A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae

Background Saccharomyces cerevisiae is an important synthetic biology chassis for microbial production of valuable molecules. Promoter engineering has been frequently applied to generate more synthetic promoters with a variety of defined characteristics in order to achieve a well-regulated genetic network for high production efficiency. Galactose-inducible (GAL) expression systems, composed of GAL promoters and multiple GAL regulators, have been widely used for protein overexpression and pathway construction in S. cerevisiae. However, the function of each element in synthetic promoters and how they interact with GAL regulators are not well known. Results Here, a library of synthetic GAL promoters demonstrate that upstream activating sequences (UASs) and core promoters have a synergistic relationship that determines the performance of each promoter under different carbon sources. We found that the strengths of synthetic GAL promoters could be fine-tuned by manipulating the sequence, number, and substitution of UASs. Core promoter replacement generated synthetic promoters with a twofold strength improvement compared with the GAL1 promoter under multiple different carbon sources in a strain with GAL1 and GAL80 engineering. These results represent an expansion of the classic GAL expression system with an increased dynamic range and a good tolerance of different carbon sources. Conclusions In this study, the effect of each element on synthetic GAL promoters has been evaluated and a series of well-controlled synthetic promoters are constructed. By studying the interaction of synthetic promoters and GAL regulators, synthetic promoters with an increased dynamic range under different carbon sources are created.

Cellular heterogeneity and MTH1 play key roles in galactose mediated signaling of the GAL switch to utilize the disaccharide melibiose

Yeast metabolizes the disaccharide melibiose by hydrolyzing it into equimolar concentrations of glucose and galactose by MEL1-encoded α-galactosidase. Galactose metabolizing genes (including MEL1) are induced by galactose and repressed by glucose, which are the products of melibiose hydrolysis. Therefore, how melibiose catabolization and utilization take place by circumventing the glucose repression is an enigma. Other than the galactose metabolizing genes MTH1, a negative regulator of glucose signal pathway has Gal4p binding sites and is induced by galactose and repressed by high glucose concentration. But, at low or no glucose MTH1 along with its paralogue STD1 represses hexose transporters, that are involved in glucose transport. This sort of tuning of glucose and galactose regulation motivated us to delineate the role of MTH1 as a regulator of MEL1 expression and melibiose utilization. The deletion mutant of MTH1 shows growth defect on melibiose and this growth defect is enhanced upon the deletion of both MTH1 and its paralogue STD1. Microscopy and flowcytometry analysis, suggest, that even though MEL1 and GAL1 promoter are under Gal4p and Gal80p regulation, upon deletion of MTH1 it hampers only MEL1 expression, but not the GAL1 gene expression. By using 2-Deoxy galactose toxicity assay, we observed phenotypic heterogeneity in cells grown on melibiose i.e. after cleaving of melibiose a fraction of cell population utilizes glucose and another fraction utilizes galactose and coexist together. Understanding GAL/MEL gene expression patterns in melibiose will have great implication to understand various other complex sugar utilizations, tunable gene expressions and complex feedback gene regulations.

Human VAMP3 Suppresses or Negatively Regulates Bax Induced Apoptosis in Yeast

Apoptosis is an essential process that is regulated genetically and could lead to a serious disease condition if not well controlled. Bax is one of the main proapoptotic proteins and actively involved in programmed cell death. It has been suggested that Bax induced apoptosis in yeast could be obstructed by enhancing vesicular membrane trafficking. Plasma membrane proteins and lipid oxidation were reduced by a vesicle-associated membrane protein (VAMP) when expressed in yeast, suggesting its potential role in repairing membranes. Membrane integrity is crucial, as the loss of membrane integrity will result in the leakage of ions from mitochondria, and ultimately cell death due to overproduction of reactive oxygen species (ROS). Expression of Arabidopsis’ VAMP has been linked to antiapoptosis activity. Since plant VAMP has been associated with antiapoptotic activities, this study investigates the possible participation of human VAMP3 in blocking human Bax mediated apoptosis. Some novel genes were identified to rescue Bax’s proapoptotic effects, in a yeast-based human hippocampal cDNA library screen. VAMP3 (a gene code for proteins involved in protein secretion) gene was chosen for further study to confirm its role in inhibiting apoptosis. VAMP3 was coexpressed with a chromosomally integrated Bax gene expression cassette driven by the GAL1 promoter. The antiapoptotic proteins of the Bcl-2 family (Bcl xL) were known to negate the proapoptotic properties of Bax. However, the new gene (VAMP3) results show that novel antiapoptotic proteins can be identified using a yeast-based assay. The findings presented here show that human VAMP3 protein has antiapoptotic property and could abrogate Bax induced apoptosis (cell death).

