Adaptation of a Saccharomyces cerevisiae strain to high copper concentrations

Transcriptomic-metabolomic analysis reveals the effect of copper toxicity on fermentation properties in Saccharomyces cerevisiae

Copper is one of the unavoidable heavy metals in wine production. In this study, the effects on fermentation performance and physiological metabolism of Saccharomyces cerevisiae under copper stress were investigated. EC1118 was the most copper-resistant among the six strains. The ethanol accumulation of EC1118 was 26.16-20 mg/L Cu2+, which was 1.90-3.15 times higher than that of other strains. The fermentation rate was significantly reduced by copper, and the inhibition was relieved after 4-10 days of adjustment. Metabolomic-transcriptomic analysis revealed that amino acid and nucleotide had the highest number of downregulated and upregulated differentially expressed metabolites, respectively. The metabolism of fructose and mannose was quickly affected, which then triggered the metabolism of galactose in copper stress. Pathways such as oxidative and organic acid metabolic processes were significantly affected in the early time, resulting in a significant decrease in the amount of carboxylic acids. The pathways related to protein synthesis and metabolism under copper stress, such as translation and peptide biosynthetic process, was also significantly affected. In conclusion, this study analyzed the metabolite-gene interaction network and molecular response during the alcohol fermentation of S. cerevisiae under copper stress, providing theoretical basis for addressing the influence of copper stress in wine production.

The trade-off of availability and growth inhibition through copper for the production of copper-dependent enzymes by Pichia pastoris

Background

Copper is an essential chemical element for life as it is a part of prosthetic groups of enzymes including super oxide dismutase and cytochrome c oxidase; however, it is also toxic at high concentrations. Here, we present the trade-off of copper availability and growth inhibition of a common host used for copper-dependent protein production, Pichia pastoris.

Results

At copper concentrations ranging from 0.1 mM (6.35 mg/L) to 2 mM (127 mg/L), growth rates of 0.25 h⁻¹ to 0.16 h⁻¹ were observed with copper uptake of as high as 20 mg_copper/g_CDW. The intracellular copper content was estimated by subtracting the copper adsorbed on the cell wall from the total copper concentration in the biomass. Higher copper concentrations led to stronger cell growth retardation and, at 10 mM (635 mg/L) and above, to growth inhibition. To test the determined copper concentration range for optimal recombinant protein production, a laccase gene from Aspergillus clavatus [EMBL: EAW07265.1] was cloned under the control of the constitutive glyceraldehyde-3-phosphate (GAP) dehydrogenase promoter for expression in P. pastoris. Notably, in the presence of copper, laccase expression improved the specific growth rate of P. pastoris. Although copper concentrations of 0.1 mM and 0.2 mM augmented laccase expression 4 times up to 3 U/mL compared to the control (0.75 U/mL), while higher copper concentrations resulted in reduced laccase production. An intracellular copper content between 1 and 2 mg_copper/g_CDW was sufficient for increased laccase activity. The physiology of the yeast could be excluded as a reason for the stop of laccase production at moderate copper concentrations as no flux redistribution could be observed by ¹³C-metabolic flux analysis.

Conclusion

Copper and its pivotal role to sustain cellular functions is noteworthy. However, knowledge on its cellular accumulation, availability and distribution for recombinant protein production is limited. This study attempts to address one such challenge, which revealed the fact that intracellular copper accumulation influenced laccase production and should be considered for high protein expression of copper-dependent enzymes when using P. pastoris. The results are discussed in the context of P. pastoris as a general host for copper -dependent enzyme production.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0251-3) contains supplementary material, which is available to authorized users.

Laboratory evolution of copper tolerant yeast strains

Background

Yeast strains endowed with robustness towards copper and/or enriched in intracellular Cu might find application in biotechnology processes, among others in the production of functional foods. Moreover, they can contribute to the study of human diseases related to impairments of copper metabolism. In this study, we investigated the molecular and physiological factors that confer copper tolerance to strains of baker's yeasts.

Results

We characterized the effects elicited in natural strains of Candida humilis and Saccharomyces cerevisiae by the exposure to copper in the culture broth. We observed that, whereas the growth of Saccharomyces cells was inhibited already at low Cu concentration, C. humilis was naturally robust and tolerated up to 1 g · L^-1 CuSO₄ in the medium. This resistant strain accumulated over 7 mg of Cu per gram of biomass and escaped severe oxidative stress thanks to high constitutive levels of superoxide dismutase and catalase. Both yeasts were then "evolved" to obtain hyper-resistant cells able to proliferate in high copper medium. While in S. cerevisiae the evolution of robustness towards Cu was paralleled by the increase of antioxidative enzymes, these same activities decreased in evolved hyper-resistant Candida cells. We also characterized in some detail changes in the profile of copper binding proteins, that appeared to be modified by evolution but, again, in a different way in the two yeasts.

