101
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Pillitteri LJ, Guo X, Dong J. Asymmetric cell division in plants: mechanisms of symmetry breaking and cell fate determination. Cell Mol Life Sci 2016; 73:4213-4229. [PMID: 27286799 PMCID: PMC5522748 DOI: 10.1007/s00018-016-2290-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 02/07/2023]
Abstract
Asymmetric cell division is a fundamental mechanism that generates cell diversity while maintaining self-renewing stem cell populations in multicellular organisms. Both intrinsic and extrinsic mechanisms underpin symmetry breaking and differential daughter cell fate determination in animals and plants. The emerging picture suggests that plants deal with the problem of symmetry breaking using unique cell polarity proteins, mobile transcription factors, and cell wall components to influence asymmetric divisions and cell fate. There is a clear role for altered auxin distribution and signaling in distinguishing two daughter cells and an emerging role for epigenetic modifications through chromatin remodelers and DNA methylation in plant cell differentiation. The importance of asymmetric cell division in determining final plant form provides the impetus for its study in the areas of both basic and applied science.
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Affiliation(s)
- Lynn Jo Pillitteri
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Xiaoyu Guo
- Waksman Institute of Microbiology, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA.
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102
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Van Leene J, Blomme J, Kulkarni SR, Cannoot B, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Vercruysse L, Vanden Bossche R, Heyndrickx KS, Vanneste S, Goossens A, Gevaert K, Vandepoele K, Gonzalez N, Inzé D, De Jaeger G. Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5825-5840. [PMID: 27660483 PMCID: PMC5066499 DOI: 10.1093/jxb/erw347] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant bZIP group I transcription factors have been reported mainly for their role during vascular development and osmosensory responses. Interestingly, bZIP29 has been identified in a cell cycle interactome, indicating additional functions of bZIP29 in plant development. Here, bZIP29 was functionally characterized to study its role during plant development. It is not present in vascular tissue but is specifically expressed in proliferative tissues. Genome-wide mapping of bZIP29 target genes confirmed its role in stress and osmosensory responses, but also identified specific binding to several core cell cycle genes and to genes involved in cell wall organization. bZIP29 protein complex analyses validated interaction with other bZIP group I members and provided insight into regulatory mechanisms acting on bZIP dimers. In agreement with bZIP29 expression in proliferative tissues and with its binding to promoters of cell cycle regulators, dominant-negative repression of bZIP29 altered the cell number in leaves and in the root meristem. A transcriptome analysis on the root meristem, however, indicated that bZIP29 might regulate cell number through control of cell wall organization. Finally, ectopic dominant-negative repression of bZIP29 and redundant factors led to a seedling-lethal phenotype, pointing to essential roles for bZIP group I factors early in plant development.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jonas Blomme
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Shubhada R Kulkarni
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Robin Vanden Bossche
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Ken S Heyndrickx
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000 Gent, Belgium Department of Biochemistry, Ghent University, B-9000 Gent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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103
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Palovaara J, de Zeeuw T, Weijers D. Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything. Annu Rev Cell Dev Biol 2016; 32:47-75. [PMID: 27576120 DOI: 10.1146/annurev-cellbio-111315-124929] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
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104
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Yoon EK, Dhar S, Lee MH, Song JH, Lee SA, Kim G, Jang S, Choi JW, Choe JE, Kim JH, Lee MM, Lim J. Conservation and Diversification of the SHR-SCR-SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots. MOLECULAR PLANT 2016; 9:1197-1209. [PMID: 27353361 DOI: 10.1016/j.molp.2016.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/04/2016] [Accepted: 06/20/2016] [Indexed: 05/25/2023]
Abstract
Development of the functional endodermis of Arabidopsis thaliana roots is controlled, in part, by GRAS transcription factors, namely SHORT-ROOT (SHR), SCARECROW (SCR), and SCARECROW-LIKE 23 (SCL23). Recently, it has been shown that the SHR-SCR-SCL23 regulatory module is also essential for specification of the endodermis (known as the bundle sheath) in leaves. Nevertheless, compared with what is known about the role of the SHR-SCR-SCL23 regulatory network in roots, the molecular interactions of SHR, SCR, and SCL23 are much less understood in shoots. Here, we show that SHR forms protein complexes with SCL23 to regulate transcription of SCL23 in shoots, similar to the regulation mode of SCR expression. Our results indicate that SHR acts as master regulator to directly activate the expression of SCR and SCL23. In the SHR-SCR-SCL23 network, we found a previously uncharacterized negative feedback loop whereby SCL23 modulates SHR levels. Through molecular, genetic, physiological, and morphological analyses, we also reveal that the SHR-SCR-SCL23 module plays a key role in the formation of the endodermis (known as the starch sheath) in hypocotyls. Taken together, our results provide new insights into the regulatory role of the SHR-SCR-SCL23 network in the endodermis development in both roots and shoots.
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Affiliation(s)
- Eun Kyung Yoon
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Souvik Dhar
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Mi-Hyun Lee
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Jae Hyo Song
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Shin Ae Lee
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Gyuree Kim
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Sejeong Jang
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Ji Won Choi
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Jeong-Eun Choe
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Jeong Hoe Kim
- Department of Biology, Kyungpook National University, Daegu 41566, Korea
| | - Myeong Min Lee
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Jun Lim
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea.
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105
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Waszczak C, Kerchev PI, Mühlenbock P, Hoeberichts FA, Van Der Kelen K, Mhamdi A, Willems P, Denecker J, Kumpf RP, Noctor G, Messens J, Van Breusegem F. SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions. THE PLANT CELL 2016; 28:1844-59. [PMID: 27432873 PMCID: PMC5006698 DOI: 10.1105/tpc.16.00038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/11/2016] [Indexed: 05/03/2023]
Abstract
Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. To analyze molecular mechanisms that regulate the response to increased H2O2 levels in plant cells, we focused on the photorespiration-dependent peroxisomal H2O2 production in Arabidopsis thaliana mutants lacking CATALASE2 (CAT2) activity (cat2-2). By screening for second-site mutations that attenuate the PSII maximum efficiency (Fv'/Fm') decrease and lesion formation linked to the cat2-2 phenotype, we discovered that a mutation in SHORT-ROOT (SHR) rescued the cell death phenotype of cat2-2 plants under photorespiration-promoting conditions. SHR deficiency attenuated H2O2-dependent gene expression, oxidation of the glutathione pool, and ascorbate depletion in a cat2-2 genetic background upon exposure to photorespiratory stress. Decreased glycolate oxidase and catalase activities together with accumulation of glycolate further implied that SHR deficiency impacts the cellular redox homeostasis by limiting peroxisomal H2O2 production. The photorespiratory phenotype of cat2-2 mutants did not depend on the SHR functional interactor SCARECROW and the sugar signaling component ABSCISIC ACID INSENSITIVE4, despite the requirement for exogenous sucrose for cell death attenuation in cat2-2 shr-6 double mutants. Our findings reveal a link between SHR and photorespiratory H2O2 production that has implications for the integration of developmental and stress responses.
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Affiliation(s)
- Cezary Waszczak
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Structural Biology Research Center, VIB, 1050 Brussels, Belgium Structural Biology Brussels Laboratory, Vrije Universiteit Brussel, 1050 Brussels, Belgium Brussels Center for Redox Biology, 1050 Brussels, Belgium Division of Plant Biology, Department of Biosciences, Viikki Plant Science Center, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pavel I Kerchev
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Per Mühlenbock
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frank A Hoeberichts
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Katrien Van Der Kelen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Amna Mhamdi
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France
| | - Patrick Willems
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jordi Denecker
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Robert P Kumpf
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Graham Noctor
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium Structural Biology Brussels Laboratory, Vrije Universiteit Brussel, 1050 Brussels, Belgium Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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106
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Clark NM, Hinde E, Winter CM, Fisher AP, Crosti G, Blilou I, Gratton E, Benfey PN, Sozzani R. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. eLife 2016; 5. [PMID: 27288545 PMCID: PMC4946880 DOI: 10.7554/elife.14770] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/10/2016] [Indexed: 01/17/2023] Open
Abstract
To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States.,Biomathematics Graduate Program, North Carolina State University, Raleigh, United States
| | - Elizabeth Hinde
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Cara M Winter
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Adam P Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Giuseppe Crosti
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University, Wageningen, Netherlands
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
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107
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Efroni I, Mello A, Nawy T, Ip PL, Rahni R, DelRose N, Powers A, Satija R, Birnbaum KD. Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions. Cell 2016; 165:1721-1733. [PMID: 27212234 DOI: 10.1016/j.cell.2016.04.046] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/02/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023]
Abstract
Plant roots can regenerate after excision of their tip, including the stem cell niche. To determine which developmental program mediates such repair, we applied a combination of lineage tracing, single-cell RNA sequencing, and marker analysis to test different models of tissue reassembly. We show that multiple cell types can reconstitute stem cells, demonstrating the latent potential of untreated plant cells. The transcriptome of regenerating cells prior to stem cell activation resembles that of an embryonic root progenitor. Regeneration defects are more severe in embryonic than in adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirror their embryonic dynamics and manipulation of both hormones alters the position of new tissues and stem cell niche markers. Our findings suggest that plant root regeneration follows, on a larger scale, the developmental stages of embryonic patterning and is guided by spatial information provided by complementary hormone domains.
