Recombination within the yeast plasmid 2mu circle is site-specific

The terminal a sequence of the herpes simplex virus genome contains the promoter of a gene located in the repeat sequences of the L component

The herpes simplex virus DNA genome consists of two covalently linked components, L and S. The unique sequences of the L component are flanked by 9-kilobase-pair inverted repeat sequences ab and b'a', whereas those of the S component are flanked by 6.5-kilobase-pair inverted repeat sequences c'a' and ca. We report that the 500-base-pair a sequence contains the promoter-regulatory domain and the transcription initiation site of a diploid gene, the coding sequences of which are located in the b sequences of the inverted repeats of the L component. The chimeric gene constructed by fusion of the a sequence to the coding sequences of the thymidine kinase gene and recombined into the viral genome was regulated as a gamma 1 gene. The size of the protein predicted from its sequence is 358 amino acids; it was designated as infected cell protein (ICP) 34.5. Thus, the inverted repeats flanking the unique sequences of the L component contain two genes specifying ICP0 and ICP34.5, respectively. Moreover, in addition to the cis-acting sites for the inversion of L and S components relative to each other, for cleavage of unit length DNA molecules from head-to-tail concatemers, and for packaging of the DNA into capsids, the a sequence also contains the promoter-regulatory domain and transcription initiation sites of a gene.

Survival strategies of the yeast plasmid two-micron circle

The multicopy yeast plasmid 2-micron circle uses a number of strategies to insure its persistence in its host. The plasmid confers no selective phenotype to the cell in which it is resident. Nonetheless, the plasmid is lost at less than 1 per 10(5) cell divisions during continuous exponential growth. We have determined that the plasmid persists at least in part due to the ability of the plasmid to amplify its mean copy number when its cellular copy level is low and to distribute plasmid molecules equally between mother and daughter cells at mitosis. We have found that amplification of plasmid copy number occurs by a novel mechanism in which site-specific recombination induces a transient shift in the mode of replication from theta to rolling circle. Equitable partitioning of plasmid molecules requires plasmid-encoded proteins and a centromere-like segment on the plasmid. We have accumulated evidence consistent with a model of partitioning in which the partitioning proteins form a transnuclear structure that is responsible for distributing plasmid molecules throughout the nucleus prior to cell division. In this chapter we describe evidence supporting the existence and mode of action of these two plasmid strategies and discuss the extent to which these strategies may be a pervasive facet of the biology of eukaryotic extrachromosomal elements.

The FLP recombinase of the Saccharomyces cerevisiae 2 microns plasmid attaches covalently to DNA via a phosphotyrosyl linkage

The FLP recombinase, encoded by the 2 micron plasmid of Saccharomyces cerevisiae, promotes efficient recombination in vivo and in vitro between its specific target sites (FLP sites). It was previously determined that FLP interacts with DNA sequences within its target site (B. J. Andrews, G. A. Proteau, L. G. Beatty, and P. D. Sadowski. Cell 40:795-803, 1985), generates a single-stranded break on both DNA strands within the FLP site, and remains covalently attached to the 3' end of each break. We now show that the FLP protein is bound to the 3' side of each break by an O-phosphotyrosyl residue and that it appears that the same tyrosyl residue(s) is used to attach to either DNA strand within the FLP site.

The FLP recombinase of the yeast 2-micron plasmid: characterization of its recombination site

The minimal size of the recombination site required for efficient FLP recombinase-catalyzed recombination in vitro is no more than 28 base pairs, which includes parts of two 13-base-pair inverted repeats and all of an 8-base-pair spacer. The FLP recombinase cleaves the DNA at the boundaries of the spacer, becomes covalently linked to the spacer DNA via a 3' phosphate, and leaves a free 5' hydroxyl at the other end of the 8-base-pair spacer. The efficiency of recombination is reduced if the size of the spacer in a recombinant site is increased or decreased by 1 base pair, while the spacer in the second site is unaltered. Recombination between two sites with identical 1-base-pair additions or deletions in the spacer, however, is relatively unaffected. This result suggests that pairing of sequences in the spacer region is important in FLP-promoted recombination events. The sequence asymmetry utilized by the recombinase to determine the orientation of the site is located uniquely within the spacer region.

