Expression of plasmid R388-encoded type II dihydrofolate reductase as a dominant selective marker in Saccharomyces cerevisiae

An Overview on Selection Marker Genes for Transformation of Saccharomyces cerevisiae

For genetic manipulation of yeast, numerous selection marker genes have been employed. These include prototrophic markers, markers conferring drug resistance, autoselection markers, and counterselectable markers. This chapter describes the different classes of selection markers and provides a number of examples for different applications.

Detecting Protein-Protein Interaction Based on Protein Fragment Complementation Assay

Proteins are the most critical executive molecules by responding to the instructions stored in the genetic materials in any form of life. More frequently, proteins do their jobs by acting as a roleplayer that interacts with other protein(s), which is more evident when the function of a protein is examined in the real context of a cell. Identifying the interactions between (or amongst) proteins is very crucial for the biochemistry investigation of an individual protein and for the attempts aiming to draw a holo-picture for the interacting members at the scale of proteomics (or protein-protein interactions mapping). Here, we introduced the currently available reporting systems that can be used to probe the interaction between candidate protein pairs based on the fragment complementation of some particular proteins. Emphasis was put on the principles and details of experimental design. These systems are dihydrofolate reductase (DHFR), β-lactamase, tobacco etch virus (TEV) protease, luciferase, β- galactosidase, GAL4, horseradish peroxidase (HRP), focal adhesion kinase (FAK), green fluorescent protein (GFP), and ubiquitin.

Puromycin- and methotrexate-resistance cassettes and optimized Cre-recombinase expression plasmids for use in yeast

Here we expand the set of tools for genetically manipulating Saccharomyces cerevisiae. We show that puromycin-resistance can be achieved in yeast through expression of a bacterial puromycin-resistance gene optimized to the yeast codon bias, which in turn serves as an easy-to-use dominant genetic marker suitable for gene disruption. We have constructed a similar DNA cassette expressing yeast codon-optimized mutant human dihydrofolate reductase (DHFR), which confers resistance to methotrexate and can also be used as a dominant selectable marker. Both of these drug-resistant marker cassettes are flanked by loxP sites, allowing for their excision from the genome following expression of Cre-recombinase. Finally, we have created a series of plasmids for low-level constitutive expression of Cre-recombinase in yeast that allows for efficient excision of loxP-flanked markers.

An overview on selection marker genes for transformation of Saccharomyces cerevisiae

For genetic manipulation of yeast, numerous selection marker genes have been employed. These include prototrophic markers, markers conferring drug resistance, autoselection markers, and counterselectable markers. This chapter describes the different classes of selection markers and provides a number of examples for different applications.

Linking amyloid protein aggregation and yeast survival

Protein aggregation and amyloid formation lie behind an increasing number of human diseases. Here we describe the application of an "aggregation reporter", in which the test protein is fused to dihydrofolate reductase, as a general method to assess the intracellular solubility of amyloid proteins in eukaryotic background. Because the aggregation state of the target protein is linked directly to yeast cells survival in the presence of methotrexate, protein solubility can be monitored in vivo without the requirement of a functional assay for the protein of interest. In addition, the approach allows the in vivo visualization of the cellular location and aggregated state of the target protein. To demonstrate the applicability of the assay in the screening of genes or compounds that modulate amyloid protein aggregation in living cells, we have used as models the Alzheimer's amyloid β peptide, polyglutamine expansions of huntingtin, α-synuclein and non-aggregating variants thereof. Moreover, the anti-aggregational properties of small molecules and the effects of the yeast protein quality control machinery have also been evaluated using this method.

Transfer and expression of heterologous genes in yeasts other than Saccharomyces cerevisiae

In the past few years, yeasts other than those belonging to the genus Saccharomyces have become increasingly important for industrial applications. Species such as Pichia pastoris, Hansenula polymorpha, Schizosaccharomyces pombe, Yarrowia lipolytica and Kluyveromyces lactis have been modified genetically and used for the production of heterologous proteins. For a number of additional yeasts such as Schwanniomyces occidentalis, Zygosaccharomyces rouxii, Trichosporon cutaneum, Pachysolen tannophilus, Pichia guilliermondii and members of the genus Candida genetic transformation systems have been worked out. Transformation was achieved using either dominant selection markers based on antibiotic resistance genes or auxotrophic markers in conjunction with cloned biosynthetic genes involved in amino acid or nucleotide metabolism.

