The long-term objectives of this proposal ar to understand global control of gene expression in plants. In particular we are investigating the mechanisms which coordinate the expression of genes belonging to integrated amino acid biosynthetic pathways. Insights into this process are beginning to emerge from recent work in our laboratory on the gene families for glutamine synthetase (GS) and asparagine synthetase (AS). The integrated expression of these key enzymes serves to regulate nitrogen assimilation and transport in plants. Our studies have revealed that individual members of the GS and AS gene families encode distinct products which are differentially expressed in particular cell-types, at particular times in development, and in response to environmental signals. Light induces the expression of the nuclear gene for chloroplast GS2 and concomitantly represses the expression of the AS1 gene. The switch from GS2 expression in the light to AS1 expression in the dark is dramatic and has biological significance to nitrogen economy in plants. We propose to elucidate the novel mechanism of light- repressed expression of AS1 with particular attention to its potential as an inducible promoter system. Several models will be tested to determine whether light-activation of GS2 and light- repression of AS1 are mediated by a """"""""repressor/activator"""""""" protein or by distinct factors. GS and AS gene expression are also coordinated when nitrogen must be mobilized from nitrogen-rich sources to metabolic sinks. Accordingly, genes for cytosolic GS3A and AS1 are coordinately induced during germination and in nitrogen-fixing root nodules. We propose to identify factors involved in the phloem- specific and developmentally-regulated expression of these genes. Preliminary results suggest that a number of factors interact with the promoters of the GS and AS genes and suggest that the mechanisms underlying the integrated regulation of these genes are complex and multifaceted. The proposed studies on factors which coordinate the regulation of GS and AS genes during development will provide some of the first insights into global control of gene expression in plants.
The specific aims of this proposal are to: 1) Define Light Regulatory Elements (LREs) involved in activation of GS2 expression and/or repression (nLRE) of AS1 expression by light using a reporter gene system in transgenic plants. We will elucidate the novel mechanism of light-repressed gene expression and develop AS1 for use as a """"""""dark"""""""" inducible promoter system in plants. 2) Determine the nature of unique binding activities in """"""""light"""""""" and """"""""dark"""""""" extracts detected with cis-elements of the GS2 and AS1 promoters. 3) Identify DNA sequences involved in phloem-specific and developmentally regulated expression of GS3A and AS1 in cotyledons and nitrogen- fixing nodules. 4) Detect phloem-specific DNA binding activities utilizing a novel purification procedure. 5) Characterize cDNA clones encoding DNA binding protein factors and determine the nature of factor:factor interactions. 6) Test ability of DNA-binding factor to activate or repress transcription in vitro. 7) Determine cell- specific and in vivo regulation of cloned factor. 8) Test models for integrated GS and AS regulation by ectopic expression of factor(s) in transgenic plants harboring GS-GUS and AS-GUS transgenes. 9) Determine whether ectopic expression of factor modulates endogenous GS and AS gene expression and/or affects nitrogen assimilation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Cytology Study Section (CTY)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
New York University
Schools of Arts and Sciences
New York
United States
Zip Code
Para, Alessia; Li, Ying; Coruzzi, Gloria M (2018) ?ChIP-Seq for Genome-Wide Mapping of In Vivo TF-DNA Interactions in Arabidopsis Root Protoplasts. Methods Mol Biol 1761:249-261
Gligorijevic, Vladimir; Barot, Meet; Bonneau, Richard (2018) deepNF: deep network fusion for protein function prediction. Bioinformatics 34:3873-3881
Tipton, Laura; Müller, Christian L; Kurtz, Zachary D et al. (2018) Fungi stabilize connectivity in the lung and skin microbial ecosystems. Microbiome 6:12
Varala, Kranthi; Marshall-Colón, Amy; Cirrone, Jacopo et al. (2018) Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proc Natl Acad Sci U S A 115:6494-6499
Swift, Joseph; Coruzzi, Gloria M (2017) A matter of time - How transient transcription factor interactions create dynamic gene regulatory networks. Biochim Biophys Acta Gene Regul Mech 1860:75-83
Raviram, Ramya; Rocha, Pedro P; Müller, Christian L et al. (2016) 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput Biol 12:e1004780
Doidy, Joan; Li, Ying; Neymotin, Benjamin et al. (2016) ""Hit-and-Run"" transcription: de novo transcription initiated by a transient bZIP1 ""hit"" persists after the ""run"". BMC Genomics 17:92
Baugh, Evan H; Simmons-Edler, Riley; Müller, Christian L et al. (2016) Robust classification of protein variation using structural modelling and large-scale data integration. Nucleic Acids Res 44:2501-13
Ristova, Daniela; Carré, Clément; Pervent, Marjorie et al. (2016) Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root. Sci Signal 9:rs13
Varala, Kranthi; Li, Ying; Marshall-Colón, Amy et al. (2015) ""Hit-and-Run"" leaves its mark: catalyst transcription factors and chromatin modification. Bioessays 37:851-6

Showing the most recent 10 out of 76 publications