101
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ten Hove CA, Lu KJ, Weijers D. Building a plant: cell fate specification in the early Arabidopsis embryo. Development 2015; 142:420-30. [DOI: 10.1242/dev.111500] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Embryogenesis is the beginning of plant development, yet the cell fate decisions and patterning steps that occur during this time are reiterated during development to build the post-embryonic architecture. In Arabidopsis, embryogenesis follows a simple and predictable pattern, making it an ideal model with which to understand how cellular and tissue developmental processes are controlled. Here, we review the early stages of Arabidopsis embryogenesis, focusing on the globular stage, during which time stem cells are first specified and all major tissues obtain their identities. We discuss four different aspects of development: the formation of outer versus inner layers; the specification of vascular and ground tissues; the determination of shoot and root domains; and the establishment of the first stem cells.
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Affiliation(s)
- Colette A. ten Hove
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Kuan-Ju Lu
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dolf Weijers
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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102
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Robert HS, Grunewald W, Sauer M, Cannoot B, Soriano M, Swarup R, Weijers D, Bennett M, Boutilier K, Friml J. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development 2015; 142:702-11. [PMID: 25617434 DOI: 10.1242/dev.115832] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop between MONOPTEROS (ARF5)-dependent auxin signalling and auxin transport. This MONOPTEROS-dependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.
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Affiliation(s)
- Hélène S Robert
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Wim Grunewald
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Michael Sauer
- University of Potsdam, Institute of Biochemistry and Biology, D-14476 Potsdam, Germany Departamento Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Madrid, Spain
| | - Bernard Cannoot
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Mercedes Soriano
- Wageningen University and Research Centre, P.O. Box 619, 6700 AP Wageningen, The Netherlands
| | - Ranjan Swarup
- School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands
| | - Malcolm Bennett
- School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Kim Boutilier
- Wageningen University and Research Centre, P.O. Box 619, 6700 AP Wageningen, The Netherlands
| | - Jiří Friml
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
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103
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Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. Proc Natl Acad Sci U S A 2014; 111:E5471-9. [PMID: 25468974 DOI: 10.1073/pnas.1413918111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Auxin polar transport, local maxima, and gradients have become an important model system for studying self-organization. Auxin distribution is regulated by auxin-dependent positive feedback loops that are not well-understood at the molecular level. Previously, we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are posttranscriptionally repressed at the site of maximum auxin accumulation at the root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential for regulating formation of auxin local maxima and gradients. ICR1 levels increase concomitant with increase in auxin response in lateral root primordia, cotyledon tips, and provascular tissues. However, in the embryo hypophysis and root meristem, when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB) [SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo hypophysis resulted in reduction of auxin accumulation and concomitant root growth arrest. ICR1 disappeared during root regeneration and lateral root initiation concomitantly with the formation of a local auxin maximum in response to external auxin treatments and transiently after gravitropic stimulation. Destabilization of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome function, and protein synthesis. A mathematical model based on these findings shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward reflux can be simulated without assuming preexisting tissue polarity. Our experimental results and mathematical modeling indicate that regulation of auxin distribution is tightly associated with auxin-dependent ICR1 levels.
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104
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Radoeva T, Weijers D. A roadmap to embryo identity in plants. TRENDS IN PLANT SCIENCE 2014; 19:709-16. [PMID: 25017700 DOI: 10.1016/j.tplants.2014.06.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/17/2014] [Accepted: 06/20/2014] [Indexed: 05/19/2023]
Abstract
Although plant embryogenesis is usually studied in the context of seed development, there are many alternative roads to embryo initiation. These include somatic embryogenesis in tissue culture and microspore embryogenesis, both widely used in breeding and crop propagation, but also include other modes of ectopic embryo initiation. In the past decades several genes, mostly transcription factors, were identified that can induce embryogenesis in somatic cells. Because the genetic networks in which such regulators operate to promote embryogenesis are largely unknown, a key question is how their activity relates to zygotic and alternative embryo initiation. We describe here the many roads to plant embryo initiation and discuss a framework for defining the developmental roles and mechanisms of plant embryogenesis regulators.
