A map of the restriction targets in yeast 2 micron plasmid DNA cloned on bacteriophage lambda

Application of a wide-range yeast vector (CoMed) system to recombinant protein production in dimorphic Arxula adeninivorans, methylotrophic Hansenula polymorpha and other yeasts

BACKGROUND

Yeasts provide attractive expression platforms in combining ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. However, early restriction to a single yeast platform can result in costly and time-consuming failures. It is therefore advisable to assess several selected systems in parallel for the capability to produce a particular protein in desired amounts and quality. A suitable vector must contain a targeting sequence, a promoter element and a selection marker that function in all selected organisms. These criteria are fulfilled by a wide-range integrative yeast expression vector (CoMed) system based on A. adeninivorans- and H. polymorpha-derived elements that can be introduced in a modular way.

RESULTS

The vector system and a selection of modular elements for vector design are presented. Individual single vector constructs were used to transform a range of yeast species. Various successful examples are described. A vector with a combination of an rDNA sequence for genomic targeting, the E. coli-derived hph gene for selection and the A. adeninivorans-derived TEF1 promoter for expression control of a GFP (green fluorescent protein) gene was employed in a first example to transform eight different species including Hansenula polymorpha, Arxula adeninivorans and others. In a second example, a vector for the secretion of IL-6 was constructed, now using an A. adeninivorans-derived LEU2 gene for selection of recombinants in a range of auxotrophic hosts. In this example, differences in precursor processing were observed: only in A. adeninivorans processing of a MFalpha1/IL-6 fusion was performed in a faithful way.

CONCLUSION

rDNA targeting provides a tool to co-integrate up to 3 different expression plasmids by a single transformation step. Thus, a versatile system is at hand that allows a comparative assessment of newly introduced metabolic pathways in several organisms or a comparative co-expression of bottleneck genes in cases where production or secretion of a certain product is impaired.

New yeast expression platforms based on methylotrophic Hansenula polymorpha and Pichia pastoris and on dimorphic Arxula adeninivorans and Yarrowia lipolytica - a comparison

Yeasts combine the ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. Yeasts thus provide attractive platforms for the production of recombinant proteins. Here, four important species are presented and compared: the methylotrophic Hansenula polymorpha and Pichia pastoris, distinguished by an increasingly large track record as industrial platforms, and the dimorphic species Arxula adeninivorans and Yarrrowia lipolytica, not yet established as industrial platforms, but demonstrating promising technological potential, as discussed in this article.

Protein binding interactions at the STB locus of the yeast 2 microns plasmid

The cis-acting STB locus has been shown to be a multiple protein binding site. STB-specific binding activity was detected in a normally insoluble yeast cell protein fraction, suggesting association with a subcellular structure. Both 2 microns-encoded and host-encoded STB-binding activities were identified. The 2 microns proteins showed contrasting STB-binding activities: C (REP2) protein acted cooperatively with the host factor to promote STB binding; B (REP1) protein also acted in association with the host factor, but showed a dual action, opposing or facilitating binding, depending upon concentration; D (RAF) exhibited rapid binding and antagonism to host factor binding. FLP did not bind, but promoted host factor dissociation. The implications of these activities for the molecular mechanism of 2 microns plasmid inheritance are considered.

Use of a cis-acting mutation to study the role of FLP-mediated recombination in the maintenance of native yeast 2 micrometer plasmids

The 2 micrometer plasmid encodes a mechanism that ensures the partitioning of the plasmid at cell division. Little is known about the detailed mechanism of this partitioning system; for example, is there equal or unequal distribution of the plasmid molecules at mitosis? The plasmid also encodes a site-specific recombination system that is thought to be involved in plasmid copy-number amplification, although to date there has been no direct evidence that the recombination process itself is important for maintenance. We have identified a natural 2 micrometer variant that has a cis-acting mutation in the FLP-mediated recombination system. We show that this plasmid is unable to amplify in vivo. Our results demonstrate that the average copy number per cell is not affected for the mutant but there is a large clonal variation. This is a direct demonstration that plasmid partitioning results in an unequal distribution of plasmids and that FLP-mediated amplification compensates for this and therefore has an important role in maintenance.