Two-micrometer circle site-specific recombination: the minimal substrate and the possible role of flanking sequences

The 2-mum circle DNA of yeast encodes a site-specific recombination system (FLP recombination). The recombination region had been mapped earlier to a 65-base-pair (bp) segment within the 599-bp-long inverted repeats of the molecule. I have shown that the "minimal" FLP substrate resides in a 13-bp dyad symmetry plus an 8-bp core located within the 65-bp recombination region. Further, as determined by different in vivo assays, sequences extraneous to the minimal FLP site and the 65-bp recombination region can affect the efficiency of the recombination reaction.

Properties of REP3: a cis-acting locus required for stable propagation of the Saccharomyces cerevisiae plasmid 2 microns circle

Stable propagation of the yeast plasmid 2 microns requires an origin of replication, a cis-active locus designated REP3, and two plasmid-encoded proteins which are the products of the REP1 and REP2 genes. The three REP loci appear to constitute a partitioning system, ensuring equal distribution of plasmid molecules to mother and daughter cells after mitosis. We have localized the REP3 site completely within a segment of five-and-one-half direct tandem repeats of a 62-base-pair unit, bordered by HpaI and AvaI restriction sites within the large unique region of the 2 microns genome. In addition, we find that the repeated elements are functionally distinct. Only a subset of the repeats is necessary to promote full partitioning activity. The other repeats appear to promote plasmid transcription. These results are discussed in the context of a model of plasmid copy control involving titration of a plasmid-specific protein by the repeated elements within REP3.

Chromatin organization of the Saccharomyces cerevisiae 2 microns plasmid depends on plasmid-encoded products

We have used gene disruptions and nuclease probes to assess the roles of yeast 2 micron plasmid genes in plasmid chromatin organization. The chromatin structure at the replication origin is not dependent on any of the four major open reading frames, A, B, C, or D. While stable plasmid maintenance is known to depend on a cis-acting locus STB and genes B and C, we find that only gene B influences STB chromatin. Other interactions between plasmid gene products and sequences may reflect gene regulation: the chromatin organization at the 5' end of gene A, which codes for a site-specific recombinase, depends on both gene B and gene C. Since disruption of gene C results in an increase in plasmid copy number that is dependent on gene A, we propose that gene C (and probably gene B) control copy number by regulating the level of the gene A recombinase.

Transformation of yeast with linearized plasmid DNA. Formation of inverted dimers and recombinant plasmid products

The molecular products of DNA double strand break repair were investigated after transformation of yeast (Saccharomyces cerevisiae) with linearized plasmid DNA. DNA of an autonomous yeast plasmid cleaved to generate free ends lacking homology with the yeast genome, when used in transformation along with sonicated non-homologous carrier DNA, gave rise to transformants with high frequency. Most of these transformants were found to harbor a head-to-head (inverted) dimer of the linearized plasmid. This outcome of transformation contrasts with that observed when the carrier DNA is not present. Transformants occur at a much reduced frequency and harbor either the parent plasmid or a plasmid with deletion at the site of the cleavage. When the linearized plasmid is introduced along with sonicated carrier DNA and a homologous DNA restriction fragment that spans the site of plasmid cleavage, homologous recombination restores the plasmid to its original circular form. Inverted dimer plasmids are not detected. This relationship between homologous recombination and a novel DNA transaction that yields rearrangement could be important to the cell, as the latter could lead to a loss of gene function and lethality.

Physical and functional structure of a yeast plasmid, pSB3, isolated from Zygosaccharomyces bisporus

The plasmid pSB3 of yeast Zygosacharomyces bisporus has been sequenced. It contains 6,615 base pairs, including a pair of inverted repeats (IR) consisting of 391 base pairs and 3 large open reading frames (ORF). One of the ORFs (A gene) participates in the recombination at the IRs and the other two (B and C genes) are necessary for the stable maintenance of this plasmid. The ARS sequence, which functions in a Saccharomyces cerevisiae host, was localized within 168 base pairs consisting of part of one of the IRs and a unique sequence contiguous to it. pSB3 can be maintained as stably in Z. rouxii as in the natural host Z.bisporus. In contrast, pSB3 is maintained fairly unstably in S.cerevisiae. The reason for this instability was found to be inefficient partitioning of pSB3 in S.cerevisiae. The molecular construction of pSB3 resembles that of 2-micron DNA, however, sequence homology at the DNA level was very poor.

