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Cat8 is a C6 zinc cluster transcription activator in yeast. It is generally recognized that the transcription of CAT8 is inhibited and that Cat8 is inactive in the presence of high concentrations of glucose. However, our recent study found that constitutively overexpressed Cat8 played a regulatory role in Saccharomyces cerevisiae in the presence of 20 g/L glucose. To explore the regulatory network of Cat8 at high glucose concentrations, CAT8 was both overexpressed and deleted in this study. Cell growth and glucose consumption in different media were significantly accelerated by the deletion of CAT8, while the lag period was greatly shortened. RNA-seq and genetic modification showed that the deletion of CAT8 changed the type of energy metabolism in yeast cells. Many genes related to the mitochondrial respiratory chain were downregulated, resulting in a reduction in aerobic respiration and the tricarboxylic acid cycle. Meanwhile, both the energy supply of anaerobic ethanol fermentation and the Crabtree effect of S. cerevisiae were enhanced by the deletion of CAT8. CAT8 knockout cells show a higher sugar uptake rate, a higher cell growth rate, and higher tolerance to glucose than the wild-type strain YS58. This study expands the understanding of the regulatory network of Cat8 and provides guidance for modulating yeast cell growth. Key points: • The deletion of CAT8 promoted cell growth of S. cerevisiae. • Transcriptome analysis revealed the regulation network of Cat8 under 1% glucose condition. • CAT8 deletion increases the glucose tolerance of cells by enhancing the Crabtree effect. [ABSTRACT FROM AUTHOR]

Abstract Background Owing to the Crabtree effect, Saccharomyces cerevisiae produces a large amount of ethanol in the presence of oxygen and excess glucose, leading to a loss of carbon for the biosynthesis of non-ethanol chemicals. In the present study, the potential of a newly constructed Crabtree negative S. cerevisiae, as a chassis cell, was explored for the biosynthesis of various non-ethanol compounds. Results To understand the metabolic characteristics of Crabtree negative S. cerevisiae sZJD-28, its transcriptional profile was compared with that of Crabtree positive S. cerevisiae CEN.PK113-11C. The reporter GO term analysis showed that, in sZJD-28, genes associated with translational processes were down-regulated, while those related to carbon metabolism were significantly up-regulated. To verify a potential increase in carbon metabolism for the Crabtree negative strain, the production of non-ethanol chemicals, derived from different metabolic nodes, was then undertaken for both sZJD-28 and CEN.PK113-11C. At the pyruvate node, production of 2,3-butanediol and lactate in sZJD-28-based strains was remarkably higher than that of CEN.PK113-11C-based ones, representing 16.8- and 1.65-fold increase in titer, as well as 4.5-fold and 0.65-fold increase in specific titer (mg/L/OD), respectively. Similarly, for shikimate derived p-coumaric acid, the titer of sZJD-28-based strain was 0.68-fold higher than for CEN.PK113-11C-based one, with a 0.98-fold increase in specific titer. While farnesene and lycopene, two acetoacetyl-CoA derivatives, showed 0.21- and 1.88-fold increases in titer, respectively. From malonyl-CoA, the titer of 3-hydroxypropionate and fatty acids in sZJD-28-based strains were 0.19- and 0.76-fold higher than that of CEN.PK113-11C-based ones, respectively. In fact, yields of products also improved by the same fold due to the absence of residual glucose. Fed-batch fermentation further showed that the titer of free fatty acids in sZJD-28-based strain 28-FFA-E reached 6295.6 mg/L with a highest reported specific titer of 247.7 mg/L/OD in S. cerevisiae. Conclusions Compared with CEN.PK113-11C, the Crabtree negative sZJD-28 strain displayed a significantly different transcriptional profile and obvious advantages in the biosynthesis of non-ethanol chemicals due to redirected carbon and energy sources towards metabolite biosynthesis. The findings, therefore, suggest that a Crabtree negative S. cerevisiae strain could be a promising chassis cell for the biosynthesis of various chemicals.

Hexokinase II (Hxk2) is a master protein in glucose-mediated transcriptional repression signaling pathway. Degrading Hxk2 through an auxin-inducible protein degradation previously doubled sesquiterpene (nerolidol) production at gram-per-liter levels in Saccharomyces cerevisiae. Global transcriptomics/proteomics profiles in Hxk2-deficient background are important to understanding genetic and molecular mechanisms for improved nerolidol production and guiding further strain optimization. Here, proteomic responses to Hxk2 depletion are investigated in the yeast strains harboring a GAL promoters-controlled nerolidol synthetic pathway, at the exponential and ethanol growth phases and in GAL80-wildtype and gal80Δ backgrounds. Carbon metabolic pathways and amino acid metabolic pathways show diversified responses to Hxk2 depletion and growth on ethanol, including upregulation of alternative carbon catabolism and respiration as well as downregulation of amino acid synthesis. De-repression of GAL genes may contribute to improved nerolidol production in Hxk2-depleted strains. Seventeen transcription factors associated with upregulated genes are enriched. Validating Ash1-mediated repression on the RIM4 promoter shows the variation on the regulatory effects of different Ash1-binding sites and the synergistic effect of Ash1 and Hxk2-mediated repression. Further validation of individual promoters shows that HXT1 promoter activities are glucose-dependent in hxk2Δ background, but much weaker than those in HXK2-wildtype background. In summary, inactivating HXK2 may relieve glucose repression on respiration and GAL promoters for improved bioproduction under aerobic conditions in S. cerevisiae. The proteomics profiles provide a better genetics overview for a better metabolic engineering design in Hxk2-deficient backgrounds.

Supply of Gibbs free energy and precursors are vital for cellular function and cell metabolism have evolved to be tightly regulated to balance their supply and consumption. Precursors and Gibbs free energy are generated in the central carbon metabolism (CCM), and fluxes through these pathways are precisely regulated. However, how fluxes through CCM pathways are affected by posttranslational modification and allosteric regulation remains poorly understood. Here, we integrated multi-omics data collected under nine different chemostat conditions to explore how fluxes in the CCM are regulated in the yeast Saccharomyces cerevisiae. We deduced a pathway- and metabolism-specific CCM flux regulation mechanism using hierarchical analysis combined with mathematical modeling. We found that increased glycolytic flux associated with an increased specific growth rate was accompanied by a decrease in flux regulation by metabolite concentrations, including the concentration of allosteric effectors, and a decrease in the phosphorylation level of glycolytic enzymes. [ABSTRACT FROM AUTHOR]

The respiro-fermentative metabolism in the yeast Saccharomyces cerevisiae, also called the Crabtree effect, results in lower energy efficiency and biomass yield which can impact yields of chemicals to be produced using this cell factory. Although it can be engineered to become Crabtree negative, the slow growth and glucose consumption rate limit its industrial application. Here the Crabtree effect in yeast can be alleviated by engineering the transcription factor Mth1 involved in glucose signaling and a subunit of the RNA polymerase II mediator complex Med2. It was found that the mutant with the MTH1A81D&MED2*432Y allele could grow in glucose rich medium with a specific growth rate of 0.30 h−1, an ethanol yield of 0.10 g g−1, and a biomass yield of 0.21 g g−1, compared with a specific growth rate of 0.40 h−1, an ethanol yield of 0.46 g g−1, and a biomass yield of 0.11 g g−1 in the wild-type strain CEN.PK 113-5D. Transcriptome analysis revealed significant downregulation of the glycolytic process, as well as the upregulation of the TCA cycle and the electron transfer chain. Significant expression changes of several reporter transcription factors were also identified, which might explain the higher energy efficiencies in the engineered strain. We further demonstrated the potential of the engineered strain with the production of 3-hydroxypropionic acid at a titer of 2.04 g L−1, i.e., 5.4-fold higher than that of a reference strain, indicating that the alleviated glucose repression could enhance the supply of mitochondrial acetyl-CoA. These results suggested that the engineered strain could be used as an efficient cell factory for mitochondrial production of acetyl-CoA derived chemicals.

