical genetic approaches to plant biology. Plant Physiol 133:448–455
Armstrong JI, Yuan S, Dale JM, Tanner VN, Theologis A (2004) Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in Arabidopsis. Proc Natl Acad Sci U S A 101:14978–14983
Walsh TA (2007) The emerging field of chemical genetics: potential applications for pesticide discovery. Pest Manag Sci 63:1165–1171
Serrano M, Robatzek S, Torres M, Kombrink E, Somssich IE, Robinson M, Schulze-Lefert P (2007) 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 282:6803–6811
Hicks GR, Raikhel NV (2009) Opportunities and challenges in plant chemical biology. Nat Chem Biol 5:268–272
Tóth R, van der Hoorn RAL (2010) Emerging principles in plant chemical genetics. Trends Plant Sci 15:81–88
McCourt P, Desveaux D (2010) Plant chemical genetics. New Phytol 185:15–26
Tornero P, Chao RA, Luthin WN, Goff SA, Dangl JL (2002) Large-scale structure-function analysis of the Arabidopsis RPM1 disease resistance protein. Plant Cell 14:435–450
Park S-Y, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Chow TF, Alfred SE, Bonetta D, Finkelstein R, Provart NJ, Desveaux D, Rodriguez PL, McCourt P, Zhu J-K, Schroeder JI, Volkman BF, Cutler SR (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324:1068–1071
Lin L-C, Hsu J-H, Wang L-C (2010) Identification of novel inhibitors of 1-aminocyclopropane-1-carboxylic acid synthase by chemical screening in Arabidopsis thaliana. J Biol Chem 285:33445–33456
Zhao Y, Dai X, Blackwell HE, Schreiber SL, Chory J (2003) SIR1, an upstream component in auxin signaling identified by chemical genetics. Science 301:1107–1110
Zouhar J, Hicks GR, Raikhel NV (2004) Sorting inhibitors (Sortins): chemical compounds to study vacuolar sorting in Arabidopsis. Proc Natl Acad Sci U S A 101:9497–9501
Surpin M, Rojas-Pierce M, Carter C, Hicks GR, Vasquez J, Raikhel NV (2005) The power of chemical genomics to study the link between endomembrane system components and the gravitropic response. Proc Natl Acad Sci U S A 102:4902–4907
Yoneda A, Higaki T, Kutsuna N, Kondo Y, Osada H, Hasezawa S, Matsui M (2007) Chemical genetic screening identifies a novel inhibitor of parallel alignment of cortical microtubules and cellulose microfibrils. Plant Cell Physiol 48:1393–1403
DeBolt S, Gutierrez R, Ehrhardt DW, Melo CV, Ross L, Cutler SR, Somerville C, Bonetta D (2007) Morlin, an inhibitor of cortical microtubule dynamics and cellulose synthase movement. Proc Natl Acad Sci U S A 104:5854–5859
Gendron JM, Haque A, Gendron N, Chang T, Asami T, Wang Z-Y (2008) Chemical genetic dissection of brassinosteroid-ethylene interaction. Mol Plant 1:368–379
Robert S, Chary SN, Drakakaki G, Li S, Yang Z, Raikhel NV, Hicks GR (2008) Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor BRI1 and the auxin transporters PIN2 and AUX1. Proc Natl Acad Sci U S A 105:8464–8469
Schreiber K, Wenzislava C, Peek J, Desveaux D (2008) A high-throughput chemical screen for resistance to Pseudomonas syringae in Arabidopsis. Plant J 54:522–531
Knoth C, Salus MS, Girke T, Eulgem T (2009) The synthetic elicitor 3,5-dichloroanthranilic acid induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis. Plant Physiol 150:333–347
Serrano M, Hubert DA, Dangl JL, Schulze-Lefert P, Kombrink E (2010) A chemical screen for suppressors of the avrRpm1-RPM1-dependent hypersensitive cell death response in Arabidopsis thaliana. Planta 231:1013–1023
Zhao Y, Chow TF, Puckrin RS, Alfred SE, Korir AK, Larive CK, Cutler SR (2007) Chemical genetic interrogation of natural variation uncovers a molecule that is glycoactivated. Nat Chem Biol 3:716–721
Savaldi-Goldstein S, Baiga TJ, Pojer F, Dabi T, Butterfield C, Parry G, Santner A, Dharmasiri N, Tao Y, Estelle M, Noel JP, Chory J (2008) New auxin analogs with growth-promoting effects in intact plants reveal a chemical strategy to improve hormone delivery. Proc Natl Acad Sci U S A 105:15190–15195
Bassel GW, Fung P, Chow TF, Foong JA, Provart NJ, Cutler SR (2008) Elucidating the germination transcriptional program using small molecules. Plant Physiol 147:143–155
De Rybel B, Audenaert D, Vert G, Rozhon W, Mayerhofer J, Peelman F, Coutuer S, Denayer T, Jansen L, Nguyen L, Vanhoutte I, Beemster GTS, Vleminckx K, Jonak C, Chory J, Inzé D, Russinova E, Beeckman T (2009) Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling. Chem Biol 16:594–604
Kim T-H, Hauser F, Ha T, Xue S, Böhmer M, Nishimura N, Munemasa S, Hubbard K, Peine N, Lee B-H, Lee S, Robert N, Parker JE, Schroeder JI (2011) Chemical genetics reveals negative regulation of abscisic acid signaling by a plant immune response pathway. Curr Biol 21:990–997
Jensen AB, Raventos D, Mundy J (2002) Fusion genetic analysis of jasmonate-signalling mutants in Arabidopsis. Plant J 29:595–606
Thorne N, Auld DS, Inglese J (2010) Apparent activity in high-throughput screening: origins of compound-dependent assay interference. Curr Opin Chem Biol 14:315–324
Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497
Schreiber SL (2000) Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 287:1964–1969
Kaiser M, Wetzel S, Kumar K, Waldmann H (2008) Biology-inspired synthesis of compound libraries. Cell Mol Life Sci 65:1186–1201
Malo N, Hanley JA, Cerquozzi S, Pelletier J, Nadon R (2006) Statistical practice in high-throughput screening data analysis. Nat Biotechnol 24:167–175
Acknowledgements
This work was supported by the Max Planck Society and a PhD fellowship from the International Max Planck Research School program (C.M.). We thank Dr. Ferenc Nagy (Institute of Plant Biology, Szeged, Hungary) for providing the Arabidopsis line harboring the CaMV35Sp::LUC gene and Dr. John Mundy (University of Copenhagen, Denmark) for providing the Arabidopsis LOX2p::LUC LOX2p::GUS line.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Meesters, C., Kombrink, E. (2014). Screening for Bioactive Small Molecules by In Vivo Monitoring of Luciferase-Based Reporter Gene Expression in Arabidopsis thaliana . In: Hicks, G., Robert, S. (eds) Plant Chemical Genomics. Methods in Molecular Biology, vol 1056. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-592-7_3
Download citation
DOI: https://doi.org/10.1007/978-1-62703-592-7_3
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-591-0
Online ISBN: 978-1-62703-592-7
eBook Packages: Springer Protocols