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Tokizawa M, Enomoto T, Chandnani R, Mora-Macías J, Burbridge C, Armenta-Medina A, Kobayashi Y, Yamamoto YY, Koyama H, Kochian LV. The transcription factors, STOP1 and TCP20, are required for root system architecture alterations in response to nitrate deficiency. Proc Natl Acad Sci U S A 2023; 120:e2300446120. [PMID: 37611056 PMCID: PMC10469342 DOI: 10.1073/pnas.2300446120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/27/2023] [Indexed: 08/25/2023] Open
Abstract
Nitrate distribution in soils is often heterogeneous. Plants have adapted to this by modifying their root system architecture (RSA). Previous studies showed that NITRATE-TRANSPORTER1.1 (NRT1.1), which also transports auxin, helps inhibit lateral root primordia (LRP) emergence in nitrate-poor patches, by preferentially transporting auxin away from the LRP. In this study, we identified the regulatory system for this response involving the transcription factor (TF), SENSITIVE-TO-PROTON-RHIZOTOXICITY1 (STOP1), which is accumulated in the nuclei of LRP cells under nitrate deficiency and directly regulates Arabidopsis NRT1.1 expression. Mutations in STOP1 mimic the root phenotype of the loss-of-function NRT1.1 mutant under nitrate deficiency, compared to wild-type plants, including increased LR growth and higher DR5promoter activity (i.e., higher LRP auxin signaling/activity). Nitrate deficiency-induced LR growth inhibition was almost completely reversed when STOP1 and the TF, TEOSINTE-BRANCHED1,-CYCLOIDEA,-PCF-DOMAIN-FAMILY-PROTEIN20 (TCP20), a known activator of NRT1.1 expression, were both mutated. Thus, the STOP1-TCP20 system is required for activation of NRT1.1 expression under nitrate deficiency, leading to reduced LR growth in nitrate-poor regions. We found this STOP1-mediated system is more active as growth media becomes more acidic, which correlates with reductions in soil nitrate as the soil pH becomes more acidic. STOP1 has been shown to be involved in RSA modifications in response to phosphate deficiency and increased potassium uptake, hence, our findings indicate that root growth regulation in response to low availability of the major fertilizer nutrients, nitrogen, phosphorus and potassium, all involve STOP1, which may allow plants to maintain appropriate root growth under the complex and varying soil distribution of nutrients.
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Affiliation(s)
- Mutsutomo Tokizawa
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SaskatchewanS7N 4J8, Canada
| | - Takuo Enomoto
- Applied Biological Sciences, Gifu University, Gifu501-1193, Japan
| | - Rahul Chandnani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SaskatchewanS7N 4J8, Canada
- NRGene Canada Inc., Saskatoon, SKS7N 3R3, Canada
| | - Javier Mora-Macías
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SaskatchewanS7N 4J8, Canada
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SaskatchewanS7N 4J8, Canada
| | - Alma Armenta-Medina
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SaskatchewanS7N 4J8, Canada
| | - Yuriko Kobayashi
- Applied Biological Sciences, Gifu University, Gifu501-1193, Japan
| | - Yoshiharu Y. Yamamoto
- Applied Biological Sciences, Gifu University, Gifu501-1193, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama230-0045, Japan
| | - Hiroyuki Koyama
- Applied Biological Sciences, Gifu University, Gifu501-1193, Japan
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SaskatchewanS7N 4J8, Canada
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Armenta-Medina A, Gillmor CS, Gao P, Mora-Macias J, Kochian LV, Xiang D, Datla R. Developmental and genomic architecture of plant embryogenesis: from model plant to crops. Plant Commun 2021; 2:100136. [PMID: 33511346 PMCID: PMC7816075 DOI: 10.1016/j.xplc.2020.100136] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 05/08/2023]
Abstract
Embryonic development represents an important reproductive phase of sexually reproducing plant species. The fusion of egg and sperm produces the plant zygote, a totipotent cell that, through cell division and cell identity specification in early embryogenesis, establishes the major cell lineages and tissues of the adult plant. The subsequent morphogenesis phase produces the full-sized embryo, while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination, ensuring continuation of the plant life cycle. In this review on embryogenesis, we compare the model eudicot Arabidopsis thaliana with monocot crops, focusing on genome activation, paternal and maternal regulation of early zygote development, and key organizers of patterning, such as auxin and WOX transcription factors. While the early stages of embryo development are apparently conserved among plant species, embryo maturation programs have diversified between eudicots and monocots. This diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation, and also assures seed germination in different environmental conditions. This review describes the most important features of embryonic development in plants, and the scope and applications of genomics in plant embryo studies.