Sensitivity to the Yeast Plasmid 2mu DNA is conferred by the nuclear allele nibl

Two strains of Saccharomyces carlsbergensis that lacked the plasmid 2mu DNA responded differently when the plasmid was introduced into them. In one strain, cells lacking 2mu DNA ("cir0") produced the normal "smooth" colony morphology, but cells bearing 2mu DNA ("cir+") produced heterogeneous "nibbled" colonies. In the second strain, both cir+ and cir0 strains exhibited a smooth colony morphology. Crosses between these strains revealed that a single recessive nuclear gene, called nibl, conferred the nibbled colony morphology in the presence of 2mu DNA. By a series of backcrosses, nibl was introduced into a Saccharomyces cerevisiae background. nibl caused a nibbled colony morphology in this background just as it did in S. carlsbergensis. nibl was mapped to the left arm of chromosome XVI. Twelve independent smooth revertants were isolated from two nibl [cir+] strains. Seven were analyzed, and all were found to be chromosome VII disomes. Chromosome VII disomy and suppression of the nibbled phenotype cosegregated in crosses. Thus, chromosome VII disomy can suppress the nibbled phenotype. The results of other experiments (C. Holm, Cell 29:585-594, 1982) indicate that the nibbled colony morphology is the result of lethal sectoring and that the lethality is caused by a high copy number of 2mu DNA. I suggest, therefore, that the product of the nibl gene may play a role in controlling the copy number of 2mu DNA. Possible models for the suppression of the nibbled phenotype by chromosome VII disomy are discussed.

Sensitivity to the Yeast Plasmid 2mu DNA is conferred by the nuclear allele nibl

Two strains of Saccharomyces carlsbergensis that lacked the plasmid 2mu DNA responded differently when the plasmid was introduced into them. In one strain, cells lacking 2mu DNA ("cir0") produced the normal "smooth" colony morphology, but cells bearing 2mu DNA ("cir+") produced heterogeneous "nibbled" colonies. In the second strain, both cir+ and cir0 strains exhibited a smooth colony morphology. Crosses between these strains revealed that a single recessive nuclear gene, called nibl, conferred the nibbled colony morphology in the presence of 2mu DNA. By a series of backcrosses, nibl was introduced into a Saccharomyces cerevisiae background. nibl caused a nibbled colony morphology in this background just as it did in S. carlsbergensis. nibl was mapped to the left arm of chromosome XVI. Twelve independent smooth revertants were isolated from two nibl [cir+] strains. Seven were analyzed, and all were found to be chromosome VII disomes. Chromosome VII disomy and suppression of the nibbled phenotype cosegregated in crosses. Thus, chromosome VII disomy can suppress the nibbled phenotype. The results of other experiments (C. Holm, Cell 29:585-594, 1982) indicate that the nibbled colony morphology is the result of lethal sectoring and that the lethality is caused by a high copy number of 2mu DNA. I suggest, therefore, that the product of the nibl gene may play a role in controlling the copy number of 2mu DNA. Possible models for the suppression of the nibbled phenotype by chromosome VII disomy are discussed.

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.

Intrachromosomal gene conversion in yeast

We have shown that the yeast Saccharomyces cerevisiae has a mechanism by which information from one gene can be transferred non-reciprocally to a repeated copy of the gene on the same chromosome. This intrachromosomal gene conversion may be important in maintaining sequence homogeneity within families of repeated eukaryotic genes.

Sequence of 863 nucleotides encompassing the PstI site of the yeast 2 micron plasmid

The sequence of part of the larger unique region of the yeast 2 micron plasmid cloned in pMB9 has been determined. The sequence extends from the single EcoRI site in this region to the AvaI site and includes the single PstI site and HpaI site. A notable feature of this sequence is the presence of tandem repeats of 124 residues beginning at the HpaI site and extending beyond the AvaI site. The sequence was determined independently by both the Maxam-Gilbert procedure applied to isolated restriction fragments, and by the chain-termination procedure applied to restriction fragments cloned in the single-stranded phage M13mp2 and purified by plaque selection.

