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Menges M, Dóczi R, Ökrész L, Morandini P, Mizzi L, Soloviev M, Murray JAH, Bögre L. Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways. New Phytol 2008; 179:643-662. [PMID: 18715324 DOI: 10.1111/j.1469-8137.2008.02552.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
* Mitogen activated protein kinase (MAPK) pathways are signal transduction modules with layers of protein kinases having c. 120 genes in Arabidopsis, but only a few have been linked experimentally to functions. * We analysed microarray expression data for 114 MAPK signalling genes represented on the ATH1 Affymetrix arrays; determined their expression patterns during development, and in a wide range of time-course microarray experiments for their signal-dependent transcriptional regulation and their coregulation with other signalling components and transcription factors. * Global expression correlation of the MAPK genes with each of the represented 21 692 Arabidopsis genes was determined by calculating Pearson correlation coefficients. To group MAPK signalling genes based on similarities in global regulation, we performed hierarchical clustering on the pairwise correlation values. This should allow inferring functional information from well-studied MAPK components to functionally uncharacterized ones. Statistical overrepresentation of specific gene ontology (GO) categories in the gene lists showing high expression correlation values with each of the MAPK components predicted biological themes for the gene functions. * The combination of these methods provides functional information for many uncharacterized MAPK genes, and a framework for complementary future experimental dissection of the function of this complex family.
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Affiliation(s)
- Margit Menges
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK
| | - Róbert Dóczi
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - László Ökrész
- Institute of Plant Biology, Biological Research Centre, POB 521, H-6701, Szeged, Hungary
| | - Piero Morandini
- Department of Biology, University of Milan and CNR Biophysics Institute (Milan Section), Via Celoria 26, I-20133 Milan, Italy
| | - Luca Mizzi
- Department of Biomolecular Sciences and Biotechnology, University of Milan and CNR Biophysics Institute (Milan Section), Via Celoria 26, I-20133 Milan, Italy
| | - Mikhail Soloviev
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - James A H Murray
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK
| | - László Bögre
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
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Farrás R, Ferrando A, Jásik J, Kleinow T, Ökrész L, Tiburcio A, Salchert K, del Pozo C, Schell J, Koncz C. SKP1-SnRK protein kinase interactions mediate proteasomal binding of a plant SCF ubiquitin ligase. EMBO J 2001; 20:2742-56. [PMID: 11387208 PMCID: PMC125500 DOI: 10.1093/emboj/20.11.2742] [Citation(s) in RCA: 188] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Arabidopsis Snf1-related protein kinases (SnRKs) are implicated in pleiotropic regulation of metabolic, hormonal and stress responses through their interaction with the kinase inhibitor PRL1 WD-protein. Here we show that SKP1/ASK1, a conserved SCF (Skp1-cullin-F-box) ubiquitin ligase subunit, which suppresses the skp1-4 mitotic defect in yeast, interacts with the PRL1-binding C-terminal domains of SnRKs. The same SnRK domains recruit an SKP1/ASK1-binding proteasomal protein, alpha4/PAD1, which enhances the formation of a trimeric SnRK complex with SKP1/ASK1 in vitro. By contrast, PRL1 reduces the interaction of SKP1/ASK1 with SnRKs. SKP1/ASK1 is co-immunoprecipitated with a cullin SCF subunit (AtCUL1) and an SnRK kinase, but not with PRL1 from Arabidopsis cell extracts. SKP1/ASK1, cullin and proteasomal alpha-subunits show nuclear co-localization in differentiated Arabidopsis cells, and are observed in association with mitotic spindles and phragmoplasts during cell division. Detection of SnRK in purified 26S proteasomes and co-purification of epitope- tagged SKP1/ASK1 with SnRK, cullin and proteasomal alpha-subunits indicate that the observed protein interactions between SnRK, SKP1/ASK1 and alpha4/PAD1 are involved in proteasomal binding of an SCF ubiquitin ligase in Arabidopsis.
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Affiliation(s)
- Rosa Farrás
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Alejandro Ferrando
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Ján Jásik
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Tatjana Kleinow
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - László Ökrész
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Antonio Tiburcio
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Klaus Salchert
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Carlos del Pozo
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Jeff Schell
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
| | - Csaba Koncz
- Max-Planck Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany, Department of Plant Physiology, Comenius University, Mlynska dolina B2, 84215 Bratislava, Slovakia, Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, Temesvári krt. 62, Hungary, Unitat de Fisiologia Vegetal, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Centro de Biologia Molecular ‘Severo Ochoa’, Cantoblanco, 28049 Madrid, Spain and Risoe National Laboratory, Plant Biology and Biogeochemistry Department, DK-4000 Roskilde, Denmark Corresponding author e-mail:
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