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Affiliation(s)
- Alma Armenta-Medina
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Javier Mora-Macias
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Daoquan Xiang
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
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Chung Y, Zhu Y, Wu MF, Simonini S, Kuhn A, Armenta-Medina A, Jin R, Østergaard L, Gillmor CS, Wagner D. Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS. Nat Commun 2019; 10:886. [PMID: 30792395 PMCID: PMC6385194 DOI: 10.1038/s41467-019-08861-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/04/2019] [Indexed: 12/19/2022] Open
Abstract
Specification of new organs from transit amplifying cells is critical for higher eukaryote development. In plants, a central stem cell pool maintained by the pluripotency factor SHOOTMERISTEMLESS (STM), is surrounded by transit amplifying cells competent to respond to auxin hormone maxima by giving rise to new organs. Auxin triggers flower initiation through Auxin Response Factor (ARF) MONOPTEROS (MP) and recruitment of chromatin remodelers to activate genes promoting floral fate. The contribution of gene repression to reproductive primordium initiation is poorly understood. Here we show that downregulation of the STM pluripotency gene promotes initiation of flowers and uncover the mechanism for STM silencing. The ARFs ETTIN (ETT) and ARF4 promote organogenesis at the reproductive shoot apex in parallel with MP via histone-deacetylation mediated transcriptional silencing of STM. ETT and ARF4 directly repress STM, while MP acts indirectly, through its target FILAMENTOUS FLOWER (FIL). Our data suggest that - as in animals- downregulation of the pluripotency program is important for organogenesis in plants.
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Affiliation(s)
- Yuhee Chung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yang Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Bayer Crop Science, St. Louis, MO, 63146, USA
| | - Sara Simonini
- Crop Genetics Dept, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, Norfolk, UK
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Andre Kuhn
- Crop Genetics Dept, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, Norfolk, UK
| | - Alma Armenta-Medina
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato C.P., 36824, Guanajuato, Mexico
| | - Run Jin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lars Østergaard
- Crop Genetics Dept, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, Norfolk, UK
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato C.P., 36824, Guanajuato, Mexico
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Abstract
MicroRNAs play important roles in posttranscriptional regulation of plant development, metabolism, and abiotic stress responses. The recent generation of massive amounts of small RNA sequence data, along with development of bioinformatic tools to identify miRNAs and their mRNA targets, has led to an explosion of newly identified putative miRNAs in plants. Genome editing techniques like CRISPR-Cas9 will allow us to study the biological role of these potential novel miRNAs by efficiently targeting both the miRNA and its mRNA target. In this chapter, we review bioinformatic tools and experimental methods for the identification and functional characterization of miRNAs and their target mRNAs in plants.
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Affiliation(s)
- Alma Armenta-Medina
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.
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Armenta-Medina A, Gillmor CS. Genetic, molecular and parent-of-origin regulation of early embryogenesis in flowering plants. Curr Top Dev Biol 2019; 131:497-543. [DOI: 10.1016/bs.ctdb.2018.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Lepe-Soltero D, Armenta-Medina A, Xiang D, Datla R, Gillmor CS, Abreu-Goodger C. Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana. Data Brief 2017; 15:642-647. [PMID: 29124087 PMCID: PMC5671514 DOI: 10.1016/j.dib.2017.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 11/03/2022] Open
Abstract
The genome annotation for the model plant Arabidopsis thaliana does not include the primary transcripts from which MIRNAs are processed. Here we present and analyze the raw mRNA sequencing data from wild type and serrate-1 globular stage embryos of A. thaliana, ecotype Columbia. Because SERRATE is required for pri-miRNA processing, these precursors accumulate in serrate-1 mutants, facilitating their detection using standard RNA-Seq protocols. We first use the mapping of the RNA-Seq reads to the reference genome to annotate the potential primary transcripts of MIRNAs expressed in the embryo. We then quantify these pri-miRNAs in wild type and serrate-1 mutants. Finally, we use differential expression analysis to determine which are up-regulated in serrate-1 compared to wild type, to select the best candidates for bona fide pri-miRNAs expressed in the globular stage embryos. In addition, we analyze a previously published RNA-Seq dataset of wild type and dicer-like 1 mutant embryos at the globular stage [1]. Our data are interpreted and discussed in a separate article [2].
