TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates

Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis

RNA polymerase III (RNAP III) holoenzyme activity and the processing of its products have been linked to several metabolic dysfunctions in lower and higher eukaryotes. Alterations in the activity of RNAP III-driven synthesis of non-coding RNA cause extensive changes in glucose metabolism. Increased RNAP III activity in the S. cerevisiae maf1Δ strain is lethal when grown on a non-fermentable carbon source. This lethal phenotype is suppressed by reducing tRNA synthesis. Neither the cause of the lack of growth nor the underlying molecular mechanism have been deciphered, and this area has been awaiting scientific explanation for a decade. Our previous proteomics data suggested mitochondrial dysfunction in the strain. Using model mutant strains maf1Δ (with increased tRNA abundance) and rpc128-1007 (with reduced tRNA abundance), we collected data showing major changes in the TCA cycle metabolism of the mutants that explain the phenotypic observations. Based on 13C flux data and analysis of TCA enzyme activities, the present study identifies the flux constraints in the mitochondrial metabolic network. The lack of growth is associated with a decrease in TCA cycle activity and downregulation of the flux towards glutamate, aspartate and phosphoenolpyruvate (PEP), the metabolic intermediate feeding the gluconeogenic pathway. rpc128-1007, the strain that is unable to increase tRNA synthesis due to a mutation in the C128 subunit, has increased TCA cycle activity under non-fermentable conditions. To summarize, cells with non-optimal activity of RNAP III undergo substantial adaptation to a new metabolic state, which makes them vulnerable under specific growth conditions. Our results strongly suggest that balanced, non-coding RNA synthesis that is coupled to glucose signaling is a fundamental requirement to sustain a cell's intracellular homeostasis and flexibility under changing growth conditions. The presented results provide insight into the possible role of RNAP III in the mitochondrial metabolism of other cell types.

13CO2-labelling and Sampling in Algae for Flux Analysis of Photosynthetic and Central Carbon Metabolism

The flux in photosynthesis can be studied by performing 13CO2 pulse labelling and analysing the temporal labelling kinetics of metabolic intermediates using gas or liquid chromatography linked to mass spectrometry. Metabolic flux analysis (MFA) is the primary approach for analysing metabolic network function and quantifying intracellular metabolic fluxes. Different MFA approaches differ based on the metabolic state (steady vs. non-steady state) and the use of stable isotope tracers. The main methodology used to investigate metabolic systems is metabolite steady state associated with stable isotope labelling experiments. Specifically, in biological systems like photoautotrophic organisms, isotopic non-stationary 113C metabolic flux analysis at metabolic steady state with transient isotopic labelling (13C-INST-MFA) is required. The common requirement for metabolic steady state, alongside its very short half-timed reactions, complicates robust MFA of photosynthetic metabolism. While custom gas chambers design has addressed these challenges in various model plants, no similar tools were developed for liquid photosynthetic cultures (e.g., algae, cyanobacteria), where diffusion and equilibration of inorganic carbon species in the medium entails a new dimension of complexity. Recently, a novel tailor-made microfluidics labelling system has been introduced, supplying short 13CO2 pulses at steady state, and resolving fluxes across most photosynthetic metabolic pathways in algae. The system involves injecting algal cultures and medium containing pre-equilibrated inorganic 13C into a microfluidic mixer, followed by rapid metabolic quenching, enabling precise seconds-level label pulses. This was complemented by a 13CO2-bubbling-based open labelling system (photobioreactor), allowing long pulses (minutes-hours) required for investigating fluxes into central C metabolism and major products. This combined labelling procedure provides a comprehensive fluxome cover for most algal photosynthetic and central C metabolism pathways, thus allowing comparative flux analyses across algae and plants.

Assessing the growth kinetics and stoichiometry of Escherichia coli at the single-cell level

Microfluidic cultivation and single-cell analysis are inherent parts of modern microbial biotechnology and microbiology. However, implementing biochemical engineering principles based on the kinetics and stoichiometry of growth in microscopic spaces remained unattained. We here present a novel integrated framework that utilizes distinct microfluidic cultivation technologies and single-cell analytics to make the fundamental math of process-oriented biochemical engineering applicable at the single-cell level. A combination of non-invasive optical cell mass determination with sub-pg sensitivity, microfluidic perfusion cultivations for establishing physiological steady-states, and picoliter batch reactors, enabled the quantification of all physiological parameters relevant to approximate a material balance in microfluidic reaction environments. We determined state variables (biomass concentration based on single-cell dry weight and mass density), biomass synthesis rates, and substrate affinities of cells grown in microfluidic environments. Based on this data, we mathematically derived the specific kinetics of substrate uptake and growth stoichiometry in glucose-grown Escherichia coli with single-cell resolution. This framework may initiate microscale material balancing beyond the averaged values obtained from populations as a basis for integrating heterogeneous kinetic and stoichiometric single-cell data into generalized bioprocess models and descriptions.

An excess of glycolytic enzymes under glucose-limited conditions may enable Saccharomyces cerevisiae to adapt to nutrient availability

Microorganisms, including the budding yeast Saccharomyces cerevisiae, express glycolytic proteins to a maximal capacity that (largely) exceeds the actual flux through the enzymes, especially at low growth rates. An open question is if this apparent expression level is really an overcapacity, or maintains the (optimal) enzyme capacity needed to carry flux at (very) low substrate availability. Here, we use computational modelling to suggest that yeast maintains a genuine excess of glycolytic enzymes at low specific growth rates. During fast fermentative growth at high glucose levels, the observed expression of the glycolytic enzymes matched the predicted optimal levels. We suggest that the excess glycolytic capacity at low glucose levels is a preparatory strategy in the adaptation to sugar fluctuations in the environment.