The FLP recombinase of the 2 micron circle DNA of yeast: interaction with its target sequences

We have studied the interaction of purified FLP protein with restriction fragments from the substrate 2mu circle DNA of yeast. We find that FLP protects about 50 bp of DNA from nonspecific nuclease digestion. The protected site consists of two 13 bp inverted repeat sequences separated by an 8 bp spacer region. A third 13 bp element is also protected by binding of the FLP protein. We demonstrate that FLP introduces single- and double-strand breaks into the substrate DNA. This site-specific cleavage occurs at the margins of the spacer region, generating 8 bp 5' protruding ends with 5'-OH and 3'-protein-bound termini. Binding to mutant sites and half-sites demonstrates that the third symmetry element is not important for binding and cleavage by the FLP protein. The integrity of the core region is important for the cleavage activity of FLP.

Molecular and functional organization of yeast plasmid pSR1

The nucleotide sequence of a 6251 base-pair plasmid, pSR1, harbored in an osmophilic haploid yeast, Zygosaccharomyces rouxii (formerly Saccharomyces rouxii), was determined. No homology was detected between the sequences of pSR1 and 2-micron DNA of Saccharomyces cerevisiae. pSR1 has a pair of inverted repeats consisting of completely homologous 959 base-pair sequences, which separate two unique sequences 2654 base-pairs and 1679 base-pairs long. Each inverted repeat has an ARS sequence functional in both Z. rouxii and S. cerevisiae hosts. Short direct repeats or dyad symmetries were observed in the inverted repeats similar to those found close to the replication origin of 2-micron DNA. Three open reading frames, P, S and R, each able to encode a protein of molecular weight larger than 10,000, were found. Insertional inactivation of R gave rise to a defect in the intramolecular recombination at the inverted repeats, and that of S reduced the copy number of pSR1 in the S. cerevisiae host. The maintenance stability of the plasmid was also tested in the heterogeneous S. cerevisiae host, but the results of the insertional inactivation of P, S and R were ambiguous. pSR1 and 2-micron DNA were compatible in S. cerevisiae cells, but the protein factors encoded by these plasmids did not complement each other.

The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize

The size of the mitochondrial genome from the fertile cytoplasm of maize has been determined by restriction mapping to be 570 kb. The entire sequence complexity of the genome can be represented on a single circular DNA species (the 'master circle'). The presence of reiterated sequences, active in recombination, results in a complex multipartite organisation.

Expression of heterologous genes in Saccharomyces cerevisiae from vectors utilizing the glyceraldehyde-3-phosphate dehydrogenase gene promoter

The promoter region from the cloned glyceraldehyde-3-phosphate dehydrogenase (GPD) gene of Saccharomyces cerevisiae (Musti et al., 1983) has been characterized. A 653-bp TaqI restriction fragment with a 3' border 24 bp upstream from the ATG initiation codon was isolated and demonstrated to contain all sequences necessary for promoter function in vivo. This DNA segment was converted to a portable promoter by cloning it into M13mp9, and the entire nucleotide sequence of the portable promoter was determined. Two generalized yeast expression vectors have been constructed utilizing the GPD portable promoter. The expression vectors include the yeast 2 mu origin of replication and amplification functions, such that the plasmids are maintained at high copy number in ciro yeast hosts. These vectors direct synthesis of a consensus alpha-interferon (IFN-alpha Con1) as 1% of total cell protein. Hepatitis B surface antigen (HBsAg) was also expressed from these vectors. The 5' end of the HBsAg gene was replaced with a synthetic DNA segment which restored the deleted GPD untranslated leader and utilized optimal yeast codons for the first 30 amino acids. The partially synthetic gene resulted in a 10- to 15-fold increased expression level from GPD vectors yielding HBsAg polypeptide as 2-4% of total cell protein.