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Affiliation(s)
- Idan Efroni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Alison Mello
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Tal Nawy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Pui-Leng Ip
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Ramin Rahni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Nicholas DelRose
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | | | - Rahul Satija
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
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108
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Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN. Transcriptional control of tissue formation throughout root development. Science 2016; 350:426-30. [PMID: 26494755 DOI: 10.1126/science.aad1171] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tissue patterns are dynamically maintained. Continuous formation of plant tissues during postembryonic growth requires asymmetric divisions and the specification of cell lineages. We show that the BIRDs and SCARECROW regulate lineage identity, positional signals, patterning, and formative divisions throughout Arabidopsis root growth. These transcription factors are postembryonic determinants of the ground tissue stem cells and their lineage. Upon further activation by the positional signal SHORT-ROOT (a mobile transcription factor), they direct asymmetric cell divisions and patterning of cell types. The BIRDs and SCARECROW with SHORT-ROOT organize tissue patterns at all formative steps during growth, ensuring developmental plasticity.
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Affiliation(s)
- Miguel A Moreno-Risueno
- Department of Biotechnology, Center for Plant Genomics and Biotechnology, Universidad Politecnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Rosangela Sozzani
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Galip Gürkan Yardımcı
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Jalean J Petricka
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 69364 Lyon, France
| | - Ikram Blilou
- Department of Plant Biology, Wageningen University Research, Wageningen, Netherlands
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Cara M Winter
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ben Scheres
- Department of Plant Biology, Wageningen University Research, Wageningen, Netherlands
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
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109
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Jöst M, Hensel G, Kappel C, Druka A, Sicard A, Hohmann U, Beier S, Himmelbach A, Waugh R, Kumlehn J, Stein N, Lenhard M. The INDETERMINATE DOMAIN Protein BROAD LEAF1 Limits Barley Leaf Width by Restricting Lateral Proliferation. Curr Biol 2016; 26:903-9. [PMID: 26996502 DOI: 10.1016/j.cub.2016.01.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/15/2015] [Accepted: 01/20/2016] [Indexed: 12/21/2022]
Abstract
Variation in the size, shape, and positioning of leaves as the major photosynthetic organs strongly impacts crop yield, and optimizing these aspects is a central aim of cereal breeding [1, 2]. Leaf growth in grasses is driven by cell proliferation and cell expansion in a basal growth zone [3]. Although several factors influencing final leaf size and shape have been identified from rice and maize [4-14], what limits grass leaf growth in the longitudinal or transverse directions during leaf development remains poorly understood. To identify factors involved in this process, we characterized the barley mutant broad leaf1 (blf1). Mutants form wider but slightly shorter leaves due to changes in the numbers of longitudinal cell files and of cells along the leaf length. These differences arise during primordia outgrowth because of more cell divisions in the width direction increasing the number of cell files. Positional cloning, analysis of independent alleles, and transgenic complementation confirm that BLF1 encodes a presumed transcriptional regulator of the INDETERMINATE DOMAIN family. In contrast to loss-of-function mutants, moderate overexpression of BLF1 decreases leaf width below wild-type levels. A functional BLF1-vYFP fusion protein expressed from the endogenous promoter shows a dynamic expression pattern in the shoot apical meristem and young leaf primordia. Thus, we propose that the BLF1 gene regulates barley leaf size by restricting cell proliferation in the leaf-width direction. Given the agronomic importance of canopy traits in cereals, identifying functionally different BLF1 alleles promises to allow for the generation of optimized cereal ideotypes.
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Affiliation(s)
- Moritz Jöst
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Götz Hensel
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Arnis Druka
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Uwe Hohmann
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Sebastian Beier
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Jochen Kumlehn
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Nils Stein
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Michael Lenhard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany.
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110
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Dou M, Cheng S, Zhao B, Xuan Y, Shao M. The Indeterminate Domain Protein ROC1 Regulates Chilling Tolerance via Activation of DREB1B/CBF1 in Rice. Int J Mol Sci 2016; 17:233. [PMID: 26927068 PMCID: PMC4813127 DOI: 10.3390/ijms17030233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/27/2016] [Accepted: 02/04/2016] [Indexed: 11/25/2022] Open
Abstract
Abiotic stress, including salinity, drought and cold, severely affect diverse aspects of plant development and production. Rice is an important crop that does not acclimate to cold; therefore, it is relatively sensitive to low temperature stress. Dehydration-responsive element-binding protein 1s (DREB1s)/C-repeat binding factors (CBFs) are well known for their function in cold tolerance, but the transcriptional regulation of CBFs remains elusive, especially in rice. Here, we performed a yeast one-hybrid assay using the promoter of CBF1, a cold-induced gene, to isolate transcriptional regulators of CBF1. Among the seven candidates identified, an indeterminate domain (IDD) protein named ROC1 (a regulator of CBF1) was further analyzed. The ROC1 transcript was induced by exogenously-treated auxin, while it was not altered by cold or ABA stimuli. ROC1-GFP was localized at the nucleus, and ROC1 showed trans-activation activity in yeast. The electrophoretic mobility shift assay (EMSA) and ChIP analyses revealed that ROC1 directly bound to the promoter of CBF1. Furthermore, ROC1 mutants exhibited chilling-sensitive symptoms and inhibited cold-mediated induction of CBF1 and CBF3, indicating that ROC1 is a positive regulator of cold stress responses. Taken together, this study identified the CBF1 regulator, and the results are important for rice plant adaptation to chilling stress.
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Affiliation(s)
- Mingzhu Dou
- College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan 250014, Shandong, China.
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Shuai Cheng
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Baotian Zhao
- College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan 250014, Shandong, China.
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, Liaoning, China.
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
| | - Minglong Shao
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
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111
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Fisher AP, Sozzani R. Uncovering the networks involved in stem cell maintenance and asymmetric cell division in the Arabidopsis root. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:38-43. [PMID: 26707611 DOI: 10.1016/j.pbi.2015.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
Stem cells are the source of different cell types and tissues in all multicellular organisms. In plants, the balance between stem cell self-renewal and differentiation of their progeny is crucial for correct tissue and organ formation. How transcriptional programs precisely control stem cell maintenance and identity, and what are the regulatory programs influencing stem cell asymmetric cell division (ACD), are key questions that researchers have sought to address for the past decade. Successful efforts in genetic, molecular, and developmental biology, along with mathematical modeling, have identified some of the players involved in stem cell regulation. In this review, we will discuss several studies that characterized many of the genetic programs and molecular mechanisms regulating stem cell ACD and their identity in the Arabidopsis root. We will also highlight how the growing use of mathematical modeling provides a comprehensive and quantitative perspective on the design rules governing stem cell ACDs.
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Affiliation(s)
- Adam P Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States.
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112
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Li J, Yang P, Kang J, Gan Y, Yu J, Calderón-Urrea A, Lyu J, Zhang G, Feng Z, Xie J. Transcriptome Analysis of Pepper (Capsicum annuum) Revealed a Role of 24-Epibrassinolide in Response to Chilling. FRONTIERS IN PLANT SCIENCE 2016; 7:1281. [PMID: 27621739 PMCID: PMC5002408 DOI: 10.3389/fpls.2016.01281] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/11/2016] [Indexed: 05/21/2023]
Abstract
Brassinosteroids (BRs) have positive effects on many processes during plant growth, development, and various abiotic stress responses. However, little information is available regarding the global gene expression of BRs in response to chilling stress in pepper. In this study, we used RNA sequencing to determine the molecular roles of 24-epibrassinolide (EBR) during a chilling stress response. There were 39,829 transcripts, and, among them, 656 were differently-expressed genes (DEGs) following EBR treatment (Chill+EBR) compared with the control (Chill only), including 335 up-regulated and 321 down-regulated DEGs. We selected 20 genes out of the 656 DEGs for RT-qPCR analysis to confirm the RNA-Seq. Based on GO enrich and KEGG pathway analysis, we found that photosynthesis was significantly up-enriched in biological processes, accompanied by significant increases in the net photosynthetic rate (Pn), Fv/Fm, and chlorophyll content. Furthermore, the results indicate that EBR enhanced endogenous levels of salicylic acid (SA) and jasmonic acid (JA) while suppressing the ethylene (ETH) biosynthesis pathway, suggesting that BRs function via a synergistic cross-talk with SA, JA, and ETH signaling pathways in response to chilling stress. In addition, EBR induced cellulose synthase-like protein and UDP-glycosyltransferase, suggesting a contribution to the formation of cell wall and hormone metabolism. EBR also triggered the calcium signaling transduction in cytoplasm, and activated the expression of cellular redox homeostasis related genes, such as GSTX1, PER72, and CAT2. This work, therefor, identified the specific genes showed different expression patterns in EBR-treated pepper and associated with the processes of hormone metabolism, redox, signaling, transcription, and defense. Our study provides the first evidence of the potent roles of BRs, at the transcription level, to induce the tolerance to chilling stress in pepper as a function of the combination of the transcriptional activities, signaling transduction, and metabolic homeostasis.
