Heritable damage to yeast caused by transformation

Genetic modification and variations in solvent increase the sensitivity of the yeast RAD54-GFP genotoxicity assay

The yeast (Saccharomyces cerevisiae) RAD54-GFP DNA repair reporter assay (GreenScreen assay, GSA) can be used for early genotoxicity screening in drug discovery. During the initial validation of this preregulatory assay, a subset of known genotoxic compounds that did not give reproducibly clear positive GSA results was identified. Cell permeability, inherent drug resistance mechanisms, metabolic activation and compound solubility were identified as possible barriers to the detection of specific compounds. In this study three types of modification to the existing assay protocol were explored in order to address these possibilities: (i) modification of the reporter host strain by deletion of genes involved in cell wall integrity or with products functioning as efflux pumps (PDR5, ERG6, SNQ2, YOR1); (ii) expression in the host yeast of human phase I metabolic activation genes and (iii) variation in the test solvent system for compounds with poor aqueous solubility. The modifications described and the assay results presented show how the assay may be tailored to suit specific classes of test compound in a more analytical mode. Improvements in assay sensitivity were seen in the detection of some genotoxins using yeast cell wall mutants and those expressing human cytochrome P450 genes.

Rad51p and Rad54p, but not Rad52p, elevate gene repair in Saccharomyces cerevisiae directed by modified single-stranded oligonucleotide vectors

Synthetic single-stranded DNA vectors have been used to correct point and frameshift mutations in episomal or chromosomal targets in the yeast Saccharomyces cerevisiae. Certain parameters, such as the length of the vector and the genetic background of the organism, have a significant impact on the process of targeted gene repair, and point mutations are corrected at a higher frequency than frameshift mutations. Genetic analyses reveal that expression levels of the recombination/repair genes RAD51, RAD52 and RAD54 can affect the frequency of gene repair. Overexpression of RAD51 enhances the frequency 4-fold for correction of an episomal target and 5-fold for correction of a chromosomal target; overexpression of RAD54 is also effective in stimulating gene repair, to the same extent as RAD51 in the chromosomal target. In sharp contrast, RAD52 gene expression serves to reduce gene repair activity in rescue experiments and in experiments where RAD52 is overexpressed in a wild-type strain. This may suggest an antagonist role for Rad52p. Consistent with this notion, the highest level of targeted repair occurs when the RAD51 gene is overexpressed in a strain of yeast deficient in RAD52 gene function.

The isolation of strains of Saccharomyces cerevisiae showing altered plasmid stability characteristics by means of selective continuous culture

A recombinant strain of Saccharomyces cerevisiae containing a plasmid-encoded lacZ gene from Escherichia coli was grown for 420 generations under selective conditions in glucose-limited continuous culture. A ura3-based auxotrophic system was used to apply selection in favour of plasmid-containing organisms. A similar strategy had previously proved successful at evolving clones of Bacillus subtilis, showing improved plasmid stability characteristics. In this study a series of clones were isolated which exhibited large variation in their ability to retain the recombinant plasmid. Clones showed both significantly increased and reduced capacity to maintain the recombinant plasmid. The probabilities of obtaining clones in either category were essentially equal so that selection was not seen to enrich for more stable clones. Periodic selection events appeared to exert a greater influence on the distribution of stability characteristics amongst clones than did the applied selective pressure. Alterations in plasmid retention characteristics could be associated with host or plasmid. The most stable clone isolated exhibited a approximately 30% improvement of its overall stability (sigma(N+)) and an 80% improvement in productivity, when compared to the parental strain CGpLG. This improved stability was associated with alterations in the plasmid genome.

From gene to screen with yeast

With the complete sequence now available, the yeast genome project enters a post-sequencing phase that will concentrate on a comprehensive determination of gene function. Novel techniques have been developed to undertake genome-wide functional analysis at the levels of phenotype, transcript and protein. These include techniques for the efficient deletion of individual genes while tagging the deletants with specific oligonucleotide signatures, as well as strategies to quantify the physiological effects of such deletions by comparing growth rates and metabolite profiles under a range of conditions. Comprehensive approaches to the study of gene expression include hybridization array technology to identify and quantify transcripts, and the exploitation of mass spectometry to identify proteins resolved by two-dimensional gel electrophoresis. Yeast presents opportunities for the discovery of new human medicines both via the recognition of functional homologies between human and yeast genes and by the use of yeast to express human coding sequences specifying potential drug targets.

Breaking the barrier: methods for reversible permeabilization of cellular membranes

Plasma membrane constitutes a major barrier for the entry of hydrophilic molecules into the cell interior. Selective and reversible permeabilization of this barrier is a prerequisite for many biotechnological applications. This article reviews general principles of membrane permeabilization based on biological, chemical, and physical methods and mechanisms of the delivery of extrinsic substances to cell interior. The emphasis is given on the methods that have significantly contributed to our understanding of biological phenomena on membrane level or have been widely used in current biotechnology, such as delivery by membrane vehicles, electropermeabilization, microinjection, and biolistics. The mechanisms of the internalization of extrinsic substances and the advantages and drawbacks of individual techniques are discussed with respect to specific applications in biotechnology.

Analysis of metabolic control in vivo using molecular genetics

The aim of this brief review has been to illustrate the enormous power of molecular genetic techniques for testing out our, sometimes old, models of metabolic control. The technology allows us to ask some very simple but direct questions about the importance of specific enzymes in the control of flux. The answers, however, may not always be straightforward in that the absence of a change in pathway flux does not necessarily indicate that the enzyme is unimportant in flux control. Rather it would seem, from the relatively few studies that have been done, that the changes in the biological system which occur in response to a change in the concentration of a specific enzyme could tell us a lot about the role of that enzyme in metabolism and how it is controlled. I have restricted my discussion to studies in which relatively large numbers of cells have been modified genetically and subsequently characterized. This ignores a large and growing area in which micro-injection techniques are being used to introduce plasmid DNA or proteins into individual cells. The resultant phenotypes are then characterized at the single cell level using very sensitive optical techniques, such as fluorescence and bioluminescence. The reader is referred to a recent article for an example of this type of approach.

Toward a science of metabolic engineering

Application of recombinant DNA methods to restructure metabolic networks can improve production of metabolite and protein products by altering pathway distributions and rates. Recruitment of heterologous proteins enables extension of existing pathways to obtain new chemical products, alter posttranslational protein processing, and degrade recalcitrant wastes. Although some of the experimental and mathematical tools required for rational metabolic engineering are available, complex cellular responses to genetic perturbations can complicate predictive design.