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NSF Arabidopsis 2010 Genome Grant IOB0519985: |
| Genotype | N Treatment | Other Treatment | Tissue | N2010 Datasets | PubMed | Experiments | External Database |
|---|---|---|---|---|---|---|---|
| Col0 | Nitrate (20min and 2hrs) | Roots and Shoots | Wang Plant Physiology 2003 | Pubmed |
Download | NASC | |
| nia1 nia2 | Nitrate (2hr) | Roots and Shoots | Wang Plant Physiology 2004 | Pubmed |
Download | NASC | |
| Col0 | Sucrose and Light (8hr) | Seedlings | Thum Genome Biology 2004 | Pubmed |
Download | ArrayExpress | |
| Col0 | Nitrate & Ammonium Nitrate (8hr) | Sucrose (8hr) | Seedlings | Palenchar Genome Biology 2004 | Pubmed |
Download | |
| Col0 | Nitrate (8hr) | Sucrose (8hr) | Roots | Gutierrez Genome Biology 2007 | Pubmed |
Download | ArrayExpress |
| Col0 | Nitrate and Nitrite(20min) | Sucrose (8hr) | Roots | Wang Plant Physiology 2007 | Pubmed |
Download | NASC |
| Col0 and nia1nia2 | Nitrate | Seedlings, Root, Shoots | Guetierrez J. Experimental Botany 2007 | Pubmed |
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| Col0 | Nitrate (2hr) | MSX (2hr) | Different Cell types, Roots | Gifford PNAS 2008 | Pubmed |
Download | GEO |
| Col0 | Nitrate & Ammonium Nitrate, Glutamate (2hr) | MSX (2hr) | Seedlings | Gutierrez PNAS 2008 | Pubmed |
Download | NASC |
Senior Personnel
Data Analysis and Tools:
Gutierrez et al 2007: Sungear Demo: This dataset was generated from published microarray studies that identified Arabidopsis genes regulated by transient treatments with the nutrients nitrogen (N) and or carbon (C) (Price, J., et al. (2004) Plant Cell 16, 2128-2150; Scheible, W.-R., et al. (2004) Plant Physiol. 136, 2483-2499; Wang, R., et al. (2004) Plant Physiol 136, 2512-2522. ). In this example, six lists of genes containing N- or CN-regulated genes (I= induced; D= depressed) provide the anchors for Sungear. These experiments conducted by three different research groups all share the feature of transiently treating Arabidopsis seedlings with nitrogen or nitrogen plus carbon nutrients, and assaying gene responses using the ATH1 Affymetrix whole genome chips. Note: You have to have Java Webstart installed on your local computer to run this demo.To learn more about Sungear visit this link. - PathExplore
- BioMaps - Find biological themes (Based on MIPS funcats or GO terms) in gene lists
PROJECT SUMMARY: This proposal involves determination of gene function for gene networks regulated by nitrogen status. Targets for functional analysis are key nodes controlling N-regulation of metabolic and developmental networks associated with growth and seed development- key agronomic traits. To identify regulatory hubs, "multinetworks" will be constructed where "edges" connecting gene "nodes" are supported by multiple data/evidence including; metabolic pathways, protein:protein, protein:DNA, and microRNA:target datasets. Microarray data from leaves, roots, cell-types and seeds of nitrogen-treated Arabidopsis will be interpreted using this multinetwork. Machine learning techniques will be used to predict mechanisms of N-regulation of networks and to identify putative regulatory nodes. Predictions will depend on expression data, number, types and weight of edges linked to a node, and will implicate transcription factors, signal transducers or genes encoding microRNAs as potential regulators. This analysis will be iterative, to refine predictions using kinetic microarray and growth data from wild-type and mutants in putative regulators. Specific aims are: Aim 1. Integrate network responses to N-sources and interactions between nitrogen, carbon and light signaling. Aim 2. Integrate N-regulatory networks and development. Aim 3: Develop tools to integrate omic-datasets and identify regulatory nodes in multinetworks. Aim 4. In vivo testing of N-network models and putative regulatory nodes.
Broader impacts of proposed research: This project involves developing new informatic & network analysis tools that integrate various types of omic data into a "multinetwork" that will enable researchers to identify networks of genes that are connected by functional, regulatory and physical interactions. The integrative genomic approaches, visualization and analysis tools developed in this project, will serve the plant genomic community at large, and the studies conducted will serve to identify networks and hubs involved in regulating all aspects of plant growth and development. The new approaches described will advance understanding of plant genomes in a network view, and will also be useful for genomic studies of any model species for which genomic data is available. This project involves a number of collaborations with other plant genome groups (Arabidopsis small RNAs, Medicago and Lotus genome groups), as well as with individuals working on tools for text mining (GeneWays) and new visualization concepts (B. Paley). Thus, these studies will have broad connections, synergies and impacts on the work of these and other genomic groups. In addition, since these studies pertain to discovering master regulatory nodes regulating nitrogen responsive gene networks controlling plant growth & development, the results should be significant for altering N-use efficiency in agriculture.