Metabolic engineering of Kluyveromyces marxianus for biomass-based applications

Kluyveromyces marxianus ATCC 26,548 was cultivated in aerobic chemostats with [1-13C] and [U-13C] glucose as carbon source under three different growth conditions (0.10, 0.25, and 0.5 h-1) to evaluate metabolic fluxes. Carbon balances closed always within 97-102%. Growth was carbon limited, and the cell yield on glucose was the same. The extracellular side-product formation was very low, totaling 0.0008 C-mol C-mol-1 substrate at 0.5 h-1. The intracellular flux ratios did not show significant variation for metabolic flux analysis from labelling and biomass composition and metabolic flux ratio analysis from labelling. The observed strictly oxidative metabolism and the stability of the metabolism in terms of fluxes even at high growth rates, without triggering out the synthesis of by-products, is an extremely desired condition that underlines the potential of K. marxianus for biotechnological biomass-related applications and the comprehension of the metabolic pools and pathways is an important step to engineering this organism.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03324-x.

Real-Time Monitoring of Dynamic Microbial Fe(III) Respiration Metabolism with a Living Cell-Compatible Electron-Sensing Probe

Monitoring microbial metabolism is vital for biomanufacturing processes optimization. However, it remains a grand challenge to offer insight into microbial metabolism due to particularly complex and dynamic processes. Here, we report an electron-sensing probe Zn₂ GeO₄ :Mn@Fe³⁺ for real-time and dynamic monitoring of Fe(III) respiration metabolism. The quenched persistent luminescence of Zn₂ GeO4:Mn@Fe³⁺ is recovered when Fe³⁺ accepted electrons from the dynamic Fe(III) respiration metabolism, enabling the real-time monitoring of microbial metabolism. The probe shows the capability to verify the role of related biomolecules in microbial Fe(III) respiration metabolism, to track the dynamic Fe(III) respiration metabolic response to environmental stress and microbial co-culture interactions. Furthermore, the Zn₂ GeO₄ :Mn@Fe³⁺ probe provides guidance for improving biosynthesis efficiency by monitoring Fe redox recycling in microbial co-culture.

Pyruvic acid stress caused color attenuation by interfering with anthocyanins metabolism during alcoholic fermentation

Anthocyanin accounts for wine color performance, while it is susceptive to saccharomyces cerevisiae, causing threatened stability. Considering pyranoanthocyanin performed better color and stability, converting anthocyanins to pyranoanthocyanins in advance during fermentation was an ideal way for color improvement. Thus, pyruvic acid (PA) as the precursor of vitisin A was applied to fermentation with cyanidin-3-O-glucoside (C3G). Results showed that PA-stress leads to a color loss associated with a decrease in C3G and cyanidin. However, the content of pyranoanthocyanins under PA stress is unvaried. LC-MS-based non-target metabolomics revealed that superfluous PA can disturb the process of glycolysis and tricarboxylic acid cycle. Importantly, 1291 molecular features were increased and 1122 were decreased under PA-stress, in which several anthocyanins derivatization and isomerization were changed, contributing to color performance. This study indicated that extra PA is unfriendly to anthocyanins during fermentation, playing an adverse effect on color, which should be avoided in wine production.

Burden Imposed by Heterologous Protein Production in Two Major Industrial Yeast Cell Factories: Identifying Sources and Mitigation Strategies

Production of heterologous proteins, especially biopharmaceuticals and industrial enzymes, in living cell factories consumes cellular resources. Such resources are reallocated from normal cellular processes toward production of the heterologous protein that is often of no benefit to the host cell. This competition for resources is a burden to host cells, has a negative impact on cell fitness, and may consequently trigger stress responses. Importantly, this often causes a reduction in final protein titers. Engineering strategies to generate more burden resilient production strains offer sustainable opportunities to increase production and profitability for this growing billion-dollar global industry. We review recently reported impacts of burden derived from resource competition in two commonly used protein-producing yeast cell factories: Saccharomyces cerevisiae and Komagataella phaffii (syn. Pichia pastoris). We dissect possible sources of burden in these organisms, from aspects related to genetic engineering to protein translation and export of soluble protein. We also summarize advances as well as challenges for cell factory design to mitigate burden and increase overall heterologous protein production from metabolic engineering, systems biology, and synthetic biology perspectives. Lastly, future profiling and engineering strategies are highlighted that may lead to constructing robust burden-resistant cell factories. This includes incorporation of systems-level data into mathematical models for rational design and engineering dynamical regulation circuits in production strains.

Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants

Photosynthesis-related pathways are regarded as a promising avenue for crop improvement. Whilst empirical studies have shown that photosynthetic efficiency is higher in microalgae than in C3 or C4 crops, the underlying reasons remain unclear. Using a tailor-made microfluidics labelling system to supply 13CO2 at steady state, we investigated in vivo labelling kinetics in intermediates of the Calvin Benson cycle and sugar, starch, organic acid and amino acid synthesis pathways, and in protein and lipids, in Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii, which is the fastest growing green alga on record. We estimated flux patterns in these algae and compared them with published and new data from C3 and C4 plants. Our analyses identify distinct flux patterns supporting faster growth in photosynthetic cells, with some of the algae exhibiting faster ribulose 1,5-bisphosphate regeneration and increased fluxes through the lower glycolysis and anaplerotic pathways towards the tricarboxylic acid cycle, amino acid synthesis and lipid synthesis than in higher plants.