Background: Owing to the Crabtree effect, Saccharomyces cerevisiae produces a large amount of ethanol in the presence of oxygen and excess glucose, leading to a loss of carbon for the biosynthesis of non-ethanol chemicals. In the present study, the potential of a newly constructed Crabtree negative S. cerevisiae, as a chassis cell, was explored for the biosynthesis of various non-ethanol compounds. Results: To understand the metabolic characteristics of Crabtree negative S. cerevisiae sZJD-28, its transcriptional profile was compared with that of Crabtree positive S. cerevisiae CEN.PK113-11C. The reporter GO term analysis showed that, in sZJD-28, genes associated with translational processes were down-regulated, while those related to carbon metabolism were significantly up-regulated. To verify a potential increase in carbon metabolism for the Crabtree negative strain, the production of non-ethanol chemicals, derived from different metabolic nodes, was then undertaken for both sZJD-28 and CEN.PK113-11C. At the pyruvate node, production of 2,3-butanediol and lactate in sZJD-28-based strains was remarkably higher than that of CEN.PK113-11C-based ones, representing 16.8- and 1.65-fold increase in titer, as well as 4.5-fold and 0.65-fold increase in specific titer (mg/L/OD), respectively. Similarly, for shikimate derived p-coumaric acid, the titer of sZJD-28-based strain was 0.68-fold higher than for CEN.PK113-11C-based one, with a 0.98-fold increase in specific titer. While farnesene and lycopene, two acetoacetyl-CoA derivatives, showed 0.21- and 1.88-fold increases in titer, respectively. From malonyl-CoA, the titer of 3-hydroxypropionate and fatty acids in sZJD-28-based strains were 0.19- and 0.76-fold higher than that of CEN.PK113-11C-based ones, respectively. In fact, yields of products also improved by the same fold due to the absence of residual glucose. Fed-batch fermentation further showed that the titer of free fatty acids in sZJD-28-based strain 28-FFA-E reached 6295.6 mg/L with a highest reported specific titer of 247.7 mg/L/OD in S. cerevisiae. Conclusions: Compared with CEN.PK113-11C, the Crabtree negative sZJD-28 strain displayed a significantly different transcriptional profile and obvious advantages in the biosynthesis of non-ethanol chemicals due to redirected carbon and energy sources towards metabolite biosynthesis. The findings, therefore, suggest that a Crabtree negative S. cerevisiae strain could be a promising chassis cell for the biosynthesis of various chemicals. [ABSTRACT FROM AUTHOR]

Since Jacob and Monod’s discovery of the lac operon ∼1960, the explanations offered for most metabolic adaptations have been genetic. The focus has been on the adaptive changes in gene expression that occur, which are often referred to as “metabolic reprogramming.” The contributions metabolism makes to adaptation have been largely ignored. Here we point out that metabolic adaptations, including the associated changes in gene expression, are highly dependent on the metabolic state of an organism prior to the environmental change to which it is adapting, and on the plasticity of that state. In support of this hypothesis, we examine the paradigmatic example of a genetically driven adaptation, the adaptation of E. coli to growth on lactose, and the paradigmatic example of a metabolic driven adaptation, the Crabtree effect in yeast. Using a framework based on metabolic control analysis, we have reevaluated what is known about both adaptations, and conclude that knowledge of the metabolic properties of these organisms prior to environmental change is critical for understanding not only how they survive long enough to adapt, but also how the ensuing changes in gene expression occur, and their phenotypes post-adaptation. It would be useful if future explanations for metabolic adaptations acknowledged the contributions made to them by metabolism, and described the complex interplay between metabolic systems and genetic systems that make these adaptations possible.

This paper proposes a general approach for building a mechanistic yeast model able to predict the shift of metabolic pathways. The mechanistic model accounts for the coexistence of several metabolic pathways (aerobic fermentation, glucose respiration, anaerobic fermentation and ethanol respiration) whose activation depends on growth conditions. This general approach is applied to a commercial strain of Saccharomyces cerevisiae. Stoichiometry and yeast kinetics were mostly determined from aerobic and completely anaerobic experiments. Known parameters were taken from the literature, and the remaining parameters were estimated by inverse analysis using the particle swarm optimization method. The optimized set of parameters allows the concentrations to be accurately determined over time, reporting global mean relative errors for all variables of less than 7 and 11% under completely anaerobic and aerobic conditions, respectively. Different affinities of yeast for glucose and ethanol tolerance under aerobic and anaerobic conditions were obtained. Finally, the model was successfully validated by simulating a different experiment, a batch fermentation process without gas injection, with an overall mean relative error of 7%. This model represents a useful tool for the control and optimization of yeast fermentation systems. More generally, the modeling framework proposed here is intended to be used as a building block of a digital twin of any bioproduction process. [ABSTRACT FROM AUTHOR]

The advancement of knowledge about the physiology of Dekkera bruxellensis has shown its potential for the production of fuel ethanol very close to the conventional fermenting yeast S. cerevisiae. However, some aspects of its metabolism remain uncovered. In the present study, the respiro-fermentative parameters of D. bruxellensis GDB 248 were evaluated under different cultivation conditions. The results showed that sucrose was more efficiently converted to ethanol than glucose, regardless the nitrogen source, which points out for the industrial efficiency of this yeast in sucrose-based substrate. The blockage of the cytosolic acetate production incremented the yeast fermentative efficiency by 27% (in glucose) and 14% (in sucrose). On the other hand, the presence of nitrate as inducer of acetate production reducing the production of ethanol. Altogether, these results settled the hypothesis that acetate metabolism is the main constraint for ethanol production. Besides, this acetate-generating pathway seems to exert some regulatory action on the flux and distribution of the carbon flowing through the central metabolism. These physiological aspects were corroborated by the relative expression analysis of key genes in the crossroad to ethanol, acetate and biomass formation. All the results were discussed in the light of the industrial potential of this yeast. [Display omitted] • D. bruxellensis directed most of carbon to fermentation even under aerobic conditions. • Disulfiram decreased growth and stimulated ethanol production in D. bruxellensis. • Acdh activity might take control of the carbon flowing in the central metabolism. • Nitrate impairs the production of ethanol in glucose. • Sucrose improved the metabolism of D. bruxellensis regardless the nitrogen source. [ABSTRACT FROM AUTHOR]

In view of unified cell bioenergetics, cell bioenergetic problems related to cell overenergization can cause excessive disturbances in current cell fate and, as a result, lead to a change of cell-fate. At the onset of the problem, cell overenergization of multicellular organisms (especially overenergization of mitochondria) is solved inter alia by activation and then stimulation of the reversible Crabtree effect by cells. Unfortunately, this apparently good solution can also lead to a much bigger problem when, despite the activation of the Crabtree effect, cell overenergization persists for a long time. In such a case, cancer transformation, along with the Warburg effect, may occur to further reduce or stop the charging of mitochondria by high-energy molecules. Understanding the phenomena of cancer transformation and cancer development has become a real challenge for humanity. To date, many models have been developed to understand cancer-related mechanisms. Nowadays, combining all these models into one coherent universal model of cancer transformation and development can be considered a new challenge. In this light, the aim of this article is to present such a potentially universal model supported by a proposed new model of cellular functionality evolution. The methods of fighting cancer resulting from unified cell bioenergetics and the two presented models are also considered. [ABSTRACT FROM AUTHOR]

Environmental conditions significantly impact the metabolism of Saccharomyces cerevisiae , a Crabtree-positive yeast that maintains a fermentative metabolism in high-sugar environments even in the presence of oxygen. Although the introduction of oxygen has been reported to induce alterations in yeast metabolism, knowledge of the mechanisms behind these metabolic adaptations in relation to redox cofactor metabolism and their implications in the context of wine fermentation remains limited. This study aimed to compare the intracellular redox cofactor levels, the cofactor ratios, and primary metabolite production in S. cerevisiae under aerobic and anaerobic conditions in synthetic grape juice. The molecular mechanisms underlying these metabolic differences were explored using a transcriptomic approach. Aerobic conditions resulted in an enhanced fermentation rate and biomass yield. Total NADP(H) levels were threefold higher during aerobiosis, while a decline in the total levels of NAD(H) was observed. However, there were stark differences in the ratio of NAD+/NADH between the treatments. Despite few changes in the differential expression of genes involved in redox cofactor metabolism, anaerobiosis resulted in an increased expression of genes involved in lipid biosynthesis pathways, while the presence of oxygen increased the expression of genes associated with thiamine, methionine, and sulfur metabolism. The production of fermentation by-products was linked with differences in the redox metabolism in each treatment. This study provides valuable insights that may help steer the production of metabolites of industrial interest during alcoholic fermentation (including winemaking) by using oxygen as a lever of redox metabolism. • S. cerevisiae NAD+/NADH ratios vary significantly between aerobic and anaerobic conditions. • B3 salvage is the preferred pathway to convert nicotinamide riboside to nicotinamide during anaerobiosis. • Total NADP(H) levels are higher during aerobiosis with no difference in the ratio. • Anaerobiosis increases the expression of genes in glycolysis and lipid biosynthetic pathways. • Increased expression of thiamine regulation genes during aerobiosis suggests an increased thiamine requirement. [ABSTRACT FROM AUTHOR]