Apoptosis, Induced by Human α-Synuclein in Yeast, Can Occur Independent of Functional Mitochondria

Human α-synuclein expression in baker’s yeast reportedly induces mitochondria-dependent apoptosis. Surprisingly, we find that, under de-repressing conditions of the inducible MET25/GAL1 promoters, yeast cells expressing chromosomally-integrated copies of the human α-synuclein gene are not killed, but spontaneously form respiration-deficient rho-minus (ρ−) petites. Although yeast cells can undergo cell death (apoptosis) from loss of mitochondrial function, they can also survive without functional mitochondria. Such cells are referred to as ρ0 or ρ− petites. This study reports that minimal expression of human α-synuclein in yeast, from MET25/GAL1 promoter, gives rise to ρ− petites. Interestingly, the full expression of α-synuclein, from the same promoters, in α-synuclein-triggered ρ− petites and also in ρ0 petites (produced by treating ρ+ cells with the mutagen ethidium bromide) initiates apoptosis. The percentages of petites increase with increasing α-synuclein gene copy-number. ρ− petites expressing α-synuclein from fully-induced MET25/GAL1 promoters exhibit increased ROS levels, loss of mitochondrial membrane potential, and nuclear DNA fragmentation, with increasing copies of α-synuclein. Our results indicate that, for the first time in yeast, α-synuclein-triggered apoptosis can occur independently of functional mitochondria. The observation that α-synuclein naturally forms petites and that they can undergo apoptosis may have important implications in understanding the pathogenesis of Parkinson’s disease.

Identification of proteins involved in transcription/translation (eEF 1A1) as an inhibitor of Bax induced apoptosis

Eukaryotic elongation factor 1A1 (eEF1A1) is central to translational activity. It is involved in complexes that form signal transduction with protein kinase C, as well as being a signal transducer and activator of transcription 3. eEF1A1 and eEF1A2 are isoforms of the alpha subunit of elongating factor 1 complex. It has been reported that eEF1A1 is expressed in most human tissues but the brain, skeletal muscle and heart. eEF1A1 has been linked to both apoptosis and anti-apoptotic activities. In this study, eEF1A1 was co-expressed with Bax, a proapoptotic protein via heterologous expression of recombinant DNA in yeast cells. Assays were carried out to monitor the fate and state of yeast cells when eEF1A1 was co-expressed with Bax. The yeast strain (bearing an integrated copy of the Bax gene) was transformed with an episomal 2-micron plasmid that encodes HA-tagged eEF1A1 gene. The resultant strain would allow co-expression of Bax and eEF1A1 in yeast cells, Bax being under the control of the GAL1 promoter, while the PGK1 promoter drives eEF1A1 expression. Bcl 2A1, a known anti-apoptotic protein, was also co-expressed with Bax in yeast cells as a positive control, to study the anti-apoptotic characteristic of eEF-1A1. The part eEF1A1 plays in apoptosis has been contentious, amidst the pro and anti-apoptotic properties of eEF1A1, it was shown clearly, in this study that eEF1A1 portrays only anti-apoptotic property in the presence of pro-apoptotic protein, Bax.

Cell-size regulation in budding yeast does not depend on linear accumulation of Whi5

Cells must couple cell-cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at a smaller size. We tested this model using the inducibleGAL1promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous andGAL1promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings indicate that size control in budding yeast does not fundamentally originate from the linear accumulation of Whi5, contradicting a previous claim and demonstrating the need for further models of cell-cycle regulation to explain how cell size controls passage through Start.