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Affiliation(s)
- Jie Li
- Department of Facility Horticulture Science, College of Horticulture, Gansu Agricultural UniversityLanzhou, China
| | - Ping Yang
- Department of Crop Cultivation and Farming System, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Jungen Kang
- Department of Vegetable Genetics and Breeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Yantai Gan
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food CanadaSwift Current, SK, Canada
- Gansu Provincial Key Lab of Aridland Crop Science, Gansu Agricultural UniversityLanzhou, China
| | - Jihua Yu
- Department of Facility Horticulture Science, College of Horticulture, Gansu Agricultural UniversityLanzhou, China
| | | | - Jian Lyu
- Department of Facility Horticulture Science, College of Horticulture, Gansu Agricultural UniversityLanzhou, China
| | - Guobin Zhang
- Department of Facility Horticulture Science, College of Horticulture, Gansu Agricultural UniversityLanzhou, China
| | - Zhi Feng
- Department of Facility Horticulture Science, College of Horticulture, Gansu Agricultural UniversityLanzhou, China
| | - Jianming Xie
- Department of Facility Horticulture Science, College of Horticulture, Gansu Agricultural UniversityLanzhou, China
- *Correspondence: Jianming Xie
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113
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Long Y, Goedhart J, Schneijderberg M, Terpstra I, Shimotohno A, Bouchet BP, Akhmanova A, Gadella TWJ, Heidstra R, Scheres B, Blilou I. SCARECROW-LIKE23 and SCARECROW jointly specify endodermal cell fate but distinctly control SHORT-ROOT movement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:773-84. [PMID: 26415082 DOI: 10.1111/tpj.13038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/15/2015] [Accepted: 09/18/2015] [Indexed: 05/27/2023]
Abstract
Intercellular signaling through trafficking of regulatory proteins is a widespread phenomenon in plants and can deliver positional information for the determination of cell fate. In the Arabidopsis root meristem, the cell fate determinant SHORT-ROOT (SHR), a GRAS domain transcription factor, acts as a signaling molecule from the stele to the adjacent layer to specify endodermal cell fate. Upon exiting the stele, SHR activates another GRAS domain transcription factor, SCARCROW (SCR), which, together with several BIRD/INDETERMINATE DOMAIN proteins, restricts movement of SHR to define a single cell layer of endodermis. Here we report that endodermal cell fate also requires the joint activity of both SCR and its closest homologue SCARECROW-LIKE23 (SCL23). We show that SCL23 protein moves with zonation-dependent directionality. Within the meristem, SCL23 exhibits short-ranged movement from ground tissue to vasculature. Away from the meristem, SCL23 displays long-range rootward movement into meristematic vasculature and a bidirectional radial spread, respectively. As a known target of SHR and SCR, SCL23 also interacts with SCR and SHR and can restrict intercellular outspread of SHR without relying on nuclear retention as SCR does. Collectively, our data show that SCL23 is a mobile protein that controls movement of SHR and acts redundantly with SCR to specify endodermal fate in the root meristem.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | | | - Inez Terpstra
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Akie Shimotohno
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Benjamin P Bouchet
- Cell Biology, Department Biology, Utrecht University, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Anna Akhmanova
- Cell Biology, Department Biology, Utrecht University, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Renze Heidstra
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
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114
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MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 2015; 112:12099-104. [PMID: 26371322 DOI: 10.1073/pnas.1515576112] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Stem cells are defined by their ability to self-renew and produce daughter cells that proliferate and mature. These maturing cells transition from a proliferative state to a terminal state through the process of differentiation. In the Arabidopsis thaliana root the transcription factors SCARECROW and SHORTROOT regulate specification of the bipotent stem cell that gives rise to cortical and endodermal progenitors. Subsequent progenitor proliferation and differentiation generate mature endodermis, marked by the Casparian strip, a cell-wall modification that prevents ion diffusion into and out of the vasculature. We identified a transcription factor, MYB DOMAIN PROTEIN 36 (MYB36), that regulates the transition from proliferation to differentiation in the endodermis. We show that SCARECROW directly activates MYB36 expression, and that MYB36 likely acts in a feed-forward loop to regulate essential Casparian strip formation genes. We show that myb36 mutants have delayed and defective barrier formation as well as extra divisions in the meristem. Our results demonstrate that MYB36 is a critical positive regulator of differentiation and negative regulator of cell proliferation.
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115
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Clevenger JP, Van Houten J, Blackwood M, Rodríguez GR, Jikumaru Y, Kamiya Y, Kusano M, Saito K, Visa S, van der Knaap E. Network Analyses Reveal Shifts in Transcript Profiles and Metabolites That Accompany the Expression of SUN and an Elongated Tomato Fruit. PLANT PHYSIOLOGY 2015; 168:1164-78. [PMID: 25941316 PMCID: PMC4741315 DOI: 10.1104/pp.15.00379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/04/2015] [Indexed: 05/04/2023]
Abstract
SUN controls elongated tomato (Solanum lycopersicum) shape early in fruit development through changes in cell number along the different axes of growth. The gene encodes a member of the IQ domain family characterized by a calmodulin binding motif. To gain insights into the role of SUN in regulating organ shape, we characterized genome-wide transcriptional changes and metabolite and hormone accumulation after pollination and fertilization in wild-type and SUN fruit tissues. Pericarp, seed/placenta, and columella tissues were collected at 4, 7, and 10 d post anthesis. Pairwise comparisons between SUN and the wild type identified 3,154 significant differentially expressed genes that cluster in distinct gene regulatory networks. Gene regulatory networks that were enriched for cell division, calcium/transport, lipid/hormone, cell wall, secondary metabolism, and patterning processes contributed to profound shifts in gene expression in the different fruit tissues as a consequence of high expression of SUN. Promoter motif searches identified putative cis-elements recognized by known transcription factors and motifs related to mitotic-specific activator sequences. Hormone levels did not change dramatically, but some metabolite levels were significantly altered, namely participants in glycolysis and the tricarboxylic acid cycle. Also, hormone and primary metabolite networks shifted in SUN compared with wild-type fruit. Our findings imply that SUN indirectly leads to changes in gene expression, most strongly those involved in cell division, cell wall, and patterning-related processes. When evaluating global coregulation in SUN fruit, the main node represented genes involved in calcium-regulated processes, suggesting that SUN and its calmodulin binding domain impact fruit shape through calcium signaling.
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Affiliation(s)
- Josh P Clevenger
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Jason Van Houten
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Michelle Blackwood
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Gustavo Rubén Rodríguez
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Yusuke Jikumaru
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Yuji Kamiya
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Miyako Kusano
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Kazuki Saito
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Sofia Visa
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Esther van der Knaap
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691 (J.P.C., J.V.H., G.R.R., E.v.d.K.);Department of Mathematics and Computer Science, The College of Wooster, Wooster, Ohio 44691 (M.B., S.V.);RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.J., Y.K., M.K., K.S.); andDepartment of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
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116
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Gallagher KL, Sozzani R, Lee CM. Intercellular protein movement: deciphering the language of development. Annu Rev Cell Dev Biol 2015; 30:207-33. [PMID: 25288113 DOI: 10.1146/annurev-cellbio-100913-012915] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Development in multicellular organisms requires the coordinated production of a large number of specialized cell types through sophisticated signaling mechanisms. Non-cell-autonomous signals are one of the key mechanisms by which organisms coordinate development. In plants, intercellular movement of transcription factors and other mobile signals, such as hormones and peptides, is essential for normal development. Through a combination of different approaches, a large number of non-cell-autonomous signals that control plant development have been identified. We review some of the transcriptional regulators that traffic between cells, as well as how changes in symplasmic continuity affect and are affected by development. We also review current models for how mobile signals move via plasmodesmata and how movement is inhibited. Finally, we consider challenges in and new tools for studying protein movement.
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Affiliation(s)
- Kimberly L Gallagher
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104; ,
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117
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Noir S, Marrocco K, Masoud K, Thomann A, Gusti A, Bitrian M, Schnittger A, Genschik P. The Control of Arabidopsis thaliana Growth by Cell Proliferation and Endoreplication Requires the F-Box Protein FBL17. THE PLANT CELL 2015; 27:1461-76. [PMID: 25944099 PMCID: PMC4456641 DOI: 10.1105/tpc.114.135301] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/31/2015] [Accepted: 04/11/2015] [Indexed: 05/18/2023]
Abstract
A key step of the cell cycle is the entry into the DNA replication phase that typically commits cells to divide. However, little is known about the molecular mechanisms regulating this transition in plants. Here, we investigated the function of FBL17 (F BOX-LIKE17), an Arabidopsis thaliana F-box protein previously shown to govern the progression through the second mitosis during pollen development. Our work reveals that FBL17 function is not restricted to gametogenesis. FBL17 transcripts accumulate in both proliferating and postmitotic cell types of Arabidopsis plants. Loss of FBL17 function drastically reduces plant growth by altering cell division activity in both shoot and root apical meristems. In fbl17 mutant plants, DNA replication is severely impaired and endoreplication is fully suppressed. At the molecular level, lack of FBL17 increases the stability of the CDK (CYCLIN-DEPENDENT KINASE) inhibitor KIP-RELATED PROTEIN2 known to switch off CDKA;1 kinase activity. Despite the strong inhibition of cell proliferation in fbl17, some cells are still able to enter S phase and eventually to divide, but they exhibit a strong DNA damage response and often missegregate chromosomes. Altogether, these data indicate that the F-box protein FBL17 acts as a master cell cycle regulator during the diploid sporophyte phase of the plant.