Exposed to changes in their environment, microorganisms will adapt their phenotype, including metabolism, to ensure survival. To understand the adaptation principles, resource allocation-based approaches were successfully applied to predict an optimal proteome allocation under (quasi) steady-state conditions. Nevertheless, for a general, dynamic environment, enzyme kinetics will have to be taken into account which was not included in the linear resource allocation models. To this end, a resource-dependent kinetic model was developed and applied to the model organism Saccharomyces cerevisiae by combining published kinetic models and calibrating the model parameters to published proteomics and fluxomics datasets. Using this approach, we were able to predict specific proteomes at different dilution rates under chemostat conditions. Interestingly, the approach suggests that the occurrence of aerobic fermentation (Crabtree effect) in S. cerevisiae is not caused by space limitation in the total proteome but rather an effect of constraints on the mitochondria. When exposing the approach to repetitive, dynamic substrate conditions, the proteome space was allocated differently. Less space was predicted to be available for non-essential enzymes (reserve space). This could indicate that the perceived “overcapacity” present in experimentally measured proteomes may very likely serve a purpose in increasing the robustness of a cell to dynamic conditions, especially an increase of proteome space for the growth reaction as well as of the trehalose cycle that was shown to be essential in providing robustness upon stronger substrate perturbations. The model predictions of proteome adaptation to dynamic conditions were additionally evaluated against respective experimentally measured proteomes, which highlighted the model’s ability to accurately predict major proteome adaptation trends. This proof of principle for the approach can be extended to production organisms and applied for both understanding metabolic adaptation and improving industrial process design.

Carcinogenesis is a complex process involving several steps, requiring the elimination of many cell-imposed barriers such as anti-proliferative responses, apoptosis inducing mechanisms and cellular ageing. This occurs mostly through mutations in oncogenes and tumor suppressor genes. These mutated cancer cells are characterized by their ability to rapidly grow and divide, and to undergo uncontrolled proliferation. There are six distinctive hallmarks that a cell acquires during its progression into malignancy: limitless replicative potential, sustained angiogenesis, evasion of apoptosis, self-sufficiency in growth signals, insensitivity to anti-growth signals and tissue invasion and metastasis. These hallmarks have been studied extensively. Two characteristics have recently been added to the list: evasion of immune destruction and reprogramming of energy metabolism. To carry out mitotic division, a cell must duplicate its genome, proteins and lipids and assemble these elements into daughter cells. Tumor cells undergo metabolic reprogramming, which are characterized by changes in the metabolic processes, to satisfy large demands for ATP, NADPH, NADH and carbon skeletons. A detailed understanding of tumour cell metabolism will not only throw light for early detection and screening of cancerous lesions, but will also pave paths for targeted therapy with better patient compliance. [ABSTRACT FROM AUTHOR]

The Crabtree effect in the yeast, Saccharomyces cerevisiae , has been extensively studied, but only few studies have analyzed the dynamic conditions across the critical specific growth rate where the Crabtree effect sets in. Here, we carried out a multi-omics analysis of S. cerevisiae undergoing a specific growth rate transition from 0.2 h−1 to 0.35 h−1. The extracellular metabolome, the transcriptome and the proteome were analyzed in an 8-h transition period after the specific growth rate shifted from 0.2 h−1 to 0.35 h−1. The changing trends of both the transcriptome and proteome were analyzed using principal component analysis, which showed that the transcriptome clustered together after 60 min, while the proteome reached steady-state much later. Focusing on central carbon metabolism, we analyzed both the changes in the transcriptome and proteome, and observed an interesting changing pattern in the tricarboxylic acid (TCA) pathway, which indicates an important role for citric acid shuttling across the mitochondrial membrane for α-ketoglutarate accumulation during the transition from respiratory to respiro-fermentative metabolism. This was supported by a change in the oxaloacetate and malate shuttle. Together, our findings shed new light into the onset of the Crabtree effect in S. cerevisiae. [ABSTRACT FROM AUTHOR]

Aerobic fermentation, also referred to as the Crabtree effect in yeast, is a well-studied phenomenon that allows many eukaryal cells to attain higher growth rates at high glucose availability. Not all yeasts exhibit the Crabtree effect, and it is not known why Crabtree-negative yeasts can grow at rates comparable to Crabtree-positive yeasts. Here, we quantitatively compared two Crabtree-positive yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and two Crabtree-negative yeasts, Kluyveromyces marxianus and Scheffersomyces stipitis, cultivated under glucose excess conditions. Combining physiological and proteome quantification with genome-scale metabolic modeling, we found that the two groups differ in energy metabolism and translation efficiency. In Crabtree-positive yeasts, the central carbon metabolism flux and proteome allocation favor a glucose utilization strategy minimizing proteome cost as proteins translation parameters, including ribosomal content and/or efficiency, are lower. Crabtree-negative yeasts, however, use a strategy of maximizing ATP yield, accompanied by higher protein translation parameters. Our analyses provide insight into the underlying reasons for the Crabtree effect, demonstrating a coupling to adaptations in both metabolism and protein translation. [ABSTRACT FROM AUTHOR]

Non-Saccharomyces wine yeasts are of increasing importance due to their influence on the organoleptic properties of wine and thus the factors influencing the biomass production of these yeasts, as starter cultures, are of commercial value. Therefore, the effects of growth rates on the biomass yield (Yx/s) and fermentation performance of non-Saccharomyces yeasts at bench and pilot scale were examined. The fermentative performance and (Yx/s) were optimised, in aerobic fed-batch cultivations, to produce commercial wine seed cultures of Lachancea thermotolerans Y1240, Issatchenkia orientalis Y1161 and Metschnikowia pulcherrima Y1337. Saccharomyces cerevisiae (Lalvin EC1118) was used as a benchmark. A Crabtree positive response was shown by L. thermotolerans in a molasses-based industrial medium, at growth rates exceeding 0.21 h−1 (µcrit), resulting in a Yx/s of 0.76 g/g at 0.21 h−1 (46% of µmax) in the aerobic bioreactor-grown fed-batch culture at bench scale. At pilot scale and 0.133 h−1 (36% of µmax), this yeast exhibited ethanol concentrations reaching 10.61 g/l, as a possible result of substrate gradients. Crabtree negative responses were observed for I. orientalis and M. pulcherrima resulting in Yx/s of 0.83 g/g and 0.68 g/g, respectively, below 32% of µmax. The Yx/s of M. pulcherrima, I. orientalis and L. thermotolerans was maximised at growth rates between 0.10 and 0.12 h−1 and the fermentative capacity of these yeasts was maximised at these lower growth rates. [ABSTRACT FROM AUTHOR]

