REGULATION OF AMINO ACID BIOSYNTHESIS GENES IN PLANTS

Summary

Principal Investigator: Gloria Coruzzi
Affiliation: New York University
Country: USA
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

Top Publications

  1. ncbi MetricMap: an embedding technique for processing distance-based queries in metric spaces
    Jason 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
  2. pmc VirtualPlant: a software platform to support systems biology research
    Manpreet 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
  3. pmc 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
  4. doi 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, BMAA
    Eric 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
  5. pmc A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis
    Gabriel 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
  6. pmc An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis
    Karen E Thum
    Department of Biology, New York University, New York, NY, 10003, USA
    BMC Syst Biol 2:31. 2008
  7. pmc Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1
    Rodrigo 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
  8. pmc Cell-specific nitrogen responses mediate developmental plasticity
    Miriam 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
  9. ncbi Insights into the genomic nitrate response using genetics and the Sungear Software System
    Rodrigo A Gutierrez
    Department of Biology, New York University, New York, NY 10003, USA
    J Exp Bot 58:2359-67. 2007
  10. pmc Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
    Rodrigo A Gutierrez
    Department of Biology, New York University, Washington Square East, New York, NY 10003, USA
    Genome Biol 8:R7. 2007

Scientific Experts

  • Damion Nero
  • Eric D Brenner
  • Jason T L Wang
  • Karen E Thum
  • Rodrigo A Gutierrez
  • Gloria M Coruzzi
  • Manpreet S Katari
  • Dennis E Shasha
  • Alexis Dean
  • Miriam L Gifford
  • Gabriel Krouk
  • Arthur P Goldberg
  • Felipe F Aceituno
  • Juan M Cabello
  • Steve D Nowicki
  • Rebecca S Davidson
  • Lee Parnell Thompson
  • Jonathan Kelfer
  • Dennis Shasha
  • Laurence Lejay
  • Daniel Tranchina
  • Alexis A Cruikshank
  • C Robertson McClung
  • Trevor L Stokes
  • Xiaodong Xu
  • KENNETH D BIRNBAUM
  • Milos Tanurdzic
  • Mariana Obertello
  • Laurence V Lejay
  • Chris Poultney
  • Nigel M Crawford
  • Francesca Chiaromonte
  • Rongchen Wang

Detail Information

Publications12

  1. ncbi MetricMap: an embedding technique for processing distance-based queries in metric spaces
    Jason 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...
  2. pmc VirtualPlant: a software platform to support systems biology research
    Manpreet 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...
  3. pmc 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...
  4. doi 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, BMAA
    Eric 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...
  5. pmc A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis
    Gabriel 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...
  6. pmc An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis
    Karen 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...
  7. pmc Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1
    Rodrigo 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...
  8. pmc Cell-specific nitrogen responses mediate developmental plasticity
    Miriam 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...
  9. ncbi Insights into the genomic nitrate response using genetics and the Sungear Software System
    Rodrigo 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...
  10. pmc Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
    Rodrigo 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...
  11. pmc In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana
    Damion 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...