1
|
New-Generation Chemical Tools for the Manipulation of Auxin Biosynthesis, Action, and Transport. Methods Mol Biol 2019. [PMID: 30694472 DOI: 10.1007/978-1-4939-9015-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Auxin is the master regulator for almost every aspect of plant growth and development. Small molecule inhibitors, fluorescently labeled molecule, and hormone analogs on auxin biosynthesis, transport, and signaling, so-called auxin chemical tools, have been widely utilized to dissect physiological functions of gene families in auxin biosynthesis, transport, and signaling. Auxin chemical tools can manipulate specific auxin-regulated events at any developmental stage. Chemical tools can modulate the function of orthologs of target proteins and also can overcome the redundant function of large family gene controlling auxin-regulated response. On the other hand, chemical tool might induce the off-target effects at high concentration, if the chemical tool shows insufficient specificity on target proteins. This chapter describes a brief overview and practical application of the auxin chemical tools.
Collapse
|
2
|
Kerchev PI, De Clercq I, Denecker J, Mühlenbock P, Kumpf R, Nguyen L, Audenaert D, Dejonghe W, Van Breusegem F. Mitochondrial perturbation negatively affects auxin signaling. MOLECULAR PLANT 2014; 7:1138-50. [PMID: 24903751 DOI: 10.1093/mp/ssu071] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Mitochondria are crucial players in the signaling and metabolic homeostasis of the plant cell. The molecular components that orchestrate the underlying processes, however, are largely unknown. Using a chemical biology approach, we exploited the responsiveness of Arabidopsis UDP-glucosyltransferase-encoding UGT74E2 towards mitochondrial perturbation in order to look for novel mechanisms regulating mitochondria-to-nucleus communication. The most potent inducers of UGT74E2 shared a (2-furyl)acrylate (FAA) substructure that negatively affected mitochondrial function and was identified before as an auxin transcriptional inhibitor. Based on these premises, we demonstrated that perturbed mitochondria negatively affect the auxin signaling machinery. Moreover, chemical perturbation of polar auxin transport and auxin biosynthesis was sufficient to induce mitochondrial retrograde markers and their transcript abundance was constitutively elevated in the absence of the auxin transcriptional activators ARF7 and ARF19.
Collapse
Affiliation(s)
- Pavel Ivanov Kerchev
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Inge De Clercq
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jordi Denecker
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | | | - Robert Kumpf
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Long Nguyen
- d VIB Compound Screening Facility, B-9052 Gent, Belgium
| | - Dominique Audenaert
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium d VIB Compound Screening Facility, B-9052 Gent, Belgium
| | - Wim Dejonghe
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Frank Van Breusegem
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| |
Collapse
|
3
|
Kania U, Fendrych M, Friml J. Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biol 2014; 4:140017. [PMID: 24740985 PMCID: PMC4043115 DOI: 10.1098/rsob.140017] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Although plant and animal cells use a similar core mechanism to deliver proteins
to the plasma membrane, their different lifestyle, body organization and
specific cell structures resulted in the acquisition of regulatory mechanisms
that vary in the two kingdoms. In particular, cell polarity regulators do not
seem to be conserved, because genes encoding key components are absent in plant
genomes. In plants, the broad knowledge on polarity derives from the study of
auxin transporters, the PIN-FORMED proteins, in the model plant
Arabidopsis thaliana. In animals, much information is
provided from the study of polarity in epithelial cells that exhibit basolateral
and luminal apical polarities, separated by tight junctions. In this review, we
summarize the similarities and differences of the polarization mechanisms
between plants and animals and survey the main genetic approaches that have been
used to characterize new genes involved in polarity establishment in plants,
including the frequently used forward and reverse genetics screens as well as a
novel chemical genetics approach that is expected to overcome the limitation of
classical genetics methods.
Collapse
Affiliation(s)
- Urszula Kania
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | | | | |
Collapse
|
4
|
Hu Y, Yang L, Na X, You J, Hu W, Liang X, Liu J, Mao L, Wang X, Wang H, Bi Y. Narciclasine inhibits the responses of Arabidopsis roots to auxin. PLANTA 2012; 236:597-612. [PMID: 22476291 DOI: 10.1007/s00425-012-1632-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/22/2012] [Indexed: 05/31/2023]
Abstract
The plant hormone auxin plays a central role in the regulation of plant growth and development, as well as in responses to environmental stimuli. Narciclasine (NCS, an Amaryllidaceae alkaloid) isolated from Narcissus tazetta bulbs has a broad range of inhibitory effects on plants. In this study, the role of NCS in responses to auxin in Arabidopsis thaliana roots was investigated. We demonstrated the inhibitory effects of NCS on auxin-inducible lateral root formation, root hair formation, primary root growth, and the expression of primary auxin-inducible genes in Arabidopsis roots using DR5::GUS reporter gene, native auxin promoters (IAA12::GUS, IAA13::GUS), and quantitative reverse transcription PCR analysis. Results also showed that NCS did not affect the expression of cytokinin-inducible ARR5::GUS reporter gene. NCS relieved the auxin-enhanced degradation of the Aux/IAA repressor modulated by the SCFTIR1 ubiquitin-proteasome pathway. In addition, NCS did not alter the auxin-stimulated interaction between IAA7/AXR2 (Aux/IAA proteins) and the F-box protein TIR1 activity of the proteasome. Taken together, these results suggest that NCS acts on the auxin signaling pathway upstream of TIR1, which modulates Aux/IAA protein degradation, and thereby affects the auxin-mediated responses in Arabidopsis roots.