Use of mutated PDR3 gene as a dominant selectable marker in transformation of prototrophic yeast strains

For successful transformation of prototrophic industrial yeast strains dominant selectable markers are necessary. In the present study we show the applicability of a selection system based on the phenotype of multidrug resistance. The mutant pdr3-9 allele on centromeric or episomal vector, encoding a more efficient transcriptional activator with Y276H amino acid substitution, was used as a dominant selectable marker for selection of transformants. The pdr3-9 allele conferred resistance of transformed cells to cycloheximide, chloramphenicol, mucidin and oligomycin both in the absence and in the presence of a chromosomal copy of the PDR3 gene. Both multicopy YEp352/pdr3-9 and centromeric pFL38/pdr3-9 vectors bearing the mutant pdr3-9 allele have proved to be a valuable tool for a direct selection of transformants of industrial strains of Saccharomyces cerevisiae.

Cre/loxP-mediated in vivo excision of large segments from yeast genome and their amplification based on the 2microm plasmid-derived system

In vivo excision and amplification of pre-determined, large genomic segments, directly from the genome of a natural host, provides an alternative to conventional cloning in foreign vectors. Using this approach, we have devised an in vivo procedure for excising large segments of Saccharomyces cerevisiae genome using Cre/loxP system of bacteriophage P1, followed by amplification of excised circles, as based on the yeast 2microm plasmid-derived ori and Flp/FRT machinery. To provide the excision and replication enzymes, trans-acting genes cre and FLP, which were under a very tight control of GAL1 and GAL10 promoters, respectively, were inserted by homologous recombination into the URA3 gene on chromosome V. Two parallel loxP sequences, which serve as the recognition sites for the Cre recombinase, were also integrated into the genome at pre-determined sites that are 50-100kb apart. Moreover, 2microm ori, REP3 and two inverted FRTs, which serve as a conditional replication system, were also integrated between the loxP sites. The strain carrying all these inserted elements was perfectly stable. Only after the induction by galactose of the Cre excision function, the genomic segment flanked by two loxP sites was excised and circularized. Applying this procedure, the 50-kb LEU2-YCR011c and 100-kb LEU2-YCR035c regions of chromosome III were successfully excised from the S. cerevisiae genome, whereas the 2microm ori, as aided by FRT/Flp, provided the amplification function. Such excised and amplified genomic segments can be used for the sequencing and functional analysis of any yeast genes.

Expression cassettes for formaldehyde and fluoroacetate resistance, two dominant markers in Saccharomyces cerevisiae

We employed two genes in constructing yeast expression cassettes for dominant, selectable markers. The Saccharomyces cerevisiae gene SFA1, encoding formaldehyde dehydrogenase, was placed under the control of the GPD1 promoter and CYC1 terminator. The Moraxella sp. strain B gene dehH1, encoding fluoroacetate dehalogenase, was placed under the control of both the GPD1 and CYC1 promoters. With these constructs it was possible to select directly for yeast strains resistant to either formaldehyde or fluoroacetate. Both selective agents are completely metabolized and inexpensive, making them very useful in the pursuit of yeast gene functions and for industrial applications. An additional advantage of the formaldehyde dehydrogenase marker is that it is an S. cerevisiae gene, thus allowing 'all yeast' constructs.

Industrial production of heterologous proteins by fed-batch cultures of the yeast Saccharomyces cerevisiae

This review concerns the issues involved in the industrial development of fed-batch culture processes with Saccharomyces cerevisiae strains producing heterologous proteins. Most of process development considerations with fed-batch recombinant cultures are linked to the reliability and reproducibility of the process for manufacturing environments where quality assurance and quality control aspects are paramount. In this respect, the quality, safety and efficacy of complex biologically active molecules produced by recombinant techniques are strongly influenced by the genetic background of the host strain, genetic stability of the transformed strain and production process factors. An overview of the recent literature of these culture-related factors is coupled with our experience in yeast fed-batch process development for producing various therapeutic grade proteins. The discussion is based around three principal topics: genetics, microbial physiology and fed-batch process design. It includes the fundamental aspects of yeast strain physiology, the nature of the recombinant product, quality control aspects of the biological product, features of yeast expression vectors, expression and localization of recombinant products in transformed cells and fed-batch process considerations for the industrial production of Saccharomyces cerevisiae recombinant proteins. It is our purpose that this review will provide a comprehensive understanding of the fed-batch recombinant production processes and challenges commonly encountered during process development.