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Affiliation(s)
- Tatyana Radoeva
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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105
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Zhang Y, Peng L, Wu Y, Shen Y, Wu X, Wang J. Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa. PLANT MOLECULAR BIOLOGY 2014; 86:425-42. [PMID: 25214014 DOI: 10.1007/s11103-014-0238-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/12/2014] [Indexed: 05/21/2023]
Abstract
Embryo development represents a crucial developmental period in the life cycle of flowering plants. To gain insights into the genetic programs that control embryo development in Brassica rapa L., RNA sequencing technology was used to perform transcriptome profiling analysis of B. rapa developing embryos. The results generated 42,906,229 sequence reads aligned with 32,941 genes. In total, 27,760, 28,871, 28,384, and 25,653 genes were identified from embryos at globular, heart, early cotyledon, and mature developmental stages, respectively, and analysis between stages revealed a subset of stage-specific genes. We next investigated 9,884 differentially expressed genes with more than fivefold changes in expression and false discovery rate ≤ 0.001 from three adjacent-stage comparisons; 1,514, 3,831, and 6,633 genes were detected between globular and heart stage embryo libraries, heart stage and early cotyledon stage, and early cotyledon and mature stage, respectively. Large numbers of genes related to cellular process, metabolism process, response to stimulus, and biological process were expressed during the early and middle stages of embryo development. Fatty acid biosynthesis, biosynthesis of secondary metabolites, and photosynthesis-related genes were expressed predominantly in embryos at the middle stage. Genes for lipid metabolism and storage proteins were highly expressed in the middle and late stages of embryo development. We also identified 911 transcription factor genes that show differential expression across embryo developmental stages. These results increase our understanding of the complex molecular and cellular events during embryo development in B. rapa and provide a foundation for future studies on other oilseed crops.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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106
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Wang R, Estelle M. Diversity and specificity: auxin perception and signaling through the TIR1/AFB pathway. CURRENT OPINION IN PLANT BIOLOGY 2014; 21:51-58. [PMID: 25032902 PMCID: PMC4294414 DOI: 10.1016/j.pbi.2014.06.006] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/15/2014] [Indexed: 05/19/2023]
Abstract
Auxin is a versatile plant hormone that plays an essential role in most aspects of plant growth and development. Auxin regulates various growth processes by modulating gene transcription through a SCF(TIR1/AFB)-Aux/IAA-ARF nuclear signaling module. Recent work has generated clues as to how multiple layers of regulation of the auxin signaling components may result in diverse and specific response outputs. In particular, interaction and structural studies of key auxin signaling proteins have produced novel insights into the molecular basis of auxin-regulated transcription and may lead to a refined auxin signaling model.
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Affiliation(s)
- Renhou Wang
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, UCSD, La Jolla, CA 92093, United States
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, UCSD, La Jolla, CA 92093, United States.
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107
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Huang JB, Liu H, Chen M, Li X, Wang M, Yang Y, Wang C, Huang J, Liu G, Liu Y, Xu J, Cheung AY, Tao LZ. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. THE PLANT CELL 2014; 26:3501-18. [PMID: 25217509 PMCID: PMC4213153 DOI: 10.1105/tpc.114.127902] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/12/2014] [Accepted: 08/22/2014] [Indexed: 05/18/2023]
Abstract
ROP GTPases are crucial for the establishment of cell polarity and for controlling responses to hormones and environmental signals in plants. In this work, we show that ROP3 plays important roles in embryo development and auxin-dependent plant growth. Loss-of-function and dominant-negative (DN) mutations in ROP3 induced a spectrum of similar defects starting with altered cell division patterning during early embryogenesis to postembryonic auxin-regulated growth and developmental responses. These resulted in distorted embryo development, defective organ formation, retarded root gravitropism, and reduced auxin-dependent hypocotyl elongation. Our results showed that the expression of AUXIN RESPONSE FACTOR5/MONOPTEROS and root master regulators PLETHORA1 (PLT1) and PLT2 was reduced in DN-rop3 mutant embryos, accounting for some of the observed patterning defects. ROP3 mutations also altered polar localization of auxin efflux proteins (PINs) at the plasma membrane (PM), thus disrupting auxin maxima in the root. Notably, ROP3 is induced by auxin and prominently detected in root stele cells, an expression pattern similar to those of several stele-enriched PINs. Our results demonstrate that ROP3 is important for maintaining the polarity of PIN proteins at the PM, which in turn ensures polar auxin transport and distribution, thereby controlling plant patterning and auxin-regulated responses.
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Affiliation(s)
- Jia-bao Huang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Huili Liu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaojuan Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mingyan Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yali Yang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chunling Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jiaqing Huang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Guolan Liu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yuting Liu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jian Xu
- Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Li-zhen Tao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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108
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Rodríguez-Sanz H, Manzanera JA, Solís MT, Gómez-Garay A, Pintos B, Risueño MC, Testillano PS. Early markers are present in both embryogenesis pathways from microspores and immature zygotic embryos in cork oak, Quercus suber L. BMC PLANT BIOLOGY 2014; 14:224. [PMID: 25162300 PMCID: PMC4147960 DOI: 10.1186/s12870-014-0224-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/11/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND In Quercus suber, cork oak, a Mediterranean forest tree of economic and social interest, rapid production of isogenic lines and clonal propagation of elite genotypes have been achieved by developing in vitro embryogenesis from microspores and zygotic embryos respectively. Despite its high potential in tree breeding strategies, due to their recalcitrancy, the efficiency of embryogenesis in vitro systems in many woody species is still very low since factors responsible for embryogenesis initiation and embryo development are still largely unknown. The search for molecular and cellular markers during early stages of in vitro embryogenesis constitutes an important goal to distinguish, after induction, responsive from non-responsive cells, and to elucidate the mechanisms involved in embryogenesis initiation for their efficient manipulation. In this work, we have performed a comparative analysis of two embryogenesis pathways derived from microspores and immature zygotic embryos in cork oak in order to characterize early markers of reprogrammed cells in both pathways. Rearrangements of the cell structural organization, changes in epigenetic marks, cell wall polymers modifications and endogenous auxin changes were analyzed at early embryogenesis stages of the two in vitro systems by a multidisciplinary approach. RESULTS Results showed that early embryo cells exhibited defined changes of cell components which were similar in both embryogenesis in vitro systems, cellular features that were not found in non-embryogenic cells. DNA methylation level and nuclear pattern, proportion of esterified pectins in cell walls, and endogenous auxin levels were different in embryo cells in comparison with microspores and immature zygotic embryo cells from which embryos originated, constituting early embryogenesis markers. CONCLUSIONS These findings suggest that DNA hypomethylation, cell wall remodeling by pectin esterification and auxin increase are involved in early in vitro embryogenesis in woody species, providing new evidences of the developmental pattern similarity between both embryogenesis pathways, from microspores and immature zygotic embryos, in woody species.