Metabolomics-driven Approaches on Interactions Between Enterococcus faecalis and Candida albicans Biofilms

Objectives

This study aimed to determine the effect of Enterococcus faecalis on the cell growth and hyphal formation of Candida albicans and to understand the exact mechanism of candidal inhibition by the existence of E. faecalis by metabolomic analysis.

Materials and Methods

Single- and dual-species biofilms of E. faecalis and C. albicans were formed in a microtiter plate, and the metabolomic profiles of both biofilms was determined by gas chromatography-mass spectrometry. The hyphal cell growth of C. albicans after treatment with both the supernatant and biofilm cells of E. faecalis was examined microscopically. The expression levels of Efg1 and the images of C. albicans cell wall in single- and dual-species biofilms were determined by real-time quantitative polymerase chain reaction and transmission electron microscopy, respectively. The violacein levels produced by Chromobacterium violaceum were measured to determine the quorum sensing (QS) inhibitory activity of single- and dual-species biofilms.

Results

The biofilm cell growth, Efg1 expression, and hyphal development of C. albicans were inhibited by E. faecalis. Compared to single-species biofilms, alterations in carbohydrate, amino acid, and polyamine metabolites were observed in the dual-species biofilm for both microorganisms. Putrescine and pipecolic acid were detected at high levels in dual-species biofilm. A thicker β-glucan chitin and a denser and narrower fibrillar mannan layer of C. albicans cell wall were observed in dual-species biofilm. QS inhibitory activity was higher in dual-species biofilm suspensions of E. faecalis and C. albicans than in their single-species biofilms.

Conclusion

E. faecalis inhibited the hyphal development and biofilm formation of C. albicans. Biofilm suspensions of C. albicans and E. faecalis showed an anti-QS activity, which increased even further in the environment where the two species coexisted. Investigation of putrescine and pipecolic acid can be an important step to understand the inhibition of C. albicans by bacteria.

Improving ethanol production by studying the effect of pH using a modified metabolic model and a systemic approach

pH is an important factor affecting the growth and production of microorganisms; especially, its effect on ethanologenic microorganisms. It can change the ionization state of metabolites via the change in the charge of their functional groups that may lead to metabolic alteration. Here, we estimated the ionization state of metabolites and balanced the charge of reactions in genome-scale metabolic models of Saccharomyces cerevisiae, Escherichia coli, and Zymomonas mobilis at pH levels 5, 6, and 7. The robustness analysis was first implemented to anticipate the effect of proton exchange flux on growth rates for the constructed metabolic models at various pH. In accordance with previous experimental reports, the models predict that Z. mobilis is more sensitive to pH rather than S. cerevisiae and the yeast is more regulated by pH rather than E. coli. Then, a systemic approach was proposed to predict the pH effect on metabolic change and to find effective reactions on ethanol production in S. cerevisiae. The correlated reactions with ethanol production at predicted optimal pH in a range of proton exchange rates determined by robustness analysis were identified using the Pearson correlation coefficient. Then, fluxes of these reactions were applied to cluster the various pHs by principal component analysis and to identify the role of these reactions on metabolic differentiation because of pH change. Finally, 12 reactions were selected for up and downregulation to improve ethanol production. Enzyme regulators of the selected reactions were identified using the BRENDA database and 11 selected regulators were screened and optimized via Plackett-Burman and two-level full factorial designs, respectively. The proposed approach has enhanced yields of ethanol from 0.18 to 0.36 mol/mol carbon. Hence, not only a comprehensive approach for understanding the effect of pH on metabolism was proposed in this study, but also it successfully introduced key manipulations for ethanol overproduction.

Stress-induced growth rate reduction restricts metabolic resource utilization to modulate osmo-adaptation time

A near-constant feature of stress responses is a downregulation or arrest of the cell cycle, resulting in transient growth slowdown. To investigate the role of growth slowdown in the hyperosmotic shock response of S. cerevisiae, we perturbed the G1/S checkpoint protein Sic1 to enable osmo-stress response activation with diminished growth slowdown. We document that in this mutant, adaptation to stress is accelerated rather than delayed. This accelerated recovery of the mutant proceeds by liquidation of internal glycogen stores, which are then shunted into the osmo-shock response. Therefore, osmo-adaptation in wild-type cells is delayed because growth slowdown prevents full accessibility to cellular glycogen stores. However, faster adaptation comes at the cost of acute sensitivity to subsequent osmo-stresses. We suggest that stress-induced growth slowdown acts as an arbiter to regulate the resources devoted to osmo-shock, balancing short-term adaptation with long-term robustness.

A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering

Background

Sub-cellular compartmentalization is used by cells to create favorable microenvironments for various metabolic reactions. These compartments concentrate enzymes, separate competing metabolic reactions, and isolate toxic intermediates. Such advantages have been recently harnessed by metabolic engineers to improve the production of various high-value chemicals via compartmentalized metabolic engineering. However, measuring sub-cellular concentrations of key metabolites represents a grand challenge for compartmentalized metabolic engineering.

