101
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Medici A, Marshall-Colon A, Ronzier E, Szponarski W, Wang R, Gojon A, Crawford NM, Ruffel S, Coruzzi GM, Krouk G. AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat Commun 2015. [PMID: 25723764 DOI: 10.1038/ncomms72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Nitrogen and phosphorus are among the most widely used fertilizers worldwide. Nitrate (NO3(-)) and phosphate (PO4(3-)) are also signalling molecules whose respective transduction pathways are being intensively studied. However, plants are continuously challenged with combined nutritional deficiencies, yet very little is known about how these signalling pathways are integrated. Here we report the identification of a highly NO3(-)-inducible NRT1.1-controlled GARP transcription factor, HRS1, document its genome-wide transcriptional targets, and validate its cis-regulatory elements. We demonstrate that this transcription factor and a close homologue repress the primary root growth in response to P deficiency conditions, but only when NO3(-) is present. This system defines a molecular logic gate integrating P and N signals. We propose that NO3(-) and P signalling converge via double transcriptional and post-transcriptional control of the same protein, HRS1.
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Affiliation(s)
- Anna Medici
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Amy Marshall-Colon
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Elsa Ronzier
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Wojciech Szponarski
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Rongchen Wang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Alain Gojon
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Gabriel Krouk
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
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102
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AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat Commun 2015; 6:6274. [PMID: 25723764 PMCID: PMC4373655 DOI: 10.1038/ncomms7274] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/12/2015] [Indexed: 12/19/2022] Open
Abstract
Nitrogen and phosphorus are among the most widely used fertilizers worldwide. Nitrate (NO3−) and phosphate (PO43−) are also signaling molecules whose respective transduction pathways are being intensively studied. However, plants are continuously challenged with combined nutritional deficiencies, yet very little is known about how these signaling pathways are integrated. Here we report the identification of a highly NO3−-inducible NRT1.1-controlled GARP transcription factor, HRS1, document its genome-wide transcriptional targets, and validate its cis-regulatory-elements. We demonstrate that this transcription factor and a close homolog repress primary root growth in response to P deficiency conditions, but only when NO3− is present. This system defines a molecular logic gate integrating P and N signals. We propose that NO3− and P signaling converge via double transcriptional and post-transcriptional control of the same protein, HRS1
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103
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Abstract
Many cell populations have been labeled using stable reporters containing a fluorescent protein. These same marker lines can be used to capture specific cell types or marked cell populations after a brief enzymatic digestion to dissociate tissues. Here, we describe the use of Fluorescence Activated Cell Sorting (FACS) to isolate a rare population of cells marked with Green Fluorescent Protein (GFP). The FACS is a powerful selection tool that can be used to isolate high-quality RNA while selecting for fluorescence, cell size, and other properties.
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104
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Salehin M, Bagchi R, Estelle M. SCFTIR1/AFB-based auxin perception: mechanism and role in plant growth and development. THE PLANT CELL 2015; 27:9-19. [PMID: 25604443 PMCID: PMC4330579 DOI: 10.1105/tpc.114.133744] [Citation(s) in RCA: 273] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/14/2014] [Accepted: 12/26/2014] [Indexed: 05/18/2023]
Abstract
Auxin regulates a vast array of growth and developmental processes throughout the life cycle of plants. Auxin responses are highly context dependent and can involve changes in cell division, cell expansion, and cell fate. The complexity of the auxin response is illustrated by the recent finding that the auxin-responsive gene set differs significantly between different cell types in the root. Auxin regulation of transcription involves a core pathway consisting of the TIR1/AFB F-box proteins, the Aux/IAA transcriptional repressors, and the ARF transcription factors. Auxin is perceived by a transient coreceptor complex consisting of a TIR1/AFB protein and an Aux/IAA protein. Auxin binding to the coreceptor results in degradation of the Aux/IAAs and derepression of ARF-based transcription. Although the basic outlines of this pathway are now well established, it remains unclear how specificity of the pathway is conferred. However, recent results, focusing on the ways that these three families of proteins interact, are starting to provide important clues.
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Affiliation(s)
- Mohammad Salehin
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
| | - Rammyani Bagchi
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
| | - Mark Estelle
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
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105
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Mironova VV, Omelyanchuk NA, Wiebe DS, Levitsky VG. Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome. BMC Genomics 2014; 15 Suppl 12:S4. [PMID: 25563792 PMCID: PMC4331925 DOI: 10.1186/1471-2164-15-s12-s4] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is restricted by consensus models that detect too many false positive sites. Using sequence analysis of experimentally proven AuxREs, we revealed both an extended nucleotide context pattern for AuxRE itself and three distinct types of its coupling motifs (Y-patch, AuxRE-like, and ABRE-like), which together with AuxRE may form the composite elements. Computational analysis of the genome-wide distribution of the predicted AuxREs and their impact on auxin responsive gene expression allowed us to conclude that: (1) AuxREs are enriched around the transcription start site with the maximum density in 5'UTR; (2) AuxREs mediate auxin responsive up-regulation, not down-regulation. (3) Directly oriented single AuxREs and reverse multiple AuxREs are mostly associated with auxin responsiveness. In the composite AuxRE elements associated with auxin response, ABRE-like and Y-patch are 5'-flanking or overlapping AuxRE, whereas AuxRE-like motif is 3'-flanking. The specificity in location and orientation of the coupling elements suggests them as potential binding sites for ARFs partners.