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Affiliation(s)
- Héctor Rodríguez-Sanz
- />Pollen Biotechnology of Crop Plants group, Biological Research Center, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José-Antonio Manzanera
- />ETSI Montes, Technical University of Madrid, UPM, Ciudad Universitaria, 28040 Madrid, Spain
| | - María-Teresa Solís
- />Pollen Biotechnology of Crop Plants group, Biological Research Center, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Aránzazu Gómez-Garay
- />Department of Plant Physiology, Faculty of Biology, Complutense University of Madrid, UCM, Ciudad Universitaria, 28040 Madrid, Spain
| | - Beatriz Pintos
- />Department of Plant Physiology, Faculty of Biology, Complutense University of Madrid, UCM, Ciudad Universitaria, 28040 Madrid, Spain
| | - María C Risueño
- />Pollen Biotechnology of Crop Plants group, Biological Research Center, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pilar S Testillano
- />Pollen Biotechnology of Crop Plants group, Biological Research Center, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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109
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Auxin inhibits stomatal development through MONOPTEROS repression of a mobile peptide gene STOMAGEN in mesophyll. Proc Natl Acad Sci U S A 2014; 111:E3015-23. [PMID: 25002510 DOI: 10.1073/pnas.1400542111] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Plants, as sessile organisms, must coordinate various physiological processes to adapt to ever-changing surrounding environments. Stomata, the epidermal pores facilitating gas and water exchange, play important roles in optimizing photosynthetic efficiency and adaptability. Stomatal development is under the control of an intrinsic program mediated by a secretory peptide gene family--namely, EPIDERMAL PATTERNING FACTOR, including positively acting STOMAGEN/EPFL9. The phytohormone brassinosteroids and environment factor light also control stomatal production. However, whether auxin regulates stomatal development and whether peptide signaling is coordinated with auxin signaling in the regulation of stomatal development remain largely unknown. Here we show that auxin negatively regulates stomatal development through MONOPTEROS (also known as ARF5) repression of the mobile peptide gene STOMAGEN in mesophyll. Through physiological, genetic, transgenic, biochemical, and molecular analyses, we demonstrate that auxin inhibits stomatal development through the nuclear receptor TIR1/AFB-mediated signaling, and that MONOPTEROS directly binds to the STOMAGEN promoter to suppress its expression in mesophyll and inhibit stomatal development. Our results provide a paradigm of cross-talk between phytohormone auxin and peptide signaling in the regulation of stomatal production.
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110
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Tian H, De Smet I, Ding Z. Shaping a root system: regulating lateral versus primary root growth. TRENDS IN PLANT SCIENCE 2014; 19:426-31. [PMID: 24513255 DOI: 10.1016/j.tplants.2014.01.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/04/2014] [Accepted: 01/14/2014] [Indexed: 05/22/2023]
Abstract
Primary and lateral roots comprise root systems, which are vital to the growth and survival of plants. Several molecular mechanisms associated with primary and lateral root growth have been described, including some common regulatory factors for their initiation and development. However, in this opinion article, we discuss the distinct growth behavior of lateral roots in response to environmental cues, such as salinity, gravity, and nutrient availability, which are mediated via specific regulators. We propose that differential growth dynamics between primary and lateral roots are crucial for plants to adapt to the ever-changing environmental conditions.
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Affiliation(s)
- Huiyu Tian
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong 250100, PR China
| | - Ive De Smet
- Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
| | - Zhaojun Ding
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong 250100, PR China.
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111
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Abstract
Auxin influences nearly every aspect of plant biology through a simple signaling pathway; however, it remains unclear how much of the diversity in auxin effects is explained by variation in the core signaling components and which properties of these components may contribute to diversification in response dynamics. Here, we recapitulated the entire Arabidopsis thaliana forward nuclear auxin signal transduction pathway in Saccharomyces cerevisiae to test whether signaling module composition enables tuning of the dynamic response. Sensitivity analysis guided by a small mathematical model revealed the centrality of auxin/indole-3-acetic acid (Aux/IAA) transcriptional corepressors in controlling response dynamics and highlighted the strong influence of natural variation in Aux/IAA degradation rates on circuit performance. When the basic auxin response circuit was expanded to include multiple Aux/IAAs, we found that dominance relationships between coexpressed Aux/IAAs were sufficient to generate distinct response modules similar to those seen during plant development. Our work provides a new method for dissecting auxin signaling and demonstrates the key role of Aux/IAAs in tuning auxin response dynamics.
