ABF1/YKL112W Summary Help

Standard Name ABF1
Systematic Name YKL112W
Alias BAF1 , OBF1 , REB2 , SBF1
Feature Type ORF, Verified
Description DNA binding protein with possible chromatin-reorganizing activity involved in transcriptional activation, gene silencing, and DNA replication and repair (1, 2, 3 and see Summary Paragraph)
Name Description ARS-Binding Factor 1
Chromosomal Location
ChrXI:226570 to 228765 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All ABF1 GO evidence and references
  View Computational GO annotations for ABF1
Molecular Function
Manually curated
High-throughput
Biological Process
Manually curated
Cellular Component
Manually curated
Regulatory Role
Binding motifs Predicted ABF1 Binding Site Locations
Resources
Mutant phenotypes All ABF1 Phenotype evidence and references
Classical genetics
overexpression
Large-scale survey
null
overexpression
reduction of function
repressible
Resources
interactions All ABF1 Interaction evidence and references
47 total interaction(s) for 37 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 11
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 2
  • Biochemical Activity: 1
  • Co-fractionation: 2
  • Reconstituted Complex: 7
Genetic Interactions
  • Dosage Rescue: 3
  • Negative Genetic: 12
  • Positive Genetic: 6
  • Synthetic Lethality: 2
Resources
Expression Summary
histogram
Resources
Protein Information All ABF1 Protein evidence and references
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXI:226570 to 228765 | ORF Map | GBrowse
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Relative
Coordinates		 Chromosomal
Coordinates		 Most Recent Updates
Coordinates Sequence
CDS 1..2196 226570..228765 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
Resources
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000001595
SUMMARY PARAGRAPH for ABF1

ABF1 encodes the multifunctional global regulator ARS (autonomously replicating sequence)-Binding Factor 1 (4, 5). Abf1p is a site-specific DNA binding protein that binds to the consensus site, 5-TnnCGTnnnnnnTGAT-3 (6), which is found at numerous locations in the yeast genome including the silent mating type loci, ARSs, telomeric X-regions, and the promoter regions of many genes (7, 8, 5). Abf1p binding to these sites directly mediates a number of different chromatin-related events such as DNA replication (9, 4), gene silencing (10, 11), chromatin remodeling (12, 13), nucleotide excision repair (2), and gene activation and repression (14, 5). The genes that Abf1p transcriptionally regulates are involved in a diverse range of cellular processes including carbon source regulation (e.g., ADH1, CDC19, PGK1, ENO1, ENO2) (15, 16, 17), nitrogen utilization (e.g., CAR1, CAR2) (18, 19), sporulation (e.g., SPR3) (20), meiosis (e.g., HOP1) (21), and ribosomal function (e.g., RPL2A, RPL2B) (7, 22, 23).

The structure of Abf1p is similar to that of many other site-specific transcription factors. It has a bipartite N-terminal DNA-binding domain (amino acids 40-91 and 323-496) and a C-terminal activation domain (amino acids 604-731) (24, 25), with both domains being essential for cell viability (26). Within the activation domain are two regions named CS1 (C-terminal sequence 1; amino acids 624-628) and CS2 (amino acids 639-662) that are responsible for mediating nuclear localization and chromatin remodeling, respectively (26, 27).

Abf1p levels are abundant in the cell and Abf1p binding sites in the genome are occupied in vivo under all conditions studied thus far (28, 29). Nevertheless, it has been shown that Abf1p is able to repress its own transcription via binding at a consensus site in the ABF1 promoter (30, 5). The binding activity of Abf1p is stimulated by Cdc6p, a protein involved in DNA replication (31). Abf1p activity also appears to depend on its phosphorylation state. Abf1p can be phosphorylated at multiple sites, partially through the action of serine/threonine kinase, and the extent of Abf1p phosphorylation depends on growth conditions and carbon source (32, 33). Changes in Abf1p phosphorylation have been shown to correlate with regulation of expression of the Abf1p target gene COX6, linking Abf1p phosphorylation with carbon-source control of COX6 (33). Dephosphorylation requires the presence of functional Cyc8p (33). Nuclear import of Abf1p is dependent on the Ran guanine nucleotide exchange factor Srm1p, but Abf1p is also found to bind to the importin protein Pse1p, suggesting that import may be mediated by more than one pathway (27). Abf1p also interacts with the mRNA export factor Yra1p (34).