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Affiliation(s)
- Sandra Noir
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Katia Marrocco
- Institut de Biologie Intégrative des Plantes, Unité de Biochimie et Physiologie Moléculaire des Plantes, 34060 Montpellier, France
| | - Kinda Masoud
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Alexis Thomann
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Andi Gusti
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Marta Bitrian
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Arp Schnittger
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France Institut de Biologie Intégrative des Plantes, Unité de Biochimie et Physiologie Moléculaire des Plantes, 34060 Montpellier, France
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118
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Long Y, Smet W, Cruz-Ramírez A, Castelijns B, de Jonge W, Mähönen AP, Bouchet BP, Perez GS, Akhmanova A, Scheres B, Blilou I. Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification. THE PLANT CELL 2015; 27:1185-99. [PMID: 25829440 PMCID: PMC4558684 DOI: 10.1105/tpc.114.132407] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 02/10/2015] [Accepted: 03/10/2015] [Indexed: 05/18/2023]
Abstract
Plant cells cannot rearrange their positions; therefore, sharp tissue boundaries must be accurately programmed. Movement of the cell fate regulator SHORT-ROOT from the stele to the ground tissue has been associated with transferring positional information across tissue boundaries. The zinc finger BIRD protein JACKDAW has been shown to constrain SHORT-ROOT movement to a single layer, and other BIRD family proteins were postulated to counteract JACKDAW's role in restricting SHORT-ROOT action range. Here, we report that regulation of SHORT-ROOT movement requires additional BIRD proteins whose action is critical for the establishment and maintenance of the boundary between stele and ground tissue. We show that BIRD proteins act in concert and not in opposition. The exploitation of asymmetric redundancies allows the separation of two BIRD functions: constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6. Our data indicate that BIRD proteins promote formative divisions and tissue specification in the Arabidopsis thaliana root meristem ground tissue by tethering and regulating transcriptional competence of SHORT-ROOT complexes. As a result, a tissue boundary is not "locked in" after initial patterning like in many animal systems, but possesses considerable developmental plasticity due to continuous reliance on mobile transcription factors.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Wouter Smet
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Alfredo Cruz-Ramírez
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Bas Castelijns
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Wim de Jonge
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Ari Pekka Mähönen
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Benjamin P Bouchet
- Cell Biology, Faculty of Science, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Gabino Sanchez Perez
- Bioinformatics, Plant Sciences, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Anna Akhmanova
- Cell Biology, Faculty of Science, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
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119
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Kinoshita A, ten Hove CA, Tabata R, Yamada M, Shimizu N, Ishida T, Yamaguchi K, Shigenobu S, Takebayashi Y, Iuchi S, Kobayashi M, Kurata T, Wada T, Seo M, Hasebe M, Blilou I, Fukuda H, Scheres B, Heidstra R, Kamiya Y, Sawa S. A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem. Development 2015; 142:444-53. [PMID: 25605779 DOI: 10.1242/dev.113167] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The root meristem (RM) is a fundamental structure that is responsible for postembryonic root growth. The RM contains the quiescent center (QC), stem cells and frequently dividing meristematic cells, in which the timing and the frequency of cell division are tightly regulated. In Arabidopsis thaliana, several gain-of-function analyses have demonstrated that peptide ligands of the Clavata3 (CLV3)/embryo surrounding region-related (CLE) family are important for maintaining RM size. Here, we demonstrate that a plant U-box E3 ubiquitin ligase, PUB4, is a novel downstream component of CLV3/CLE signaling in the RM. Mutations in PUB4 reduced the inhibitory effect of exogenous CLV3/CLE peptide on root cell proliferation and columella stem cell maintenance. Moreover, pub4 mutants grown without exogenous CLV3/CLE peptide exhibited characteristic phenotypes in the RM, such as enhanced root growth, increased number of cortex/endodermis stem cells and decreased number of columella layers. Our phenotypic and gene expression analyses indicated that PUB4 promotes expression of a cell cycle regulatory gene, CYCD6;1, and regulates formative periclinal asymmetric cell divisions in endodermis and cortex/endodermis initial daughters. These data suggest that PUB4 functions as a global regulator of cell proliferation and the timing of asymmetric cell division that are important for final root architecture.
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Affiliation(s)
- Atsuko Kinoshita
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Colette A ten Hove
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, Wageningen 6703HA, The Netherlands
| | - Ryo Tabata
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Masashi Yamada
- Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University, Durham, NC 27708, USA
| | - Noriko Shimizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Takashi Ishida
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki 444-8585, Japan School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Satoshi Iuchi
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masatomo Kobayashi
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tetsuya Kurata
- Graduate School of Biological Sciences, NAIST, Ikoma 630-0192, Japan
| | - Takuji Wada
- Graduate School of Biosphere Sciences, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Mitsuyasu Hasebe
- School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Ikram Blilou
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6700AP, The Netherlands
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ben Scheres
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6700AP, The Netherlands
| | - Renze Heidstra
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6700AP, The Netherlands
| | - Yuji Kamiya
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
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120
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Long Y, Scheres B, Blilou I. The logic of communication: roles for mobile transcription factors in plants. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1133-44. [PMID: 25635110 DOI: 10.1093/jxb/eru548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mobile transcription factors play many roles in plant development. Here, we compare the use of mobile transcription factors as signals with some canonical signal transduction processes in prokaryotes and eukaryotes. After an initial survey, we focus on the SHORT-ROOT pathway in Arabidopsis roots to show that, despite the simplicity of the concept of mobile transcription factor signalling, many lines of evidence reveal a surprising complexity in control mechanisms linked to this process. We argue that these controls bestow precision, robustness, and versatility on mobile transcription factor signalling.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands.
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121
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Yi G, Neelakandan AK, Gontarek BC, Vollbrecht E, Becraft PW. The naked endosperm genes encode duplicate INDETERMINATE domain transcription factors required for maize endosperm cell patterning and differentiation. PLANT PHYSIOLOGY 2015; 167:443-56. [PMID: 25552497 PMCID: PMC4326753 DOI: 10.1104/pp.114.251413] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/30/2014] [Indexed: 05/18/2023]
Abstract
The aleurone is the outermost layer of cereal endosperm and functions to digest storage products accumulated in starchy endosperm cells as well as to confer important dietary health benefits. Whereas normal maize (Zea mays [Zm]) has a single aleurone layer, naked endosperm (nkd) mutants produce multiple outer cell layers of partially differentiated cells that show sporadic expression of aleurone identity markers such as a viviparous1 promoter-β-glucuronidase transgene. The 15:1 F2 segregation ratio suggested that two recessive genes were involved, and map-based cloning identified two homologous genes in duplicated regions of the genome. The nkd1 and nkd2 genes encode the INDETERMINATE1 domain (IDD) containing transcription factors ZmIDDveg9 and ZmIDD9 on chromosomes 2 and 10, respectively. Independent mutant alleles of nkd1 and nkd2, as well as nkd2-RNA interference lines in which both nkd genes were knocked down, also showed the nkd mutant phenotype, confirming the gene identities. In wild-type kernels, the nkd transcripts were most abundant around 11 to 16 d after pollination. The NKD proteins have putative nuclear localization signals, and green fluorescent protein fusion proteins showed nuclear localization. The mutant phenotype and gene identities suggest that NKD controls a gene regulatory network involved in aleurone cell fate specification and cell differentiation.
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Affiliation(s)
- Gibum Yi
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Anjanasree K Neelakandan
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Bryan C Gontarek
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Erik Vollbrecht
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Philip W Becraft
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
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122
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Drisch RC, Stahl Y. Function and regulation of transcription factors involved in root apical meristem and stem cell maintenance. FRONTIERS IN PLANT SCIENCE 2015; 6:505. [PMID: 26217359 PMCID: PMC4491714 DOI: 10.3389/fpls.2015.00505] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/23/2015] [Indexed: 05/20/2023]
Abstract
Plant roots are essential for overall plant development, growth, and performance by providing anchorage in the soil and uptake of nutrients and water. The primary root of higher plants derives from a group of pluripotent, mitotically active stem cells residing in the root apical meristem (RAM) which provides the basis for growth, development, and regeneration of the root. The stem cells in the Arabidopsis thaliana RAM are surrounding the quiescent center (QC), which consists of a group of rarely dividing cells. The QC maintains the stem cells in a non-cell-autonomous manner and prevents them from differentiation. The necessary dynamic but also tight regulation of the transition from stem cell fate to differentiation most likely requires complex regulatory mechanisms to integrate external and internal cues. Transcription factors play a central role in root development and are regulated by phytohormones, small signaling molecules, and miRNAs. In this review we give a comprehensive overview about the function and regulation of specific transcription factors controlling stem cell fate and root apical meristem maintenance and discuss the possibility of TF complex formation, subcellular translocations and cell-to-cell movement functioning as another level of regulation.
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Affiliation(s)
| | - Yvonne Stahl
- *Correspondence: Yvonne Stahl, Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstrasse 1, Düsseldorf, NRW, Germany,
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123
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Wu S, Lee CM, Hayashi T, Price S, Divol F, Henry S, Pauluzzi G, Perin C, Gallagher KL. A plausible mechanism, based upon Short-Root movement, for regulating the number of cortex cell layers in roots. Proc Natl Acad Sci U S A 2014; 111:16184-9. [PMID: 25352666 PMCID: PMC4234584 DOI: 10.1073/pnas.1407371111] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Formation of specialized cells and tissues at defined times and in specific positions is essential for the development of multicellular organisms. Often this developmental precision is achieved through intercellular signaling networks, which establish patterns of differential gene expression and ultimately the specification of distinct cell fates. Here we address the question of how the Short-root (SHR) proteins from Arabidopsis thaliana (AtSHR), Brachypodium distachyon (BdSHR), and Oryza sativa (OsSHR1 and OsSHR2) function in patterning the root ground tissue. We find that all of the SHR proteins function as mobile signals in A. thaliana and all of the SHR homologs physically interact with the AtSHR binding protein, Scarecow (SCR). Unlike AtSHR, movement of the SHR homologs was not limited to the endodermis. Instead, the SHR proteins moved multiple cell layers and determined the number of cortex, not endodermal, cell layers formed in the root. Our results in A. thaliana are consistent with a mechanism by which the regulated movement of the SHR transcription factor determines the number of cortex cell layers produced in the roots of B. distachyon and O. sativa. These data also provide a new model for ground tissue patterning in A. thaliana in which the ability to form a functional endodermis is spatially limited independently of SHR.