Conclusions

Following evolution, both Candida and Saccharomyces cells were able to proliferate up to 2.5 g · L^-1 CuSO₄ and to accumulate high amounts of intracellular copper. The comparison of yeasts differing in their robustness, allowed highlighting physiological and molecular determinants of natural and acquired copper tolerance. We observed that different mechanisms contribute to confer metal tolerance: the control of copper uptake, changes in the levels of enzymes involved in oxidative stress response and changes in the copper-binding proteome. However, copper elicits different physiological and molecular reactions in yeasts with different backgrounds.

Optimization of bioprocess for production of copper-enriched biomass of industrially important microorganism Saccharomyces cerevisiae

The production of Saccharomyces cerevisiae cells enriched with copper and the effects of adding copper ions to different media on yeast cell growth and ethanol production were studied. In the media Cu(2+) concentrations of up to 0.094 mM had no effect on alcoholic fermentation, whereas higher Cu(2+) concentrations markedly decreased yeast cell growth rate and ethanol production. Under static conditions, the maximum amounts of copper uptake (i.e., 1.16 mg/g, 1.2 mg/g and 0.81 mg/g dry matter yeast biomass for glucose, sucrose and molasses media, respectively) were obtained after 8 h of fermentation, whereas under dynamic conditions smaller amounts of copper uptake (i.e., 0.98 mg/g, 1.02 mg/g and 0.7 mg/g dry matter yeast biomass for glucose, sucrose and molasses media, respectively) were obtained after 6 h of fermentation.

Characteristics of copper tolerance in Yarrowia lipolytica

We discovered that a mutant strain of the dimorphic yeast Yarrowia lipolytica could grow in the yeast form in high concentrations of copper sulfate. The amount of metal accumulated by Y. lipolytica increased with increasing copper concentrations in the medium. Washing with 100 mM EDTA released at least 60% of the total metal from the cells, but about 20-25 micromol/g DW persisted, which represented about 30% of the soluble fraction of cultured cells. The soluble fraction (mainly cytosol) contained only about 10% of the total metal content within cells cultured in medium supplemented with 6 mM copper. We suggest that although a high copper concentration induces an efflux mechanism, the released copper becomes entrapped in the periplasm and in other parts of the cell wall. Washing with EDTA liberated not only copper ions, but also melanin, a brown pigment that can bind metal and which located at the cell wall. These findings indicated that melanin participates in the mechanism of metal accumulation. Culture in medium supplemented with copper obviously enhanced the activities of Cu, Zn-SOD, but not of Mn-SOD.

Copper adaptation and methylotrophic metabolism in Candida boidinii

The importance of the antioxidant enzyme superoxide dismutase (CuZnSOD) in the metabolic switch from normotrophic to methylotrophic conditions was studied in the facultative methylotrophic yeast Candida boidinii. Copper adaptation was performed to qualify C. boidinii as a suitable cellular system to study the effect of induction of CuZnSOD, and other biochemical components along the copper detoxification system, on methanol adaptation. Copper adaptation results in the induction of CuZnSOD peroxidase activity as well as of glutathione. The effects at the metabolic level of exposure to both copper and methanol were also studied: the results suggest that the effect on antioxidant enzyme levels as a function of the change of trophic condition are predominant with respect to the effects of copper administration. Thus, the methanol-dependent induction of such enzymes is likely to provide a sufficient protection for the cells against toxic effects depending on copper administration. Administration of copper under methylotrophic conditions decreases the growth rate in spite of the high levels of antioxidant enzymes that are elicited by copper treatment. The adaptation to methanol metabolism was studied alsoafter methanol-independent induction of CuZnSOD, glutathione and catalase levels, obtained by exposure to high copper concentrations in glucose-containing medium. The metabolic changes induced by copper are persistent over several re-inoculations in normo-cupric glucose medium, thus allowing the study of the glucose-to-methanol switch on cells exhibiting high levels of antioxidant enzyme activities. Under such conditions the lag time observed during the transition from normotrophic to methylotrophic conditions is strongly reduced.

The influence of Cu concentration on ethanolic fermentation by Saccharomyces cerevisiae

In the present work, the influence of Cu concentration on alcoholic fermentation by Saccharomyces cerevisiae was studied in white grape musts and in YNB medium containing glucose. In the YNB medium, the yield of ethanol, relative to the control, doubled in the presence of 0.50 and 1.0 mM Cu. As for production of ethanol from musts, only minor effects were observed at different Cu concentrations, which indicates that Cu levels do not effect changes in fermentation, and, therefore, are below any toxic level regarding the yeast performance.