Real-time flow cytometric quantification of GFP expression and Gfp-fluorescence generation in Saccharomyces cerevisiae

Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

The relationship between co-fitness and co-inhibition of genes in chemicogenomic yeast screens provides insights into gene function and drug target prediction.

We systematically analyzed the relationships between gene fitness profiles (co-fitness) and drug inhibition profiles (co-inhibition) from several hundred chemogenomic screens in yeast. Co-fitness predicted gene functions distinct from those derived from other assays and identified conditionally dependent protein complexes. Co-inhibitory compounds were weakly correlated by structure and therapeutic class. We developed an algorithm predicting protein targets of chemical compounds and verified its accuracy with experimental testing. Fitness data provide a novel, systems-level perspective on the cell.

Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways

The dynamic features of a genetic network's response to environmental fluctuations represent essential functional specifications and thus may constrain the possible choices of network architecture and kinetic parameters. To explore the connection between dynamics and network design, we have analyzed a general regulatory architecture that is commonly found in many metabolic pathways. Such architecture is characterized by a dual control mechanism, with end product feedback inhibition and transcriptional regulation mediated by an intermediate metabolite. As a case study, we measured with high temporal resolution the induction profiles of the enzymes in the leucine biosynthetic pathway in response to leucine depletion, using an automated system for monitoring protein expression levels in single cells. All the genes in the pathway are known to be coregulated by the same transcription factors, but we observed drastically different dynamic responses for enzymes upstream and immediately downstream of the key control point—the intermediate metabolite α-isopropylmalate (αIPM), which couples metabolic activity to transcriptional regulation. Analysis based on genetic perturbations suggests that the observed dynamics are due to differential regulation by the leucine branch-specific transcription factor Leu3, and that the downstream enzymes are strictly controlled and highly expressed only when αIPM is available. These observations allow us to build a simplified mathematical model that accounts for the observed dynamics and can correctly predict the pathway's response to new perturbations. Our model also suggests that transient dynamics and steady state can be separately tuned and that the high induction levels of the downstream enzymes are necessary for fast leucine recovery. It is likely that principles emerging from this work can reveal how gene regulation has evolved to optimize performance in other metabolic pathways with similar architecture.

Single-cell organisms must constantly adjust their gene expression programs to survive in a changing environment. Interactions between different molecules form a regulatory network to mediate these changes. While the network connections are often known, figuring out how the network responds dynamically by looking at a static picture of its structure presents a significant challenge. Measuring the response at a finer time scales could reveal the link between the network's function and its structure. The architecture of the system we studied in this work—the leucine biosynthesis pathway in yeast—is shared by other metabolic pathways: a metabolic intermediate binds to a transcription factor to activate the pathway genes, creating an intricate feedback structure that links metabolism with gene expression. We measured protein abundance at high temporal resolution for genes in this pathway in response to leucine depletion and studied the effects of various genetic perturbations on gene expression dynamics. Our measurements and theoretical modeling show that only the genes immediately downstream from the intermediate are highly regulated by the metabolite, a feature that is essential to fast recovery from leucine depletion. Since the architecture we studied is common, we believe that our work may lead to general principles governing the dynamics of gene expression in other metabolic pathways.

A quantitative, high-temporal resolution study of gene induction in a metabolic pathway reveals an intricate connection between the regulatory architecture and the dynamic response of the system, pointing to possible principles underlying the design of these pathways.

In vivo optimizing of intracellular production of heterologous protein in Pichia pastoris by fluorescent scanning

Specific monitoring of recombinant protein titer in DNA recombinant biotechnology traditionally has relied on SDS-PAGE, Western blotting, or bioactivity-based assays, but these are labor-intensive, time-consuming, and destructive and are not a good choice for the optimization of recombinant protein production. We describe a study in which enhanced green fluorescence protein (EGFP) was fused to the C terminus of a model protein glutathione S-transferase (GST) to optimize the chimeric protein production in Pichia pastoris by measurements of fluorescence of living cells in a 96-well microtiter plate using simple fluorescent scanning. Several common factors (e.g., time course of expression, effect of methanol concentration, frequency of methanol addition, medium pH) were tested using this strategy. Western blotting assay showed that the correct full-length GST-EGFP chimeric protein was expressed intracellularly in P. pastoris. The fluorescence intensity and GST bioactivity of cell extract yielded a direct correlation. The results show that the reported method provides an attractive platform for the optimization of recombinant protein production in vivo in real time as well as handling at least 96 samples in parallel.