Methods

To this end, we developed a synthetic biosensor to measure a key metabolite, acetyl-CoA, in a representative compartment of yeast, the peroxisome. This synthetic biosensor uses enzyme re-localization via PTS1 signal peptides to construct a metabolic pathway in the peroxisome which converts acetyl-CoA to polyhydroxybutyrate (PHB) via three enzymes. The PHB is then quantified by HPLC.

Results

The biosensor demonstrated the difference in relative peroxisomal acetyl-CoA availability under various culture conditions and was also applied to screening a library of single knockout yeast mutants. The screening identified several mutants with drastically reduced peroxisomal acetyl-CoA and one with potentially increased levels. We expect our synthetic biosensors can be widely used to investigate sub-cellular metabolism and facilitate the “design-build-test” cycle of compartmentalized metabolic engineering.

Nitrate removal characteristics and 13C metabolic pathways of aerobic denitrifying bacterium Paracoccus denitrificans Z195

Strain Z195 was isolated and identified as Paracoccus denitrificans. Z195 exhibited efficient aerobic denitrification and carbon removal abilities, and removed 93.74% of total nitrogen (TN) and 97.81% of total organic carbon.71.88% of nitrogen was lost as gaseous products.¹³C-metabolic flux analysis revealed that 95% and 132% of the carbon fluxes entered the Entner-Doudoroff (ED) pathway and tricarboxylic acid (TCA) cycle, respectively. Electrons produced by carbon metabolism markedly promoted the processes of nitrogen metabolism process and aerobic respiration. A response surface methodology model demonstrated that the optimal conditions for the maximum TN removal were a C/N ratio of 7.47, shaking speed of 108 rpm, temperature of 31 °C and initial pH of 8.02. Additionally, the average TN and chemical oxygen demand removal efficiencies of raw wastewater were 89% and 91%, respectively. The results give new insight for understanding metabolic flux analysis of aerobic denitrifying bacteria.

Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

Microbial co-cultures have been used in several biotechnological applications. Within these co-cultures, the microorganisms tend to interact with each other and perform complex actions. Investigating metabolic interactions in microbial co-cultures is crucial in designing microbial consortia. Here, we present a pipeline integrating modelling and experimental approaches to understand metabolic interactions between organisms in a community. We define a new index named "Metabolic Support Index (MSI)", which quantifies the benefits derived by each organism in the presence of the other when grown as a co-culture. We computed MSI for several experimentally demonstrated co-cultures and showed that MSI, as a metric, accurately identifies the organism that derives the maximum benefit. We also computed MSI for a commonly used yeast co-culture consisting of Saccharomyces cerevisiae and Pichia stipitis and observed that the latter derives higher benefit from the interaction. Further, we designed two-stage experiments to study mutual interactions and showed that P. stipitis indeed derives the maximum benefit from the interaction, as shown from our computational predictions. Also, using our previously developed computational tool MetQuest, we identified all the metabolic exchanges happening between these organisms by analysing the pathways spanning the two organisms. By analysing the HPLC profiles and studying the isotope labelling, we show that P. stipitis consumes the ethanol produced by S. cerevisiae when grown on glucose-rich medium under aerobic conditions, as also indicated by our in silico pathway analyses. Our approach represents an important step in understanding metabolic interactions in microbial communities through an integrated computational and experimental workflow.

Tracing metabolic flux through time and space with isotope labeling experiments

Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.

Chemical Compositions of Propolis from China and the United States and their Antimicrobial Activities Against Penicillium notatum

The chemical compositions of ethanol extracts of propolis from China (EEP-C) and the United States (EEP-A) and their antifungal activity against Penicillium notatum were determined. The result showed that a total of 49 compounds were detected by UPLC-Q-TOF-MS, 30 of which were present in samples from two regions. The major compounds of EEP-C and EEP-A were similar, including pinocembrin, pinobanksin-3-O-acetate, galanin, chrysin, pinobanksin, and pinobanksin-methyl ether, and both of them showed antifungal activity against P. notatum with same minimum inhibitory concentration (MIC) value of 0.8 mg·mL-1. In the presence of propolis, the mycelial growth was inhibited, the hyphae became shriveled and wrinkled, the extracellular conductivities were increased, and the activities of succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) were decreased. In addition, iTRAQ-based quantitative proteomic analysis of P. notatum in response to propolis revealed that a total of 341 proteins were differentially expressed, of which 88 (25.8%) were upregulated and 253 (74.2%) were downregulated. Meanwhile, the differentially expressed proteins (DEPs) involved in energy production and conversion, carbohydrate transport and metabolism, and the sterol biosynthetic pathway were identified. This study revealed that propolis could affect respiration, interfere with energy metabolism, and influence steroid biosynthesis to inhibit the growth of P. notatum.

Elevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts

BACKGROUND

Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of thermotolerance in yeast impede its full comprehension and the rare physiological data at elevated temperatures has so far not been matched with corresponding metabolic analyses.

RESULTS

To elaborate on the metabolic network response to increased fermentation temperatures of up to 49 °C, comprehensive physiological datasets of several Kluyveromyces and Ogataea strains were generated and used for 13C-metabolic flux analyses. While the maximum growth temperature was very similar in all investigated strains, the metabolic network response to elevated temperatures was not conserved among the different species. In fact, metabolic flux distributions were remarkably irresponsive to increasing temperatures in O. polymorpha, while the K. marxianus strains exhibited extensive flux rerouting at elevated temperatures.

CONCLUSIONS

While a clear mechanism of thermotolerance is not deducible from the fluxome level alone, the generated data can be valued as a knowledge repository for using temperature to modulate the metabolic activity towards engineering goals.