Wang Plant Physiology 2003
Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism.
Wang R, Okamoto M, Xing X, Crawford NM.
The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 microm nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism.
Wang Plant Physiology 2004
Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis.
Wang R, Tischner R, Gutierrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM.
A nitrate reductase (NR)-null mutant of Arabidopsis was constructed that had a deletion of the major NR gene NIA2 and an insertion in the NIA1 NR gene. This mutant had no detectable NR activity and could not use nitrate as the sole nitrogen source. Starch mobilization was not induced by nitrate in this mutant but was induced by ammonium, indicating that nitrate was not the signal for this process. Microarray analysis of gene expression revealed that 595 genes responded to nitrate (5 mm nitrate for 2 h) in both wild-type and mutant plants. This group of genes was overrepresented most significantly in the functional categories of energy, metabolism, and glycolysis and gluconeogenesis. Because the nitrate response of these genes was NR independent, nitrate and not a downstream metabolite served as the signal. The microarray analysis also revealed that shoots can be as responsive to nitrate as roots, yet there was substantial organ specificity to the nitrate response.
Thum Genome Biology 2004
Genome-wide investigation of light and carbon signaling interactions in Arabidopsis.
Thum KE, Shin MJ, Palenchar PM, Kouranov A, Coruzzi GM.
BACKGROUND: Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS: Microarrays are used to investigate carbon and light signaling interactions at a genome-wide level in Arabidopsis thaliana. A classification system, 'InterAct Class', is used to classify genes on the basis of their expression profiles. InterAct classes and the genes within them are placed into theoretical models describing interactions between carbon and light signaling. Within InterAct classes there are genes regulated by carbon (201 genes), light (77 genes) or through carbon and light interactions (1,247 genes). We determined whether genes involved in specific biological processes are over-represented in the population of genes regulated by carbon and/or light signaling. Of 29 primary functional categories identified by the Munich Information Center for Protein Sequences, five show over-representation of genes regulated by carbon and/or light. Metabolism has the highest representation of genes regulated by carbon and light interactions and includes the secondary functional categories of carbon-containing-compound/carbohydrate metabolism, amino-acid metabolism, lipid metabolism, fatty-acid metabolism and isoprenoid metabolism. Genes that share a similar InterAct class expression profile and are involved in the same biological process are used to identify putative cis elements possibly involved in responses to both carbon and light signals. CONCLUSIONS: The work presented here represents a method to organize and classify microarray datasets, enabling one to investigate signaling interactions and to identify putative cis elements in silico through the analysis of genes that share a similar expression profile and biological function.
Palenchar Genome Biology 2004
Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants.
Palenchar PM, Kouranov A, Lejay LV, Coruzzi GM.
BACKGROUND: carbon and nitrogen are two signals that influence plant growth and development. It is known that carbon- and nitrogen-signaling pathways influence one another to affect gene expression, but little is known about which genes are regulated by interactions between carbon and nitrogen signaling or the mechanisms by which the different pathways interact. RESULTS: Microarray analysis was used to study global changes in mRNA levels due to carbon and nitrogen in Arabidopsis thaliana. An informatic analysis using InterAct Class enabled us to classify genes on the basis of their responses to carbon or nitrogen treatments. This analysis provides in vivo evidence supporting the hypothesis that plants have a carbon/nitrogen (CN)-sensing/regulatory mechanism, as we have identified over 300 genes whose response to combined CN treatment is different from that expected from expression values due to carbon and nitrogen treatments separately. Metabolism, energy and protein synthesis were found to be significantly affected by interactions between carbon and nitrogen signaling. Identified putative cis-acting regulatory elements involved in mediating CN-responsive gene expression suggest multiple mechanisms for CN responsiveness. One mechanism invokes the existence of a single CN-responsive cis element, while another invokes the existence of cis elements that promote nitrogen-responsive gene expression only when present in combination with a carbon-responsive cis element. CONCLUSION: This study has allowed us to identify genes and processes regulated by interactions between carbon and nitrogen signaling and take a first step in uncovering how carbon- and nitrogen-signaling pathways interact to regulate transcription.
Gutierrez Genome Biology 2007
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.
Gutierrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM.
BACKGROUND: carbon (C) and nitrogen (N) metabolites can regulate gene expression in Arabidopsis thaliana. Here, we use multi-network analysis of microarray data to identify molecular networks regulated by C and N in the Arabidopsis root system. RESULTS: We used the Arabidopsis whole genome Affymetrix gene chip to explore global gene expression responses in plants exposed transiently to a matrix of C and N treatments. We used ANOVA analysis to define quantitative models of regulation for all detected genes. Our results suggest that about half of the Arabidopsis transcriptome is regulated by C, N or CN interactions. We found ample evidence for interactions between C and N that include genes involved in metabolic pathways, protein degradation and auxin signaling. To provide a global, yet detailed, view of how the cell molecular network is adjusted in response to the CN treatments, we constructed a qualitative multi-network model of the Arabidopsis metabolic and regulatory molecular network, including 6,176 genes, 1,459 metabolites and 230,900 interactions among them. We integrated the quantitative models of CN gene regulation with the wiring diagram in the multi-network, and identified specific interacting genes in biological modules that respond to C, N or CN treatments. CONCLUSION: Our results indicate that CN regulation occurs at multiple levels, including potential post-transcriptional control by microRNAs. The network analysis of our systematic dataset of CN treatments indicates that CN sensing is a mechanism that coordinates the global and coordinated regulation of specific sets of molecular machines in the plant cell.