Abstract Background The four-carbon dicarboxylic acids of the tricarboxylic acid cycle (malate, fumarate and succinate) remain promising bio-based alternatives to various precursor chemicals derived from fossil-based feed stocks. The double carbon bond in fumarate, in addition to the two terminal carboxylic groups, opens up an array of downstream reaction possibilities, where replacement options for petrochemical derived maleic anhydride are worth mentioning. To date the most promising organism for producing fumarate is Rhizopus oryzae (ATCC 20344, also referred to as Rhizopus delemar) that naturally excretes fumarate under nitrogen-limited conditions. Fumarate excretion in R. oryzae is always associated with the co-excretion of ethanol, an unwanted metabolic product from the fermentation. Attempts to eliminate ethanol production classically focus on enhanced oxygen availability within the mycelium matrix. In this study our immobilised R. oryzae process was employed to investigate and utilise the Crabtree characteristics of the organism in order to establish the limits of ethanol by-product formation under growth and non-growth conditions. Results All fermentations were performed with either nitrogen excess (growth phase) or nitrogen limitation (production phase) where medium replacements were done between the growth and the production phase. Initial experiments employed excess glucose for both growth and production, while the oxygen partial pressure was varied between a dissolved oxygen of 18.4% and 85%. Ethanol was formed during both growth and production phases and the oxygen partial pressure had zero influence on the response. Results clearly indicated that possible anaerobic zones within the mycelium were not responsible for ethanol formation, hinting that ethanol is formed under fully aerobic conditions as a metabolic overflow product. For Crabtree-positive organisms like Saccharomyces cerevisiae ethanol overflow is manipulated by controlling the glucose input to the fermentation. The same strategy was employed for R. oryzae for both growth and production fermentations. It was shown that all ethanol can be eliminated during growth for a glucose addition rate of $$0.07\,\hbox {g}\,\hbox {L}^{-1}\,\hbox {h}^{-1}$$ 0.07 g L - 1 h - 1 . The production phase behaved in a similar manner, where glucose addition of $$0.197\,\hbox {g}\,\hbox {L}^{-1}\,\hbox {h}^{-1}$$ 0.197 g L - 1 h - 1 resulted in fumarate production of $$0.150\,\hbox {g}\,\hbox {L}^{-1}\,\hbox {h}^{-1}$$ 0.150 g L - 1 h - 1 and a yield of $$0.802\,\hbox {g}\,\hbox {g}^{-1}$$ 0.802 g g - 1 fumarate on glucose. Further investigation into the effect of glucose addition revealed that ethanol overflow commences at a glucose addition rate of $$0.395\,\hbox {g}\,\hbox {g}^{-1}\,\hbox {h}^{-1}$$ 0.395 g g - 1 h - 1 on biomass, while the maximum glucose uptake rate was established to be between 0.426 and $$0.533\,\hbox {g}\,\hbox {g}^{-1}\,\hbox {h}^{-1}$$ 0.533 g g - 1 h - 1 . Conclusions The results conclusively prove that R. oryzae is a Crabtree-positive organism and that the characteristic can be utilised to completely discard ethanol by-product formation. A state referred to as “homofumarate production” was illustrated, where all carbon input exits the cell as either fumarate or respiratory $$\hbox {CO}_{2}$$ CO 2 . The highest biomass-based “homofumarate production”: rate of $$0.243\,\hbox {g}\,\hbox {g}^{-1}\,\hbox {h}^{-1}$$ 0.243 g g - 1 h - 1 achieved a yield of $$0.802\,\hbox {g}\,\hbox {g}^{-1}$$ 0.802 g g - 1 on glucose, indicating the bounds for developing an ethanol free process. The control strategy employed in this study in conjunction with the uncomplicated scalability of the immobilised process provides new direction for further developing bio-fumarate production.

This paper proposes a general approach for building a mechanistic yeast model able to predict the shift of metabolic pathways. The mechanistic model accounts for the coexistence of several metabolic pathways (aerobic fermentation, glucose respiration, anaerobic fermentation and ethanol respiration) whose activation depends on growth conditions. This general approach is applied to a commercial strain of Saccharomyces cerevisiae. Stoichiometry and yeast kinetics were mostly determined from aerobic and completely anaerobic experiments. Known parameters were taken from the literature, and the remaining parameters were estimated by inverse analysis using the particle swarm optimization method. The optimized set of parameters allows the concentrations to be accurately determined over time, reporting global mean relative errors for all variables of less than 7 and 11% under completely anaerobic and aerobic conditions, respectively. Different affinities of yeast for glucose and ethanol tolerance under aerobic and anaerobic conditions were obtained. Finally, the model was successfully validated by simulating a different experiment, a batch fermentation process without gas injection, with an overall mean relative error of 7%. This model represents a useful tool for the control and optimization of yeast fermentation systems. More generally, the modeling framework proposed here is intended to be used as a building block of a digital twin of any bioproduction process.

Metabolic reprogramming and mitochondrial dysfunction are central elements in a broad variety of physiological and pathological processes. While cell culture established itself as a versatile technique for the elaboration of physiology and disease, studying metabolism using standard cell culture protocols is profoundly interfered by the Crabtree effect. This phenomenon refers to the adaptation of cultured cells to a glycolytic phenotype, away from oxidative phosphorylation in glucose-containing medium, and questions the applicability of cell culture in certain fields of research. In this systematic review we aim to provide a comprehensive overview and critical appraisal of strategies reported to circumvent the Crabtree effect. [ABSTRACT FROM AUTHOR]

In view of unified cell bioenergetics, cell bioenergetic problems related to cell overenergization can cause excessive disturbances in current cell fate and, as a result, lead to a change of cell-fate. At the onset of the problem, cell overenergization of multicellular organisms (especially overenergization of mitochondria) is solved inter alia by activation and then stimulation of the reversible Crabtree effect by cells. Unfortunately, this apparently good solution can also lead to a much bigger problem when, despite the activation of the Crabtree effect, cell overenergization persists for a long time. In such a case, cancer transformation, along with the Warburg effect, may occur to further reduce or stop the charging of mitochondria by high-energy molecules. Understanding the phenomena of cancer transformation and cancer development has become a real challenge for humanity. To date, many models have been developed to understand cancer-related mechanisms. Nowadays, combining all these models into one coherent universal model of cancer transformation and development can be considered a new challenge. In this light, the aim of this article is to present such a potentially universal model supported by a proposed new model of cellular functionality evolution. The methods of fighting cancer resulting from unified cell bioenergetics and the two presented models are also considered.

The yeast trehalose-6-phosphate synthase (Tps1) catalyzes the formation of trehalose-6-phosphate (T6P) in trehalose synthesis. Besides, Tps1 plays a key role in carbon and energy homeostasis in this microbial cell, as shown by the well documented loss of ATP and hyper accumulation of sugar phosphates in response to glucose addition in a mutant defective in this protein. The inability of a Saccharomyces cerevisiae tps1 mutant to cope with fermentable sugars is still a matter of debate. We reexamined this question through a quantitative analysis of the capability of TPS1 homologues from different origins to complement phenotypic defects of this mutant. Our results allowed to classify this complementation in three groups. A first group enclosed TPS1 of Klyveromyces lactis with that of S. cerevisiae as their expression in Sctps1 cells fully recovered wild type metabolic patterns and fermentation capacity in response to glucose. At the opposite was the group with TPS1 homologues from the bacteria Escherichia coli and Ralstonia solanacearum, the plant Arabidopsis thaliana and the insect Drosophila melanogaster whose metabolic profiles were comparable to those of a tps1 mutant, notably with almost no accumulation of T6P, strong impairment of ATP recovery and potent reduction of fermentation capacity, albeit these homologous genes were able to rescue growth of Sctps1 on glucose. In between was a group consisting of TPS1 homologues from other yeast species and filamentous fungi characterized by 5 to 10 times lower accumulation of T6P, a weaker recovery of ATP and a 3-times lower fermentation capacity than wild type. Finally, we found that glucose repression of gluconeogenic genes was strongly dependent on T6P. Altogether, our results suggest that the TPS protein is indispensable for growth on fermentable sugars, and points to a critical role of T6P as a sensing molecule that promotes sugar fermentation and glucose repression..

