GLN3/YER040W Summary Help

Standard Name GLN3 1
Systematic Name YER040W
Feature Type ORF, Verified
Description Transcriptional activator of genes regulated by nitrogen catabolite repression; localization and activity regulated by quality of nitrogen source and Ure2p (2, 3 and see Summary Paragraph)
Name Description GLutamiNe metabolism 1
Chromosomal Location
ChrV:229795 to 231987 | ORF Map | GBrowse
Genetic position: 38 cM
Gene Ontology Annotations All GLN3 GO evidence and references
  View Computational GO annotations for GLN3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Targets 132 genes
Regulators 9 genes
Classical genetics
Large-scale survey
198 total interaction(s) for 148 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 7
  • Affinity Capture-RNA: 2
  • Affinity Capture-Western: 3
  • Biochemical Activity: 1
  • Co-localization: 3
  • PCA: 2
  • Reconstituted Complex: 4
  • Two-hybrid: 12

Genetic Interactions
  • Dosage Rescue: 7
  • Negative Genetic: 92
  • Phenotypic Enhancement: 21
  • Phenotypic Suppression: 9
  • Positive Genetic: 15
  • Synthetic Growth Defect: 5
  • Synthetic Lethality: 2
  • Synthetic Rescue: 13

Expression Summary
Length (a.a.) 730
Molecular Weight (Da) 79,382
Isoelectric Point (pI) 10.39
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrV:229795 to 231987 | ORF Map | GBrowse
Genetic position: 38 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..2193 229795..231987 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000842

GLN3 encodes a transcriptional activator that is involved in positively regulating genes that are subject to nitrogen catabolite repression (NCR) (4). Gln3p, via a zinc finger binding domain (5), binds to the sequence 5-GATAAG-3 in the UASNTR found in the promoters of many genes involved in nitrogen utilization (6, 7). When nitrogen is limiting, Gln3p is localized to the nucleus and the expression of NCR-sensitive genes is upregulated (8). In contrast, when optimal nitrogen sources are available, Gln3p is localized to the cytoplasm and transcription of NCR-sensitive genes is minimal (8). Nuclear import and export of Gln3p depends on the proteins Srp1p and Crm1p respectively (9). The Ran GTPase pathway and an intact actin cytoskeleton and are also required for proper Gln3p nuclear translocation (9, 10).

Gln3p is a phosphoprotein, and phosphorylation appears to be dependent on the quality of the nitrogen source in the media. When cells are provided with good nitrogen sources, Gln3p is phosphorylated by the TOR kinases Tor1p and Tor2p (8, 11). While the TOR kinases are the primary mediators of Gln3p phosphorylation, there is evidence that the kinases Snf1p and Npr1p may also be involved in Gln3p regulation (9, 12, 13). The phosphorylated form of the Gln3p is bound by the regulatory protein Ure2p and sequestered in the cytosol (14, 15). The Gln3p:Ure2p complex is significantly more resistant to dephosphorylation than free Gln3p (11). Gln3p dephosphorylation and subsequent activation can be induced by: nitrogen limitation (8), glutamine starvation (16), treatment with the TOR inhibitor drug rapamycin (8), regulation by the phosphatases Pph3p or Sit4p (8, 11), or the loss of the regulatory subunit of Sit4p, Tap42p (8, 11). While most studies indicate it is the dephosphorylated form of Gln3p that is active, treatment of cells with the glutamine synthetase inhibitor methionine sulfoximine increases the phosphorylation state of Gln3p but results in nuclear localization and activation of the protein (17). In addition to phosphorylation, protein stability might also be an important aspect of Gln3p regulation. Under poor nitrogen conditions, Gln3p activation is dependent on the E3/E4 ubiquitin-protein ligase protein Rsp5p and the Rsp5-associated proteins Bul1p and Bul2p (13).

Although an increase in copies of GLN3 causes drastic decreases in the cellular growth rate, GLN3 is not essential for growth (5). Loss of Gln3p also confers resistance to the drug rapamycin (18), and for some genes the absence of Gln3p results in a longer mRNA transcript because the GATAAG binding sites can serve as a surrogate TATA transcription initiation site (14).