Expression and secretion of Bacillus amyloliquefaciens alpha-amylase by using the yeast pheromone alpha-factor promoter and leader sequence in Saccharomyces cerevisiae

Replacement of the regulatory and secretory signals of the alpha-amylase gene (AMY) from Bacillus amylolique-faciens with the complete yeast pheromone alpha-factor prepro region (MF alpha 1p) resulted in increased levels of extracellular alpha-amylase production in Saccharomyces cerevisiae. However, the removal of the (Glu-Ala)2 peptide from the MF alpha 1 spacer region (Lys-Arg-Glu-Ala-Glu-Ala) yielded decreased levels of extracellular alpha-amylase.

Synthesis and secretion of an Erwinia chrysanthemi pectate lyase in Saccharomyces cerevisiae regulated by different combinations of bacterial and yeast promoter and signal sequences

Nine different expression-secretion cassettes, comprising novel combinations of yeast and bacterial gene promoters and secretion signal sequences, were constructed and evaluated. A pectate lyase-encoding gene (pelE) from Erwinia chrysanthemi was inserted between each one of these expression-secretion cassettes and a yeast gene terminator, generating recombinant yeast-integrating shuttle plasmids pAMS1 through pAMS9. These YIp5-derived plasmids were transformed and stably integrated into the genome of a laboratory strain of Saccharomyces cerevisiae, and the pectate lyase production was monitored. Transcription initiation signals for pelE expression were derived from the yeast alcohol dehydrogenase (ADC1P), the yeast mating pheromone alpha-factor (MF alpha 1P) and the Bacillus amyloliquefaciens alpha-amylase (AMYP) gene promoters. The transcription termination signals were derived from the yeast tryptophan synthase gene terminator (TRP5T). Secretion of pectate lyase (PLe) was directed by the signal sequences of the yeast mating pheromone alpha-factor (MF alpha 1S), B. amyloliquefaciens alpha-amylase (AMYS) and Er. chrysanthemi pectate lyase (pelES). The ADC1P-MF alpha 1S expression-secretion system proved to be the most efficient control cassette for the expression of pelE and the secretion of PLe in S. cerevisiae.

The yeast heat shock transcription factor contains a transcriptional activation domain whose activity is repressed under nonshock conditions

Transcription of heat shock genes is induced by exposure of cells to elevated temperatures or other stress conditions. In yeast, it is thought that induction of transcription is mediated by conversion of a DNA-bound transcriptionally inactive form of the heat shock transcription factor (HSTF) to a DNA-bound transcriptionally active form. We have identified domains in HSTF involved in transcriptional activation and in repression of transcriptional activation at non-shock temperatures. We present evidence that a temperature-regulated transcriptional activation domain exists in HSTF and that this domain is essential for survival of yeast cells at heat shock temperatures. We propose a model for temperature-regulated transcriptional activation by a derepression mechanism.

Yeast 2 micron vectors replicate and undergo recombination in Torulaspora delbrueckii

In order to develop a procedure for transformation of the industrial yeast Torulaspora delbrueckii, we have constructed a set of recombinant plasmids carrying Saccharomyces cerevisiae ARS and 2 microns origin of replication and kanamycin-G418 resistance gene of Tn903(601) as a selective marker. In this paper we show that S. cerevisiae ARS vectors can replicate autonomously and that vectors bearing the whole S. cerevisiae 2 microns sequence yield stable transformants. We also present evidence to show that 2 microns vectors undergo an FLP-mediated inter- and intramolecular recombination, which suggests that T. delbrueckii can support the amplification and partition mechanisms of these plasmids.

Regulated secretion of MuGM-CSF in Saccharomyces cerevisiae via GAL1:MF alpha 1 prepro sequences

Murine granulocyte-macrophage colony-stimulating factor (GM-CSF) was expressed in Saccharomyces cerevisiae using a novel regulated secretion system. This system involves the fusion of the GAL1 upstream regulatory region to the signal sequence of the alpha mating pheromone, and the integration of this GAL1:MF alpha 1 prepro:MuGM-CSF construct into the yeast chromosome. These constructs were very stable under both selective and nonselective conditions: after 30 generations of growth no plasmid loss was observed. The expression and secretion of MuGM-CSF were analyzed by biological assays and Western blots of yeast culture medium and yeast cell extracts. Expression of MuGM-CSF was regulated by galactose induction. In addition, expression levels were proportional to the number of tandem copies of the gene inserted into the yeast chromosome.