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Affiliation(s)
- Shuang Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Chin-Mei Lee
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Tomomi Hayashi
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Simara Price
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Fanchon Divol
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Cultivées (AGAP), F34398 Montpellier, France
| | - Sophia Henry
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Cultivées (AGAP), F34398 Montpellier, France
| | - Germain Pauluzzi
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Cultivées (AGAP), F34398 Montpellier, France
| | - Christophe Perin
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Cultivées (AGAP), F34398 Montpellier, France
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124
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Wu S, Gallagher KL. The movement of the non-cell-autonomous transcription factor, SHORT-ROOT relies on the endomembrane system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:396-409. [PMID: 25124761 DOI: 10.1111/tpj.12640] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 07/29/2014] [Accepted: 08/04/2014] [Indexed: 05/08/2023]
Abstract
Plant cells are able to convey positional and developmental information between cells through the direct transfer of transcription factors. One well studied example of this is the SHORT-ROOT (SHR) protein, which moves from the stele into the neighboring ground tissue layer to specify endodermis. While it has been shown that SHR trafficking relies on plasmodesmata (PD), and interaction with the SHR INTERACTING EMBRYONIC LETHAL (SIEL) protein, little information is known about how SHR trafficking is controlled or how SIEL promotes the movement of SHR. Here we show that SHR can move from multiple different cell types in the root. Analysis of subcellular localization indicates that in the cytoplasm of root or leaf cells, SHR localizes to endosomes in a SIEL-dependent manner. Interference of early and late endosomes disrupts intercellular movement of SHR. Our findings reveal an essential role for the plant endomembrane, independent of secretion, in the intercellular trafficking of SHR.
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Affiliation(s)
- Shuang Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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125
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Petti C, Nair M, DeBolt S. The involvement of J-protein AtDjC17 in root development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2014; 5:532. [PMID: 25339971 PMCID: PMC4189540 DOI: 10.3389/fpls.2014.00532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/18/2014] [Indexed: 05/29/2023]
Abstract
In a screen for root hair morphogenesis mutants in Arabidopsis thaliana L. we identified a T-DNA insertion within a type III J-protein AtDjC17 caused altered root hair development and reduced hair length. Root hairs were observed to develop from trichoblast and atrichoblast cell files in both Atdjc17 and 35S::AtDJC17. Localization of gene expression in the root using transgenic plants expressing proAtDjC17::GUS revealed constitutive expression in stele cells. No AtDJC17 expression was observed in epidermal, endodermal, or cortical layers. To explore the contrast between gene expression in the stele and epidermal phenotype, hand cut transverse sections of Atdjc17 roots were examined showing that the endodermal and cortical cell layers displayed increased anticlinal cell divisions. Aberrant cortical cell division in Atdjc17 is proposed as causal in ectopic root hair formation via the positional cue requirement that exists between cortical and epidermal cell in hair cell fate determination. Results indicate a requirement for AtDJC17 in position-dependent cell fate determination and illustrate an intriguing requirement for molecular co-chaperone activity during root development.
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Affiliation(s)
| | | | - Seth DeBolt
- Department of Horticulture, University of KentuckyLexington, KY, USA
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126
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Fouracre JP, Ando S, Langdale JA. Cracking the Kranz enigma with systems biology. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3327-39. [PMID: 24510938 DOI: 10.1093/jxb/eru015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Leaves with Kranz anatomy exhibit a highly characteristic arrangement of closely spaced veins surrounded by concentric wreaths of bundle sheath and mesophyll cells. This anatomical framework is vital for effective C4 photosynthesis in nearly all known land plant lineages and has evolved independently on over 60 occasions. Over the last 3 years, technological advances, particularly in high-throughput DNA sequencing, have allowed the development of Kranz anatomy to be interrogated at unprecedented depth. This review highlights the recent advances in our understanding that have been facilitated by systems biology approaches, and proposes a testable model for the regulation of Kranz development.
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Affiliation(s)
- Jim P Fouracre
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Sayuri Ando
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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127
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Jang G, Lee JY. Intercellular trafficking of transcription factors in the vascular tissue patterning. PHYSIOLOGIA PLANTARUM 2014; 151:184-91. [PMID: 24329715 DOI: 10.1111/ppl.12140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/21/2013] [Accepted: 11/24/2013] [Indexed: 05/25/2023]
Abstract
Throughout life cycles, plants grow in an indeterminate manner by adding new cells and organs with specialized functions. Newly emerging cells acquire their identities depending on their positions relative to the neighboring cells. Exchanging positional signals between cells is critical in this process. Recent studies showed that many transcription factors move between cells or between organs in forms of proteins and messenger RNA (mRNA). Some of these were found to be important positional signals for cell type patterning. Cell type patterning in the vascular system is no exception from this. In this review, we describe recent discoveries of mobile transcription factors that function as positional signals for vascular tissue patterning and propose how these transcription factors integrate with other forms of signals.
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Affiliation(s)
- Geupil Jang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
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128
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Kajala K, Ramakrishna P, Fisher A, C. Bergmann D, De Smet I, Sozzani R, Weijers D, Brady SM. Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants. ANNALS OF BOTANY 2014; 113:1083-1105. [PMID: 24825294 PMCID: PMC4030820 DOI: 10.1093/aob/mcu065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/06/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic ('niche-controlled') or intrinsic regulatory mechanisms and are fundamentally important in plant development. SCOPE This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. CONCLUSIONS Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Priya Ramakrishna
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Adam Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dominique C. Bergmann
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, The Netherlands
| | - Siobhan M. Brady
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
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129
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Horstman A, Tonaco IAN, Boutilier K, Immink RGH. A cautionary note on the use of split-YFP/BiFC in plant protein-protein interaction studies. Int J Mol Sci 2014; 15:9628-43. [PMID: 24886811 PMCID: PMC4100113 DOI: 10.3390/ijms15069628] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/17/2014] [Accepted: 05/20/2014] [Indexed: 12/16/2022] Open
Abstract
Since its introduction in plants 10 years ago, the bimolecular fluorescence complementation (BiFC) method, or split-YFP (yellow fluorescent protein), has gained popularity within the plant biology field as a method to study protein-protein interactions. BiFC is based on the restoration of fluorescence after the two non-fluorescent halves of a fluorescent protein are brought together by a protein-protein interaction event. The major drawback of BiFC is that the fluorescent protein halves are prone to self-assembly independent of a protein-protein interaction event. To circumvent this problem, several modifications of the technique have been suggested, but these modifications have not lead to improvements in plant BiFC protocols. Therefore, it remains crucial to include appropriate internal controls. Our literature survey of recent BiFC studies in plants shows that most studies use inappropriate controls, and a qualitative rather than quantitative read-out of fluorescence. Therefore, we provide a cautionary note and beginner’s guideline for the setup of BiFC experiments, discussing each step of the protocol, including vector choice, plant expression systems, negative controls, and signal detection. In addition, we present our experience with BiFC with respect to self-assembly, peptide linkers, and incubation temperature. With this note, we aim to provide a guideline that will improve the quality of plant BiFC experiments.
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Affiliation(s)
- Anneke Horstman
- Plant Research International, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | | | - Kim Boutilier
- Plant Research International, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Richard G H Immink
- Plant Research International, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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130
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DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins. Proc Natl Acad Sci U S A 2014; 111:7861-6. [PMID: 24821766 DOI: 10.1073/pnas.1321669111] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DELLA protein is a key negative regulator of gibberellin (GA) signaling. Although how DELLA regulates downstream gene expression remains unclear, DELLA has been proposed to function as a transcriptional activator. However, because DELLA lacks a DNA-binding domain, intermediate protein(s) mediating the DELLA/DNA interaction are believed to be necessary for activating DELLA target genes. Here, using yeast hybrid screenings, we identified five members of indeterminate domain (IDD) protein family which bind physically to both DELLA and the promoter sequence of the GA-positive regulator SCARECROW-LIKE 3 (SCL3), which previously was characterized as a DELLA direct target gene. Transient assays using Arabidopsis protoplasts demonstrated that a luciferase reporter controlled by the SCL3 promoter was additively transactivated by REPRESSOR of ga1-3 (RGA) and IDDs. Phenotypic analysis of transgenic plants expressing AtIDD3 (one of the 16 IDDs in the Arabidopsis genome) fused with the plant-specific repression domain (SRDX) supported the possibility that AtIDD3 is positively involved in GA signaling. In addition, we found that SCL3 protein also interacts with IDDs, resulting in the suppression of its target gene expression. In this context, DELLA and SCL3 interact competitively with IDD proteins to regulate downstream gene expression. These results suggest that the coregulators DELLA and SCL3, using IDDs as transcriptional scaffolds for DNA binding, antagonistically regulate the expression of their downstream targets to control the GA signaling pathway.
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131
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Chávez Montes RA, Coello G, González-Aguilera KL, Marsch-Martínez N, de Folter S, Alvarez-Buylla ER. ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks. BMC PLANT BIOLOGY 2014; 14:97. [PMID: 24739361 PMCID: PMC4021103 DOI: 10.1186/1471-2229-14-97] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/27/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Uncovering the complex transcriptional regulatory networks (TRNs) that underlie plant and animal development remains a challenge. However, a vast amount of data from public microarray experiments is available, which can be subject to inference algorithms in order to recover reliable TRN architectures. RESULTS In this study we present a simple bioinformatics methodology that uses public, carefully curated microarray data and the mutual information algorithm ARACNe in order to obtain a database of transcriptional interactions. We used data from Arabidopsis thaliana root samples to show that the transcriptional regulatory networks derived from this database successfully recover previously identified root transcriptional modules and to propose new transcription factors for the SHORT ROOT/SCARECROW and PLETHORA pathways. We further show that these networks are a powerful tool to integrate and analyze high-throughput expression data, as exemplified by our analysis of a SHORT ROOT induction time-course microarray dataset, and are a reliable source for the prediction of novel root gene functions. In particular, we used our database to predict novel genes involved in root secondary cell-wall synthesis and identified the MADS-box TF XAL1/AGL12 as an unexpected participant in this process. CONCLUSIONS This study demonstrates that network inference using carefully curated microarray data yields reliable TRN architectures. In contrast to previous efforts to obtain root TRNs, that have focused on particular functional modules or tissues, our root transcriptional interactions provide an overview of the transcriptional pathways present in Arabidopsis thaliana roots and will likely yield a plethora of novel hypotheses to be tested experimentally.