Cell size regulation in budding yeast does not depend on linear accumulation of Whi5

Cells must couple cell cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at smaller size. We tested this model using the inducible GAL1 promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous and GAL1 promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings contradict the previously proposed model for cell size control in budding yeast and demonstrate the need for a molecular mechanism that explains how cell size controls passage through Start.Author ContributionsFB performed the experiments, data analysis and simulations. All authors designed the experiments and wrote the manuscript.Significance StatementDespite decades of research, the question of how single cells regulate their size remains unclear. Here we demonstrate that a widely supported molecular model for the fundamental origin of size control in budding yeast is inconsistent with a set of experiments testing the model’s key prediction. We therefore conclude that the problem of cell size control in budding yeast remains unsolved. This work highlights the need for rigorous testing of future models of size control in order to make progress on this fundamental question.

Independent manipulation of histone H3 modifications in individual nucleosomes reveals the contributions of sister histones to transcription

Histone tail modifications can greatly influence chromatin-associated processes. Asymmetrically modified nucleosomes exist in multiple cell types, but whether modifications on both sister histones contribute equally to chromatin dynamics remains elusive. Here, we devised a bivalent nucleosome system that allowed for the constitutive assembly of asymmetrically modified sister histone H3s in nucleosomes in Saccharomyces cerevisiae. The sister H3K36 methylations independently affected cryptic transcription in gene coding regions, whereas sister H3K79 methylation had cooperative effects on gene silencing near telomeres. H3K4 methylation on sister histones played an independent role in suppressing the recruitment of Gal4 activator to the GAL1 promoter and in inhibiting GAL1 transcription. Under starvation stress, sister H3K4 methylations acted cooperatively, independently or redundantly to regulate transcription. Thus, we provide a unique tool for comparing symmetrical and asymmetrical modifications of sister histone H3s in vivo.

The histone variant H2A.Z interconverts two stable epigenetic chromatin states

The nucleosomes occupying the chromosomal start sites of transcription contain the histone H2A variant H2A.Z in place of H2A. Upon galactose induction, nucleosomes are evicted from the GAL1 locus in Saccharomyces cerevisiae cells. H2A.Z (which is encoded by the HTZ1 gene in S. cerevisiae) is required for the eviction of the GAL1 promoter nucleosome and for the transcriptional activation of the GAL1 gene; however, histones are also important for transcriptional repression and we asked in the present paper if H2A.Z also plays a role in the glucose repression of the GAL1 promoter. With the help of a fusion of the URA3 ORF (open reading frame) to the GAL1 promoter, we were able to detect two different epigenetic transcription states of the GAL1 promoter in glucose-grown cells lacking H2A.Z: a repressed state that is occupied by a H2A-containing nucleosome and a derepressed state that is nucleosome-free. These two chromatin states are inherited stably through many cell divisions. According to the model described in the present paper, the role of H2A.Z is to facilitate the addition and removal of promoter nucleosomes and to prevent the formation of unfavourable stable epigenetic chromatin structures, which are not in accordance with the environmental conditions.

Research on Construction of a Whole-Cell Biocatalyst for Xylan Degradation

Endo-1,4-β-xylanase (E.C.3.2.1.8) is a family of glycoside hydrolase. It is capable of hydrolyzing the backbone of substituted xylan polymers into fragments of random size. Due to this ability, xylanase can serve the degradation of lignocellulose, and facilitate the application of xylan. Cell-surface display of enzymes is one of the most attractive applications in yeast. It is a promising utilization in constructing the whole-cell biocatalyst of xylanase. For this purpose, a cDNA sequence of endo-1,4-β-xylanase B (XylB) from Aspergillus niger BCC14405 was optimized and synthesized according to the codon bias of Saccharomyces cerevisiae. The genes encoding galactokinase (GAL1) promoter, α-mating factor 1 (MFα1) pre-pro secretion signal, fully codon-optimized XylB, the 320 amino acids of C terminal of α-agglutinin, alcohol dehydrogenase (ADH1) terminator and kanMX cassette were amplified and cloned into YEplac181 to construct a cell-surface display vector called pGMAAK-XylB with α-agglutinin as an anchor. Then pGMAAK-XylB was transformed into S. cerevisiae. The results show XylB was immobilized and actively expressed on S. cerevisiae. Meanwhile, a secretion expression plasmid was also constructed using the above elements except α-agglutinin as a control strain in the study of characteristic of XylB. After an induction of 48 h by 2% galactose, the activity of displayed XylB reached 63 U/g dry-cell weight. The optimal pH of displayed XylB has changed from 5 to 6 and the optimal temperature has changed from 50 °C to 60 °C, comparing to the recombinant secretion XylB.