Background: Evolution of aerobic fermentation (crabtree effect) in yeast is associated with the whole genome duplication (WGD) event, suggesting that duplication of certain genes may have altered yeast metabolism. The pyruvate kinase (PYK) gene is associated with alterations in cell metabolism, and duplicated during the WGD, generating PYK1 and PYK2. Thus, the impact of WGD on PYK activity and role of PYK in yeast metabolism were explored.Methods: PYK activity in the presence or absence of fructose-1,6-bisphosphate (FBP) was compared between pre- and post-WGD yeast. Glucose consumption, ethanol production, and oxygen consumption were measured in wildtype yeast and yeast with a T403E point mutation, which alters FBP binding affinity.Results: FBP stimulated increased PYK activity in pre-WGD yeast and in the PYK1 isoforms of post-WGD yeast, but not in the PYK2 isoforms of post-WGD yeast. Compared to wildtype, T403E mutant yeast displayed reduced glucose consumption, reduced ethanol production, and increased mitochondrial metabolism.Conclusion: The WGD event impacted the sensitivity of PYK activity to FBP. Mutations in the FBP binding domain of PYK induce metabolic shifts that favor respiration and suppress fermentation.

Fumaric acid is widely used in the food and beverage, pharmaceutical and polyester resin industries. Rhizopus oryzae is the most successful microorganism at excreting fumaric acid compared to all known natural and genetically modified organisms. It has previously been discovered that careful control of the glucose feed rate can eliminate the by-product formation of ethanol. Two key parameters affecting fumaric acid excretion were identified, namely the medium pH and the urea feed rate. A continuous fermentation with immobilised R. oryzae was utilised to determine the effect of these parameters. It was found that the selectivity for fumaric acid production increased at high glucose consumption rates for a pH of 4, different from the trend for pH 5 and 6, achieving a yield of 0.93 gg−1. This yield is higher than previously reported in the literature. Varying the urea feed rate to 0.255 mgL−1h−1 improved the yield of fumaric acid but experienced a lower glucose uptake rate compared to higher urea feed rates. An optimum region has been found for fumaric acid production at pH 4, a urea feed rate of 0.625 mgL−1h−1 and a glucose feed rate of 0.329 gL−1h−1.

Small-molecule compound-based therapies have provided new insights into cancer treatment against mitochondrial impairment. N6-furfuryladenosine (kinetin riboside, KR) is a purine derivative and an anticancer agent that selectively affects the molecular pathways crucial for cell growth and apoptosis by interfering with mitochondrial functions and thus might be a potential mitotoxicant. Metabolism of cancer cells is predominantly based on the Crabtree effect that relies on glucose-induced inhibition of cell respiration and thus on oxidative phosphorylation (OXPHOS), which supports the survival of cancer cells in metabolic stress conditions. The simplest way to circumvent this phenomenon is to replace glucose with galactose in the culture environment. Consequently, cells become more sensitive to mitochondrial perturbations caused by mitotoxicants. In the present study, we evaluated several cellular parameters and investigated the effect of KR on mitochondrial functions in HepG2 cells forced to rely mainly on OXPHOS. We showed that KR in the galactose environment is a more potent apoptosis-inducing agent. KR decreases the mitochondrial membrane potential, reduces glutathione level, depletes cellular ATP, and induces reactive oxygen species (ROS) production in the OXPHOS state, leading to the loss of cell viability. Taken together, these results demonstrate that KR directly acts on the mitochondria to limit their function and that the sensitivity of cells is dependent on their ability to cope with energetic stress. [ABSTRACT FROM AUTHOR]

Abstract Background The yeast Saccharomyces cerevisiae is a promising host cell for producing a wide range of chemicals. However, attempts to metabolically engineer Crabtree-positive S. cerevisiae invariably face a common issue: how to reduce dominant ethanol production. Here, we propose a yeast metabolic engineering strategy for decreasing ethanol subgeneration involving tugging the carbon flux at an important hub branching point (e.g., pyruvate). Tugging flux at a central glycolytic overflow metabolism point arising from high glycolytic activity may substantially increase higher alcohol production in S. cerevisiae. We validated this possibility by testing 2,3-butanediol (2,3-BDO) production, which is routed via pyruvate as the important hub compound. Results By searching for high-activity acetolactate synthase (ALS) enzymes that catalyze the important first-step reaction in 2,3-BDO biosynthesis, and tuning several fermentation conditions, we demonstrated that a stronger pyruvate pulling effect (tugging of pyruvate carbon flux) is very effective for increasing 2,3-BDO production and reducing ethanol subgeneration by S. cerevisiae. To further confirm the validity of the pyruvate carbon flux tugging strategy, we constructed an evolved pyruvate decarboxylase (PDC)-deficient yeast (PDCΔ) strain that lacked three isozymes of PDC. In parallel with re-sequencing to identify genomic mutations, liquid chromatography–tandem mass spectrometry analysis of intermediate metabolites revealed significant accumulation of pyruvate and NADH in the evolved PDCΔ strain. Harnessing the high-activity ALS and additional downstream enzymes in the evolved PDCΔ strain resulted in a high yield of 2,3-BDO (a maximum of 0.41 g g−1 glucose consumed) and no ethanol subgeneration, thereby confirming the utility of our strategy. Using this engineered strain, we demonstrated a high 2,3-BDO titer (81.0 g L−1) in a fed-batch fermentation using a high concentration of glucose as the sole carbon source. Conclusions We demonstrated that the pyruvate carbon flux tugging strategy is very effective for increasing 2,3-BDO production and decreasing ethanol subgeneration in Crabtree-positive S. cerevisiae. High activity of the common first-step enzyme for the conversion of pyruvate, which links to both the TCA cycle and amino acid biosynthesis, is likely important for the production of various chemicals by S. cerevisiae.

Abstract Background Growth conditions that bring about stress on Phaffia rhodozyma cells encourage the synthesis of astaxanthin, an antioxidant carotenoid, which protects cells against oxidative damage. Using P. rhodozyma cultures performed with and without copper limitation, we examined the kinetics of astaxanthin synthesis along with the expression of asy, the key astaxanthin synthesis gene, as well as aox, which encodes an alternative oxidase protein. Results Copper deficiency had a detrimental effect on the rates of oxygen consumption and ethanol reassimilation at the diauxic shift. In contrast, copper deficiency prompted alcoholic fermentation under aerobic conditions and had a favorable effect on the astaxanthin content of cells, as well as on aox expression. Both cultures exhibited strong aox expression while consuming ethanol, but particularly when copper was absent. Conclusion We show that the induction of either astaxanthin production, aox expression, or aerobic fermentation exemplifies the crucial role that redox imbalance plays in triggering any of these phenomena. Based on our own results and data from others, we propose a mechanism that rationalizes the central role played by changes of respiratory activity, which lead to redox imbalances, in triggering both the short-term antioxidant response as well as fermentation in yeasts and other cell types.

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Amebiasis caused by Entamoeba histolytica parasite is among the worst gut diseases worldwide. The study involved detection of gut mycobiome signature of the infected subjects in a trial to improve ability to diagnose and treat this disease. The results indicated that diversity of samples slightly changed due to infection. Dendrogram indicated that the most common phyla in the human gut are Ascomycota, Basidiomycota and Zygomycota. Species Pichia kudriavzevii, Candida glabrata, Saccharomyces cerevisiae of phylum Ascomycota and Rhodotorula mucilaginosa of phylum Basidiomycota were found highly OTU abundant. Weighted unifrac diversity distances resulted in complete separation of the two groups. Differential abundance analysis indicated that four phyla, six families, nine genera and ten species showed considerable changes in gut mycobiome signatures within and among groups. Unclassified species of genus Malassezia (phylum Basidiomycota) showed high abundance in infected subjects as compared to healthy subjects, while families Saccharomycetaceae and Trichocomaceae, genus Saccharomyces and species S. cerevisiae showed opposite results. Linear discriminant analysis effect size (LEFSE) indicated that family Saccharomycetaceae, of which S. cerevisiae is a downstream taxon, can be a negative biomarker for amebiasis. In conclusion, the study provides new insights into possible use of Saccharomyces as a probiotic against amebiasis. [ABSTRACT FROM AUTHOR]

