SPT3/YDR392W Summary Help

Standard Name SPT3 1
Systematic Name YDR392W
Feature Type ORF, Verified
Description Subunit of the SAGA and SAGA-like transcriptional regulatory complexes; interacts with Spt15p to activate transcription of some RNA polymerase II-dependent genes, also functions to inhibit transcription at some promoters; relocalizes to the cytosol in response to hypoxia (2, 3, 4, 5 and see Summary Paragraph)
Name Description SuPpressor of Ty's 1
Chromosomal Location
ChrIV:1258696 to 1259709 | ORF Map | GBrowse
Gene Ontology Annotations All SPT3 GO evidence and references
  View Computational GO annotations for SPT3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Targets 523 genes
Regulators 3 genes
Classical genetics
Large-scale survey
672 total interaction(s) for 372 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 86
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 27
  • Biochemical Activity: 2
  • Co-fractionation: 1
  • Co-localization: 2
  • Co-purification: 7
  • PCA: 2
  • Reconstituted Complex: 8

Genetic Interactions
  • Dosage Lethality: 1
  • Dosage Rescue: 3
  • Negative Genetic: 326
  • Phenotypic Enhancement: 8
  • Phenotypic Suppression: 1
  • Positive Genetic: 66
  • Synthetic Growth Defect: 59
  • Synthetic Lethality: 54
  • Synthetic Rescue: 18

Expression Summary
Length (a.a.) 337
Molecular Weight (Da) 38,800
Isoelectric Point (pI) 8.16
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrIV:1258696 to 1259709 | ORF Map | GBrowse
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1014 1258696..1259709 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 SGDIDS000002800

SPT3 encodes a subunit of SAGA, a multi-subunit complex that either activates or inhibits transcription of some RNA polymerase II-dependent genes (4). In its role as an activator, Spt3p interacts with the TATA-binding protein (TBP), encoded by SPT15 (3), and has been shown to be required for recruitment of TBP to the SAGA-dependent promoters GAL1 (6, 7), VTC3, BDF2, PHO84, and ADH1 (8). Studies of activation at the GAL1 promoter indicate that the activator protein Gal4p recruits SAGA to the upstream activation sequence (UAS), and that SAGA subsequently recruits TBP via Spt3p and Spt20p (7). During SAGA-mediated transcriptional inhibition, which has been demonstrated at the HIS3 and TRP3 promoters, Spt3p and Spt8p prevent TBP binding to the TATA box (2).

SPT3 was originally identified in a genetic screen for mutations that suppress Ty or solo Delta element insertions in the HIS4 or LYS2 promoters (9, 1). Null mutations in SPT3 confer defects in mating (10), sporulation (11), diploid pseudohyphal growth, and haploid invasive growth (12). SPT3 homologs have been identified in humans (13, 14) and other fungi (15, 12). Candida albicans SPT3, which complements an S. cerevisiae spt3 null mutation, is required for normal filamentation and for virulence in C. albicans . Interestingly, null mutations in C. albicans SPT3 cause hyperfilamentation, the opposite effect of that observed in S. cerevisiae spt3 null mutants (12).

Characterized subunits of the SAGA complex include: Hfi1p, Ada2p, Ngg1p, Spt20p, Gcn5p, Spt3p, Spt7p, Spt8p, Tra1p, Taf5p, Taf6p, Taf9p, Taf10p, Taf12p, Ubp8p, and Sgf11p (16, 17; reviewed in 18). Cells also contain an altered form of SAGA, referred to as SLIK (SAGA-like) or SALSA (SAGA altered, Spt8 absent), which is also involved in transcription activation (19, 18). This complex contains Spt3p, but it lacks Spt8p and has a truncated form of Spt7p.

Last updated: 2006-07-03 Contact SGD

References cited on this page View Complete Literature Guide for SPT3
1) Winston F, et al.  (1984) Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics 107(2):179-97
2) Belotserkovskaya R, et al.  (2000) Inhibition of TATA-binding protein function by SAGA subunits Spt3 and Spt8 at Gcn4-activated promoters. Mol Cell Biol 20(2):634-47
3) Eisenmann DM, et al.  (1992) SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev 6(7):1319-31
4) Grant PA, et al.  (1997) Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev 11(13):1640-50
5) Ghosh Dastidar R, et al.  (2012) The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. Cell Biosci 2(1):30
6) Dudley AM, et al.  (1999) The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes Dev 13(22):2940-5
7) Larschan E and Winston F  (2001) The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev 15(15):1946-56
8) Bhaumik SR and Green MR  (2002) Differential requirement of SAGA components for recruitment of TATA-box-binding protein to promoters in vivo. Mol Cell Biol 22(21):7365-71
9) Simchen G, et al.  (1984) Ty-mediated gene expression of the LYS2 and HIS4 genes of Saccharomyces cerevisiae is controlled by the same SPT genes. Proc Natl Acad Sci U S A 81(8):2431-4
10) Hirschhorn JN and Winston F  (1988) SPT3 is required for normal levels of a-factor and alpha-factor expression in Saccharomyces cerevisiae. Mol Cell Biol 8(2):822-7
11) Winston F, et al.  (1984) The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae. Cell 39(3 Pt 2):675-82
12) Laprade L, et al.  (2002) Spt3 plays opposite roles in filamentous growth in Saccharomyces cerevisiae and Candida albicans and is required for C. albicans virulence. Genetics 161(2):509-19
13) Martinez E, et al.  (1998) A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID. J Biol Chem 273(37):23781-5
14) Yu J, et al.  (1998) Characterization of a human homologue of the Saccharomyces cerevisiae transcription factor spt3 (SUPT3H). Genomics 53(1):90-6
15) Madison JM and Winston F  (1998) Identification and analysis of homologues of Saccharomyces cerevisiae Spt3 suggest conserved functional domains. Yeast 14(5):409-17
16) Henry KW, et al.  (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev 17(21):2648-63
17) Lee KK, et al.  (2005) The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol Cell Biol 25(3):1173-82
18) Sterner DE, et al.  (2002) SALSA, a variant of yeast SAGA, contains truncated Spt7, which correlates with activated transcription. Proc Natl Acad Sci U S A 99(18):11622-7
19) Pray-Grant MG, et al.  (2002) The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway. Mol Cell Biol 22(24):8774-86