Synthesis of a chicken ovalbumin-like protein in the yeast Saccharomyces cerevisiae

A cDNA sequence coding for chicken ovalbumin was fused to the beginning of the Escherichia coli lactose operon and recombined in vitro with a composite vector plasmid which can be propagated in both E. coli and Saccharomyces cerevisiae. Such plasmids direct the synthesis of an ovalbumin-like protein (OLP) in both microorganisms, probably because the E. coli lac regulatory region has some promoter activity in yeast. The yeast strains produce about 1 000 to 5 000 molecules of ovalbumin-like protein per cell.

Replication and recombination functions associated with the yeast plasmid, 2 mu circle

By examining both the transformation efficiency of yeast of various plasmids containing defined regions of the 2 mu circle genome and the characteristics of the resultant transformants, we have identified several regions of the 2 mu circle genome which are involved in 2 mu circle replication or recombination. First, by identifying those DNA fragments from the molecule which promote high frequency transformation of yeast, we have localized the origin of replication to a sequence partially within the large unique region, which, as determined by subsequent deletion analysis, extends from the middle of the inverted repeat region into the contiguous unique region. Second, by examining the relative efficiency of replication in yeast of hybrid plasmids containing either the entire 2 mu circle genome or a fragment of 2 mu circle encompassing the origin of replication, we have determined that efficient use of the 2 mu circle origin requires some function or functions encoded in the molecule at a site away from the origin. Third, by examining the ability of a mutant 2 mu circle molecule to undergo intramolecular recombination in yeast, we have identified a 2 mu circle gene which codes for a product required for this process.

Nucleotide sequence of the yeast plasmid

The nucleotide sequence of the yeast DNA plasmid (2 mu circle) from Saccharomyces cerevisiae strain A364A D5 has been determined. The plasmid contains 6,318 base pairs, including two identical inverted repeats of 599 base pairs. Possible functions are suggested, and attributes of an improved vector for cloning foreign DNAs in yeast are discussed.

Saccharomyces cerevisiae plasmid, Scp or 2 mum: intracellular distribution, stability and nucleosomal-like packaging

Cell fractions from yeast strains known to harbor the plasmic 2 mum or Scp were treated with nucleases used to probe eukaryotic chromosome structure. Scp and subfragments were identified by hybridization to natural or cloned Scp probes according to Southern (34). Specificity was confirmed with non-Scp probes. Copy/haploid nuclear genome(n) was estimated from reconstructions at a resolution of 0.5/n. About 43-67% of the total cellular copy exists as nucleoprotein complexes which separate from other debris on isokinetic sucrose gradients with s-values of 67-110. These complexes are totally degraded by DNAase I. Digestion with micrococcal nuclease produced integral-sized fragments; they are not generated by direct mixing of pure Scp with nuclear chromatin from a[cir] strain. Initial digests gave a repeat of 168 +/- 3 base pairs (bp) for both Scp and nuclear nucleoprotein; advanced digests reduced the nuclear repeat relative to Scp by 8 bp. Of a potential 37 repeat units/plasmid, 31-32 were directly measured. A strain difference in Scp autodegradation was found. A partial nuclease resistant form was also demonstrated whose abundance was cell strain and growth stage dependent. Both Scp isomers exist in these complexes which are structurally similar to simian viral 40 minichromosomes.

Identification and mapping of the transcriptional and translational products of the yeast plasmid, 2mu circle

We have identified two major and approximately ten minor poly(A)-containing RNA species in S. cerevisiae which arise from in vivo transcription of the yeast plasmid, known as 2mu circle. The two major species, which are 1325 and 1275 bases in length, are transcribed from the two unique halves of the plasmid and extend into the inverted repeat sequences which separate the unique regions. The map positions of the minor transcripts, which range in length from 350 to 2600 bases, indicate that except for a small region of the genome in which no transcription is observed, both strands of the entire 2mu circle genome are transcribed. We also present evidence demonstrating that RNA transcribed from 2mu circular DNA is used to program the synthesis of specific proteins in yeast: that is, yeast RNA complementary to 2mu circle DNA can be translated in vitro to produce specific polypeptides of substantial size. Finally, the pattern of transcription of 2mu circle suggests the possibility that messenger RNA species are derived by cleavage of larger transcripts, and in addition, that the intramolecular recombination of 2mu circle which occurs in yeast functions as a genetic switch to allow separate expression of two sets of genes on the 2mu circle genome.