The ability of the oleaginous yeast Trichosporon fermentans to efficiently produce lipids when cultivated in dried sweet sorghum was evaluated. First, lipid production was evaluated in synthetic media mimicking the composition of sweet sorghum stalks and optimized based on the nitrogen source and C: N ratio. Under optimum conditions, the lipid production reached 3.66 g/L with 21.91% w/w lipid content by using a mixture of sucrose, glucose and fructose and peptone at C: N ratio 160. Cultivation on pre-saccharified sweet sorghum stalks offered 1.97 g/L, while it was found that sweet sorghum stalks can support yeast growth and lipid production without the need for external nitrogen source addition. At an attempt to increase the carbon source concentration for optimizing lipid production, the Crabtree effect was observed in T. fermentans. To this end, the yeast was evaluated for its potential to produce ethanol under anaerobic conditions in synthetic media and sweet sorghum. The ethanol concentration at 100 g/L glucose was 40.31 g/L, while utilizing sweet sorghum by adding a distinct saccharification step and external nitrogen source offered ethanol concentration equal to 23.5 g/L. To the authors' knowledge, this is the first time that the Crabtree effect is observed in T. fermentans. • Lipid production was evaluated in synthetic media and sweet sorghum. • Lipid production in sweet sorghum was 1.97 g/L adding a saccharification step and no nitrogen source. • Crabtree effect was observed in Trichosporon fermentans. • Ethanol production in 20% w/v sweet sorghum was 23.5 g/L. [ABSTRACT FROM AUTHOR]

Background: The four-carbon dicarboxylic acids of the tricarboxylic acid cycle (malate, fumarate and succinate) remain promising bio-based alternatives to various precursor chemicals derived from fossil-based feed stocks. The double carbon bond in fumarate, in addition to the two terminal carboxylic groups, opens up an array of downstream reaction possibilities, where replacement options for petrochemical derived maleic anhydride are worth mentioning. To date the most promising organism for producing fumarate is Rhizopus oryzae (ATCC 20344, also referred to as Rhizopus delemar) that naturally excretes fumarate under nitrogen-limited conditions. Fumarate excretion in R. oryzae is always associated with the co-excretion of ethanol, an unwanted metabolic product from the fermentation. Attempts to eliminate ethanol production classically focus on enhanced oxygen availability within the mycelium matrix. In this study our immobilised R. oryzae process was employed to investigate and utilise the Crabtree characteristics of the organism in order to establish the limits of ethanol by-product formation under growth and non-growth conditions. Results: All fermentations were performed with either nitrogen excess (growth phase) or nitrogen limitation (production phase) where medium replacements were done between the growth and the production phase. Initial experiments employed excess glucose for both growth and production, while the oxygen partial pressure was varied between a dissolved oxygen of 18.4% and 85%. Ethanol was formed during both growth and production phases and the oxygen partial pressure had zero influence on the response. Results clearly indicated that possible anaerobic zones within the mycelium were not responsible for ethanol formation, hinting that ethanol is formed under fully aerobic conditions as a metabolic overflow product. For Crabtree-positive organisms like Saccharomyces cerevisiae ethanol overflow is manipulated by controlling the glucose input to the fermentation. The same strategy was employed for R. oryzae for both growth and production fermentations. It was shown that all ethanol can be eliminated during growth for a glucose addition rate of 0.07 g L - 1 h - 1 . The production phase behaved in a similar manner, where glucose addition of 0.197 g L - 1 h - 1 resulted in fumarate production of 0.150 g L - 1 h - 1 and a yield of 0.802 g g - 1 fumarate on glucose. Further investigation into the effect of glucose addition revealed that ethanol overflow commences at a glucose addition rate of 0.395 g g - 1 h - 1 on biomass, while the maximum glucose uptake rate was established to be between 0.426 and 0.533 g g - 1 h - 1 . Conclusions: The results conclusively prove that R. oryzae is a Crabtree-positive organism and that the characteristic can be utilised to completely discard ethanol by-product formation. A state referred to as "homofumarate production" was illustrated, where all carbon input exits the cell as either fumarate or respiratory CO 2 . The highest biomass-based "homofumarate production": rate of 0.243 g g - 1 h - 1 achieved a yield of 0.802 g g - 1 on glucose, indicating the bounds for developing an ethanol free process. The control strategy employed in this study in conjunction with the uncomplicated scalability of the immobilised process provides new direction for further developing bio-fumarate production. [ABSTRACT FROM AUTHOR]

Summary: Yeast activity in solution can be quantified by its production of Carbon Dioxide which affects the compressibility of the solution which can be tracked acoustically with a microphone. Yeast is found to respond predictably to a fixed amount of glusose. • BARDS is a rapid method for real-time analysis of CO 2 production by yeast cells via the Crabtree Effect. • Yeast strains can be differentiated by real-time CO 2 production profiling. • BARDS detects intracellular v extra-cellular timelines for CO 2 production. • BARDS can determine cellular CO 2 gaseous production using the Crawford Equation. • BARDS can detect metabolic pathway switching depening on the carbon source bolus used. In this study, a new approach to measure metabolic activity of yeast via the Crabtree effect is described. BARDS is an analytical technique developed to aid powder and tablet characterisation by monitoring changes in the compressibility of a solvent during solute dissolution. It is a rapid and simple method which utilises a magnetic stir bar to mix added solute and induce the acoustic resonance of a vessel containing a fixed volume of solvent. In this study it is shown that initiation of fermentation in a yeast suspension, in aqueous buffer, is accompanied by reproducible changes in the frequency of induced acoustic resonance. These changes signify increased compressibility of the suspension due to CO 2 release by the yeast. A simple standardised BARDS protocol reveals yeast carbon source preferences and can generate quantitative kinetic data on carbon source metabolism which are characteristic of each yeast strain. The Crawford-Woods equation can be used to quantify total gaseous CO 2 produced by a given number of viable yeast when supplied with a fixed amount of carbon source. This allows for a value to be calculated for the amount of gaseous CO 2 produced by each yeast cell. The approach has the potential to transform the way in which yeast metabolism is tracked and potentially provide an orthogonal or surrogate method to determining viability, vitality and attenuation measurements in the future. [ABSTRACT FROM AUTHOR]

Hyperosmotic conditions are associated to several pathological states. In this article, we evaluate the consequence of hyperosmotic medium on cellular energy metabolism. We demonstrate that exposure of cells to hyperosmotic conditions immediately reduces the mitochondrial oxidative phosphorylation rate. This causes an increase in glycolysis, which represses further respiration. This is known as the Warburg or Crabtree effect. In addition to aerobic glycolysis, we observed two other cellular responses that would help to preserve cellular ATP level and viability: A reduction in the cellular ATP turnover rate and a partial mitochondrial uncoupling which is expected to enhance ATP production by Krebs cycle. The latter is likely to constitute another metabolic adaptation to compensate for deficient oxidative phosphorylation that, importantly, is not dependent on glucose. [ABSTRACT FROM AUTHOR]

The Crabtree effect involves energy management in which yeasts utilize glycolysis as the terminal electron acceptor instead of oxygen, despite the presence of sufficient dissolved oxygen, when oxygen concentrations exceed a certain limit. The Crabtree effect is detrimental to bakery yeast production, because it results in lower cellular glucose yields. Batch culture of Saccharomyces cerevisiae , a Crabtree positive yeast, decreased the cell yield of glucose and produced large amounts of ethanol despite a high specific glucose consumption rate compared to Candida utilis, a Crabtree negative yeast. This study investigated the effect of these characteristics on metabolite levels. We performed metabolome analysis of both yeasts during each growth phase of batch culture using liquid chromatography-tandem mass spectrometry and gas chromatography-mass spectrometry. Principle component analysis of metabolome data indicated that the Crabtree effect affected metabolites related to NADH synthesis in central metabolism. The amount of these metabolites in S. cerevisiae was lower than that in C. utilis. However, to maintain the specific glucose consumption rate at high levels, yeasts must avoid depletion of NAD+, which is essential for glucose utilization. Our results indicated that NADH was oxidized by converting acetaldehyde to ethanol in S. cerevisiae , which is in accordance with previous reports. Therefore, the specific NADH production rates of S. cerevisiae and C. utilis did not show a difference. This study suggested that NAD+/NADH ratio is disrupted by the Crabtree effect, which in turn influenced central metabolism and that S. cerevisiae maintained the NAD+/NADH ratio by producing ethanol. [ABSTRACT FROM AUTHOR]

Biofilm formation is a survival strategy for microorganisms facing a hostile environment. Under biofilm, bacteria are better protected against antibacterial drugs and the immune response, increasing treatment difficulty, as persistent populations recalcitrant to chemotherapy are promoted. Deciphering mechanisms leading to biofilms could, thus, be beneficial to obtain new antibacterial drug candidates. Here, we show that mycobacterial biofilm formation is linked to excess glycerol adaptation and the concomitant establishment of the Crabtree effect. This effect is characterized by respiratory reprogramming, ATP downregulation, and secretion of various metabolites including pyruvate, acetate, succinate, and glutamate. Interestingly, the Crabtree effect was abnormal in a mycobacterial strain deficient for Cpn60.1 (GroEL1). Indeed, this mutant strain had a compromised ability to downregulate ATP and secreted more pyruvate, acetate, succinate, and glutamate in the culture medium. Importantly, the mutant strain had higher intracellular pyruvate and produced more toxic methylglyoxal, suggesting a glycolytic stress leading to growth stasis and consequently biofilm failure. This study demonstrates, for the first time, the link between mycobacterial biofilm formation and the Crabtree effect.