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Affiliation(s)
- Ricardo A Chávez Montes
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología and Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F. 04510, Mexico
- Present address: Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, AP 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Gerardo Coello
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F. 04510, Mexico
| | - Karla L González-Aguilera
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, AP 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnologıa y Bioquımica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, AP 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, AP 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Elena R Alvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología and Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F. 04510, Mexico
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132
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Han X, Kumar D, Chen H, Wu S, Kim JY. Transcription factor-mediated cell-to-cell signalling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1737-49. [PMID: 24347464 DOI: 10.1093/jxb/ert422] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant cells utilize mobile transcription factors to transmit intercellular signals when they perceive environmental stimuli or initiate developmental programmes. Studies on these novel cell-to-cell signals have accumulated multiple pieces of evidence showing that non-cell-autonomous transcription factors play pivotal roles in most processes related to the formation and development of plant organs. Recent studies have explored the evolution of mobile transcription factors and proposed mechanisms for their trafficking through plasmodesmata, where a selective system exists to facilitate this process. Mobile transcription factors contribute to the diversity of the intercellular signalling network, which is also established by peptides, hormones, and RNAs. Crosstalk between mobile transcription factors and other intercellular molecules leads to the development of complex biological signalling networks in plants. The regulation of plasmodesmata appears to have been another major step in controlling the intercellular trafficking of transcription factors based on studies of many plasmodesmal components. Furthermore, diverse omics approaches are being successfully applied to explore a large number of candidate transcription factors as mobile signals in plants. Here, we review these fascinating discoveries to integrate current knowledge of non-cell-autonomous transcription factors.
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Affiliation(s)
- Xiao Han
- Division of Applied Life Science (BK21plus/WCU Program), Graduate School of Gyeongsang National University, Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Jinju 660-701, Korea
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133
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Cui H, Kong D, Liu X, Hao Y. SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath cell fate and function in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:319-27. [PMID: 24517883 DOI: 10.1111/tpj.12470] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/30/2014] [Accepted: 02/03/2014] [Indexed: 05/25/2023]
Abstract
Bundle sheath (BS) cells form a single cell layer surrounding the vascular tissue in leaves. In C3 plants, photosynthesis occurs in both the BS and mesophyll cells, but the BS cells are the major sites of photosynthesis in C4 plants, whereas the mesophyll cells are only involved in CO2 fixation. Because C4 plants are more efficient photosynthetically, introduction of the C4 mechanism into C3 plants is considered a key strategy to improve crop yield. One prerequisite for such C3-to-C4 engineering is the ability to manipulate the number and physiology of the BS cells, but the molecular basis of BS cell-fate specification remains unclear. Here we report that mutations in three GRAS family transcription factors, SHORT-ROOT (SHR), SCARECROW (SCR) and SCARECROW-LIKE 23 (SCL23), affect BS cell fate in Arabidopsis thaliana. SCR and SCL23 are expressed specifically in the BS cells and act redundantly in BS cell-fate specification, but their expression pattern and function diverge at later stages of leaf development. Using ChIP-chip experiments and sugar assays, we show that SCR is primarily involved in sugar transport whereas SCL23 functions in mineral transport. SHR is also essential for BS cell-fate specification, but it is expressed in the central vascular tissue. However, the SHR protein moves into the BS cells, where it directly regulates SCR and SCL23 expression. SHR, SCR and SCL23 homologs are present in many plant species, suggesting that this developmental pathway for BS cell-fate specification is likely to be evolutionarily conserved.
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Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
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134
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Sozzani R, Iyer-Pascuzzi A. Postembryonic control of root meristem growth and development. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:7-12. [PMID: 24507488 DOI: 10.1016/j.pbi.2013.10.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 10/10/2013] [Indexed: 05/08/2023]
Abstract
Organ development in multicellular organisms is dependent on the proper balance between cell proliferation and differentiation. In the Arabidopsis root apical meristem, meristem growth is the result of cell divisions in the proximal meristem and cell differentiation in the elongation and differentiation zones. Hormones, transcription factors and small peptides underpin the molecular mechanisms governing these processes. Computer modeling has aided our understanding of the dynamic interactions involved in stem cell maintenance and meristem activity. Here we review recent advances in our understanding of postembryonic root stem cell maintenance and control of meristem size.
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Affiliation(s)
- Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Anjali Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States.
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135
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Regulatory Networks Acted Upon by the GID1–DELLA System After Perceiving Gibberellin. SIGNALING PATHWAYS IN PLANTS 2014; 35:1-25. [DOI: 10.1016/b978-0-12-801922-1.00001-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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136
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Yoshida H, Ueguchi-Tanaka M. DELLA and SCL3 balance gibberellin feedback regulation by utilizing INDETERMINATE DOMAIN proteins as transcriptional scaffolds. PLANT SIGNALING & BEHAVIOR 2014; 9:e29726. [PMID: 25763707 PMCID: PMC4205140 DOI: 10.4161/psb.29726] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 06/25/2014] [Indexed: 05/20/2023]
Abstract
DELLA proteins are key negative regulators in the phytohormone gibberellin's (GA) signaling. In addition to this role, the DELLA proteins upregulate the gene expression levels of the positive regulators in GA signaling, such as GA 20-oxidase, GA receptor, and a transcriptional regulator, SCARECROW-LIKE3 (SCL3), which enables the regulation of GA feedback. Since DELLAs lack a known DNA binding domain, other transcription factor(s) that recruit DELLAs to DNA are essential for this regulation. Recently, we showed that the INDETERMINATE DOMAIN family proteins serve as transcriptional scaffolds to exert the transactivation activity of DELLAs. This finding and further analyses regarding the function of SCL3 indicate that the balance of the DELLAs and SCL3 protein levels (both are GRAS proteins) regulates downstream gene expression through IDDs binding to DNA. Here, we review the regulatory system in plants similar to ours and also discuss the interactive network between GRAS and IDD proteins.
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137
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Dehghan Nayeri F. Identification of transcription factors linked to cell cycle regulation in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2014; 9:e972864. [PMID: 25482767 PMCID: PMC4622563 DOI: 10.4161/15592316.2014.972864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 06/04/2023]
Abstract
Cell cycle is an essential process in growth and development of living organisms consists of the replication and mitotic phases separated by 2 gap phases; G1 and G2. It is tightly controlled at the molecular level and especially at the level of transcription. Precise regulation of the cell cycle is of central significance for plant growth and development and transcription factors are global regulators of gene expression playing essential roles in cell cycle regulation. This study has uncovered TFs that are involved in the control of cell cycle progression. With the aid of multi-parallel quantitative RT-PCR, the expression changes of 1880 TFs represented in the Arabidopsis TF platform was monitored in Arabidopsis synchronous MM2d cells during a 19 h period representing different time points corresponding to the 4 cell cycle phases after treatment of MM2d cells with Aphidicolin. Comparative TF expression analyses performed on synchronous cells resulted in the identification of 239 TFs differentially expressed during the cell cycle, while about one third of TFs were constitutively expressed through all time points. Phase-specific TFs were also identified.
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Affiliation(s)
- Fatemeh Dehghan Nayeri
- Max-Planck Institute of Molecular Plant Physiology; Am Mühlenberg 1; Potsdam-Golm, Germany
- Department of Agricultural Biotechnology; Faculty of Engineering and Technology; Imam Khomeini International University; Qazvin, Iran
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138
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Song XM, Liu TK, Duan WK, Ma QH, Ren J, Wang Z, Li Y, Hou XL. Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis). Genomics 2013; 103:135-46. [PMID: 24365788 DOI: 10.1016/j.ygeno.2013.12.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 11/08/2013] [Accepted: 12/16/2013] [Indexed: 12/23/2022]
Abstract
The GRAS gene family is one of the most important families of transcriptional regulators. In this study, 48 GRAS genes are identified from Chinese cabbage, and they are classified into eight groups according to the classification of Arabidopsis. The characterization, classification, gene structure and phylogenetic construction of GRAS proteins are performed. Distribution mapping shows that GRAS proteins are nonrandomly localized in 10 chromosomes. Fifty-five orthologous gene pairs are shared by Chinese cabbage and Arabidopsis, and interaction networks of these orthologous genes are constructed. The expansion of GRAS genes in Chinese cabbage results from genome triplication. Among the 17 species examined, 14 higher plants carry the GRAS genes, whereas two lower plants and one fungi species do not. Furthermore, the expression patterns of GRAS genes exhibit differences in three tissues based on RNA-seq data. Taken together, this comprehensive analysis will provide rich resources for studying GRAS protein functions in Chinese cabbage.
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Affiliation(s)
- Xiao-Ming Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong-Kun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei-Ke Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing-Hua Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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139
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Eveland AL, Goldshmidt A, Pautler M, Morohashi K, Liseron-Monfils C, Lewis MW, Kumari S, Hiraga S, Yang F, Unger-Wallace E, Olson A, Hake S, Vollbrecht E, Grotewold E, Ware D, Jackson D. Regulatory modules controlling maize inflorescence architecture. Genome Res 2013; 24:431-43. [PMID: 24307553 PMCID: PMC3941108 DOI: 10.1101/gr.166397.113] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures.