'Candidatus Liberibacter asiaticus' and Its Vector, Diaphorina citri, Augment the Tricarboxylic Acid Cycle of Their Host via the γ-Aminobutyric Acid Shunt and Polyamines Pathway

Huanglongbing (HLB), a destructive citrus disease, is associated with 'Candidatus Liberibacter asiaticus', which is transmitted by the Asian citrus psyllid Diaphorina citri. Both 'Ca. L. asiaticus' and its vector manipulate the host metabolism for their benefit, to meet their nutritional needs and neutralize the host defense responses. We used a targeted gas chromatography-mass spectrometry-based method to explore the connection between the tricarboxylic acid (TCA) cycle, γ-aminobutyric acid (GABA) shunt, and polyamines (PAs) pathways in citrus. 'Ca. L. asiaticus' and D. citri accelerated the conversion of α-ketoglutarate to glutamate, then to GABA, causing an accumulation of GABA in the cytosol. In silico analysis showed that the citrus genome possesses a putative GABA permease that connects the GABA shunt with the TCA cycle and supports the accumulation of succinate, fumarate, and citrate. Additionally, the PAs biosynthetic pathway might be connected directly to the TCA cycle, through the production of fumarate, or indirectly, via enhancement of GABA shunt. Taken together, we suggest that GABA shunt and PAs pathways are alternative pathways that contribute to the flux toward succinate rather than an intact TCA cycle in citrus. Both 'Ca. L. asiaticus' and its vector enhance these pathways. This study provides more insights into citrus responses to the HLB pathosystem and could be a further step toward clues for understanding the nutritional needs of 'Ca. L. asiaticus', which could help in culturing 'Ca. L. asiaticus'.

Methionine supplementation stimulates mitochondrial respiration

Mitochondria play essential metabolic functions in eukaryotes. Although their major role is the generation of energy in the form of ATP, they are also involved in maintenance of cellular redox state, conversion and biosynthesis of metabolites and signal transduction. Most mitochondrial functions are conserved in eukaryotic systems and mitochondrial dysfunctions trigger several human diseases. By using multi-omics approach, we investigate the effect of methionine supplementation on yeast cellular metabolism, considering its role in the regulation of key cellular processes. Methionine supplementation induces an up-regulation of proteins related to mitochondrial functions such as TCA cycle, electron transport chain and respiration, combined with an enhancement of mitochondrial pyruvate uptake and TCA cycle activity. This metabolic signature is more noticeable in cells lacking Snf1/AMPK, the conserved signalling regulator of energy homeostasis. Remarkably, snf1Δ cells strongly depend on mitochondrial respiration and suppression of pyruvate transport is detrimental for this mutant in methionine condition, indicating that respiration mostly relies on pyruvate flux into mitochondrial pathways. These data provide new insights into the regulation of mitochondrial metabolism and extends our understanding on the role of methionine in regulating energy signalling pathways.

The combination of NAD+-dependent deacetylase gene deletion and the interruption of gluconeogenesis causes increased glucose metabolism in budding yeast

Metabolic engineering focuses on rewriting the metabolism of cells to enhance native products or endow cells with the ability to produce new products. This engineering has the potential for wide-range application, including the production of fuels, chemicals, foods and pharmaceuticals. Glycolysis manages the levels of various secondary metabolites by controlling the supply of glycolytic metabolites. Metabolic reprogramming of glycolysis is expected to cause an increase in the secondary metabolites of interest. In this study, we constructed a budding yeast strain harboring the combination of triple sirtuin gene deletion (hst3∆ hst4∆ sir2∆) and interruption of gluconeogenesis by the deletion of the FBP1 gene encoding fructose-1,6-bisphosphatase (fbp1∆). hst3∆ hst4∆ sir2∆ fbp1∆ cells harbored active glycolysis with high glucose consumption and active ethanol productivity. Using capillary electrophoresis–time-of-flight mass spectrometry (CE–TOF/MS) analysis, hst3∆ hst4∆ sir2∆ fbp1∆ cells accumulated not only glycolytic metabolites but also secondary metabolites, including nucleotides that were synthesized throughout the pentose phosphate (PP) pathway, although various amino acids remained at low levels. Using the stable isotope labeling assay for metabolites, we confirmed that hst3∆ hst4∆ sir2∆ fbp1∆ cells directed the metabolic fluxes of glycolytic metabolites into the PP pathway. Thus, the deletion of three sirtuin genes (HST3, HST4 and SIR2) and the FBP1 gene can allow metabolic reprogramming to increase glycolytic metabolites and several secondary metabolites except for several amino acids.

Metabolic construction strategies for direct methanol utilization in Saccharomyces cerevisiae

The aim of this study was to metabolically construct Saccharomyces cerevisiae for achievement of direct methanol utilization and value added product (mainly pyruvate) production. After successful integration of methanol oxidation pathway originated from Pichia pastoris into the chromosome of S. cerevisiae, the recombinant showed 1.04g/L consumption of methanol and 3.13% increase of cell growth (OD₆₀₀) when using methanol as the sole carbon source. Moreover, 0.26g/L of pyruvate was detected in the fermentation broth. The supplementation of 1g/L yeast extract could further improve cell growth with increase of 11.70% and methanol consumption to 2.35g/L. This represents the first genetically modified non-methylotrophic eukaryotic microbe for direct methanol utilization and would be of great value concerning the development of biotechnological processes.