ABSTRACT When faced with environmental changes, microbes often enter a temporary growth arrest during which they reprogram the expression of specific genes to adapt to the new conditions. A prime example of such a lag phase occurs when microbes need to switch from glucose to other, less-preferred carbon sources. Despite its industrial relevance, the genetic network that determines the duration of the lag phase has not been studied in much detail. Here, we performed a genome-wide Bar-Seq screen to identify genetic determinants of the Saccharomyces cerevisiae glucose-to-galactose lag phase. The results show that genes involved in respiration, and specifically those encoding complexes III and IV of the electron transport chain, are needed for efficient growth resumption after the lag phase. Anaerobic growth experiments confirmed the importance of respiratory energy conversion in determining the lag phase duration. Moreover, overexpression of the central regulator of respiration, HAP4, leads to significantly shorter lag phases. Together, these results suggest that the glucose-induced repression of respiration, known as the Crabtree effect, is a major determinant of microbial fitness in fluctuating carbon environments. IMPORTANCE The lag phase is arguably one of the prime characteristics of microbial growth. Longer lag phases result in lower competitive fitness in variable environments, and the duration of the lag phase is also important in many industrial processes where long lag phases lead to sluggish, less efficient fermentations. Despite the immense importance of the lag phase, surprisingly little is known about the exact molecular processes that determine its duration. Our study uses the molecular toolbox of S. cerevisiae combined with detailed growth experiments to reveal how the transition from fermentative to respirative metabolism is a key bottleneck for cells to overcome the lag phase. Together, our findings not only yield insight into the key molecular processes and genes that influence lag duration but also open routes to increase the efficiency of industrial fermentations and offer an experimental framework to study other types of lag behavior.

The switch between mitochondrial respiration and fermentation as the main ATP production pathway through an increase glycolytic flux is known as the Crabtree effect. The elucidation of the molecular mechanism of the Crabtree effect may have important applications in ethanol production and lay the groundwork for the Warburg effect, which is essential in the molecular etiology of cancer. A key piece in this mechanism could be Snf1p, which is a protein that participates in the nutritional response including glucose metabolism. Thus, this work aimed to recognize the role of the SNF1 gene on the glycolytic flux and mitochondrial respiration through the glucose concentration variation to gain insights about its relationship with the Crabtree effect. Herein, we found that SNF1 deletion in Saccharomyces cerevisiae cells grown at 1% glucose, decreased glycolytic flux, increased NAD(P)H concentration, enhanced HXK2 gene transcription, and decreased mitochondrial respiration. Meanwhile, the same deletion increased the mitochondrial respiration of cells grown at 10% glucose. Altogether, these findings indicate that SNF1 is important to respond to glucose concentration variation and is involved in the switch between mitochondrial respiration and fermentation. [ABSTRACT FROM AUTHOR]

• Accumulation of malic acid due to overflow carbon metabolism. • Influence of ambient pH on sclerotiorin biosynthesis. • Repression of sclerotiorin biosynthesis by Crabtree effect. • Efficient biosynthesis of sclerotiorin via carbon metabolite repression. Sclerotiorin is the secondary metabolite of Penicillium sclerotiorum , which is usually produced by solid state fermentation or liquid culture without stirring (formation of mycelial mat on air-liquid surface). In the present work, it was confirmed that malic acid was produced during cell suspension culture in a liquid medium (mycelia acting as planktonic cells) using resting cells as whole cell biocatalyst. The accumulation of malic acid was caused by overflow carbon metabolism at high glucose concentration (Crabtree effect), which led to low ambient pH value. The low ambient pH repressed sclerotiorin biosynthesis. In order to overcome the low pH caused by Crabtree effect, many influenced factors, such as phosphate buffer system, initial pH, biomass loading, slowly metabolized carbon resource, and mixed sugars as carbon resource, were investigated. Finally, the low pH caused by Crabtree effect was eliminated by taking the advantage of carbon metabolite repression via utilization of mixed sugars (glucose and lactose) as carbon resource. And then, an ideal pH approximately 3.8 was maintained and corresponding high concentration of sclerotiorin (150 absorbance unit at 365 nm, corresponding to 1.9 g/l) was achieved by cell suspension culture with a relatively high biomass loading 11.7 g/l DCW (dry cell weight). [ABSTRACT FROM AUTHOR]

Mucor circinelloides is a dimorphic Zygomycete fungus that produces ethanol under aerobic conditions in the presence of glucose, which indicates that it is a Crabtree-positive fungus. To determine the physiological role of the alcohol dehydrogenase (ADH) activity elicited under these conditions, we obtained and characterized an allyl alcohol-resistant mutant that was defective in ADH activity, and examined the effect of adh mutation on physiological parameters related to carbon and energy metabolism. Compared to the Adh+ strain R7B, the ADH-defective (Adh-) strain M5 was unable to grow under anaerobic conditions, exhibited a considerable reduction in ethanol production in aerobic cultures when incubated with glucose, had markedly reduced growth capacity in the presence of oxygen when ethanol was the sole carbon source, and exhibited very low levels of NAD+-dependent alcohol de-hydrogenase activity in the cytosolic fraction. Further characterization of the M5 strain showed that it contains a 10-bp deletion that interrupts the coding region of the adhl gene. Complementation with the wild-type allele adh1+ by transformation of M5 remedied all the defects caused by the adh1 mutation. These findings indicate that in M. circinelloides, the product of the adh1 gene mediates the Crabtree effect, and can act as either a fermentative or an oxidative enzyme, depending on the nutritional conditions, thereby participating in the association between fermentative and oxidative metabolism. It was found that the spores of M. circinelloides possess low mRNA levels of the ethanol assimilation genes (adl2 and acs2), which could explain their inability to grow in the alcohol. [ABSTRACT FROM AUTHOR]

Biofilm formation is a survival strategy for microorganisms facing a hostile environment. Under biofilm, bacteria are better protected against antibacterial drugs and the immune response, increasing treatment difficulty, as persistent populations recalcitrant to chemotherapy are promoted. Deciphering mechanisms leading to biofilms could, thus, be beneficial to obtain new antibacterial drug candidates. Here, we show that mycobacterial biofilm formation is linked to excess glycerol adaptation and the concomitant establishment of the Crabtree effect. This effect is characterized by respiratory reprogramming, ATP downregulation, and secretion of various metabolites including pyruvate, acetate, succinate, and glutamate. Interestingly, the Crabtree effect was abnormal in a mycobacterial strain deficient for Cpn60.1 (GroEL1). Indeed, this mutant strain had a compromised ability to downregulate ATP and secreted more pyruvate, acetate, succinate, and glutamate in the culture medium. Importantly, the mutant strain had higher intracellular pyruvate and produced more toxic methylglyoxal, suggesting a glycolytic stress leading to growth stasis and consequently biofilm failure. This study demonstrates, for the first time, the link between mycobacterial biofilm formation and the Crabtree effect. [ABSTRACT FROM AUTHOR]