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112
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Soriano M, Li H, Jacquard C, Angenent GC, Krochko J, Offringa R, Boutilier K. Plasticity in Cell Division Patterns and Auxin Transport Dependency during in Vitro Embryogenesis in Brassica napus. THE PLANT CELL 2014; 26:2568-2581. [PMID: 24951481 PMCID: PMC4114952 DOI: 10.1105/tpc.114.126300] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/29/2014] [Accepted: 06/09/2014] [Indexed: 05/19/2023]
Abstract
In Arabidopsis thaliana, zygotic embryo divisions are highly regular, but it is not clear how embryo patterning is established in species or culture systems with irregular cell divisions. We investigated this using the Brassica napus microspore embryogenesis system, where the male gametophyte is reprogrammed in vitro to form haploid embryos in the absence of exogenous growth regulators. Microspore embryos are formed via two pathways: a zygotic-like pathway, characterized by initial suspensor formation followed by embryo proper formation from the distal cell of the suspensor, and a pathway characterized by initially unorganized embryos lacking a suspensor. Using embryo fate and auxin markers, we show that the zygotic-like pathway requires polar auxin transport for embryo proper specification from the suspensor, while the suspensorless pathway is polar auxin transport independent and marked by an initial auxin maximum, suggesting early embryo proper establishment in the absence of a basal suspensor. Polarity establishment in this suspensorless pathway was triggered and guided by rupture of the pollen exine. Irregular division patterns did not affect cell fate establishment in either pathway. These results confirm the importance of the suspensor and suspensor-driven auxin transport in patterning, but also uncover a mechanism where cell patterning is less regular and independent of auxin transport.
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Affiliation(s)
- Mercedes Soriano
- Plant Research International, 6700 AP Wageningen, The Netherlands
| | - Hui Li
- Plant Research International, 6700 AP Wageningen, The Netherlands
| | - Cédric Jacquard
- Université de Reims Champagne-Ardenne, Unité de Recherche Vignes et Vins de Champagne-EA 4707, Laboratoire de Stress, Défenses et Reproduction des Plantes, Moulin de la Housse, 51687 REIMS Cedex 2, France
| | - Gerco C Angenent
- Plant Research International, 6700 AP Wageningen, The Netherlands Laboratory for Molecular Biology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Joan Krochko
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon S7N 0W9, Canada
| | - Remko Offringa
- Molecular and Developmental Genetics, Institute Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Kim Boutilier
- Plant Research International, 6700 AP Wageningen, The Netherlands
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113
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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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Bhalerao RP, Fischer U. Auxin gradients across wood-instructive or incidental? PHYSIOLOGIA PLANTARUM 2014; 151:43-51. [PMID: 24286229 DOI: 10.1111/ppl.12134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 05/21/2023]
Abstract
Various aspects of wood formation have been linked to the action of auxin, e.g. cambial activity, dormancy, secondary cell wall deposition and tension wood formation. The presence of a radial auxin concentration gradient across wood-forming tissue has been suggested to regulate cambial activity and differentiation of cambial derivatives by providing positional information to cells within the tissue. Similar patterning mechanisms that depend on the interpretation of auxin thresholds have subsequently been proposed for shoot and root apical meristems. However, direct evidence for the existence of auxin gradients has only been obtained for the cambium of various tree species. While the auxin gradient theory is based on a plethora of descriptive and pharmacological experiments, in recent years, auxin function on wood formation has been underpinned by molecular and functional data. Here, we review the latest progress in understanding the role of auxin in wood formation and discuss how auxin concentration gradients could be established and interpreted in wood-forming tissues.
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Affiliation(s)
- Rishikesh P Bhalerao
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, SE-90183, Sweden
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115
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Abstract
Auxin signaling through the SCF(TIR1)-Aux/IAA-ARF pathway is one of the best-studied plant hormone response pathways. Components of this pathway, from receptors through to transcription factors, have been identified and analyzed in detail. Although we understand elementary aspects of how the auxin signal is perceived and leads to a transcriptional response, many questions remain about the in vivo function of the pathway. Two crucial issues are the tissue specificity of the response, i.e. how distinct cell types can interpret the same auxin signal differently, and the response to a signaling gradient, i.e. how a graded distribution of auxin can elicit distinct expression patterns along its range. Here, we speculate on how signaling through the canonical SCF(TIR1)-Aux/IAA-ARF pathway may achieve divergent responses.
