RAF1/R0030W Summary Help

Standard Name RAF1 1
Systematic Name R0030W
Feature Type ORF, Verified
Description Anti-repressor that increases 2 micron plasmid copy number; increases 2 micron plasmid copy number by relieving repression of the FLP1 site-specific recombinase caused by the Rep1-Rep2p trascription regulator; also itself repressed by the Rep1p-Rep2p complex (1 and see Summary Paragraph)
Name Description REP Antagonizing Factor or Recombinase Activating Factor 1
Chromosomal Location
2-micron:3271 to 3816 | ORF Map | GBrowse
Gene Ontology Annotations All RAF1 GO evidence and references
Molecular Function
Biological Process
Manually curated
Cellular Component
Manually curated
Length (a.a.) 181
Molecular Weight (Da) 21,289
Isoelectric Point (pI) 6.02
Phosphorylation PhosphoPep Database
sequence information
2-micron:3271 to 3816 | ORF Map | GBrowse
Last Update Coordinates: 2006-10-06 | Sequence: 2004-02-11
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..546 3271..3816 2006-10-06 2004-02-11
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000029674

The 2-micron plasmid is a relatively small (6318 bp) nuclear multicopy extrachromosomal element found in most common strains of Saccharomyces cerevisiae. Its presence confers no obvious advantage to its host, nor does it appear to impose any disadvantage at its steady-state copy number of 40-60 molecules (2). The plasmid contains 4 protein-coding loci (FLP1, REP1, REP2, RAF1) and 4 cis-acting loci (an origin of replication, a partitioning locus called STB, and 2 Flp Recombination Targets or FRTs) (3).

Raf1p (REP Antagonizing Factor or Recombinase Activating Factor), the product of the "D ORF", is an anti-repressor that positively regulates the plasmid amplification process by relieving repression of the FLP1 site-specific recombinase by the Rep1-Rep2p bipartite transcription regulator (1). RAF1 is itself repressed by the Rep1p-Rep2p complex, but requires a higher level of repressor activity for complete inhibition than does FLP1 (1).

The 2-micron plasmid propagates itself with chromosome-like stability through the combined action of a plasmid amplification system and a plasmid partitioning system. The amplification system compensates for any copy number decreases caused by missegregation events, and consists of Flp1p along with a pair of 599-bp FRT sites present in the plasmid genome in a head-to-head orientation (4). The partitioning system ensures roughly equal distribution of replicated plasmids to daughter cells by overcoming the normal segregation bias that favors the mother cell over daughters in plasmid retention (4). This system comprises Rep1p, Rep2p, and the partitioning locus STB which consists of two subloci, one containing approximately six iterations of a consensus 65-bp repeat, and another which is involved in maintaining the active configuration of STB and contains the termination site for two transcripts directed toward the plasmid replication origin (4). Multiple copies of the 2-micron plasmid exist as a tight-knit cluster within the nucleus that stays together throughout the cell cycle (5), and this plasmid cluster is the segregation entity, effectively reducing copy number to one (5, 6).

Last updated: 2006-08-17 Contact SGD

References cited on this page View Complete Literature Guide for RAF1
1) Murray JA, et al.  (1987) Antagonistic controls regulate copy number of the yeast 2 mu plasmid. EMBO J 6(13):4205-12
2) Futcher AB  (1988) The 2 micron circle plasmid of Saccharomyces cerevisiae. Yeast 4(1):27-40
3) Ahn YT, et al.  (1997) The 2microm-plasmid-encoded Rep1 and Rep2 proteins interact with each other and colocalize to the Saccharomyces cerevisiae nucleus. J Bacteriol 179(23):7497-506
4) Ghosh SK, et al.  (2006) Mechanisms for chromosome and plasmid segregation. Annu Rev Biochem 75:211-41
5) Velmurugan S, et al.  (2000) Partitioning of the 2-microm circle plasmid of Saccharomyces cerevisiae. Functional coordination with chromosome segregation and plasmid-encoded rep protein distribution. J Cell Biol 149(3):553-66
6) Scott-Drew S, et al.  (2002) DNA plasmid transmission in yeast is associated with specific sub-nuclear localisation during cell division. Cell Biol Int 26(5):393-405