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Affiliation(s)
- Andrea L Eveland
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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140
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Racolta A, Bryan AC, Tax FE. The receptor-like kinases GSO1 and GSO2 together regulate root growth in Arabidopsis through control of cell division and cell fate specification. Dev Dyn 2013; 243:257-78. [PMID: 24123341 DOI: 10.1002/dvdy.24066] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 09/19/2013] [Accepted: 09/19/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The root apical meristem of Arabidopsis is established post-embryonically as the main source of root cells, and its activity is maintained by complex bidirectional signaling between stem cells and mature cells. The receptor-like kinases GASSHO1 (GSO1) and GSO2 have been shown to regulate aerial epidermal function and seedling growth in Arabidopsis. RESULTS Here we show that gso1; gso2 seedlings also have root growth and patterning defects. Analyses of mutant root morphology indicate abnormal numbers of cells in longitudinal files and radial cell layers, as well as aberrant stem cell division planes. gso1; gso2 double mutants misexpress markers for stem cells and differentiated root cell types. In addition, gso1; gso2 root growth defects, but not marker missexpression or patterning phenotypes, are rescued by growth on media containing metabolizable sugars. CONCLUSIONS We conclude that GSO1 and GSO2 function together in intercellular signaling to positively regulate cell proliferation, differentiation of root cell types, and stem cell identity. In addition, GSO1 and GSO2 control seedling root growth by modulating sucrose response after germination.
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Affiliation(s)
- Adriana Racolta
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona
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141
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Garay-Arroyo A, Ortiz-Moreno E, de la Paz Sánchez M, Murphy AS, García-Ponce B, Marsch-Martínez N, de Folter S, Corvera-Poiré A, Jaimes-Miranda F, Pacheco-Escobedo MA, Dubrovsky JG, Pelaz S, Álvarez-Buylla ER. The MADS transcription factor XAL2/AGL14 modulates auxin transport during Arabidopsis root development by regulating PIN expression. EMBO J 2013; 32:2884-95. [PMID: 24121311 DOI: 10.1038/emboj.2013.216] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 08/28/2013] [Indexed: 12/29/2022] Open
Abstract
Elucidating molecular links between cell-fate regulatory networks and dynamic patterning modules is a key for understanding development. Auxin is important for plant patterning, particularly in roots, where it establishes positional information for cell-fate decisions. PIN genes encode plasma membrane proteins that serve as auxin efflux transporters; mutations in members of this gene family exhibit smaller roots with altered root meristems and stem-cell patterning. Direct regulators of PIN transcription have remained elusive. Here, we establish that a MADS-box gene (XAANTAL2, XAL2/AGL14) controls auxin transport via PIN transcriptional regulation during Arabidopsis root development; mutations in this gene exhibit altered stem-cell patterning, root meristem size, and root growth. XAL2 is necessary for normal shootward and rootward auxin transport, as well as for maintaining normal auxin distribution within the root. Furthermore, this MADS-domain transcription factor upregulates PIN1 and PIN4 by direct binding to regulatory regions and it is required for PIN4-dependent auxin response. In turn, XAL2 expression is regulated by auxin levels thus establishing a positive feedback loop between auxin levels and PIN regulation that is likely to be important for robust root patterning.
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Affiliation(s)
- Adriana Garay-Arroyo
- Depto. de Ecología Funcional. Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, México
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142
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Inoue T, Kondo Y, Naramoto S, Nakano A, Ueda T. RAB5 activation is required for multiple steps in Arabidopsis thaliana root development. PLANT & CELL PHYSIOLOGY 2013; 54:1648-59. [PMID: 23893024 DOI: 10.1093/pcp/pct109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Rab GTPases regulate the tethering and fusion of transport vesicles to target membranes in membrane trafficking by acting as a molecular switch, cycling between GDP- and GTP-bound states. RAB5 is a member of the Rab GTPase family, the members of which have been shown to perform various functions in the endocytic pathway, including the regulation of endosomal fusion and motility in animal cells. RAB5-mediated endosomal trafficking has also been found to play important roles in various higher order plant functions, which include the regulation of the polar transport of auxin and responses to environmental conditions. The regulatory mechanisms and functions of plant RAB5 have also been investigated at the molecular and cellular levels. However, the significance of RAB5 activity at the tissue and organ levels has hardly been investigated thus far. In the present study, we examined the effect of a mutation in VPS9a, which encodes the sole guanine nucleotide exchange factor for all RAB5s in the vegetative stages of Arabidopsis thaliana. We found that multiple developmental processes were impaired in the mutant plants, including the growth and pattern formation of the roots and establishment of auxin maxima. Our results indicate that RAB5 plays distinctive pivotal roles in the development of plants.
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Affiliation(s)
- Takeshi Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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143
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Cui D, Zhao J, Jing Y, Fan M, Liu J, Wang Z, Xin W, Hu Y. The arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport. PLoS Genet 2013; 9:e1003759. [PMID: 24039602 PMCID: PMC3764202 DOI: 10.1371/journal.pgen.1003759] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 07/12/2013] [Indexed: 12/20/2022] Open
Abstract
The plant hormone auxin plays a critical role in regulating various aspects of plant growth and development, and the spatial accumulation of auxin within organs, which is primarily attributable to local auxin biosynthesis and polar transport, is largely responsible for lateral organ morphogenesis and the establishment of plant architecture. Here, we show that three Arabidopsis INDETERMINATE DOMAIN (IDD) transcription factors, IDD14, IDD15, and IDD16, cooperatively regulate auxin biosynthesis and transport and thus aerial organ morphogenesis and gravitropic responses. Gain-of-function of each IDD gene in Arabidopsis results in small and transversally down-curled leaves, whereas loss-of-function of these IDD genes causes pleiotropic phenotypes in aerial organs and defects in gravitropic responses, including altered leaf shape, flower development, fertility, and plant architecture. Further analyses indicate that these IDD genes regulate spatial auxin accumulation by directly targeting YUCCA5 (YUC5), TRYPTOPHAN AMINOTRANSFERASE of ARABIDOPSIS1 (TAA1), and PIN-FORMED1 (PIN1) to promote auxin biosynthesis and transport. Moreover, mutation or ectopic expression of YUC suppresses the organ morphogenic phenotype and partially restores the gravitropic responses in gain- or loss-of-function idd mutants, respectively. Taken together, our results reveal that a subfamily of IDD transcription factors plays a critical role in the regulation of spatial auxin accumulation, thereby controlling organ morphogenesis and gravitropic responses in plants. Auxin is a key plant hormone and the spatial accumulation of auxin is essential for lateral organ morphogenesis and gravitropic responses in higher plants. However, the various mechanisms through which spatial auxin accumulation is regulated remain to be fully elucidated. Here, we identify a gain-of-function mutant of Arabidopsis IDD14 that exhibits small and transversally down-curled leaves. Further characterization of both gain- and loss-of-function mutants in IDD14 and its close homologs, IDD15 and IDD16, reveals that these three IDD transcription factors function redundantly and cooperatively in the regulation of multiple aspects of lateral organ morphogenesis and gravitropic responses. We further demonstrate that these IDD transcription factors influence the spatial accumulation of auxin by directly targeting auxin biosynthetic and transport genes to activate their expression. These findings identify a subfamily of IDD transcription factors that coordinates spatial auxin gradients and thus directs lateral organ morphogenesis and gravitropic responses in plants.
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Affiliation(s)
- Dayong Cui
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jingbo Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjun Jing
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mingzhu Fan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jing Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhicai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Xin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- National Center for Plant Gene Research, Beijing, China
- * E-mail:
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144
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Reinhart BJ, Liu T, Newell NR, Magnani E, Huang T, Kerstetter R, Michaels S, Barton MK. Establishing a framework for the Ad/abaxial regulatory network of Arabidopsis: ascertaining targets of class III homeodomain leucine zipper and KANADI regulation. THE PLANT CELL 2013; 25:3228-49. [PMID: 24076978 PMCID: PMC3809529 DOI: 10.1105/tpc.113.111518] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/08/2013] [Accepted: 08/27/2013] [Indexed: 05/18/2023]
Abstract
The broadly conserved Class III homeodomain leucine zipper (HD-ZIPIII) and KANADI transcription factors have opposing and transformational effects on polarity and growth in all tissues and stages of the plant's life. To obtain a comprehensive understanding of how these factors work, we have identified transcripts that change in response to induced HD-ZIPIII or KANADI function. Additional criteria used to identify high-confidence targets among this set were presence of an adjacent HD-ZIPIII binding site, expression enriched within a subdomain of the shoot apical meristem, mutant phenotype showing defect in polar leaf and/or meristem development, physical interaction between target gene product and HD-ZIPIII protein, opposite regulation by HD-ZIPIII and KANADI, and evolutionary conservation of the regulator-target relationship. We find that HD-ZIPIII and KANADI regulate tissue-specific transcription factors involved in subsidiary developmental decisions, nearly all major hormone pathways, and new actors (such as indeterminate domain4) in the ad/abaxial regulatory network. Multiple feedback loops regulating HD-ZIPIII and KANADI are identified, as are mechanisms through which HD-ZIPIII and KANADI oppose each other. This work lays the foundation needed to understand the components, structure, and workings of the ad/abaxial regulatory network directing basic plant growth and development.