Amplification of plasmid copy number by thymidine kinase expression in Saccharomyces cerevisiae

A 2 micron circle-based chimaeric plasmid containing the yeast LEU2 and the Herpes Simplex Virus type 1 thymidine kinase (HSV-1 TK) genes was constructed. Transformants grown under selective conditions for the LEU2 gene harboured the plasmid at about 15 copies per cell whilst selection for the HSV-1 TK gene led to an increase to about 100 copies per cell. Furthermore, the plasmid copy number could be controlled by the stringency of selection for the TK gene, and the increase in TK gene dosage was reflected in an increase in intracellular thymidine kinase activity. The mitotic stability of the plasmid in "high-copy" and "low-copy" number cells was determined. "High-copy" number cells showed a greater mitotic stability. The relationship of TK expression to plasmid copy number may be useful for the isolation of plasmid copy number mutants in yeast and the control of heterologous gene expression.

Cloning in Saccharomyces cerevisiae of a cycloheximide resistance gene from the Candida maltosa genome which modifies ribosomes

We have previously shown that cycloheximide resistance can be induced in a strain of Candida maltosa by modifying ribosomes (M. Takagi, S. Kawai, Y. Takata, N. Tanaka, M. Sunairi, M. Miyazaki, and K. Yano, J. Gen. Appl. Microbiol. 31:267-275, 1985). The present paper describes the cloning of the gene involved in this resistance (designated RIM-C for ribosome modification by cycloheximide) by using a host-vector system of Saccharomyces cerevisiae.

Construction of stable laboratory and industrial yeast strains expressing a foreign gene by integrative transformation using a dominant selection system

An expression cassette of mouse dihydrofolate reductase (Mdhfr) cDNA under control of the yeast cytochrome c promoter was inserted in a yeast plasmid containing the ARS1 sequence. The ARS replicating function was destroyed by BglII treatment prior to yeast transformation. Using this linearized plasmid, genomic transformants could be obtained from either laboratory or industrial strains of bakers' yeast based on direct methotrexate (MTX)-resistance selection. The entire sequence of the linearized plasmid was integrated by homologous recombination at the ARS region of the host chromosome. The results indicate that repetitive and homologous recombination occurs readily in such transformations. The stability of the constructed integrants was more than 99.95% per generation in non-selective medium, and tandem repeats of up to six copies (i.e., about 44 kb) were not changed even after 30 generations in rich medium. Expression in rich medium of cointegrated, human interleukin 2 cDNA under control of the triose phosphate isomerase promoter was shown by Western blot experiments in both laboratory and industrial yeast strains. Furthermore, a comparison of the transcription efficiency of the Mdhfr gene in the chromosome with that in the plasmid revealed that the efficiency was almost proportional to the number of gene copies, irrespective of the location of the transcription unit. These results show that by using the MTX/Mdhfr dominant selection-amplification system one can construct stable recombinant yeast strains suitable for heterologous gene expression in laboratory as well as in industrial fermentation conditions.

Use of bacterial DHFR-II fusion proteins to elicit specific antibodies

Plasmids containing the coding region of the type II dihydrofolate reductase (DHFR) specified by R388 have been used to alter the amino acid (aa) sequence at the C-terminus of this protein. These plasmids have a unique cloning site in the C-terminal portion of the 78-aa coding region. Insertions of DNA fragments into this site produced plasmids that code for proteins with 6- to 80-aa extensions. The vectors were constructed to terminate translation in all three phases beyond the position of insertion of foreign DNA. Random DNA fragments from the major sperm protein (MSP) gene of Caenorhabditis elegans produced by DNase I cleavage were inserted into these vectors. Cell extracts from colonies containing MSP sequences were examined by gel electrophoresis and immunoblotting. One of the hybrid DHFR-MSP proteins was isolated and antibody was prepared to it. This antibody preparation reacted with MSP in immunoblots of purified MSP and whole cell extracts of the worm. A rapid purification procedure for the DHFR is presented.

Restriction enzyme map of cryptic plasmid accompanying pR711b and pR409; identity of pR409 and pR388

A reference strain containing the IncW plasmid, pR409, was found to contain also a cryptic, conjugative plasmid, here named pJR15. After the separation of the two plasmids into different strains of bacteria, pR409 was found to have an identical restriction enzyme map to the IncW plasmid, pR388. Both pR409 and pR388 were isolated from the same hospital in London and confer sulphonamide and trimethoprim resistance. Originally pR409 was reported to confer resistance to tetracycline, but this was not confirmed by the Plasmid Reference Center. pR409 appears to represent another isolate of pR388 in a different host background. The restriction enzyme map of the cryptic plasmid, pJR15 (39 kb), has been determined. pJR15 was found compatible with plasmids from 15 different incompatibility groups and has been found also in the reference strain of the IncD plasmid, pR711b. The HindIII and BglII digests of pR711b are shown. The possible presence of the conjugative plasmid, pJR15, should be examined for studies on the sex pili or chromosomal mobilization properties of pR711b.