Identification of sites required for repression of a silent mating type locus in yeast

There are three loci in the yeast Saccharomyces, each containing one of two possible genetic elements that can determine cell type. At one of these loci, MAT, this information is expressed to establish the mating type of the cell. At the other two loci, HML and HMR, this same information is phenotypically and transcriptionally silent, even though a large amount of identical sequence flanks MAT, HML and HMR coding regions. Transcriptional repression of HML and HMR requires the trans active gene products of four loci, designated variously as MAR or SIR, that are unlinked to each other or to MAT, HML or HMR. We have examined the phenotypic expression of a cloned, plasmid-borne copy of HML and of various deletion and insertion derivatives of this plasmid following their reintroduction into Mar+/Sir+ yeast strains. From these data, we have identified two sites flanking the locus, both of which are required for MAR/SIR repression of the locus. In addition, we demonstrate that each of these sites promotes autonomous replication in yeast. Abraham et al. (1984) have presented evidence demonstrating that a similar regulatory structure exists at the other silent locus, HMR. From an analysis of the sequences of these four regulatory sites, we have identified several specific sequences that may be involved in mediating repression of these loci and in promoting replication in yeast. These results are discussed in the context of potential models for the mechanism of regulation of the silent mating type loci.

Recombination sequences in plant mitochondrial genomes: diversity and homologies to known mitochondrial genes

Several plant mitochondrial genomes contain repeated sequences that are postulated to be sites of homologous intragenomic recombination (1-3). In this report, we have used filter hybridizations to investigate sequence relationships between the cloned mitochondrial DNA (mtDNA) recombination repeats from turnip, spinach and maize and total mtDNA isolated from thirteen species of angiosperms. We find that strong sequence homologies exist between the spinach and turnip recombination repeats and essentially all other mitochondrial genomes tested, whereas a major maize recombination repeat does not hybridize to any other mtDNA. The sequences homologous to the turnip repeat do not appear to function in recombination in any other genome, whereas the spinach repeat hybridizes to reiterated sequences within the mitochondrial genomes of wheat and two species of pokeweed that do appear to be sites of recombination. Thus, although intragenomic recombination is a widespread phenomenon in plant mitochondria, it appears that different sequences either serve as substrates for this function in different species, or else surround a relatively short common recombination site which does not cross-hybridize under our experimental conditions. Identified gene sequences from maize mtDNA were used in heterologous hybridizations to show that the repeated sequences implicated in recombination in turnip and spinach/pokeweed/wheat mitochondria include, or are closely linked to genes for subunit II of cytochrome c oxidase and 26S rRNA, respectively. Together with previous studies indicating that the 18S rRNA gene in wheat mtDNA is contained within a recombination repeat (3), these results imply an unexpectedly frequent association between recombination repeats and plant mitochondrial genes.

Illegitimate recombination generates a class switch from C mu to C delta in an IgD-secreting plasmacytoma

We present here the sequence characterization of a C mu----C delta immunoglobulin (Ig) heavy chain class switch. In the murine IgD-secreting plasmacytoma TEPC 1017, deletion of most of the mu switch recombination region (S mu) and the entire C mu gene occurred in the absence of switch region sequences 5' to C delta. This unique rearrangement resulted from an illegitimate recombination of sequences with only patchy homology to each other. The infrequent and variable nature of illegitimate recombination may explain the low frequency of IgD-secreting plasma cells in normal mouse tissues.

A review of the structure and organization of the mitochondrial genome of higher plants

The structure, organisation and functions of the mitochondrial genome of most groups of eukaryotic organisms are known to varying degrees with the notable exception of higher plants. With the recent completion of physical mapping studies on the Brassica campestris (Chinese cabbage, turnip) and Zea mays (maize) mitochondrial genomes, many of the apparent problems of plant mitochondrial genome structure can now be answered. In this manuscript I review the literature relating to the physical observations on plant mitochondrial DNA (mtDNA) and assess the data in relation to our current understanding of mitochondrial genome structure.