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Affiliation(s)
- Brenda J. Reinhart
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Tie Liu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Nicole R. Newell
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Enrico Magnani
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Tengbo Huang
- Rutgers University of New Jersey, New Brunswick, New Jersey 08901
| | | | | | - M. Kathryn Barton
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Address correspondence to
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145
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Wang P, Kelly S, Fouracre JP, Langdale JA. Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:656-70. [PMID: 23647263 DOI: 10.1111/tpj.12229] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 05/09/2023]
Abstract
Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit 'Kranz' anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell types. Although Kranz anatomy evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene so far implicated in Kranz patterning. To provide a broader insight into the regulation of Kranz differentiation, we performed a genome-wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network, and suggests likely components of that network. Furthermore, the data imply a role for additional pathways in the development of Kranz leaves.
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Affiliation(s)
- Peng Wang
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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146
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Slewinski TL. Using evolution as a guide to engineer kranz-type c4 photosynthesis. FRONTIERS IN PLANT SCIENCE 2013; 4:212. [PMID: 23847626 PMCID: PMC3696737 DOI: 10.3389/fpls.2013.00212] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/03/2013] [Indexed: 05/07/2023]
Abstract
Kranz-type C4 photosynthesis has independently and rapidly evolved over 60 times to dramatically increase radiation use efficiency in both monocots and eudicots. Indeed, it is one of the most exceptional examples of convergent evolution in the history of life. The repeated and rapid evolution of Kranz-type C4 suggests that it may be a derivative of a conserved developmental pathway that is present in all angiosperms. Here, I argue that the Kranz-type C4 photosynthetic system is an extension of the endodermis/starch sheath, that is normally only found in the roots and stems, into photosynthetic structures such as leaves. Support for this hypothesis was recently provided by a study that showed that the same genetic pathway that gives rise to the endodermis in roots, the SCARECROW/SHORT-ROOT radial patterning system, also regulates the development of Kranz anatomy and C4 physiology in leaves. This new hypothesis for the evolution of Kranz-type C4 photosynthesis has opened new opportunities to explore the underlying genetic networks that regulate the development and physiology of C4 and provides new potential avenues for the engineering of the mechanism into C3 crops.
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147
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Koizumi K, Gallagher KL. Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning. Development 2013; 140:1292-300. [PMID: 23444357 DOI: 10.1242/dev.090761] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The timing and extent of cell division is particularly important for the growth and development of multicellular organisms. Roots of the model organism Arabidopsis thaliana have been widely studied as a paradigm for organ development in plants. In the Arabidopsis root, the plant-specific GRAS family transcription factors SHORT-ROOT (SHR) and SCARECROW (SCR) are key regulators of root growth and of the asymmetric cell divisions that separate the ground tissue into two separate layers: the endodermis and cortex. To elucidate the role of SHR in root development, we identified 17 SHR-interacting proteins. Among those isolated was At5g24740, which we named SHRUBBY (SHBY). SHBY is a vacuolar sorting protein with similarity to the gene responsible for Cohen syndrome in humans. Hypomorphic alleles of shby caused poor root growth, decreased meristematic activity and defects in radial patterning that are characterized by an increase in the number of cell divisions in the ground tissue that lead to extra cells in the cortex and endodermis, as well as additional cell layers. Analysis of genetic and molecular markers indicates that SHBY acts in a pathway that partially overlaps with SHR, SCR, PLETHORA1 and PLETHORA2 (PLT1 and PLT2). The shby-1 root phenotype was partially phenocopied by treatment of wild-type roots with the proteosome inhibitor MG132 or the gibberellic acid (GA) synthesis inhibitor paclobutrazol (PAC). Our results indicate that SHBY controls root growth downstream of GA in part through the regulation of SHR and SCR.
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Affiliation(s)
- Koji Koizumi
- 121 Carolyn Lynch Laboratories, Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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148
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Peng Y, Ma W, Chen L, Yang L, Li S, Zhao H, Zhao Y, Jin W, Li N, Bevan MW, Li X, Tong Y, Li Y. Control of root meristem size by DA1-RELATED PROTEIN2 in Arabidopsis. PLANT PHYSIOLOGY 2013; 161:1542-56. [PMID: 23296689 PMCID: PMC3585615 DOI: 10.1104/pp.112.210237] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/03/2013] [Indexed: 05/21/2023]
Abstract
The control of organ growth by coordinating cell proliferation and differentiation is a fundamental developmental process. In plants, postembryonic root growth is sustained by the root meristem. For maintenance of root meristem size, the rate of cell differentiation must equal the rate of cell division. Cytokinin and auxin interact to affect the cell proliferation and differentiation balance and thus control root meristem size. However, the genetic and molecular mechanisms that determine root meristem size still remain largely unknown. Here, we report that da1-related protein2 (dar2) mutants produce small root meristems due to decreased cell division and early cell differentiation in the root meristem of Arabidopsis (Arabidopsis thaliana). dar2 mutants also exhibit reduced stem cell niche activity in the root meristem. DAR2 encodes a Lin-11, Isl-1, and Mec-3 domain-containing protein and shows an expression peak in the border between the transition zone and the elongation zone. Genetic analyses show that DAR2 functions downstream of cytokinin and SHORT HYPOCOTYL2 to maintain normal auxin distribution by influencing auxin transport. Further results indicate that DAR2 acts through the PLETHORA pathway to influence root stem cell niche activity and therefore control root meristem size. Collectively, our findings identify the role of DAR2 in root meristem size control and provide a novel link between several key regulators influencing root meristem size.
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149
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Miyashima S, Honda M, Hashimoto K, Tatematsu K, Hashimoto T, Sato-Nara K, Okada K, Nakajima K. A comprehensive expression analysis of the Arabidopsis MICRORNA165/6 gene family during embryogenesis reveals a conserved role in meristem specification and a non-cell-autonomous function. PLANT & CELL PHYSIOLOGY 2013; 54:375-84. [PMID: 23292599 DOI: 10.1093/pcp/pcs188] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
One of the most fundamental events in plant ontogeny is the specification of the shoot and root apical meristem (SAM and RAM) in embryogenesis. In Arabidopsis, the restricted expression of class III homeodomain leucine zipper (HD-ZIP III) transcription factors (TFs) at the central-apical domain of early embryos is required for the correct specification of the SAM and RAM. Because the expression of HD-ZIP III TFs is suppressed by microRNA165/166 (miR165/6), elucidation of the sites of miR165/6 production and their activity range is a key to understanding the molecular basis of SAM and RAM specification in embryogenesis. Here, we present a comprehensive reporter analysis of all nine Arabidopsis MICRORNA165/166 (MIR165/6) genes during embryogenesis. We show that five MIR165/6 genes are transcribed in a largely conserved pattern in embryos, with their expression being preferentially focused at the basal-peripheral region of embryos. Our analysis also indicated that MIR165/6 transcription does not depend on SCARECROW (SCR) function in early embryos, in contrast to its requirement in post-embryonic roots. Furthermore, by observing the expression pattern of the miR-resistant PHBmu-GFP (green fluorescent protein) reporter, in either the presence or absence of the MIR165Amu transgene, which targets PHBmu-GFP, we obtained data that indicate a non-cell-autonomous function for miR165 in early embryos. These results suggest that miR165, and possibly miR166 as well, has the capacity to act as a positional cue from the basal-peripheral region of early embryos, and remotely controls SAM and RAM specification with their non-cell-autonomous function.
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Affiliation(s)
- Shunsuke Miyashima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan
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150
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Xuan YH, Priatama RA, Huang J, Je BI, Liu JM, Park SJ, Piao HL, Son DY, Lee JJ, Park SH, Jung KH, Kim TH, Han CD. Indeterminate domain 10 regulates ammonium-mediated gene expression in rice roots. THE NEW PHYTOLOGIST 2013; 197:791-804. [PMID: 23278238 DOI: 10.1111/nph.12075] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 10/30/2012] [Indexed: 05/22/2023]
Abstract
Indeterminate domain (IDD) genes are a family of plant transcriptional regulators that function in the control of development and metabolism during growth. Here, the function of Oryza sativa indeterminate domain 10 (OsIDD10) has been explored in rice plants. Compared with wild-type roots, idd10 mutant roots are hypersensitive to exogenous ammonium. This work aims to define the action of IDD10 on gene expression involved in ammonium uptake and nitrogen (N) metabolism. The ammonium induction of key ammonium uptake and assimilation genes was examined in the roots of idd10 mutants and IDD10 overexpressors. Molecular studies and transcriptome analysis were performed to identify target genes and IDD10 binding cis-elements. IDD10 activates the transcription of AMT1;2 and GDH2 by binding to a cis-element motif present in the promoter region of AMT1;2 and in the fifth intron of GDH2. IDD10 contributes significantly to the induction of several genes involved in N-linked metabolic and cellular responses, including genes encoding glutamine synthetase 2, nitrite reductases and trehalose-6-phosphate synthase. Furthermore, the possibility that IDD10 might influence the N-mediated feedback regulation of target genes was examined. This study demonstrates that IDD10 is involved in regulatory circuits that determine N-mediated gene expression in plant roots.
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Affiliation(s)
- Yuan Hu Xuan
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
| | - Ryza A Priatama
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
| | - Jin Huang
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
| | - Byoung Il Je
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
| | - Jing Miao Liu
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
| | - Soon Ju Park
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
| | - Hai Long Piao
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
| | - Dae Young Son
- Department of Applied Biology, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Jeung Joo Lee
- Department of Applied Biology, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Sung Han Park
- National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-857, South Korea
| | - Ki Hong Jung
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea
| | - Tae Ho Kim
- Genomics Division, Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), RDA, Suwon, 441-707, South Korea
| | - Chang-Deok Han
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 660-701, South Korea
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