Comprehensive Real-Time Analysis of the Yeast Volatilome

While yeast is one of the most studied organisms, its intricate biology remains to be fully mapped and understood. This is especially the case when it comes to capture rapid, in vivo fluctuations of metabolite levels. Secondary electrospray ionization-high resolution mass spectrometry SESI-HRMS is introduced here as a sensitive and noninvasive analytical technique for online monitoring of microbial metabolic activity. The power of this technique is exemplarily shown for baker’s yeast fermentation, for which the time-resolved abundance of about 300 metabolites is demonstrated. The results suggest that a large number of metabolites produced by yeast from glucose neither are reported in the literature nor are their biochemical origins deciphered. With the technique demonstrated here, researchers interested in distant disciplines such as yeast physiology and food quality will gain new insights into the biochemical capability of this simple eukaryote.

Integration of the tricarboxylic acid (TCA) cycle with cAMP signaling and Sfl2 pathways in the regulation of CO2 sensing and hyphal development in Candida albicans

Morphological transitions and metabolic regulation are critical for the human fungal pathogen Candida albicans to adapt to the changing host environment. In this study, we generated a library of central metabolic pathway mutants in the tricarboxylic acid (TCA) cycle, and investigated the functional consequences of these gene deletions on C. albicans biology. Inactivation of the TCA cycle impairs the ability of C. albicans to utilize non-fermentable carbon sources and dramatically attenuates cell growth rates under several culture conditions. By integrating the Ras1-cAMP signaling pathway and the heat shock factor-type transcription regulator Sfl2, we found that the TCA cycle plays fundamental roles in the regulation of CO₂ sensing and hyphal development. The TCA cycle and cAMP signaling pathways coordinately regulate hyphal growth through the molecular linkers ATP and CO₂. Inactivation of the TCA cycle leads to lowered intracellular ATP and cAMP levels and thus affects the activation of the Ras1-regulated cAMP signaling pathway. In turn, the Ras1-cAMP signaling pathway controls the TCA cycle through both Efg1- and Sfl2-mediated transcriptional regulation in response to elevated CO₂ levels. The protein kinase A (PKA) catalytic subunit Tpk1, but not Tpk2, may play a major role in this regulation. Sfl2 specifically binds to several TCA cycle and hypha-associated genes under high CO₂ conditions. Global transcriptional profiling experiments indicate that Sfl2 is indeed required for the gene expression changes occurring in response to these elevated CO₂ levels. Our study reveals the regulatory role of the TCA cycle in CO₂ sensing and hyphal development and establishes a novel link between the TCA cycle and Ras1-cAMP signaling pathways.

Energy metabolism through the TCA cycle and mitochondrial electron transport are critical for the human fungal pathogen Candida albicans to survive and propagate in the host. This is, in part, due to the fact that C. albicans is a Crabtree-negative species, and thus exclusively uses respiration when oxygen is available. Here, we investigate the roles of the TCA cycle in hyphal development and CO₂ sensing in C. albicans. Through the use of ATP and the cellular signaling molecule CO₂, the TCA cycle integrates with the Ras1-cAMP signaling pathway, which is a central regulator of hyphal growth, to govern basic cellular biological processes. Together with Efg1, a downstream transcription factor of the cAMP signaling pathway, the heat shock factor-type transcription regulator Sfl2 controls CO₂-induced hyphal growth in C. albicans. Deletion of SFL2 results in the loss of global transcriptional responses under elevated CO₂ levels. Our study indicates that the TCA cycle not only occupies the central position of cellular metabolism but also regulates other biological processes such as CO₂ sensing and hyphal development through integration with the Ras1-cAMP signaling pathway in C. albicans.

Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism

¹³C metabolic flux analysis (¹³C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant of ¹³C MFA known as 2-Scale ¹³C metabolic flux analysis (2S-¹³C MFA). In this study, all strains have the galactose metabolism deactivated (gal1Δ background) so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP) flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specific growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments near a critical sugar ratio that is known to allow galactose to enter the cell. Additionally, we report a number of fluxomic changes associated with these growth rate increases and unexpected flux profile redistributions resulting from deletion of SIP1 in glucose-only medium.

Dynamic substrate preferences predict metabolic properties of a simple microbial consortium

Background

Mixed cultures of different microbial species are increasingly being used to carry out a specific biochemical function in lieu of engineering a single microbe to do the same task. However, knowing how different species’ metabolisms will integrate to reach a desired outcome is a difficult problem that has been studied in great detail using steady-state models. However, many biotechnological processes, as well as natural habitats, represent a more dynamic system. Examining how individual species use resources in their growth medium or environment (exometabolomics) over time in batch culture conditions can provide rich phenotypic data that encompasses regulation and transporters, creating an opportunity to integrate the data into a predictive model of resource use by a mixed community.

Results

Here we use exometabolomic profiling to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by two Pseudomonas and one Bacillus species isolated from ground water. Contrary to studies in model organisms, we found surprisingly few correlations between resource preferences and maximal growth rate or biomass composition. We then modeled patterns of substrate depletion, and used these models to examine if substrate usage preferences and substrate depletion kinetics of individual isolates can be used to predict the metabolism of a co-culture of the isolates. We found that most of the substrates fit the model predictions, except for glucose and histidine, which were depleted more slowly than predicted, and proline, glycine, glutamate, lysine and arginine, which were all consumed significantly faster.

