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Bhosale R, Jewell JB, Hollunder J, Koo AJ, Vuylsteke M, Michoel T, Hilson P, Goossens A, Howe GA, Browse J, Maere S. Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants. Plant Cell 2013; 25:2865-77. [PMID: 23943861 PMCID: PMC3784585 DOI: 10.1105/tpc.113.112268] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/16/2013] [Accepted: 07/18/2013] [Indexed: 05/20/2023]
Abstract
Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene network structure as expression profiles of pooled plant samples under controlled experimental perturbations. We advocate the use of subtle uncontrolled variations in gene expression between individuals to uncover functional links between genes and unravel regulatory influences. As a case study, we use this approach to identify ILL6 as a new regulatory component of the jasmonate response pathway.
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Affiliation(s)
- Rahul Bhosale
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jeremy B. Jewell
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
| | - Jens Hollunder
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Abraham J.K. Koo
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Tom Michoel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Gregg A. Howe
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
| | - Steven Maere
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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Nakata M, Mitsuda N, Herde M, Koo AJ, Moreno JE, Suzuki K, Howe GA, Ohme-Takagi M. A bHLH-type transcription factor, ABA-INDUCIBLE BHLH-TYPE TRANSCRIPTION FACTOR/JA-ASSOCIATED MYC2-LIKE1, acts as a repressor to negatively regulate jasmonate signaling in arabidopsis. Plant Cell 2013; 25:1641-56. [PMID: 23673982 PMCID: PMC3694697 DOI: 10.1105/tpc.113.111112] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/19/2013] [Accepted: 04/25/2013] [Indexed: 05/20/2023]
Abstract
Jasmonates (JAs) are plant hormones that regulate the balance between plant growth and responses to biotic and abiotic stresses. Although recent studies have uncovered the mechanisms for JA-induced responses in Arabidopsis thaliana, the mechanisms by which plants attenuate the JA-induced responses remain elusive. Here, we report that a basic helix-loop-helix-type transcription factor, ABA-INDUCIBLE BHLH-TYPE TRANSCRIPTION FACTOR/JA-ASSOCIATED MYC2-LIKE1 (JAM1), acts as a transcriptional repressor and negatively regulates JA signaling. Gain-of-function transgenic plants expressing the chimeric repressor for JAM1 exhibited substantial reduction of JA responses, including JA-induced inhibition of root growth, accumulation of anthocyanin, and male fertility. These plants were also compromised in resistance to attack by the insect herbivore Spodoptera exigua. Conversely, jam1 loss-of-function mutants showed enhanced JA responsiveness, including increased resistance to insect attack. JAM1 and MYC2 competitively bind to the target sequence of MYC2, which likely provides the mechanism for negative regulation of JA signaling and suppression of MYC2 functions by JAM1. These results indicate that JAM1 negatively regulates JA signaling, thereby playing a pivotal role in fine-tuning of JA-mediated stress responses and plant growth.
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Affiliation(s)
- Masaru Nakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Marco Herde
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Abraham J.K. Koo
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Javier E. Moreno
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Kaoru Suzuki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Gregg A. Howe
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
- Institute for Environmental Science and Technology, Saitama University, Saitama 338-8770, Japan
- Address correspondence to
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Abstract
Plant tissues are highly vulnerable to injury by herbivores, pathogens, mechanical stress, and other environmental insults. Optimal plant fitness in the face of these threats relies on complex signal transduction networks that link damage-associated signals to appropriate changes in metabolism, growth, and development. Many of these wound-induced adaptive responses are triggered by de novo synthesis of the plant hormone jasmonate (JA). Recent studies provide evidence that JA mediates systemic wound responses through distinct cell autonomous and non-autonomous pathways. In both pathways, bioactive JAs are recognized by an F-box protein-based receptor system that couples hormone binding to ubiquitin-dependent degradation of transcriptional repressor proteins. These results provide a framework for understanding how plants recognize and respond to tissue injury.
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Affiliation(s)
- Abraham J.K. Koo
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Gregg A. Howe
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Corresponding author: Tel.: 1-517-355-5159; Fax: 1-517-353-9168. E-mail address:
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Katsir L, Chung HS, Koo AJ, Howe GA. Jasmonate signaling: a conserved mechanism of hormone sensing. Curr Opin Plant Biol 2008; 11:428-35. [PMID: 18583180 PMCID: PMC2560989 DOI: 10.1016/j.pbi.2008.05.004] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 05/12/2008] [Accepted: 05/16/2008] [Indexed: 05/20/2023]
Abstract
The lipid-derived hormone jasmonate (JA) regulates diverse aspects of plant immunity and development. Among the central components of the JA signaling cascade are the E3 ubiquitin ligase SCFCOI1 and Jasmonate ZIM-domain (JAZ) proteins that repress transcription of JA-responsive genes. Recent studies provide evidence that amino acid-conjugated forms of JA initiate signal transduction upon formation of a coronatine-insensitive1 (COI1)-JA-JAZ ternary complex in which JAZs are ubiquitinated and subsequently degraded. Coronatine, a virulence factor produced by the plant pathogen Pseudomonas syringae, is a potent agonist of this hormone receptor system. Coronatine-induced targeting of JAZs to COI1 obstructs host immune responses to P. syrinage, providing a striking example of how pathogens exploit hormone signaling pathways in the host to promote disease. These findings, together with homology between COI1 and the auxin receptor, TIR1, extend the paradigm of F-box proteins as intracellular sensors of small molecules, and suggest a common evolutionary origin of the auxin and JA response pathways.
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