Last updated: 2005-10-19

References cited on this page View Complete Literature Guide for ABF1
1) de Boer M, et al.  (2000) Stp1p, Stp2p and Abf1p are involved in regulation of expression of the amino acid transporter gene BAP3 of Saccharomyces cerevisiae. Nucleic Acids Res 28(4):974-81
2) Reed SH, et al.  (1999) Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. Genes Dev 13(23):3052-8
3) Schroeder SC and Weil PA  (1998) Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box bindng protein-encoding gene, SPT15. J Biol Chem 273(31):19884-91
4) Rhode PR, et al.  (1989) The gene encoding ARS-binding factor I is essential for the viability of yeast. Genes Dev 3(12A):1926-39
5) Miyake T, et al.  (2004) Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation in Saccharomyces cerevisiae. J Biol Chem 279(33):34865-72
6) Beinoraviciute-Kellner R, et al.  (2005) In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS Lett 579(20):4535-40
7) Della Seta F, et al.  (1990) The ABF1 factor is the transcriptional activator of the L2 ribosomal protein genes in Saccharomyces cerevisiae. Mol Cell Biol 10(5):2437-41
8) Lee TI, et al.  (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594):799-804
9) Wiltshire S, et al.  (1997) An Abf1p C-terminal region lacking transcriptional activation potential stimulates a yeast origin of replication. Nucleic Acids Res 25(21):4250-6
10) Pryde FE and Louis EJ  (1999) Limitations of silencing at native yeast telomeres. EMBO J 18(9):2538-50
11) Loo S, et al.  (1995) Roles of ABF1, NPL3, and YCL54 in silencing in Saccharomyces cerevisiae. Genetics 141(3):889-902
12) Lascaris RF, et al.  (2000) Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res 28(6):1390-6
13) Venditti P, et al.  (1994) ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim Biophys Acta 1219(3):677-89
14) Buchman AR and Kornberg RD  (1990) A yeast ARS-binding protein activates transcription synergistically in combination with other weak activating factors. Mol Cell Biol 10(3):887-97
15) Yoo HY, et al.  (1995) Transcriptional control of the Saccharomyces cerevisiae ADH1 gene by autonomously replicating sequence binding factor 1. Curr Microbiol 31(3):163-8
16) Chambers A, et al.  (1990) ARS binding factor 1 binds adjacent to RAP1 at the UASs of the yeast glycolytic genes PGK and PYK1. Nucleic Acids Res 18(18):5393-9
17) Brindle PK, et al.  (1990) Multiple factors bind the upstream activation sites of the yeast enolase genes ENO1 and ENO2: ABFI protein, like repressor activator protein RAP1, binds cis-acting sequences which modulate repression or activation of transcription. Mol Cell Biol 10(9):4872-85
18) Kovari LZ and Cooper TG  (1991) Participation of ABF-1 protein in expression of the Saccharomyces cerevisiae CAR1 gene. J Bacteriol 173(20):6332-8
19) Park HD, et al.  (1999) Synergistic operation of the CAR2 (Ornithine transaminase) promoter elements in Saccharomyces cerevisiae. J Bacteriol 181(22):7052-64
20) Ozsarac N, et al.  (1997) Regulation of gene expression during meiosis in Saccharomyces cerevisiae: SPR3 is controlled by both ABFI and a new sporulation control element. Mol Cell Biol 17(3):1152-9
21) Gailus-Durner V, et al.  (1996) Participation of the yeast activator Abf1 in meiosis-specific expression of the HOP1 gene. Mol Cell Biol 16(6):2777-86
22) Planta RJ, et al.  (1995) Global regulators of ribosome biosynthesis in yeast. Biochem Cell Biol 73(11-12):825-34
23) Planta RJ  (1997) Regulation of ribosome synthesis in yeast. Yeast 13(16):1505-18
24) Cho G, et al.  (1995) Structure-function analysis of the DNA binding domain of Saccharomyces cerevisiae ABF1. Nucleic Acids Res 23(15):2980-7
25) Li R, et al.  (1998) Activation of chromosomal DNA replication in Saccharomyces cerevisiae by acidic transcriptional activation domains. Mol Cell Biol 18(3):1296-302
26) Miyake T, et al.  (2002) Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing. Mol Cell Biol 22(2):505-16
27) Loch CM, et al.  (2004) Functional and physical interactions between autonomously replicating sequence-binding factor 1 and the nuclear transport machinery. Traffic 5(12):925-35
28) Buchman AR, et al.  (1988) Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol Cell Biol 8(1):210-25
29) Kraakman LS, et al.  (1993) Growth-related expression of ribosomal protein genes in Saccharomyces cerevisiae. Mol Gen Genet 239(1-2):196-204
30) Halfter H, et al.  (1989) Sequence, expression and mutational analysis of BAF1, a transcriptional activator and ARS1-binding protein of the yeast Saccharomyces cerevisiae. EMBO J 8(13):4265-72
31) Feng L, et al.  (1998) Saccharomyces cerevisiae Cdc6 stimulates Abf1 DNA binding activity. J Biol Chem 273(3):1298-302
32) Upton T, et al.  (1995) ABF1 Ser-720 is a predominant phosphorylation site for casein kinase II of Saccharomyces cerevisiae. J Biol Chem 270(27):16153-9
33) Silve S, et al.  (1992) ABF1 is a phosphoprotein and plays a role in carbon source control of COX6 transcription in Saccharomyces cerevisiae. Mol Cell Biol 12(9):4197-208
34) Hieronymus H and Silver PA  (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat Genet 33(2):155-61
35) Harbison CT, et al.  (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004):99-104
36) Matys V, et al.  (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31(1):374-8
37) 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