Expression of an artificial yeast TRP-gene cluster in yeast and Escherichia coli

All five tryptophan biosynthetic genes of Saccharomyces cerevisiae were unified on plasmid pME554, which is based on 2 micrometer DNA and pBR322 sequences allowing for autonomous replication in yeast and E. coli. Homologous and heterologous expression of this artificial yeast TRP-gene cluster was studied. Plasmid pME554 allowed for nearly normal growth of a yeast strain bearing auxotrophic mutations in all five TRP-genes. The plasmid-borne genes TRP2 to TRP5 were expressed and regulated normally in the frame of the general control. Gene TRP1, carried on an EcoRI/Bg/II fragment lacking the ARS1 function, was expressed poorly and did not respond to the general control like the chromosomally-borne TRP1 gene. Plasmid pME554 allowed for poor growth of E. coli strain W3110 tna- delta trpEA2 on minimal medium. Marked stimulation was observed, however, when anthranilic acid or indole were added. Accordingly, poor expression of the first Trp-enzyme anthranilate synthase and the last enzyme tryptophan synthase was found, whereas the other three genes were moderately well expressed in E. coli.

Involvement of the invertible G segment in bacteriophage mu tail fiber biosynthesis

The orientation [G(+) or G(-)] of the invertible G segment of bacteriophage Mu DNA determines the host range specificity of the phage particles. In this study the hypothesis that the G segment genes are involved in synthesis of Mu tail fibers has been tested. Serum blocking power (SBP) assays demonstrated that among Mu late gene mutants only those defective in genes S or U encoded by the G segment were defective in G(+) SBP and that they lacked the same antigens. Electron microscopy of lysates produced by inversion-defective gin mutants (isolated by their inability to complement a hin inversion-defective mutant of the Salmonella phase variation segment) showed that G(+) phages with amber mutations in S or U made tail-fiberless particles with contracted tail sheaths. Inversion of G to the G(-) orientation or suppression of the amber mutations restored the normal phage particle morphology. These experiments demonstrate that genes S and U are required for Mu G(+) tail fiber biosynthesis and/or attachment.

Recombinational instability of a chimeric plasmid in Saccharomyces cerevisiae

Wild-type strains of Saccharomyces cerevisiae exhibit mitotic recombination between the chimeric plasmid TLC-1 and the endogenous 2mu circle that involves sequence homologies between the two plasmids that are not acted on by the 2mu circle site-specific recombination system. This generalized recombination can be detected because it separates the LEU2 and CAN1 markers of TLC-1 from each other through the formation of a plasmid containing only the S. cerevisiae LEU2 region and the 2mu circle. This derivative plasmid is maintained more stably during vegetative growth than TLC-1, and strains which carry it frequently lose the endogenous 2mu circle. Therefore, TLC-1 can provide a convenient selection for [cir0] cells. Formation of this new plasmid is greatly reduced, but not eliminated, in strains containing the rad52-1 mutation. This indicates that generalized mitotic recombination between plasmid sequences utilizes functions required for chromosomal recombination in S. cerevisiae.

Location of DNAase I sensitive cleavage sites in the yeast 2 micron plasmid DNA chromosome

We have studied the uniformity with which the yeast 2 micron plasmid DNA within its nucleoprotein complex is protected from digestion by DNAase I. To probe for relatively unprotected regions, plasmid nucleoprotein complexes were digested with DNAase I to yield a preparation in which approximately half of the circular DNA molecules had been converted to full-length linear molecules. The sites of the double-strand breaks were then mapped in relation to restriction endonuclease sites using end-label probes. The most prominent sensitive sites were found at positions very close to the beginning and end of a 122 base-pair sequence with dyad symmetry located within the 599 base-pair inverted repetition of the plasmid. The sequence is known to be necessary for plasmid site-specific recombination. Other sensitive sites were mapped to the 5'-side of known coding regions. A unique plasmid sequence located to one side of the replication origin was also sensitive to DNAase I digestion yet did not yield discrete cleavage sites. Cleavage of plasmid DNA stripped of proteins did not result in the appearance of distinct fragments as found after cleavage of the same DNA within the nucleoprotein complex. We conclude from these results that, when complexed with proteins, specific plasmid DNA sequences involved in transcription, replication and recombination are more accessible to nuclease digestion.