Transformation of yeast by a replicating hybrid plasmid

Chimaeric plasmids have been constructed containing a yeast plasmid and fragments of yeast nuclear DNA linked to pMB9, a derivative of the ColEl plasmid from E. coli. Two plasmids were isolated which complement leuB mutations in E. coli. These plasmids have been used to develop a method for transforming a leu2 strain of S. cerevisiae to Leu+ with high frequency. The yeast transformants contained multiple plasmid copies which were recovered by transformation in E. coli. The yeast plasmid sequence recombined intramolecularly during propagation in yeast.

Regulation of gene expression by site-specific inversion

A site-specific inversion event is responsible for phase transition in Salmonella, as indicated by heteroduplex analysis of recombinant molecules carrying the gene coding for H2 flagellin in Salmonella. The inversion region corresponds to approximately 800 base pairs in length, and the inversion process does not appear to be dependent upon the E. coli RecA recombination pathway. Specific deletion derivatives of the cloned fragments no longer produce H2-specific flagella, effectively mapping the H2 gene within about 300 bp of the inversion region. Recombinant products of the hybrid molecules arose spontaneously, and they were used in the mapping of restriction sites within the inversion region. The restriction maps further demonstrate the extent and nature of the inversion.

Mapping of regions on cloned Saccharomyces cerevisiae 2-mum DNA coding for polypeptides synthesized in Escherichia coli minicells

Saccharomyces cerevisiae 2-mum DNA and some of its restriction fragments were integrated in vector pCR1 ,pBR313 or pBR322 and their expression in Escherichia coli P678-54 minicells was analyzed. 2mum DNA inserted at the EcoRI site of pCR1 or pBR313 and at the PstI site of pBR322 promoted the synthesis of polypeptides of 48,000, 37,000, 35,000 and 19,000 daltons. The DNA regions coding for these polypeptides were mapped on the 2-mum DNA molecule by insertion of single EcoRI or HindIII restriction fragments and comparison of the polypeptides produced. For the synthesis of the 37,000 dalton polypeptide, intact sites RIB and H3 were required. The disappearance of the 37,000 dalton polypeptide on interruption of one of these sites by insertion of the vector, was correlated with the appearance of a polypeptide of 22,000 or 23,500 daltons respectively. The DNA sequence coding for the 37,000 daltons polypeptide, therefore, has to be located in the S-loop region close to or overlapping with the site RIB and H3. Assuming that the 22,000 and the 23,500 dalton polypeptides are truncated forms of the 37,000 dalton polypeptide, the last polypeptide can be exactly mapped. The polypeptide of 48,000 daltons was mapped to that half of the L-loop segment containing the sites H1 and H2. If, however, HindIII fragment H1-H2 was expressed, the 48,000 dalton polypeptide was lost and concomitantly a 43,000 dalton polypeptide appeared. We assume that this polypeptide results from early termination of the polypeptide of 48,000 daltons. The 35,000 and 9,000 dalton polypeptides were mapped to the S-loop region. The integrated inverted repeat sequence of yeast 2-mum Dna did not induce any detectable insert-specific polypeptide synthesis.

Lambdoid phages that simplify the recovery of in vitro recombinants

Derivatives of phage lambda are described for use as vectors for fragments of DNA generated with the HindIII and EcoRI restriction enzymes. With some vectors, hybrid molecules are recognised by a change from a turbid to a clear plaque morphology resulting from the insertion of a fragment of DNA into the lambda gene coding for the phage regressor. Other vectors contain a central, replaceable fragment of DNA which imparts a readily recognisable phenotype. This central fragment may include either a gene for a mutant transfer RNA (suppressor) or a part of the lacZ gene of E. coli able to complement a lacZ host. The appropriate lacZ host and indicator plates permit the ready distinction between recombinant and vector phages by the colour of the plaques.