Wang Plant Physiology 2007
Nitrite Acts as a Transcriptome Signal at Micromolar Concentrations in Arabidopsis Roots
Rongchen Wang, Xiujuan Xing, and Nigel Crawford
Nitrate serves as a potent signal to control gene expression in plants and algae, but little is known about the signaling role of nitrite, the direct product of nitrate reduction. Analysis of several nitrate-induced genes showed that nitrite increases mRNA levels as rapidly as nitrate in nitrogen-starved Arabidopsis (Arabidopsis thaliana) roots. Both nitrite and nitrate induction are apparent at concentrations as low as 100 nM. The response at low nitrite concentrations was not due to contaminating nitrate, which was present at <1% of the nitrite concentration. High levels of ammonium (20 mM) in the growth medium suppressed induction of several genes by nitrate, but had varied effects on the nitrite response. Transcriptome analysis using 250 or 5 µM nitrate or nitrite showed that over one-half of the nitrate-induced genes, which included genes involved in nitrate and ammonium assimilation, energy production, and carbon and nitrogen metabolism responded equivalently to nitrite; however, the nitrite response was more robust and there were many genes that responded specifically to nitrite. Thus, nitrite can serve as a signal as well as if not better than nitrate.
Gutierrez J. Experimental Botany 2007
Insights into the genomic nitrate response using genetics and the Sungear Software System.
Gutierrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM.
Nitrate is both a nutrient and a potent signal that stimulates plant growth. Initial experiments in the late 1950s showing that nitrate enhances nitrate reductase (NR) activity after several hours of treatment have now progressed to transcriptome studies identifying over 1000 genes that respond to muM levels of nitrate within minutes. The use of an Arabidopsis NR-null mutant allowed the identification of genes that respond to nitrate when the production of downstream metabolites of nitrate is blocked. Further dissection of the nitrate response is now possible using new bioinformatic tools such as Sungear to perform comparative studies of multiple transcriptome responses across different laboratories and environmental conditions. These analyses have identified genes and pathways (e.g. nitrate assimilation, pentose phosphate pathway, and glycolysis) that respond to nitrate under a variety of conditions (context-independent). Most of these genes and pathways are ones that were identified using the NR-null mutant as responding directly to nitrate. By contrast, other processes such as protein synthesis respond only under a subset of conditions (context-dependent). Data from the NR-null mutant suggest these latter processes may be regulated by downstream nitrogen metabolites.
Gifford PNAS 2008
Cell-specific nitrogen responses mediate developmental plasticity.
Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD.
The organs of multicellular species consist of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change. Some cell-specific responses to changes in environmental conditions are known, but the scale of cell-specific responses within an entire organ as it perceives an environmental flux has not been well characterized in plants or any other multicellular organism. Here, we use cellular profiling of five Arabidopsis root cell types in response to an influx of a critical resource, nitrogen, to uncover a vast and predominantly cell-specific response. We show that cell-specific profiling increases sensitivity several-fold, revealing highly localized regulation of transcripts that were largely hidden from previous global analyses. The cell-specific data revealed responses that suggested a coordinated developmental response in distinct cell types or tissues. One example is the cell-specific regulation of a transcriptional circuit that we showed mediates lateral root outgrowth in response to nitrogen via microRNA167, linking small RNAs to nitrogen responses. Together, these results reveal a previously cryptic component of cell-specific responses to nitrogen. Thus, the results make an important advance in our understanding of how multicellular organisms cope with environmental change at the cell level.
Gutierrez PNAS 2008
Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1.
Gutierrez RA, Stokes TL, Thum K, Xu X, Obertello M, Katari MS, Tanurdzic M, Dean A, Nero DC, McClung CR, Coruzzi GM.
Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of MSX, an inhibitor of glutamine synthetase, resulting in a block of Glu/Gln synthesis. Genes that responded to organic N were identified as those whose response to ammonium nitrate treatment was blocked in the presence of MSX. We showed that some genes previously identified to be regulated by nitrate are under the control of an organic N-metabolite. Using an integrated network model of molecular interactions, we uncovered a subnetwork regulated by organic N that included CCA1 and target genes involved in N-assimilation. We validated some of the predicted interactions and showed that regulation of the master clock control gene CCA1 by Glu or a Glu-derived metabolite in turn regulates the expression of key N-assimilatory genes. Phase response curve analysis shows that distinct N-metabolites can advance or delay the CCA1 phase. Regulation of CCA1 by organic N signals may represent a novel input mechanism for N-nutrients to affect plant circadian clock function.