Genomes and Genes
REGULATION OF AMINO ACID BIOSYNTHESIS GENES IN PLANTS
Principal Investigator: Gloria Coruzzi
Affiliation: New York University
Abstract: The overall goal of our research is to gain a molecular understanding of the regulatory processes that control the assimilation of inorganic nitrogen in plants. This process plays a central role in the regulation of plant growth and development. Using molecular-genetic approaches in Arabidopsis, we identified isoenzymes of GS, GOGAT and GDH that control the assimilation of inorganic-N into Glu/Gln, key amino acids used to transport nitrogen within and between cells. Our studies indicate that expression of these genes is regulated by the metabolic status of the plant. For example, transcriptional induction of GS by light, can be mimicked by sucrose in the absence of light. Moreover, sucrose induction of GS expression can be antagonized by amino acids, which results in repression of GS activity. This led us to hypothesize that plants have a mechanism to sense internal levels of amino acids. This would allow a plant to turn off assimilation of inorganic-N when internal levels of amino acid are high. Testing this hypothesis, defining it mechanistically, and identifying components thereof, is the focus of this renewal. Towards this goal, we have begun to characterize amino acid sensing/signaling components in Arabidopsis using molecular-genetic, cell biological, and biochemical approaches. Our reverse genetic studies are driven by the hypothesis that amino acid sensing is primitive and conserved in evolution. In support of this, the repression of GS expression by amino acids in plants is mechanistically reminiscent of the Ntr system in E. coli. Moreover, we identified a plant homologue of an Ntr component, PII, and showed using PII transgenic plants that PII appears to play a role in C:N sensing in chloroplasts an in GS regulation, as it does in Ntr. The amino acid products of N-assimilation are exported from chloroplasts and transported to other cells, and we have evidence that Glu, the prinicple intermediate, may serve as an extracellular signal . In support of this, we identified putative sensors of extracellular Glu, plant homologues of animal glutamate receptors (iGluRs). We showed plant GluRs function as ligand-gated ion channels, and studies of GLR transgenic plants indicate they may play a role in light signal transduction, reminiscent of their counterparts in the retina and brain. These findings suggest iGluRs are derived from a primitive amino acid signaling mechanism that existed before plants and animals diverged. We propose to exploit this evolutionary conservation and test whether Arabidopsis (or GLR mutants we isolate) can be used in a bioassay for drugs to treat GluR-related diseases in humans. We will also use forward genetic approaches to isolate amino acid sensing/signaling mutants in Arabidopsis which may identify components of these evolutionarily conserved amino acid signaling pathways or novel pathways.
Funding Period: 1983-12-01 - 2004-02-29
more information: NIH RePORT
- Semisynthesis of peptoid-protein hybrids by chemical ligation at serinePaul M Levine
Department of Chemistry and Center for Genomics and Systems Biology, New York University, New York, New York 10003, United States
Org Lett 16:512-5. 2014..This technique will expand the repertoire of strategies to enable design of hybrid macromolecules with novel structures and functions not accessible to fully biosynthesized proteins. ..
- Network news: prime time for systems biology of the plant circadian clockC Robertson McClung
Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 3576, USA
Curr Opin Genet Dev 20:588-98. 2010..This approach, coupled with advances from the genetic and biochemical analyses of clock function, is accelerating our progress towards a comprehensive understanding of the plant circadian clock network...
- Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thalianaElena A Vidal
Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Santiago, Chile
Wiley Interdiscip Rev Syst Biol Med 2:683-93. 2010..Here, we provide an update on recent advances to identify the components involved in N sensing and signaling in Arabidopsis and their importance for the plant response to N...
- Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrateGabriel Krouk
Department of Biology, New York University, Center for Genomics and Systems Biology, New York, NY 10003, USA
Genome Biol 11:R123. 2010..Nitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified...
- Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thalianaElena A Vidal
Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Santiago 8331010, Chile
Proc Natl Acad Sci U S A 107:4477-82. 2010....
- miR-EdiTar: a database of predicted A-to-I edited miRNA target sitesAlessandro Laganà
Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
Bioinformatics 28:3166-8. 2012..In fact, edited forms of mature miRNAs can target sets of genes that differ from the targets of their unedited forms. The specific deamination of mRNAs can generate novel binding sites in addition to potentially altering existing ones...
- Parametric Bayesian priors and better choice of negative examples improve protein function predictionNoah Youngs
Department of Computer Science, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
Bioinformatics 29:1190-8. 2013..The improper choice of negative examples, in particular, can hamper the accuracy of protein function prediction...
- Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architectureUlises Rosas
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
Proc Natl Acad Sci U S A 110:15133-8. 2013..This finding supports a role for plasticity responses in phenotypic evolution in natural environments. ..
- Plasticity regulators modulate specific root traits in discrete nitrogen environmentsMiriam L Gifford
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America School of Life Sciences, University of Warwick, Coventry, United Kingdom Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
PLoS Genet 9:e1003760. 2013..The overall results suggest that there is a pool of genetic variability in plants that controls traits in specific environments, with opportunity to tune crop plants to a given environment. ..
- Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana rootsElena A Vidal
FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago 8331010, Chile
BMC Genomics 14:701. 2013..Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out...
- GRAPES: a software for parallel searching on biological graphs targeting multi-core architecturesRosalba Giugno
Department Clinical and Molecular Biomedicine, University of Catania, Catania, Italy
PLoS ONE 8:e76911. 2013..We show the performance of GRAPES on representative biological datasets containing antiviral chemical compounds, DNA, RNA, proteins, protein contact maps and protein interactions networks. ..
- High nitrogen insensitive 9 (HNI9)-mediated systemic repression of root NO3- uptake is associated with changes in histone methylationThomas Widiez
Biochimie et Physiologie Moleculaire des Plantes, Unité Mixte de Recherche 5004, Institut National de la Recherche Agronomique Centre National de la Recherche Scientifique Sup Agro UM2, Institut de Biologie Integrative des Plantes, F 34060 Montpellier, France
Proc Natl Acad Sci U S A 108:13329-34. 2011..1 locus. Our findings highlight the hypothesis that posttranslational chromatin modifications control nutrient acquisition in plants...
- A framework integrating plant growth with hormones and nutrientsGabriel Krouk
Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
Trends Plant Sci 16:178-82. 2011..We believe this model will provide a useful concept for past and future research in this field...
- Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demandSandrine Ruffel
Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
Proc Natl Acad Sci U S A 108:18524-9. 2011....
- Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in ArabidopsisMariana Obertello
Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Main Building, New York, NY 10003, USA
BMC Syst Biol 4:111. 2010..We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide...
- Nitrate signaling: adaptation to fluctuating environmentsGabriel Krouk
Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, NY 10003, USA
Curr Opin Plant Biol 13:266-73. 2010....
- Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in ArabidopsisRodrigo A Gutierrez
Department of Biology, New York University, Washington Square East, New York, NY 10003, USA
Genome Biol 8:R7. 2007..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...
- Insights into the genomic nitrate response using genetics and the Sungear Software SystemRodrigo A Gutierrez
Department of Biology, New York University, New York, NY 10003, USA
J Exp Bot 58:2359-67. 2007..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...
- Cell-specific nitrogen responses mediate developmental plasticityMiriam L Gifford
Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
Proc Natl Acad Sci U S A 105:803-8. 2008..Thus, the results make an important advance in our understanding of how multicellular organisms cope with environmental change at the cell level...
- Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1Rodrigo A Gutierrez
Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY 10003, USA
Proc Natl Acad Sci U S A 105:4939-44. 2008..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...
- An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in ArabidopsisKaren E Thum
Department of Biology, New York University, New York, NY, 10003, USA
BMC Syst Biol 2:31. 2008..This study integrates genetic, genomic and systems approaches to identify a genetically perturbed gene network that is regulated by the interaction of carbon and light signaling in Arabidopsis...
- A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in ArabidopsisGabriel Krouk
Center for Genomics and Systems Biology, New York University, Department of Biology, New York, New York, United States of America
PLoS Comput Biol 5:e1000326. 2009..These results uncovered a strong constraining structure in plant cell signaling pathways, which prompted us to propose the existence of a "code" of signal integration...
- A mutation in the Proteosomal Regulatory Particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAAEric D Brenner
The International Plant Science Center, The New York Botanical Garden, 200th and Kazimiroff Blvd, Bronx, NY 10458, USA
Plant Mol Biol 70:523-33. 2009..The mutation in bim409 was identified to be in a gene encoding the Proteosomal Regulatory Particle AAA-ATPase-3 (RPT3). Possible roles of the proteosome in Glu-mediated signaling in plants is discussed...
- A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"Damion Nero
Department of Biology, New York University, Center for Genomics and Systems Biology, New York 10003, USA
BMC Syst Biol 3:59. 2009..Herein, a systems biology approach was developed to identify the components and role of cross-talk between nitrate and hormone signals, likely to be involved in the conditional response of NO3- signaling...
- VirtualPlant: a software platform to support systems biology researchManpreet S Katari
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
Plant Physiol 152:500-15. 2010..VirtualPlant is freely available at www.virtualplant.org...
- In silico evaluation of predicted regulatory interactions in Arabidopsis thalianaDamion Nero
Department of Biology, New York University, Center for Genomics and Systems Biology, New York, NY 10003, USA
BMC Bioinformatics 10:435. 2009..However, to date there has been no quantitative assessment as to which correlation measures or CRE detection methods used alone or in combination are most effective in predicting TF-->target relationships on a genome-wide scale...
- MetricMap: an embedding technique for processing distance-based queries in metric spacesJason T L Wang
Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
IEEE Trans Syst Man Cybern B Cybern 35:973-87. 2005..Experimental results on both protein and RNA data show the good performance and the superiority of MetricMap over the other methods...