RFA1/YAR007C Summary Help

Standard Name RFA1 1
Systematic Name YAR007C
Alias BUF2 , FUN3 2 , RPA1 3 , RPA70 4
Feature Type ORF, Verified
Description Subunit of heterotrimeric Replication Protein A (RPA); RPA is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination; RPA protects against inappropriate telomere recombination, and upon telomere uncapping, prevents cell proliferation by a checkpoint-independent pathway; role in DNA catenation/decatenation pathway of chromosome disentangling; relocalizes to the cytosol in response to hypoxia (1, 5, 6, 7, 8, 9 and see Summary Paragraph)
Name Description Replication Factor A 1
Chromosomal Location
ChrI:158619 to 156754 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -3 cM
Gene Ontology Annotations All RFA1 GO evidence and references
  View Computational GO annotations for RFA1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 8 genes
Classical genetics
reduction of function
Large-scale survey
reduction of function
303 total interaction(s) for 165 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 125
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 32
  • Biochemical Activity: 6
  • Co-localization: 9
  • Co-purification: 2
  • Reconstituted Complex: 10
  • Two-hybrid: 14

Genetic Interactions
  • Dosage Growth Defect: 4
  • Dosage Lethality: 1
  • Dosage Rescue: 2
  • Negative Genetic: 32
  • Phenotypic Enhancement: 26
  • Phenotypic Suppression: 12
  • Positive Genetic: 1
  • Synthetic Growth Defect: 9
  • Synthetic Lethality: 7
  • Synthetic Rescue: 8

Expression Summary
Length (a.a.) 621
Molecular Weight (Da) 70,347
Isoelectric Point (pI) 6.13
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrI:158619 to 156754 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -3 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1866 158619..156754 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 SGDIDS000000065

RFA1, RFA2, and RFA3 encode the three subunits of the heterotrimeric complex Replication protein A (RPA). RPA is a highly conserved single-stranded DNA (ssDNA) binding protein that removes secondary structure from ssDNA. RPA plays a key role in DNA metabolic pathways that have a ssDNA intermediate such as replication, recombination, transcription, checkpoints, telomere maintenance, and DNA repair (reviewed in 10 and 11). Some specific instances of RPA function in yeast include loading the telomerase component Est1p onto telomeres (12), enabling the efficient assembly of the Rad51p presynaptic filament (13, 14), and providing specificity of Rad17p/Mec3p/Ddc1p loading at 5'-junctions (15).

RPA binds ssDNA with high affinity and has no sequence specificity but does preferentially bind to pyrimidines over purines (6, 16). RPA interaction with DNA is mediated by binding domains in Rfa1p and Rfa2p (17). In response to DNA damage, Rfa1p and Rfa2p are phosphorylated by overlapping mechanisms that involve the kinases Mec1p and Tel1p (18, 19, 20). These same kinases also mediate Rfa2p phosphorylation during the normal cell cycle and during meiosis (18, 21).

All three RFA subunits are essential for viability in yeast, but reduction of function mutations in RPA result in various defects such as sensitivity to DNA damaging agents, altered mitotic and meiotic recombination, failure in mating type switching, severe telomere shortening, and chromosomal instability (12, 14 and reviewed in 11, 22). Gross chromosomal rearrangements found in rfa1 mutants are similar to those seen in some human cancers, and corresponding mutations in mice lead to tumor development (23 and references therein).

Last updated: 2007-08-09 Contact SGD

References cited on this page View Complete Literature Guide for RFA1
1) Brill SJ and Stillman B  (1991) Replication factor-A from Saccharomyces cerevisiae is encoded by three essential genes coordinately expressed at S phase. Genes Dev 5(9):1589-600
2) Steensma HY, et al.  (1987) Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: isolation and analysis of the CEN1-ADE1-CDC15 region. Mol Cell Biol 7(1):410-9
3) Heyer WD, et al.  (1990) An essential Saccharomyces cerevisiae single-stranded DNA binding protein is homologous to the large subunit of human RP-A. EMBO J 9(7):2321-9
4) Hegnauer AM, et al.  (2012) An N-terminal acidic region of Sgs1 interacts with Rpa70 and recruits Rad53 kinase to stalled forks. EMBO J 31(18):3768-83
5) Longhese MP, et al.  (1994) Replication factor A is required in vivo for DNA replication, repair, and recombination. Mol Cell Biol 14(12):7884-90
6) Alani E, et al.  (1992) Characterization of DNA-binding and strand-exchange stimulation properties of y-RPA, a yeast single-strand-DNA-binding protein. J Mol Biol 227(1):54-71
7) Cejka P, et al.  (2012) Decatenation of DNA by the S. cerevisiae Sgs1-Top3-Rmi1 and RPA complex: a mechanism for disentangling chromosomes. Mol Cell 47(6):886-96
8) Ghosh Dastidar R, et al.  (2012) The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. Cell Biosci 2(1):30
9) Grandin N and Charbonneau M  (2013) RPA provides checkpoint-independent cell cycle arrest and prevents recombination at uncapped telomeres of Saccharomyces cerevisiae. DNA Repair (Amst) 12(3):212-26
10) Sung P, et al.  (2003) Rad51 recombinase and recombination mediators. J Biol Chem 278(44):42729-32
11) Symington LS  (2002) Role of RAD52 epistasis group genes in homologous recombination and double-strand break repair. Microbiol Mol Biol Rev 66(4):630-70, table of contents
12) Schramke V, et al.  (2004) RPA regulates telomerase action by providing Est1p access to chromosome ends. Nat Genet 36(1):46-54
13) Hays SL, et al.  (1998) Studies of the interaction between Rad52 protein and the yeast single-stranded DNA binding protein RPA. Mol Cell Biol 18(7):4400-6
14) Kantake N, et al.  (2003) The recombination-deficient mutant RPA (rfa1-t11) is displaced slowly from single-stranded DNA by Rad51 protein. J Biol Chem 278(26):23410-7
15) Majka J, et al.  (2006) Replication protein A directs loading of the DNA damage checkpoint clamp to 5'-DNA junctions. J Biol Chem 281(38):27855-61
16) Kim C, et al.  (1992) Binding properties of replication protein A from human and yeast cells. Mol Cell Biol 12(7):3050-9
17) Brill SJ and Bastin-Shanower S  (1998) Identification and characterization of the fourth single-stranded-DNA binding domain of replication protein A. Mol Cell Biol 18(12):7225-34
18) Brush GS, et al.  (1996) The ATM homologue MEC1 is required for phosphorylation of replication protein A in yeast. Proc Natl Acad Sci U S A 93(26):15075-80
19) Brush GS and Kelly TJ  (2000) Phosphorylation of the replication protein A large subunit in the Saccharomyces cerevisiae checkpoint response. Nucleic Acids Res 28(19):3725-32
20) Kim HS and Brill SJ  (2003) MEC1-dependent phosphorylation of yeast RPA1 in vitro. DNA Repair (Amst) 2(12):1321-35
21) Brush GS, et al.  (2001) Replication protein A is sequentially phosphorylated during meiosis. Nucleic Acids Res 29(23):4808-17
22) Sung P, et al.  (2000) Recombination factors of Saccharomyces cerevisiae. Mutat Res 451(1-2):257-75
23) Wang Y, et al.  (2005) Mutation in Rpa1 results in defective DNA double-strand break repair, chromosomal instability and cancer in mice. Nat Genet 37(7):750-5