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106
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Ruffel S, Gojon A, Lejay L. Signal interactions in the regulation of root nitrate uptake. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5509-17. [PMID: 25165146 DOI: 10.1093/jxb/eru321] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In most aerobic soils, nitrate (NO3(-)) is the main nitrogen source for plants and is often limiting for plant growth and development. To adapt to a changing environment, plants have developed complex regulatory mechanisms that involve short and long-range signalling pathways in response to both NO3(-) availability in the soil and other physiological processes like growth or nitrogen (N) and carbon (C) metabolisms. Over the past decade, transcriptomic approaches largely contributed to the identification of molecular elements involved in these regulatory mechanisms, especially at the level of root NO3(-)uptake. Most strikingly, the data obtained revealed the high level of interaction between N and both hormone and C signalling pathways, suggesting a strong dependence on growth, development, and C metabolism to adapt root NO3(-) uptake to both external NO3(-) availability and the N status of the plant. However, the signalling mechanisms involved in the cross-talk between N, C, and hormones for the regulation of root NO3(-) uptake remain largely obscure. The aim of this review is to discuss the recent advances concerning the regulatory pathways controlling NO3(-) uptake in response to N signalling, hormones, and C in the model plant Arabidopsis thaliana. Then, to further characterize the level of interaction between these signalling pathways we built on publicly available transcriptome data to determine how hormones and C treatments modify the gene network connecting root NO3(-) transporters and their regulators.
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Affiliation(s)
- Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
| | - Alain Gojon
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
| | - Laurence Lejay
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
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107
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Del Pozo JC, Manzano C. Auxin and the ubiquitin pathway. Two players-one target: the cell cycle in action. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2617-2632. [PMID: 24215077 DOI: 10.1093/jxb/ert363] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Plants are sessile organisms that have to adapt their growth to the surrounding environment. Concomitant with this adaptation capability, they have adopted a post-embryonic development characterized by continuous growth and differentiation abilities. Constant growth is based on the potential of stem cells to divide almost incessantly and on a precise balance between cell division and cell differentiation. This balance is influenced by environmental conditions and by the genetic information of the cell. Among the internal cues, the cross-talk between different hormonal signalling pathways is essential to control this division/differentiation equilibrium. Auxin, one of the most important plant hormones, regulates cell division and differentiation, among many other processes. Amazing advances in auxin signal transduction at the molecular level have been reported, but how this signalling is connected to the cell cycle is, so far, not well known. Auxin signalling involves the auxin-dependent degradation of transcription repressors by F-box-containing E3 ligases of ubiquitin. Recently, SKP2A, another F-box protein, was shown to bind auxin and to target cell-cycle repressors for proteolysis, representing a novel mechanism that links auxin to cell division. In this review, a general vision of what is already known and the most recent advances on how auxin signalling connects to cell division and the role of the ubiquitin pathway in plant cell cycle will be covered.
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Affiliation(s)
- Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Concepción Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
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108
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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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109
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Perrot-Rechenmann C. Auxin Signaling in Plants. Mol Biol 2014. [DOI: 10.1007/978-1-4614-7570-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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110
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Clark NM, de Luis Balaguer MA, Sozzani R. Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root. FRONTIERS IN PLANT SCIENCE 2014; 5:328. [PMID: 25071810 PMCID: PMC4083358 DOI: 10.3389/fpls.2014.00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/23/2014] [Indexed: 05/04/2023]
Abstract
The presence of an auxin gradient in the Arabidopsis root is crucial for proper root development and importantly, for stem cell niche (SCN) maintenance. Subsequently, developmental pathways in the root SCN regulate the formation of the auxin gradient. Combinations of experimental data and computational modeling enable the identification of pathways involved in establishing and maintaining the auxin gradient. We describe how the predictive power of these computational models is used to find how genes and their interactions tightly control the formation of an auxin maximum in the SCN. In addition, we highlight known connections between signaling pathways involving auxin and controlling patterning and development in Arabidopsis.
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Affiliation(s)
| | | | - Rosangela Sozzani
- *Correspondence: Rosangela Sozzani, Department of Plant and Microbial Biology, North Carolina State University, 2577 Thomas Hall, P. O. Box 7612, Raleigh, NC 27695, USA e-mail:
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111
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Signaling: Auxin Signaling. Mol Biol 2014. [DOI: 10.1007/978-1-4939-0263-7_15-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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