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116
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Boer DR, Freire-Rios A, van den Berg WAM, Saaki T, Manfield IW, Kepinski S, López-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D, Coll M. Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors. Cell 2014; 156:577-89. [PMID: 24485461 DOI: 10.1016/j.cell.2013.12.027] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/22/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022]
Abstract
Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Alejandra Freire-Rios
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Willy A M van den Berg
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Terrens Saaki
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology (IWM) and Centre for Plant Sciences (SK), Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Stefan Kepinski
- Astbury Centre for Structural Molecular Biology (IWM) and Centre for Plant Sciences (SK), Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Irene López-Vidrieo
- Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Jose Manuel Franco-Zorrilla
- Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Sacco C de Vries
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Roberto Solano
- Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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117
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Costa LM, Marshall E, Tesfaye M, Silverstein KAT, Mori M, Umetsu Y, Otterbach SL, Papareddy R, Dickinson HG, Boutiller K, VandenBosch KA, Ohki S, Gutierrez-Marcos JF. Central Cell-Derived Peptides Regulate Early Embryo Patterning in Flowering Plants. Science 2014; 344:168-72. [DOI: 10.1126/science.1243005] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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118
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Yoshida S, Barbier de Reuille P, Lane B, Bassel G, Prusinkiewicz P, Smith R, Weijers D. Genetic Control of Plant Development by Overriding a Geometric Division Rule. Dev Cell 2014; 29:75-87. [DOI: 10.1016/j.devcel.2014.02.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/20/2014] [Accepted: 02/04/2014] [Indexed: 01/25/2023]
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119
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Abstract
Plants can grow complex and elaborate structures, in some species for thousands of years. Despite the diversity in form and shape, plants are built from a limited number of fundamental tissue types, and their arrangement is deeply conserved in the plant kingdom. A key question in biology is how these fundamental tissues, i.e. epidermal, ground and vascular tissue, are specified and organized in time and space. In the present paper, I discuss the use of the early Arabidopsis embryo as a model system to dissect the control of tissue formation and patterning, as well as the specification of the stem cells that sustain post-embryonic growth. I present recent insights into the molecules and mechanisms that control both the specification and the subsequent growth of the different cell types within the embryonic root. Finally, I discuss major unanswered questions and future challenges in using the embryo as a model to decipher the regulatory logic of plant development.
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120
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Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing. PLoS One 2014; 9:e84203. [PMID: 24427281 PMCID: PMC3888382 DOI: 10.1371/journal.pone.0084203] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/13/2013] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The phytohormone auxin is involved in a wide range of developmental processes and auxin signaling is known to modulate the expression of target genes via two types of transcriptional regulators, namely, Aux/IAA and Auxin Response Factors (ARF). ARFs play a major role in transcriptional activation or repression through direct binding to the promoter of auxin-responsive genes. The present study aims at gaining better insight on distinctive structural and functional features among ARF proteins. RESULTS Building on the most updated tomato (Solanum lycopersicon) reference genome sequence, a comprehensive set of ARF genes was identified, extending the total number of family members to 22. Upon correction of structural annotation inconsistencies, renaming the tomato ARF family members provided a consensus nomenclature for all ARF genes across plant species. In silico search predicted the presence of putative target site for small interfering RNAs within twelve Sl-ARFs while sequence analysis of the 5'-leader sequences revealed the presence of potential small uORF regulatory elements. Functional characterization carried out by transactivation assay partitioned tomato ARFs into repressors and activators of auxin-dependent gene transcription. Expression studies identified tomato ARFs potentially involved in the fruit set process. Genome-wide expression profiling using RNA-seq revealed that at least one third of the gene family members display alternative splicing mode of regulation during the flower to fruit transition. Moreover, the regulation of several tomato ARF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signaling pathways of these two hormones. CONCLUSION All together, the data bring new insight on the complexity of the expression control of Sl-ARF genes at the transcriptional and post-transcriptional levels supporting the hypothesis that these transcriptional mediators might represent one of the main components that enable auxin to regulate a wide range of physiological processes in a highly specific and coordinated manner.
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121
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Huang S, Hill RD, Stasolla C. Plant hemoglobin participation in cell fate determination. PLANT SIGNALING & BEHAVIOR 2014; 9:e29485. [PMID: 25763627 PMCID: PMC4205130 DOI: 10.4161/psb.29485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/05/2014] [Indexed: 05/27/2023]
Abstract
Plant hemoglobins (Hbs) have been identified as master regulators in determining the developmental fate of specific cells during maize embryogenesis. Whether an embryogenic cell lives or undergoes programmed cell death (PCD) is modulated by Hbs, through their tight interactions with nitric oxide (NO) and auxin. During maize embryogenesis, Hb-suppressing cells accumulate NO, are depleted of auxin, and are committed to die. We propose that Hbs control cell fate by regulating NO and auxin homeostasis, and that this type of mechanism may influence other hormonal responses modulating plant behavior during development and stress conditions.
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122
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Sparks E, Wachsman G, Benfey PN. Spatiotemporal signalling in plant development. Nat Rev Genet 2013; 14:631-44. [PMID: 23949543 DOI: 10.1038/nrg3541] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plants, being sessile organisms, need to respond to changing environments, and as a result they have evolved unique signalling mechanisms that allow rapid communication between different parts of the plant. The signalling mechanisms that direct plant development include long-range effectors, such as phytohormones, and molecules with a local intra-organ range, such as peptides, transcription factors and some small RNAs. In this Review, we highlight recent advances in understanding plant signalling mechanisms and discuss how different classes of signalling networks can integrate with gene regulatory networks and contribute to plant development. In some cases, we also address the evolutionary context of mechanisms and discuss possible links between the lifestyle of plants and selection for different signalling mechanisms.
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Affiliation(s)
- Erin Sparks
- 1] Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA. [2]
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123
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Wabnik K, Robert HS, Smith RS, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Curr Biol 2013; 23:2513-8. [PMID: 24291090 DOI: 10.1016/j.cub.2013.10.038] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/17/2013] [Accepted: 10/15/2013] [Indexed: 11/17/2022]
Abstract
The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters, whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development.