Interaction of the bacteriophage P1 recombinase Cre with the recombining site loxP

The interaction between the P1 recombinase protein Cre and the DNA site at which it acts, loxP, has been studied by using nuclease protection techniques. The region of DNA protected by Cre against nuclease attack by DNase I or neocarzinostatin is a 34-base-pair (bp) region containing two 13-bp inverted repeats separated by an 8-bp spacer region. These protected sequences have previously been shown to be required for efficient Cre-mediated recombination at loxP. The results of the above protection experiments suggest (i) that no more than 34 bp may be required for loxP recombination and (ii) that the asymmetry of loxP recombination is due to the 8-bp spacer sequence. With neocarzinostatin, a specific nucleotide within the 8-bp spacer region is not protected. This nucleotide is located in a 2-bp sequence shown to be involved in a loxP crossover event, suggesting that this region remains exposed after Cre binding. Protection experiments have also been done with loxP sites that have either the left or right inverted repeat deleted. The nuclease protection pattern of these sites reveals that each loxP site consists of two binding domains for Cre, each being composed of one 13-bp inverted repeat and the contiguous 4 bp of the 8-bp spacer region.

Recombinational instability of a chimeric plasmid in Saccharomyces cerevisiae

Wild-type strains of Saccharomyces cerevisiae exhibit mitotic recombination between the chimeric plasmid TLC-1 and the endogenous 2mu circle that involves sequence homologies between the two plasmids that are not acted on by the 2mu circle site-specific recombination system. This generalized recombination can be detected because it separates the LEU2 and CAN1 markers of TLC-1 from each other through the formation of a plasmid containing only the S. cerevisiae LEU2 region and the 2mu circle. This derivative plasmid is maintained more stably during vegetative growth than TLC-1, and strains which carry it frequently lose the endogenous 2mu circle. Therefore, TLC-1 can provide a convenient selection for [cir0] cells. Formation of this new plasmid is greatly reduced, but not eliminated, in strains containing the rad52-1 mutation. This indicates that generalized mitotic recombination between plasmid sequences utilizes functions required for chromosomal recombination in S. cerevisiae.

Cloning of the vaccinia virus telomere in a yeast plasmid vector

The vaccinia virus DNA telomere, which contains a covalently closed hairpin structure, has been cloned in a yeast plasmid vector. Restriction mapping indicates that the cloned vaccinia telomere is maintained in yeast not in its native hairpin configuration but as an inverted repeat structure, within a circular plasmid, with the sequences of the viral hairpin now at the axis of symmetry of an imperfect palindrome. As such, the cloned telomere resembles the telomeric replicative intermediate observed during vaccinia virus DNA replication. Small deletions and duplications in the viral inverted repeats of different clones suggest a model in which the observed circular plasmids were generated in yeast by the replication of hybrid linear DNA molecules consisting of the linearized yeast vector flanked by two hairpin-containing vaccinia termini.

Site-specific recombination of yeast 2-micron DNA in vitro

Most strains of the yeast Saccharomyces cerevisiae harbor several copies of a 2-micron plasmid circle DNA termed "2 micron." This circular plasmid contains two 599-base-pair precise inverted repeats across which a site-specific inversion event occurs in vivo. This inversion is promoted by a plasmid-encoded function called "FLP." We have cloned the FLP gene of 2-micron DNA under control of a strong yeast promoter and transformed yeast cells with a plasmid containing the cloned FLP gene. Cell-free extracts from such a transformant promote highly efficient inversion of 2-micron DNA in vitro. The reaction requires a cation and works efficiently on supercoiled, relaxed circular, or linear DNA. The FLP activity bears certain similarities to the cre protein, a site-specific recombinase encoded by bacteriophage P1.

Yeast plasmid requires a cis-acting locus and two plasmid proteins for its stable maintenance

Unstable ars1 (autonomously replicating sequence)-containing plasmids can be stabilized by connecting particular DNA segments of yeast 2 mu-plasmid. A cis-acting locus for the plasmid's stability (the STB locus) was found in the large unique region and separated from the replication origin of 2 mu-plasmid. Several direct repeats found in this region were essential for its function. Two proteins encoded by the plasmid (B and C) were required as trans-acting factors. The average copy number of the plasmid was not affected whether the plasmid carried the stability system or not, suggesting that the system was not directly associated with the replication function but was involved in partitioning at cell division.