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Affiliation(s)
- Daniel Lepe-Soltero
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - Alma Armenta-Medina
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - Daoquan Xiang
- Plant Biotechnology Institute, National Research Council, Saskatoon, Saskatchewan, Canada
| | - Raju Datla
- Plant Biotechnology Institute, National Research Council, Saskatoon, Saskatchewan, Canada
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico
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Armenta-Medina A, Huanca-Mamani W, Sanchez-León N, Rodríguez-Arévalo I, Vielle-Calzada JP. Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana. PLoS One 2013; 8:e76977. [PMID: 24194852 PMCID: PMC3806734 DOI: 10.1371/journal.pone.0076977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/28/2013] [Indexed: 01/07/2023] Open
Abstract
To investigate the genetic and molecular regulation that the female gametophyte could exert over neighboring sporophytic regions of the ovule, we performed a quantitative comparison of global expression in wild-type and nozzle/sporocyteless (spl) ovules of Arabidopsis thaliana (Arabidopsis), using Massively Parallel Signature Sequencing (MPSS). This comparison resulted in 1517 genes showing at least 3-fold increased expression in ovules lacking a female gametophyte, including those encoding 89 transcription factors, 50 kinases, 25 proteins containing a RNA-recognition motif (RRM), and 20 WD40 repeat proteins. We confirmed that eleven of these genes are either preferentially expressed or exclusive of spl ovules lacking a female gametophyte as compared to wild-type, and showed that six are also upregulated in determinant infertile1 (dif1), a meiotic mutant affected in a REC8-like cohesin that is also devoided of female gametophytes. The sporophytic misexpression of IOREMPTE, a WD40/transducin repeat gene that is preferentially expressed in the L1 layer of spl ovules, caused the arrest of female gametogenesis after differentiation of a functional megaspore. Our results show that in Arabidopsis, the sporophytic-gametophytic cross talk includes a negative regulation of the female gametophyte over specific genes that are detrimental for its growth and development, demonstrating its potential to exert a repressive control over neighboring regions in the ovule.
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Affiliation(s)
- Alma Armenta-Medina
- Grupo de Desarrollo Reproductivo y Apomixis, Laboratorio Nacional de Genómica para la Biodiversidad y Departamento de Ingeniería Genética de Plantas, CINVESTAV Irapuato, Irapuato, Mexico
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Vielle-Calzada JP, Hernández-Lagana E, Rodríguez-Leal D, Rodríguez-Arévalo I, León-Martínez G, Abad-Vivero U, Demesa-Arévalo E, Armenta-Medina A, Alvarez-Mejía C. Reproductive versatility and the epigenetic control of female gametogenesis. Cold Spring Harb Symp Quant Biol 2012; 77:17-21. [PMID: 23250990 DOI: 10.1101/sqb.2012.77.014894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Each year, plants and animals perform the task of repopulating the planet through patterns of courtship and mating that have a unifying and compelling logic: the production of offspring. Although life of nearly all organisms is organized around sex and breeding, Darwinian thinking focused more on the struggle for existence than on evolutionary significance of this frantic race to reproduce. In Darwin's own words, "We do not know the final cause of sexuality; why new beings should be produced by the union of the two sexual elements. The whole subject is hidden in darkness…" (Darwin 1862). In plants, a major consequence of this search for survival is the evolution of a multitude of reproductive alternatives that have intrigued botanists, geneticists, and evolutionary biologists for more than 100 years. Because sexually derived genetic diversity is interpreted as essential for adaptation, it is often thought that sex is necessary for the perpetuation of a species; however, many organisms--including several hundred families of flowering plants--are going efficiently about propagating their kind without bothering with meiosis and mating. Whereas many plants can undergo vegetative propagation, through the production of stolons, bulbs, or rhizomes, for example, many others have developed methods to produce an embryo from a single cell whose nucleus is not formed by the fusion of two gametes, offering a direct developmental and evolutionary challenge to sexual reproduction. Recent evidence suggests that epigenetic mechanisms that control transcriptional silencing of DNA repetitive elements and heterochromatin are crucial for the acquisition of cell identity in the ovule, opening the possibility that the developmental distinction between sexual development and apomixis might have evolved as an adaptive response to evolutionary forces that modulate structural variation and reproductive versatility in flowering plants.
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Affiliation(s)
- J-P Vielle-Calzada
- Group of Reproductive Development and Apomixis, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, México.
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Armenta-Medina A, Demesa-Arévalo E, Vielle-Calzada JP. Epigenetic control of cell specification during female gametogenesis. ACTA ACUST UNITED AC 2011; 24:137-47. [PMID: 21484604 DOI: 10.1007/s00497-011-0166-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 03/17/2011] [Indexed: 11/29/2022]
Abstract
In flowering plants, the formation of gametes depends on the differentiation of cellular precursors that divide meiotically before giving rise to a multicellular gametophyte. The establishment of this gametophytic phase presents an opportunity for natural selection to act on the haploid plant genome by means of epigenetic mechanisms that ensure a tight regulation of plant reproductive development. Despite this early acting selective pressure, there are numerous examples of naturally occurring developmental alternatives that suggest a flexible regulatory control of cell specification and subsequent gamete formation in flowering plants. In this review, we discuss recent findings indicating that epigenetic mechanisms related to the activity of small RNA pathways prevailing during ovule formation play an essential role in cell specification and genome integrity. We also compare these findings to small RNA pathways acting during gametogenesis in animals and discuss their implications for the understanding of the mechanisms that control the establishment of the female gametophytic lineage during both sexual reproduction and apomixis.
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Affiliation(s)
- Alma Armenta-Medina
- Grupo de Desarrollo Reproductivo y Apomixis, Laboratorio Nacional de Genómica para la Biodiversidad y Departamento de Ingeniería Genética de Plantas, CINVESTAV, Irapuato, Mexico
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