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Affiliation(s)
- Krzysztof Wabnik
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Hélène S Robert
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium; Mendel Centre for Genomics and Proteomics of Plants Systems, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
| | - Richard S Smith
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland; Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Jiří Friml
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium; Mendel Centre for Genomics and Proteomics of Plants Systems, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.
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124
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Palovaara J, Saiga S, Weijers D. Transcriptomics approaches in the early Arabidopsis embryo. TRENDS IN PLANT SCIENCE 2013; 18:514-21. [PMID: 23726727 DOI: 10.1016/j.tplants.2013.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/24/2013] [Accepted: 04/30/2013] [Indexed: 05/20/2023]
Abstract
Early plant embryogenesis condenses the fundamental processes underlying plant development into a short sequence of predictable steps. The main tissues, as well as stem cells for their post-embryonic maintenance, are specified through genetic control networks. A key question is how cell fates are instructed by unique cellular transcriptomes, and important insights have recently been gained through cell type-specific transcriptomics during post-embryonic development. However, the poor accessibility and small size of Arabidopsis (Arabidopsis thaliana) embryos have obstructed similar progress during embryogenesis. Here, we review the current situation in plant embryo transcriptomics, and discuss how the recent development of novel cell-specific analysis technologies will enable the identification of cellular transcriptomes in the early Arabidopsis embryo.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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125
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Carabelli M, Turchi L, Ruzza V, Morelli G, Ruberti I. Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development. PLANT SIGNALING & BEHAVIOR 2013; 8:25447. [PMID: 23838958 PMCID: PMC4002598 DOI: 10.4161/psb.25447] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 06/18/2013] [Indexed: 05/20/2023]
Abstract
The Arabidopsis genome encodes 10 Homeodomain-Leucine Zipper (HD-Zip) II transcription factors that can be subdivided into 4 clades (α-δ). All the γ (ARABIDOPSIS THALIANA HOMEOBOX 2 [ATHB2], HOMEOBOX ARABIDOPSIS THALIANA 1 [HAT1], HAT2) and δ (HAT3, ATHB4) genes are regulated by light quality changes (Low Red [R]/Far-Red [FR]) that induce the shade avoidance response in most of the angiosperms. HD-Zip IIγ and HD-Zip IIδ transcription factors function as positive regulators of shade avoidance, and there is evidence that at least ATHB2 is directly positively regulated by the basic Helix-Loop-Helix (bHLH) proteins PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5. Recent evidence demonstrate that, in addition to their function in shade avoidance, HD-Zip IIγ and HD-Zip IIδ proteins play an essential role in plant development from embryogenesis onwards in a white light environment.
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Affiliation(s)
- Monica Carabelli
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
| | - Luana Turchi
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
| | - Valentino Ruzza
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
| | - Giorgio Morelli
- Food and Nutrition Research Centre; Agricultural Research Council (CRA); Rome, Italy
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
- Correspondence to: Ida Ruberti,
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126
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Wendrich JR, Weijers D. The Arabidopsis embryo as a miniature morphogenesis model. THE NEW PHYTOLOGIST 2013; 199:14-25. [PMID: 23590679 DOI: 10.1111/nph.12267] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/12/2013] [Indexed: 05/06/2023]
Abstract
Four basic ingredients of morphogenesis, oriented cell division and expansion, cell-cell communication and cell fate specification allow plant cells to develop into a wide variety of organismal architectures. A central question in plant biology is how these cellular processes are regulated and orchestrated. Here, we present the advantages of the early Arabidopsis embryo as a model for studying the control of morphogenesis. All ingredients of morphogenesis converge during embryogenesis, and the highly predictable nature of embryo development offers unprecedented opportunities for understanding their regulation in time and space. In this review we describe the morphogenetic principles underlying embryo patterning and discuss recent advances in their regulation. Morphogenesis is under tight transcriptional control and most genes that were identified as important regulators of embryo patterning encode transcription factors or components of signaling pathways. There exists, therefore, a large gap between the transcriptional control of embryo morphogenesis and the cellular execution. We describe the first such connections, and propose future directions that should help bridge this gap and generate comprehensive understanding of the control of morphogenesis.
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Affiliation(s)
- Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
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127
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Pierre-Jerome E, Moss BL, Nemhauser JL. Tuning the auxin transcriptional response. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2557-63. [PMID: 23630231 DOI: 10.1093/jxb/ert100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
How does auxin provoke such a diverse array of responses? This long-standing question is further complicated by a remarkably short nuclear auxin signalling pathway. To crack the auxin code, several potential sources of specificity need to be evaluated. These include: specificity of interactions among the core auxin response components, specificity resulting from higher order complex dynamics, and specificity in interactions with global factors controlling protein turnover and transcriptional repression. Here, we review recent progress towards characterizing and quantifying these interactions and highlight key gaps that remain.