When faced with environmental changes, microbes enter a lag phase during which cell growth is arrested, allowing cells to adapt to the new situation. The discovery of the lag phase started the field of gene regulation and led to the unraveling of underlying mechanisms. However, the factors determining the exact duration and dynamics of the lag phase remain largely elusive. Naively, one would expect that cells adapt as quickly as possible, so they can resume growth and compete with other organisms. However, recent studies show that the lag phase can last from several hours up to several days. Moreover, some cells within the same population take much longer than others, despite being genetically identical. In addition, the lag phase duration is also influenced by the past, with recent exposure to a given environment leading to a quicker adaptation when that environment returns. Genome-wide screens in Saccharomyces cerevisiae on carbon source shifts now suggest that the length of the lag phase, the heterogeneity in lag times of individual cells, and the history-dependent behavior are not determined by the time it takes to induce a few specific genes related to uptake and metabolism of a new carbon source. Instead, a major shift in general metabolism, and in particular a switch between fermentation and respiration, is the major bottleneck that determines lag duration. This suggests that there may be a fitness trade-off between complete adaptation of a cell's metabolism to a given environment, and a short lag phase when the environment changes. [ABSTRACT FROM AUTHOR]

The high cell density culture of baker's yeast FX‐2 was investigated in a 50 L(A) automatic bioreactor. Herein, it was found firstly that the Crabtree effect clearly existed in batch fermentation with higher glucose content, then the critical initial glucose content range (≤2.00 g L−1) was reasonably ascertained to effectively avoid Crabtree effect. In the next fed‐batch fermentations with different strategies, the second strategy (maintain ethanol concentration lower than 0.10% and pH around 4.80) was confirmed to be more beneficial to yeast growth than the first strategy (keep reducing sugar not more than 2.00 g L−1 and control steady Carbon/Nitrogen ratio 3.05:1.00). After that, one optimal control strategy (maintain pH around 4.80 and keep respiratory quotient in the range of 0.90–1.00) was constructed to further enhance cell yield. Under an optimal control strategy, four schemes with the aim of achieving pH‐stat were compared, and yeast extract instead of other alkaline materials was selected as a better regulator. As a result, 148.37 g L−1 dry cell weight, 38.25 × 108 mL−1 living cells, and 8.24 g L−1 h−1 productivity were harvested, which respectively elevated 23.74%, 135.38%, and 24.47% compared to that obtained under the traditional scheme (regulate pH with ammonia); meanwhile, the maximum oxygen uptake rate and carbon dioxide excretion rate were both more than 250.00 mmol L−1 min−1. [ABSTRACT FROM AUTHOR]

publisher‐imprint‐name Springer volume‐issue‐count 1 issue‐article‐count 0 issue‐toc‐levels 0 issue‐pricelist‐year 2018 issue‐copyright‐holder The Author(s) issue‐copyright‐year 2018 article‐contains‐esm No article‐numbering‐style Unnumbered article‐registration‐date‐year 2018 article‐registration‐date‐month 5 article‐registration‐date‐day 29 article‐toc‐levels 0 toc‐levels 0 volume‐type Regular journal‐product ArchiveJournal numbering‐style Unnumbered article‐grants‐type OpenChoice metadata‐grant OpenAccess abstract‐grant OpenAccess bodypdf‐grant OpenAccess bodyhtml‐grant OpenAccess bibliography‐grant OpenAccess esm‐grant OpenAccess online‐first false pdf‐file‐reference BodyRef/PDF/40169_2018_Article_193.pdf target‐type OnlinePDF issue‐type Regular article‐type OriginalPaper journal‐subject‐primary Medicine & Public Health journal‐subject‐secondary Medicine/Public Health, general journal‐subject‐collection Medicine open‐access true --> Maintenance of health involves a synchronized network of catabolic and anabolic signals among organs/tissues/cells that requires differential bioenergetics from mitochondria and glycolysis (biological laws or biorhythms). We defined biological circadian rhythms as Yin (tumoricidal) and Yang (tumorigenic) arms of acute inflammation (effective immunity) involving immune and non‐immune systems. Role of pathogens in altering immunity and inducing diseases and cancer has been documented for over a century. However, in 1955s decision makers in cancer/medical establishment allowed public (current baby boomers) to consume million doses of virus‐contaminated polio vaccines. The risk of cancer incidence and mortality sharply rose from 5% (rate of hereditary/genetic or innate disease) in 1900s, to its current scary status of 33% or 50% among women and men, respectively. Despite better hygiene, modern detection technologies and discovery of antibiotics, baby boomers and subsequent 2–3 generations are sicker than previous generations at same age. American health status ranks last among other developed nations while America invests highest amount of resources for healthcare. In this perspective we present evidence that cancer is an induced disease of twentieth century, facilitated by a great deception of cancer/medical establishment for huge corporate profits. Unlike popularized opinions that cancer is 100, 200 or 1000 diseases, we demonstrate that cancer is only one disease; the severe disturbances in biorhythms (differential bioenergetics) or loss of balance in Yin and Yang of effective immunity. Cancer projects that are promoted and funded by decision makers are reductionist approaches, wrong and unethical and resulted in loss of millions of precious lives and financial toxicity to society. Public vaccination with pathogen‐specific vaccines (e.g., flu, hepatitis, HPV, meningitis, measles) weakens, not promotes, immunity. Results of irresponsible projects on cancer sciences or vaccines are increased population of drug‐dependent sick society. Outcome failure rates of claimed 'targeted' drugs, 'precision' or 'personalized' medicine are 90% (± 5) for solid tumors. We demonstrate that aging, frequent exposures to environmental hazards, infections and pathogen‐specific vaccines and ingredients are 'antigen overload' for immune system, skewing the Yin and Yang response profiles and leading to induction of 'mild', 'moderate' or 'severe' immune disorders. Induction of decoy or pattern recognition receptors (e.g., PRRs), such as IRAK‐M or IL‐1dRs ('designer' molecules) and associated genomic instability and over‐expression of growth promoting factors (e.g., pyruvate kinases, mTOR and PI3Ks, histamine, PGE2, VEGF) could lead to immune tolerance, facilitating cancer cells to hijack anabolic machinery of immunity (Yang) for their increased growth requirements. Expression of constituent embryonic factors would negatively regulate differentiation of tumor cells through epithelial–mesenchymal‐transition and create "dual negative feedback loop" that influence tissue metabolism under hypoxic conditions. It is further hypothesized that induction of tolerance creates 'dark energy' and increased entropy and temperature in cancer microenvironment allowing disorderly cancer proliferation and mitosis along with increased glucose metabolism via Crabtree and Pasteur Effects, under mitophagy and ribophagy, conditions that are toxic to host survival. Effective translational medicine into treatment requires systematic and logical studies of complex interactions of tumor cells with host environment that dictate clinical outcomes. Promoting effective immunity (biological circadian rhythms) are fundamental steps in correcting host differential bioenergetics and controlling cancer growth, preventing or delaying onset of diseases and maintaining public health. The author urges independent professionals and policy makers to take a closer look at cancer dilemma and stop the 'scientific/medical ponzi schemes' of a powerful group that control a drug‐dependent sick society before all hopes for promoting public health evaporate. [ABSTRACT FROM AUTHOR]

In this article, some new aspects of unified cell bioenergetics are presented. From the perspective of unified cell bioenergetics certain subsequent stages of cancer development, from initiation stage, through transformation to metastasis, are analyzed. Here we show that after transformation, cancer cells are permanently exposed to reactive oxygen species, that causes continual random DNA mutations and as a result genome and chromosomal destabilizations. The modern cancer attractor hypothesis has been extended in explaining cancer development. Discussion is conducted in light of current cancerogenesis research, including bioenergetic cancer initiation, the somatic mutation theory and the tissue organization field theory. In the article reasons complicating the discovery of patterns of cancer genome changes and cancer evolution are presented. In addition certain cancer therapeutic aspects are given attention to. [ABSTRACT FROM AUTHOR]

Chronic hyperglycemia has been found to be the major etiologic factor causing diabetic retinopathy (DR) and accelerating its progression. The exact biochemical mechanism of the same is still unclear. Although multiple metabolic pathways have been implicated in DR, there is no existing treatment for causing regression / slowing the progression of DR apart from strict systemic glycemic control. We describe the possible role of Crabtree effect in causing DR and postulate novel treatment strategies by controlling the flux of glucose metabolic pathways. [ABSTRACT FROM AUTHOR]