Collapse
Affiliation(s)
- Yanfeng Hu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
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
|
6
|
De Rybel B, Audenaert D, Beeckman T, Kepinski S. The past, present, and future of chemical biology in auxin research. ACS Chem Biol 2009; 4:987-98. [PMID: 19736989 DOI: 10.1021/cb9001624] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Research into the plant hormone auxin has always been tightly linked with the use of small molecules. In fact, most of the known players in auxin signaling and transport in the model plant Arabidopsis thaliana were identified by screening for resistance to auxin analogues. The use of high-throughput screening technologies has since yielded many novel molecules, opening the way for the identification of new target proteins to further elucidate known pathways. Here, we give an overview of well-established and novel molecules used in auxin research and highlight the current status and future perspectives of chemical biology approaches to auxin biology.
Collapse
Affiliation(s)
- Bert De Rybel
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
- Department Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Dominique Audenaert
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
- Department Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
- Department Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Stefan Kepinski
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, U.K
| |
Collapse
|
7
|
Hayashi KI, Kamio S, Oono Y, Townsend LB, Nozaki H. Toyocamycin specifically inhibits auxin signaling mediated by SCFTIR1 pathway. PHYTOCHEMISTRY 2009; 70:190-197. [PMID: 19171357 DOI: 10.1016/j.phytochem.2008.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 11/25/2008] [Accepted: 12/16/2008] [Indexed: 05/27/2023]
Abstract
The auxins, plant hormones, play a crucial role in many aspects of plant development by regulating cell division, elongation and differentiation. Toyocamycin, a nucleoside-type antibiotic, was identified as auxin signaling inhibitor in a screen of microbial extracts for inhibition of the auxin-inducible reporter gene assay. Toyocamycin specifically inhibited auxin-responsive gene expression, but did not affect other hormone-inducible gene expression. Toyocamycin also blocked auxin-enhanced degradation of the Aux/IAA repressor modulated by the SCF(TIR1) ubiquitin-proteasome pathway without inhibiting proteolytic activity of proteasome. Furthermore, toyocamycin inhibited auxin-induced lateral root formation and epinastic growth of cotyledon in the Arabidopsis thaliana plant. This evidence suggested that toyocamycin would act on the ubiquitination process regulated by SCF(TIR1) machineries. To address the structural requirements for the specific activity of toyocamycin on auxin signaling, the structure-activity relationships of nine toyocamycin-related compounds, including sangivamycin and tubercidin, were investigated.
Collapse
Affiliation(s)
- Ken-ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, 1-1 Ridai-cho, Okayama City 700-0005, Japan.
| | | | | | | | | |
Collapse
|
8
|
Robert S, Raikhel NV, Hicks GR. Powerful partners: Arabidopsis and chemical genomics. THE ARABIDOPSIS BOOK 2009; 7:e0109. [PMID: 22303245 PMCID: PMC3243329 DOI: 10.1199/tab.0109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chemical genomics (i.e. genomics scale chemical genetics) approaches capitalize on the ability of low molecular mass molecules to modify biological processes. Such molecules are used to modify the activity of a protein or a pathway in a manner that it is tunable and reversible. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. A major advantage of this approach as a powerful addition to conventional plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Furthermore, the ability of chemicals to be added at will and to act quickly can permit the study of processes that are highly dynamic such as endomembrane trafficking. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure-activity relationships and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms from which the results can be translated to plants. In addition, there are approaches utilizing "tagged" chemical libraries that possess reactive moieties permitting the immobilization of active compounds. This opens the possibility for biochemical purification of putative cognate targets. We will review approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis and provide several examples of the power and challenges inherent in this new approach in plant biology.
Collapse
Affiliation(s)
- Stéphanie Robert
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
- Current address: VIB Department of Plant Systems Biology, University of Ghent, 9052 Ghent, Belgium
| | - Natasha V. Raikhel
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Glenn R. Hicks
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
- Address correspondence to
| |
Collapse
|