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128
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Wang L, Ruan YL. Regulation of cell division and expansion by sugar and auxin signaling. FRONTIERS IN PLANT SCIENCE 2013; 4:163. [PMID: 23755057 PMCID: PMC3667240 DOI: 10.3389/fpls.2013.00163] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/10/2013] [Indexed: 05/18/2023]
Abstract
Plant growth and development are modulated by concerted actions of a variety of signaling molecules. In recent years, evidence has emerged on the roles of sugar and auxin signals network in diverse aspects of plant growth and development. Here, based on recent progress of genetic analyses and gene expression profiling studies, we summarize the functional similarities, diversities, and their interactions of sugar and auxin signals in regulating two major processes of plant development: cell division and cell expansion. We focus on roles of sugar and auxin signaling in both vegetative and reproductive tissues including developing seed.
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Affiliation(s)
- Lu Wang
- Department of Biology, School of Environmental and Life Sciences, The University of NewcastleCallaghan, NSW, Australia
- Australia-China Research Centre for Crop Improvement, The University of NewcastleCallaghan, NSW, Australia
| | - Yong-Ling Ruan
- Department of Biology, School of Environmental and Life Sciences, The University of NewcastleCallaghan, NSW, Australia
- Australia-China Research Centre for Crop Improvement, The University of NewcastleCallaghan, NSW, Australia
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129
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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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130
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Yoshida S, Saiga S, Weijers D. Auxin regulation of embryonic root formation. PLANT & CELL PHYSIOLOGY 2013; 54:325-32. [PMID: 23220820 DOI: 10.1093/pcp/pcs170] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The plant hormone auxin was initially identified as the bioactive substance that induces roots in plant tissue culture. In the past decades, mechanisms for auxin action, including its transport and response, have been described in detail. However, a molecular and cellular description of its role in root initiation is far from complete. In this review, we discuss recent advances in our understanding of auxin-dependent embryonic root formation. During this process, a root meristem is initiated in a precise and predictable position, and at a stage when the organism consists of relatively few cells. Recent studies have revealed mechanisms for local control of auxin transport, for cellular differences in auxin response components and cell type-specific chromatin regulation. The recent identification of biologically relevant target genes for auxin regulation during embryonic root initiation now also allows dissection of auxin-activated cellular processes. Finally, we discuss the potential for hormonal cross-regulation in embryonic root formation.
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Affiliation(s)
- Saiko Yoshida
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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131
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De Rybel B, Möller B, Yoshida S, Grabowicz I, Barbier de Reuille P, Boeren S, Smith R, Borst J, Weijers D. A bHLH Complex Controls Embryonic Vascular Tissue Establishment and Indeterminate Growth in Arabidopsis. Dev Cell 2013; 24:426-37. [DOI: 10.1016/j.devcel.2012.12.013] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/19/2012] [Accepted: 12/20/2012] [Indexed: 01/21/2023]
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132
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Bargmann BOR, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann DC, Estelle M, Birnbaum KD. A map of cell type-specific auxin responses. Mol Syst Biol 2013; 9:688. [PMID: 24022006 PMCID: PMC3792342 DOI: 10.1038/msb.2013.40] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/23/2013] [Indexed: 12/31/2022] Open
Abstract
In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.
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Affiliation(s)
- Bastiaan O R Bargmann
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes—Claude Grignon, Montpellier, France
| | - Tal Nawy
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Idan Efroni
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Eilon Shani
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Goh Choe
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Jiří Friml
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | | | - Mark Estelle
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Kenneth D Birnbaum
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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133
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Tantikanjana T, Nasrallah JB. Non-cell-autonomous regulation of crucifer self-incompatibility by Auxin Response Factor ARF3. Proc Natl Acad Sci U S A 2012; 109:19468-73. [PMID: 23129621 PMCID: PMC3511119 DOI: 10.1073/pnas.1217343109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many angiosperms, outcrossing is enforced by genetic self-incompatibility (SI), which allows cells of the pistil to recognize and specifically inhibit "self" pollen. SI is often associated with increased stigma-anther separation, a morphological trait that promotes cross-pollen deposition on the stigma. However, the gene networks responsible for coordinate evolution of these complex outbreeding devices are not known. In self-incompatible members of the Brassicaceae (crucifers), the inhibition of "self"-pollen is triggered within the stigma epidermal cell by allele-specific interaction between two highly polymorphic proteins, the stigma-expressed S-locus receptor kinase (SRK) and its pollen coat-localized ligand, the S-locus cysteine-rich (SCR) protein. Using Arabidopsis thaliana plants that express SI as a result of transformation with a functional SRK-SCR gene pair, we identify Auxin Response Factor 3 (ARF3) as a mediator of cross-talk between SI signaling and pistil development. We show that ARF3, a regulator of pistil development that is expressed in the vascular tissue of the style, acts non-cell-autonomously to enhance the SI response and simultaneously down-regulate auxin responses in stigma epidermal cells, likely by regulating a mobile signal derived from the stylar vasculature. The inverse correlation we observed in stigma epidermal cells between the strength of SI and the levels of auxin inferred from activity of the auxin-responsive reporter DR5::GUS suggests that the dampening of auxin responses in the stigma epidermis promotes inhibition of "self" pollen in crucifer SI.