Yeast plasmid 2-micron circle promotes recombination within bacterial transposon Tn5

The site-specific recombination system (FLP) encoded by the yeast plasmid 2-micron circle can also act in yeast on the inverted repeats of the bacterial transposon Tn5. The efficiency of this recombination is dependent on the location of Tn5 within the 2-micron circle genome but can be as high as that observed for 2-micron circle itself. Comparison of the DNA sequences between the Tn5 repeat and the 2-micron circle recombination region reveals certain strikingly similar structural features that might be important in the recombination reaction.

Pedigree analysis of plasmid segregation in yeast

We have used pedigree analysis to investigate the mitotic segregation of circular and linear DNA plasmids in Saccharomyces cerevisae. Circular ARS plasmids, which bear putative chromosomal replication origins, have a high segregation frequency and a strong bias to segregate to the mother cell at mitosis. The segregation bias explains how the fraction of plasmid-bearing cells can be small despite the high average copy number of circular ARS plasmids. Linear ARS plasmids do not show strong segregation bias, nor does the 2 mu ori-containing plasmid YEp 13, when it is present in strains containing intact 2 mu circles. In the absence of endogenous 2 mu circles, YEp 13 behaves like an ARS plasmid, showing a strong maternal segregation bias. The presence of a centromere on circular ARS plasmids eliminates segregation bias. We discuss a model for plasmid segregation, which explains these findings and the possible biological significance of mother-daughter segregation bias.

The new yeast genetics

Gene cloning and yeast DNA transformation techniques have greatly enhanced the power of classical yeast genetics. It is now possible to isolate any classically defined gene, to alter the yeast genome at will by replacing normal chromosomal sequences with mutated derivatives produced in vitro, and to create DNA molecules that behave as autonomous replicons or minichromosomes. These unique features of the new yeast genetics have been used to study many problems in eukaryotic molecular biology.

In vivo ligation of linear DNA molecules to circular forms in the yeast Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae was transformed with restriction endonuclease-digested (linear) DNAs containing the replication origin of the yeast 2 microns plasmid and selectable markers with efficiencies of 10(3) to 10(4), 10(3), and 10(2) to 10(3) transformants per microgram of DNA in the cases of transformations with linear DNAs containing the same cohesive ends, flush ends, and non-complementary cohesive ends, respectively. The results of a restriction analysis of the circular plasmids recovered from transformed cells suggested that the linear DNA molecules were ligated to produce circular forms in the recipient protoplasts.

Copy number control by a yeast centromere

Plasmids containing a cloned yeast (Saccharomyces cerevisiae) centromere (CEN3) in combination with a suitable DNA replication system are maintained in yeast at the low copy number typical of a chromosome. In composite plasmids containing CEN3 plus the yeast 2 mu plasmid, the CEN3 copy number control is dominant over the amplification system that normally drives the 2 mu plasmids to high copy number. The CEN3-2 mu composite plasmids are relatively stably maintained in yeast at a copy number of about one per haploid genome, and segregate through meiosis in a typical Mendelian pattern. Some of the CEN3-2 mu composite plasmids isolated from yeast contain deletions of variable size that remove the functional centromere, resulting in loss of the CEN3 control and reversion to high copy number. Formation of the CEN3 deletions requires the specialized recombination system (inverted repeat sequences and FLP gene) of the yeast 2 mu plasmid.

The yeast plasmid 2mu circle encodes components required for its high copy propagation

The yeast plasmid 2mu and certain hybrid plasmids constructed from it are maintained stably and at high copy number in yeast cells. By examining various mutant hybrid 2mu plasmids, we show that these properties require the integrity of four plasmid loci. Two of these, designated REP1 and REP2, are active in trans and correspond to two open coding regions of 2mu. The other two loci are active only in cis and correspond to the origin of replication and to a region, designated REP3, located several hundred bp away from the origin and consisting of direct repeats of a 62 bp sequence. We propose that the REP loci constitute a copy control system that overrides normal cellular restriction on plasmid replication and amplifies the plasmid when copy number is low.