Production of hantavirus Puumala nucleocapsid protein in Saccharomyces cerevisiae for vaccine and diagnostics

The production of hantavirus Puumala nucleocapsid (N) protein for potential applications as a vaccine and for diagnostic purposes was investigated with Saccharomyces cerevisiae as a recombinant host. The N protein gene and the hexahistidine tagged N (h-N) protein gene were expressed intracellular from a 2-microm plasmid vectors under the control of a fused galactose inducible GAL10-PYK promoter. For monitoring the recombinant gene expression, a h-N and a GFP fusion protein was used. Different cultivation strategies and growth media compositions were tested in shake flasks and a 5 l bioreactor. When using defined YNB growth medium, we found the biomass yield to be unsatisfactorily low. Higher concentrated YNB medium, promoted cell growth but showed a pronounced inhibitory effect on heterologous gene expression. This phenomenon could not be attributed to plasmid losses, as we could demonstrate high stability of the vector under the applied cultivation conditions. Supplementation of YNB medium with extracts of plant origin resulted in increased biomass yields with concomitant high expression levels of the recombinant gene. The modified medium was used for fed-batch cultivations where basic metabolic features as well as growth parameters were determined in addition to recombinant gene expression. The maximal volumetric yield of N protein was 316 mg l(-1), the respective yield of h-N protein was 284 mg l(-1). Our study provides a basis for large-scale production of hantavirus vaccines, which satisfies economic efficiency as well as biosafety regulations for human applications.

A novel GAL recombinant yeast strain for enhanced protein production

A novel strain of Saccharomyces cerevisiae in which the GAL1 gene was replaced with the GAL4 gene has been designed. The GAL1 gene encodes galactokinase (Gal1p), an enzyme that phosphorylates galactose. Gal4p activates genes necessary for galactose metabolism and is among the best characterized transcription activators. Here we describe a GAL recombinant strain that contains the GAL4 gene fused to the natural GAL1 promoter in addition to the normal constitutively expressed chromosomal GAL4 gene. To evaluate whether both gratuitous induction and regulated overexpression of the positive regulator improve protein production, low- and multi-copy expression vectors containing the GAL1 promoter fused to the structural gene for green fluorescent protein (GFP) were introduced into wild-type, gal1 and GAL recombinant strains. In yeast containing the multi-copy plasmid there was an approximately 3.3-fold increase in GFP production in the gal1 mutant strain. Moreover, in the resulting GAL recombinant cells a 4.6-fold increase in fluorescence relative to the wild-type was observed. The GAL recombinant strain should therefore prove useful for maximal expression of heterologous genes driven by a galactose-inducible promoter.

Fluorescence based assay ofGALsystem in yeastSaccharomyces cerevisiae

The GAL1 promoter is one of the strongest inducible promoters in the yeast Saccharomyces cerevisiae. In order to improve recombinant protein production we have developed a fluorescence based method for screening and evaluating the contribution of various gene deletions to protein expression from the GAL1 promoter. The level of protein synthesis was determined in 28 selected mutant strains simultaneously, by direct measurement of fluorescence in living cells using a microplate reader. The highest, 2.4-fold increase in GFP production was observed in a gal1 mutant strain. Deletion of GAL80 caused a 1.3-fold increase in fluorescence relative to the isogenic strain. GAL3, GAL4 and MTH1 gene deletion completely abrogated GFP synthesis. Growth of gal7, gal10 and gal3 also exhibited reduced fitness in galactose medium. Other genetic perturbations affected the GFP expression level only moderately. The fluorescence based method proved to be useful for screening genes involved in GAL1 promoter regulation and provides insight into more efficient manipulation of the GAL system.

Single-cell variability in growing Saccharomyces cerevisiae cell populations measured with automated flow cytometry

Cell cultures normally are heterogeneous due to factors such as the cell cycle, inhomogeneous cell microenvironments, and genetic differences. However, distributions of cell properties usually are not taken into account in the characterization of a culture when only population averaged values are measured. In this study, the cell size, green fluorescence protein (Gfp) content, and viability after automated staining with propidium iodide (PI) are monitored at the single-cell level in Saccharomyces cerevisiae cultures growing in a batch bioreactor using an automated flow injection flow cytometer system. To demonstrate the wealth of information that can be obtained with this system, three cultures containing three different plasmids are compared. The first plasmid is a centromeric plasmid expressing under the control of a TEF2 promoter the S65T mutant form of Gfp. The other two plasmids are 2 microm plasmids and express the FM2 mutant of Gfp under the control of either the TEF1 or the TEF2 promoter. The automated sampling, cell preparation, and analysis permitted frequent quantification of the culture characteristics. The time course of the data representing not only population average values but also their variability, provides a detailed and reproducible "fingerprint" of the culture dynamics. The data demonstrate that small changes in the genetic make up of the recombinant system can result in large changes in the culture Gfp production and viability. Thus, the developed instrumentation is valuable for rapidly testing promoter strength, plasmid stability, cell viability, and culture variability.