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134
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Azpeitia E, Alvarez-Buylla ER. A complex systems approach to Arabidopsis root stem-cell niche developmental mechanisms: from molecules, to networks, to morphogenesis. PLANT MOLECULAR BIOLOGY 2012; 80:351-63. [PMID: 22945341 DOI: 10.1007/s11103-012-9954-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 08/15/2012] [Indexed: 05/11/2023]
Abstract
Recent reports have shown that the molecular mechanisms involved in root stem-cell niche development in Arabidopsis thaliana are complex and contain several feedback loops and non-additive interactions that need to be analyzed using computational and formal approaches. Complex systems cannot be understood in terms of the behavior of their isolated components, but they emerge as a consequence of largely non-linear interactions among their components. The study of complex systems has provided a useful approach for the exploration of system-level characteristics and behaviors of the molecular networks involved in cell differentiation and morphogenesis during development. We analyzed the complex molecular networks underlying stem-cell niche patterning in the A. thaliana root in terms of some of the key dynamic traits of complex systems: self-organization, modularity and structural properties. We use these analyses to integrate the available root stem-cell niche molecular mechanisms data and postulate novel hypotheses, missing components and interactions and explain apparent contradictions in the literature.
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Affiliation(s)
- Eugenio Azpeitia
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Coyoacán, Mexico, DF, Mexico
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135
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Guilfoyle TJ, Hagen G. Getting a grasp on domain III/IV responsible for Auxin Response Factor-IAA protein interactions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 190:82-8. [PMID: 22608522 DOI: 10.1016/j.plantsci.2012.04.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 04/04/2012] [Accepted: 04/05/2012] [Indexed: 05/18/2023]
Abstract
Auxin Response Factors (ARFs) and Indole Acetic Acid (IAA) proteins contain a similar carboxyl-terminal domain (domain III/IV) that facilitates interactions among these transcription factors as well as other proteins. The specificity of these interactions is controversial, and the mechanisms involved in these interactions have not been investigated. Here, we review some of the controversies about the specificities and requirements for ARF and IAA interactions and discuss some of the technical problems that might contribute to differences reported for these interactions. We make some preliminary conclusions that ARF activator-IAA, ARF activator-ARF activator, and ARF repressor-ARF repressor interactions are favored over ARF repressor-IAA and ARF repressor-ARF activator interactions, and we suggest that IAA-IAA interactions are largely indiscriminant. Based upon the predicted secondary structure of domain III/IV, we introduce a model for how ARF and IAA proteins might interact with one another through a ubiquitin-like β-grasp fold.
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Affiliation(s)
- Tom J Guilfoyle
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.
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136
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Finet C, Jaillais Y. Auxology: when auxin meets plant evo-devo. Dev Biol 2012; 369:19-31. [PMID: 22687750 DOI: 10.1016/j.ydbio.2012.05.039] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/09/2012] [Accepted: 05/31/2012] [Indexed: 11/27/2022]
Abstract
Auxin is implicated throughout plant growth and development. Although the effects of this plant hormone have been recognized for more than a century, it is only in the past two decades that light has been shed on the molecular mechanisms that regulate auxin homeostasis, signaling, transport, crosstalk with other hormonal pathways as well as its roles in plant development. These discoveries established a molecular framework to study the role of auxin in land plant evolution. Here, we review recent advances in auxin biology and their implications in both micro- and macro-evolution of plant morphology. By analogy to the term 'hoxology', which refers to the critical role of HOX genes in metazoan evolution, we propose to introduce the term 'auxology' to take into account the crucial role of auxin in plant evo-devo.
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Affiliation(s)
- Cédric Finet
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, WI 53706, USA.
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137
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Ben-Gera H, Shwartz I, Shao MR, Shani E, Estelle M, Ori N. ENTIRE and GOBLET promote leaflet development in tomato by modulating auxin response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:903-15. [PMID: 22332729 DOI: 10.1111/j.1365-313x.2012.04939.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Compound leaves produce leaflets in a highly controlled yet flexible pattern. Here, we investigate the interaction between auxin, the putative auxin response inhibitor ENTIRE (E, SlIAA9) and the CUC transcription factor GOBLET (GOB) in compound-leaf development in tomato (Solanum lycopersicum). Auxin maxima, monitored by the auxin response sensor DR5, marked and preceded leaflet and lobe initiation. The DR5 signal increased, but maxima were partially retained in response to the external or internal elevation of auxin levels. E directly interacted with the auxin receptors SlTIR1 and SlAFB6. Furthermore, E was stabilized by a mutation in domain II of the protein and by the inhibition of auxin or proteasome activity, implying that E is subjected to auxin-mediated degradation. In e mutants the DR5 signal expanded to include the complete leaf margin, and leaf-specific overexpression of a stabilized form of E inhibited the DR5 signal and lamina expansion. Genetic manipulation of GOB activity altered the distribution of the DR5 signal, and the inhibition of auxin transport or activity suppressed the GOB overexpression phenotype, suggesting that auxin mediates GOB-regulated leaf patterning. Whereas leaves of single e or gob mutants developed only primary leaflets, the downregulation of both E and GOB resulted in the complete abolishment of leaflet initiation, and in a strong DR5 signal throughout the leaf margin. These results suggest that E and GOB modulate auxin response and leaflet morphogenesis via partly redundant pathways, and that proper leaflet initiation and separation requires distinct boundaries between regions of lamina growth and adjacent regions in which growth is inhibited.
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Affiliation(s)
- Hadas Ben-Gera
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
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