The FLP protein of the yeast 2-microns plasmid: expression of a eukaryotic genetic recombination system in Escherichia coli

The FLP gene of the yeast 2-microns plasmid is involved in a site-specific recombination event that results in the inversion of a set of sequences within the plasmid. This gene has been cloned and expressed in Escherichia coli. Expression of the FLP gene results in efficient recombination within the bacterial cell, which is specific for plasmids containing at least one 2-microns plasmid recombination site. This work demonstrates that (i) FLP protein is actively involved in 2-microns plasmid recombination; (ii) no other factors specific to yeast are required for the reaction; (iii) FLP protein acts efficiently in trans; (iv) FLP protein will promote site-specific insertion and deletion reactions in addition to the inversion reaction; and (v) FLP-promoted recombination is not dependent upon any DNA structural features unique to yeast chromatin.

Site-specific recombination by Gin of bacteriophage Mu: inversions and deletions

A 3000-bp invertible segment in the DNA of bacteriophage Mu determines the host range of the phage. The inversion is catalyzed by the phage-coded protein Gin; the recombination sites are short inverted repeats. Gin protein is only made in low amounts by Mu. To further investigate the Gin-mediated recombination reaction a Gin overproducing strain was constructed. The gin gene was cloned on a plasmid behind the PL-promotor of phage lambda. This results in a 100-fold higher inversion frequency of a Mu gin phage as compared to the situation when Gin is expressed from its own promoter. A test system was developed suitable for the detection of Gin action in vivo and in vitro: the lacZ gene of E. coli was cloned within the invertible region in such a way that it is only expressed when the region is in one specific orientation. Thus inversions can be detected or selected as a switch from Lac- to Lac+. This system was used to determine the inversion frequency under different experimental conditions. The ability of Gin to catalyze deletions was investigated by inverting in vitro one of the two recombination sites using restriction enzymes and genetically marking the DNA between those sites. Deletions do occur, although at a lower frequency than inversions.

Genome fusion mediated by the site specific DNA inversion system of bacteriophage P1

The genome of bacteriophage P1 contains a segment which is invertible by site specific recombination between sequences near the outside ends of the inverted repeats which flank it. Immediately adjacent to this C segment is the coding sequence for cin, the enzyme catalyzing inversion. We show that multicopy plasmids carrying cin and the sequences at which it acts (cix) can form dimers in the absence of the host recA function. Further, such plasmids can be cotransduced with P1 markers at high frequency from recA lysogens, indicating cointegration with the P1 genome. It is thus demonstrated that a system whose primary role is the inversion of a specific DNA segment can also mediate intermolecular recombination.

Structure and role of the herpes simplex virus DNA termini in inversion, circularization and generation of virion DNA

The herpes simplex virus genome consists of two components, L and S, which invert relative to each other during viral replication. The a sequence is present at the genomic termini in direct orientation and at the L-S junction in inverted orientation. Previously, we showed that insertion of a fragment spanning the L-S junction into the viral genome causes additional inversions. In this study, we determine the nucleotide sequence of the genomic termini and show that insertion of either the free S terminus or the L terminus causes inversions in the viral genome. We conclude that the a sequence is the inversion-specific sequence, that linear unit-length molecules packaged in virions are generated by cleavage between adjacent copies of the a sequence, that cleavage produces 3' single-base extensions on the genomic termini and that the signal for cleavage is contained within the a sequence.

Genetic properties of chromosomally integrated 2 mu plasmid DNA in yeast

We obtained strains of yeast with large segments of 2 mu plasmid DNA integrated at several chromosomal locations by selecting genetically for recombination between a chromosomal sequence carried on a 2 mu-circle-containing hybrid plasmid and a homologous sequence on the chromosome. In all diploids examined, the presence of 2 mu circle sequences causes a marked instability of the chromosome into which the 2 mu DNA is inserted. Although in some cases the loss of genetic markers is due to physical loss of the entire chromosome, in most cases the loss of markers appears to be due to a mitotic homozygotization of markers: the allelic information from the homologous chromosome replaces the information distal to the integrated 2 mu DNA. The instability caused by integrated 2 mu DNA sequences requires the activity of the specialized site-specific recombination system encoded by the 2 mu plasmid. We propose that the presence of integrated 2 mu DNA allows efficient integration of additional copies of the intact 2 mu plasmid by the action of the plasmid-coded special recombination system. Unequal sister-strand exchanges within the inverted repetition would result in the formation of dicentric chromosomes whose breakage during mitosis might begin a cycle analogous to the breakage-fusion-bridge cycle described many years ago in maize.