Evaluation of the GFP signal and its aptitude for novel on-line monitoring strategies of recombinant fermentation processes

A high number of economically important recombinant proteins are produced in Escherichia coli based host/vector systems. The major obstacle for improving current processes is a lack of appropriate on-line in situ methods for the monitoring of metabolic burden and critical state variables. Here, a pre-evaluation of the reporter green fluorescent protein (GFP) was undertaken to assess its use as a reporter of stress associated promoter regulation. The investigation of GFP and its blue fluorescent variant BFP was done in model fermentations using E. coli HMS 174(DE3)/pET11 aGFPmut3.1 and E. coli HMS174(DE3)/pET1aBFP host/vector systems cultured in fed-batch and chemostat regime. Our results prove the suitability of the fluorescent reporter proteins for the design of new strategies of on-line bioprocess monitoring. GFPmut3.1 variant can be detected after a short lag-phase of only 10 min, it shows a high fluorescence yield in relation to the amount of reporter protein, a good signal to noise ratio and a low detection limit. The fluorescence-signal and the amount of fluorescent protein, determined by ELISA, showed a close correlation in all fermentations performed. A combination of reporter technology with state of the art sensors helps to develop new strategies for efficient on-line monitoring needed for industrial process optimisation. The development of efficient monitoring will contribute to advanced control of recombinant protein production and accelerate the development of optimised production processes.

Nucleo-mitochondrial interactions in Saccharomyces cerevisiae: characterization of a nuclear gene suppressing a defect in mitochondrial tRNA(Asp) processing

We utilized the heat-sensitive mutant strain (Ts932), bearing a mutation at position 61 in the mitochondrial tRNA(Asp) gene, to identify nuclear genes involved in tRNA biogenesis; this mutant is defective in 3'-end processing and consequently in the production of mature mitochondrial tRNA(Asp). We transformed this strain with a yeast nuclear library and we isolated among other suppressors, an unknown, non-essential gene (called SMM1, corresponding to open reading frame YNR015w), which restored the growth on glycerol and a normal amount of processed tRNA(Asp) in the mutant. The gene contains a domain highly conserved in evolution from bacteria to human and its product has been recently shown to have dihydrouridine synthase activity.

Heterogeneity of stress gene expression and stress resistance among individual cells of Saccharomyces cerevisiae

Knowledge of gene expression and cellular responses in microorganisms is derived from analyses of populations consisting of millions of cells. Analytical techniques that provide data as population averages fail to inform of culture heterogeneity. Flow cytometry and fluorescence techniques were used to provide information on the heterogeneity of stress-responsive gene expression and stress tolerance in individual cells within populations. A sequence of DNA encoding the heat shock and stress response elements of the Saccharomyces cerevisiae HSP104 gene was used to express enhanced green fluorescent protein (EGFP). When integrated into the genome of yeast strain W303-1A, intrinsic expression of EGFP increased about twofold as cells progressed from growth on glucose to ethanol utilization in aerobic batch cultures. Staining of cells with orange/red fluorescent propidium iodide (PI), which only enters cells that have compromised membrane integrity, revealed that the population became more tolerant to 52 degrees C heat stress as it progressed from growth on glucose and through the ethanol utilization phase of aerobic batch culture. Exposure of cultures growing on glucose to a mild heat shock (shift from 25 degrees C to 37 degrees C) resulted in significantly increased expression of EGFP in the population. However, there was heterogeneity in the intensity of fluorescence of individual cells from heat-shocked cultures, indicating variability in the strength of stress response in the clonal population. Detailed analysis of the heterogeneity showed a clear positive trend between intensity of stress response and individual cell resistance, measured in terms of PI exclusion, to heat stress at 52 degrees C. Further experiments indicated that, although the mean gene expression by a population is influenced by the genetic background, the heterogeneity among individual cells in clonal populations is largely physiologically based.

Microbial analysis at the single-cell level: tasks and techniques

The heterogeneity of microorganisms themselves is orders of magnitude greater than the heterogeneity of perspectives from which they are contemplated by human observers. Even closely related species may exhibit marked differences in biochemistry and behavior, and, under many conditions, similar, striking heterogeneity may exist within a clonal population of organisms which, in the aggregate, occupy too small a region of space to be visible to the unaided human eye. Using methods of microscopy, microspectrophotometry, and cytometry developed and refined since the 1960s, it is now possible to characterize the physiology and pharmacology of individual microorganisms, and, in many cases, to isolate organisms with selected characteristics for culture and/or further analysis. These methods include fluorescent and confocal microscopy, scanning and image cytometry, and flow cytometry. Fluorescence measurements are particularly important in single-cell analysis; they allow demonstration and quantification of cells' nucleic acid content and sequence, of the presence of specific antigens, and of physiologic characteristics such as enzyme activity and membrane potential. Multiparameter cytometry, combined with cell sorting, provides insight into population heterogeneity and allows selected cells to be separated for further analysis and culture. The technology is applicable to a wide range of problems in contemporary microbiology, including strain selection and the development of antimicrobial agents.