Last updated: 2005-09-29 Contact SGD

References cited on this page View Complete Literature Guide for GLN3
1) Mitchell AP and Magasanik B  (1984) Regulation of glutamine-repressible gene products by the GLN3 function in Saccharomyces cerevisiae. Mol Cell Biol 4(12):2758-66
2) Magasanik B and Kaiser CA  (2002) Nitrogen regulation in Saccharomyces cerevisiae. Gene 290(1-2):1-18
3) Feller A, et al.  (2013) Alterations in the Ure2 aCap domain elicit different GATA factor responses to rapamycin treatment and nitrogen limitation. J Biol Chem 288(3):1841-55
4) Courchesne WE and Magasanik B  (1988) Regulation of nitrogen assimilation in Saccharomyces cerevisiae: roles of the URE2 and GLN3 genes. J Bacteriol 170(2):708-13
5) Minehart PL and Magasanik B  (1991) Sequence and expression of GLN3, a positive nitrogen regulatory gene of Saccharomyces cerevisiae encoding a protein with a putative zinc finger DNA-binding domain. Mol Cell Biol 11(12):6216-28
6) Bysani N, et al.  (1991) Saturation mutagenesis of the UASNTR (GATAA) responsible for nitrogen catabolite repression-sensitive transcriptional activation of the allantoin pathway genes in Saccharomyces cerevisiae. J Bacteriol 173(16):4977-82
7) Blinder D and Magasanik B  (1995) Recognition of nitrogen-responsive upstream activation sequences of Saccharomyces cerevisiae by the product of the GLN3 gene. J Bacteriol 177(14):4190-3
8) Beck T and Hall MN  (1999) The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402(6762):689-92
9) Bertram PG, et al.  (2002) Convergence of TOR-nitrogen and Snf1-glucose signaling pathways onto Gln3. Mol Cell Biol 22(4):1246-52
10) Cox KH, et al.  (2004) Actin cytoskeleton is required for nuclear accumulation of Gln3 in response to nitrogen limitation but not rapamycin treatment in Saccharomyces cerevisiae. J Biol Chem 279(18):19294-301
11) Bertram PG, et al.  (2000) Tripartite regulation of Gln3p by TOR, Ure2p, and phosphatases. J Biol Chem 275(46):35727-33
12) Cox KH, et al.  (2002) Cytoplasmic compartmentation of Gln3 during nitrogen catabolite repression and the mechanism of its nuclear localization during carbon starvation in Saccharomyces cerevisiae. J Biol Chem 277(40):37559-66
13) Crespo JL, et al.  (2004) NPR1 kinase and RSP5-BUL1/2 ubiquitin ligase control GLN3-dependent transcription in Saccharomyces cerevisiae. J Biol Chem 279(36):37512-7
14) Cox KH, et al.  (2000) Saccharomyces cerevisiae GATA sequences function as TATA elements during nitrogen catabolite repression and when Gln3p is excluded from the nucleus by overproduction of Ure2p. J Biol Chem 275(23):17611-8
15) Kulkarni AA, et al.  (2001) Gln3p nuclear localization and interaction with Ure2p in Saccharomyces cerevisiae. J Biol Chem 276(34):32136-44
16) Crespo JL, et al.  (2002) The TOR-controlled transcription activators GLN3, RTG1, and RTG3 are regulated in response to intracellular levels of glutamine. Proc Natl Acad Sci U S A 99(10):6784-9
17) Tate JJ, et al.  (2005) Methionine sulfoximine treatment and carbon starvation elicit Snf1-independent phosphorylation of the transcription activator Gln3 in Saccharomyces cerevisiae. J Biol Chem 280(29):27195-204
18) Cardenas ME, et al.  (1999) The TOR signaling cascade regulates gene expression in response to nutrients. Genes Dev 13(24):3271-9
19) Harbison CT, et al.  (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004):99-104
20) Rowen DW, et al.  (1997) Role of GATA factor Nil2p in nitrogen regulation of gene expression in Saccharomyces cerevisiae. J Bacteriol 179(11):3761-6
21) Badis G, et al.  (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87
22) Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66