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Steenackers W, Cesarino I, Klíma P, Quareshy M, Vanholme R, Corneillie S, Kumpf RP, Van de Wouwer D, Ljung K, Goeminne G, Novák O, Zažímalová E, Napier R, Boerjan W, Vanholme B. The Allelochemical MDCA Inhibits Lignification and Affects Auxin Homeostasis. PLANT PHYSIOLOGY 2016; 172:874-888. [PMID: 27506238 PMCID: PMC5047068 DOI: 10.1104/pp.15.01972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 08/03/2016] [Indexed: 05/05/2023]
Abstract
The phenylpropanoid 3,4-(methylenedioxy)cinnamic acid (MDCA) is a plant-derived compound first extracted from roots of Asparagus officinalis and further characterized as an allelochemical. Later on, MDCA was identified as an efficient inhibitor of 4-COUMARATE-CoA LIGASE (4CL), a key enzyme of the general phenylpropanoid pathway. By blocking 4CL, MDCA affects the biosynthesis of many important metabolites, which might explain its phytotoxicity. To decipher the molecular basis of the allelochemical activity of MDCA, we evaluated the effect of this compound on Arabidopsis thaliana seedlings. Metabolic profiling revealed that MDCA is converted in planta into piperonylic acid (PA), an inhibitor of CINNAMATE-4-HYDROXYLASE (C4H), the enzyme directly upstream of 4CL. The inhibition of C4H was also reflected in the phenolic profile of MDCA-treated plants. Treatment of in vitro grown plants resulted in an inhibition of primary root growth and a proliferation of lateral and adventitious roots. These observed growth defects were not the consequence of lignin perturbation, but rather the result of disturbing auxin homeostasis. Based on DII-VENUS quantification and direct measurement of cellular auxin transport, we concluded that MDCA disturbs auxin gradients by interfering with auxin efflux. In addition, mass spectrometry was used to show that MDCA triggers auxin biosynthesis, conjugation, and catabolism. A similar shift in auxin homeostasis was found in the c4h mutant ref3-2, indicating that MDCA triggers a cross talk between the phenylpropanoid and auxin biosynthetic pathways independent from the observed auxin efflux inhibition. Altogether, our data provide, to our knowledge, a novel molecular explanation for the phytotoxic properties of MDCA.
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Affiliation(s)
- Ward Steenackers
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Igor Cesarino
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Petr Klíma
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Mussa Quareshy
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Ruben Vanholme
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Sander Corneillie
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Robert Peter Kumpf
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Dorien Van de Wouwer
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Karin Ljung
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Geert Goeminne
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Ondřej Novák
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Eva Zažímalová
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Richard Napier
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Wout Boerjan
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
| | - Bartel Vanholme
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (W.S., I.C., R.V., S.C., R.P.K., D.V.d.W., G.G., W.B., B.V.);Department of Botany, Institute of Biosciences, University of São Paulo, 05508-090 Butantã, São Paulo, Brazil (I.C.);Institute of Experimental Botany, the Czech Academy of Sciences, 16502 Prague, the Czech Republic (P.K., E.Z.);School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom (M.Q., R.N.);Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden (K.L., O.N.); andLaboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic (O.N.)
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9
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Takahashi H, Nakayama R, Hayashi S, Nemoto T, Murase Y, Nomura K, Takahashi T, Kubo K, Marui S, Yasuhara K, Nakamura T, Sueo T, Takahashi A, Tsutsumiuchi K, Ohta T, Kawai A, Sugita S, Yamamoto S, Kobayashi T, Honda H, Yoshida T, Hasegawa T. Macrophage migration inhibitory factor and stearoyl-CoA desaturase 1: potential prognostic markers for soft tissue sarcomas based on bioinformatics analyses. PLoS One 2013; 8:e78250. [PMID: 24167613 PMCID: PMC3805525 DOI: 10.1371/journal.pone.0078250] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 09/10/2013] [Indexed: 11/18/2022] Open
Abstract
The diagnosis and treatment of soft tissue sarcomas (STSs) has been particularly difficult, because STSs are a group of highly heterogeneous tumors in terms of histopathology, histological grade, and primary site. Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis, treatment selection, and investigation of therapeutic targets. We had previously developed a novel bioinformatics method for marker gene selection and applied this method to gene expression data from STS patients. This previous analysis revealed that the extracted gene combination of macrophage migration inhibitory factor (MIF) and stearoyl-CoA desaturase 1 (SCD1) is an effective diagnostic marker to discriminate between subtypes of STSs with highly different outcomes. In the present study, we hypothesize that the combination of MIF and SCD1 is also a prognostic marker for the overall outcome of STSs. To prove this hypothesis, we first analyzed microarray data from 88 STS patients and their outcomes. Our results show that the survival rates for MIF- and SCD1-positive groups were lower than those for negative groups, and the p values of the log-rank test are 0.0146 and 0.00606, respectively. In addition, survival rates are more significantly different (p = 0.000116) between groups that are double-positive and double-negative for MIF and SCD1. Furthermore, in vitro cell growth inhibition experiments by MIF and SCD1 inhibitors support the hypothesis. These results suggest that the gene set is useful as a prognostic marker associated with tumor progression.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Robert Nakayama
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Transcriptome Project, National Cancer Center Research Institute, Tokyo, Japan
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shuhei Hayashi
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Nemoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Dermatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuyuki Murase
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Koji Nomura
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruyoshi Takahashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Kenji Kubo
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Shigetaka Marui
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Koji Yasuhara
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tetsuro Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Takuya Sueo
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Kaname Tsutsumiuchi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tsutomu Ohta
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Kawai
- Orthopedics Division, National Cancer Center Hospital, Tokyo, Japan
| | - Shintaro Sugita
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Shinjiro Yamamoto
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Kobayashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Hiroyuki Honda
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
- Pathology Division, National Cancer Center Hospital, Tokyo, Japan,
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13
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Takahashi H, Iwakawa H, Ishibashi N, Kojima S, Matsumura Y, Prananingrum P, Iwasaki M, Takahashi A, Ikezaki M, Luo L, Kobayashi T, Machida Y, Machida C. Meta-analyses of microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and their modifying mutants reveal a critical role for the ETT pathway in stabilization of adaxial-abaxial patterning and cell division during leaf development. PLANT & CELL PHYSIOLOGY 2013; 54:418-31. [PMID: 23396601 PMCID: PMC3589830 DOI: 10.1093/pcp/pct027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/01/2013] [Indexed: 05/22/2023]
Abstract
It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial-abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1-AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1-AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1-AS2-ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba, 271-8510 Japan
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
| | - Hidekazu Iwakawa
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
- Present address: Department of Biological Sciences, Purdue University, West, Lafayette, IN 47907-1392, USA
| | - Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- These authors contributed equally to this work
| | - Shoko Kojima
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Pratiwi Prananingrum
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Mayumi Iwasaki
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Present address: Department of Plant Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Masaya Ikezaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Takeshi Kobayashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
| | - Chiyoko Machida
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
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