Conclusions

Our results indicate that a significant portion of a model community’s overall metabolism can be predicted based on the metabolism of the individuals. Based on the nature of our model, the resources that significantly deviate from the prediction highlight potential metabolic pathways affected by species-species interactions, which when further studied can potentially be used to modulate microbial community structure and/or function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1478-2) contains supplementary material, which is available to authorized users.

The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-production

The growth characteristics and underlying metabolism of microbial production hosts are critical to the productivity of metabolically engineered pathways. Production in parallel with growth often leads to biomass/bio-product competition for carbon. The growth arrest phenotype associated with the Saccharomyces cerevisiae pheromone-response is potentially an attractive production phase because it offers the possibility of decoupling production from population growth. However, little is known about the metabolic phenotype associated with the pheromone-response, which has not been tested for suitability as a production phase. Analysis of extracellular metabolite fluxes, available transcriptomic data, and heterologous compound production (para-hydroxybenzoic acid) demonstrate that a highly active and distinct metabolism underlies the pheromone-response. These results indicate that the pheromone-response is a suitable production phase, and that it may be useful for informing synthetic biology design principles for engineering productive stationary phase phenotypes.

Phenotypic plasticity within yeast colonies: differential partitioning of cell fates

Across many phyla, a common aspect of multicellularity is the organization of different cell types into spatial patterns. In the budding yeast Saccharomyces cerevisiae, after diploid colonies have completed growth, they differentiate to form alternating layers of sporulating cells and feeder cells. In the current study, we found that as yeast colonies developed, the feeder cell layer was initially separated from the sporulating cell layer. Furthermore, the spatial pattern of sporulation in colonies depended on the colony's nutrient environment; in two environments in which overall colony sporulation efficiency was very similar, the pattern of feeder and sporulating cells within the colony was very different. As noted previously, under moderately suboptimal conditions for sporulation-low acetate concentration or high temperature-the number of feeder cells increases as does the dependence of sporulation on the feeder-cell transcription factor, Rlm1. Here we report that even under a condition that is completely blocked sporulation, the number of feeder cells still increased. These results suggest broader implications to our recently proposed "Differential Partitioning provides Environmental Buffering" or DPEB hypothesis.

Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway

Background

In the future, oil- and gas-derived polymers may be replaced with bio-based polymers, produced from renewable feedstocks using engineered cell factories. Acrylic acid and acrylic esters with an estimated world annual production of approximately 6 million tons by 2017 can be derived from 3-hydroxypropionic acid (3HP), which can be produced by microbial fermentation. For an economically viable process 3HP must be produced at high titer, rate and yield and preferably at low pH to minimize downstream processing costs.

Results

Here we describe the metabolic engineering of baker’s yeast Saccharomyces cerevisiae for biosynthesis of 3HP via a malonyl-CoA reductase (MCR)-dependent pathway. Integration of multiple copies of MCR from Chloroflexus aurantiacus and of phosphorylation-deficient acetyl-CoA carboxylase ACC1 genes into the genome of yeast increased 3HP titer fivefold in comparison with single integration. Furthermore we optimized the supply of acetyl-CoA by overexpressing native pyruvate decarboxylase PDC1, aldehyde dehydrogenase ALD6, and acetyl-CoA synthase from Salmonella entericaSEacs^L641P. Finally we engineered the cofactor specificity of the glyceraldehyde-3-phosphate dehydrogenase to increase the intracellular production of NADPH at the expense of NADH and thus improve 3HP production and reduce formation of glycerol as by-product. The final strain produced 9.8 ± 0.4 g L⁻¹ 3HP with a yield of 13 % C-mol C-mol⁻¹ glucose after 100 h in carbon-limited fed-batch cultivation at pH 5. The 3HP-producing strain was characterized by ¹³C metabolic flux analysis and by transcriptome analysis, which revealed some unexpected consequences of the undertaken metabolic engineering strategy, and based on this data, future metabolic engineering directions are proposed.

Conclusions

In this study, S. cerevisiae was engineered for high-level production of 3HP by increasing the copy numbers of biosynthetic genes and improving flux towards precursors and redox cofactors. This strain represents a good platform for further optimization of 3HP production and hence an important step towards potential commercial bio-based production of 3HP.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0451-5) contains supplementary material, which is available to authorized users.

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.

Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae

A mass spectrometry–based tandem mass tag 9-plex strategy was used to determine alterations in relative protein abundance due to three carbon sources—glucose, galactose, and raffinose. More than 4700 proteins were quantified across all nine samples; 1003 demonstrated statistically significant differences in abundance in at least one condition.

The global proteomic alterations in the budding yeast Saccharomyces cerevisiae due to differences in carbon sources can be comprehensively examined using mass spectrometry–based multiplexing strategies. In this study, we investigate changes in the S. cerevisiae proteome resulting from cultures grown in minimal media using galactose, glucose, or raffinose as the carbon source. We used a tandem mass tag 9-plex strategy to determine alterations in relative protein abundance due to a particular carbon source, in triplicate, thereby permitting subsequent statistical analyses. We quantified more than 4700 proteins across all nine samples; 1003 proteins demonstrated statistically significant differences in abundance in at least one condition. The majority of altered proteins were classified as functioning in metabolic processes and as having cellular origins of plasma membrane and mitochondria. In contrast, proteins remaining relatively unchanged in abundance included those having nucleic acid–related processes, such as transcription and RNA processing. In addition, the comprehensiveness of the data set enabled the analysis of subsets of functionally related proteins, such as phosphatases, kinases, and transcription factors. As a resource, these data can be mined further in efforts to understand better the roles of carbon source fermentation in yeast metabolic pathways and the alterations observed therein, potentially for industrial applications, such as biofuel feedstock production.

Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

Recent advances in 13C-Metabolic flux analysis (13C-MFA) have increased its capability to accurately resolve fluxes using a genome-scale model with narrow confidence intervals without pre-judging the activity or inactivity of alternate metabolic pathways. However, the necessary precautions, computational challenges, and minimum data requirements for successful analysis remain poorly established. This review aims to establish the necessary guidelines for performing 13C-MFA at the genome-scale for a compartmentalized eukaryotic system such as yeast in terms of model and data requirements, while addressing key issues such as statistical analysis and network complexity. We describe the various approaches used to simplify the genome-scale model in the absence of sufficient experimental flux measurements, the availability and generation of reaction atom mapping information, and the experimental flux and metabolite labeling distribution measurements to ensure statistical validity of the obtained flux distribution. Organism-specific challenges such as the impact of compartmentalization of metabolism, variability of biomass composition, and the cell-cycle dependence of metabolism are discussed. Identification of errors arising from incorrect gene annotation and suggested alternate routes using MFA are also highlighted.

How to measure metabolic fluxes: a taxonomic guide for (13)C fluxomics

Metabolic reaction rates (fluxes) contribute fundamentally to our understanding of metabolic phenotypes and mechanisms of cellular regulation. Stable isotope-based fluxomics integrates experimental data with biochemical networks and mathematical modeling to 'measure' the in vivo fluxes within an organism that are not directly observable. In recent years, (13)C fluxomics has evolved into a technology with great experimental, analytical, and mathematical diversity. This review aims at establishing a unified taxonomy by means of which the various fluxomics methods can be compared to each other. By linking the developed modeling approaches to recent studies, their challenges and opportunities are put into perspective. The proposed classification serves as a guide for scientific 'travelers' who are striving to resolve research questions with the currently available (13)C fluxomics toolset.

A minimal growth medium for the basidiomycete Pleurotus sapidus for metabolic flux analysis

Background

Pleurotus sapidus secretes a huge enzymatic repertoire including hydrolytic and oxidative enzymes and is an example for higher basidiomycetes being interesting for biotechnology. The complex growth media used for submerged cultivation limit basic physiological analyses of this group of organisms. Using undefined growth media, only little insights into the operation of central carbon metabolism and biomass formation, i.e., the interplay of catabolic and anabolic pathways, can be gained.

Results

The development of a chemically defined growth medium allowed rapid growth of P. sapidus in submerged cultures. As P. sapidus grew extremely slow in salt medium, the co-utilization of amino acids using ¹³C-labelled glucose was investigated by gas chromatography–mass spectrometry (GC-MS) analysis. While some amino acids were synthesized up to 90% in vivo from glucose (e.g., alanine), asparagine and/or aspartate were predominantly taken up from the medium. With this information in hand, a defined yeast free salt medium containing aspartate and ammonium nitrate as a nitrogen source was developed. The observed growth rates of P. sapidus were well comparable with those previously published for complex media. Importantly, fast growth could be observed for 4 days at least, up to cell wet weights (CWW) of 400 g L^-1. The chemically defined medium was used to carry out a ¹³C-based metabolic flux analysis, and the in vivo reactions rates in the central carbon metabolism of P. sapidus were investigated. The results revealed a highly respiratory metabolism with high fluxes through the pentose phosphate pathway and TCA cycle.

Conclusions

The presented chemically defined growth medium enables researchers to study the metabolism of P. sapidus, significantly enlarging the analytical capabilities. Detailed studies on the production of extracellular enzymes and of secondary metabolites of P. sapidus may be designed based on the reported data.

Electronic supplementary material

The online version of this article (doi:10.1186/s40694-014-0009-4) contains supplementary material, which is available to authorized users.

Dynamic flux balance analysis for synthetic microbial communities

Dynamic flux balance analysis (DFBA) is an extension of classical flux balance analysis that allows the dynamic effects of the extracellular environment on microbial metabolism to be predicted and optimised. Recently this computational framework has been extended to microbial communities for which the individual species are known and genome-scale metabolic reconstructions are available. In this review, the authors provide an overview of the emerging DFBA approach with a focus on two case studies involving the conversion of mixed hexose/pentose sugar mixtures by synthetic microbial co-culture systems. These case studies illustrate the key requirements of the DFBA approach, including the incorporation of individual species metabolic reconstructions, formulation of extracellular mass balances, identification of substrate uptake kinetics, numerical solution of the coupled linear program/differential equations and model adaptation for common, suboptimal growth conditions and identified species interactions. The review concludes with a summary of progress to date and possible directions for future research.

Synthetic promoter library for modulation of actinorhodin production in Streptomyces coelicolor A3(2)

The objective of this study was the application of the synthetic promoter library (SPL) technology for modulation of actinorhodin production in Streptomyces coelicolor A3(2). The SPL technology was used to optimize the expression of a pathway specific positive transcriptional regulator ActII orf4, which activates the transcription of the S. coelicolor actinorhodin biosynthetic gene cluster. The native actII orf4 promoter was replaced with synthetic promoters, generating a S. coelicolor library with a broad range of expression levels of actII orf4. The resulting library was screened based on the yield of actinorhodin. Selected strains were further physiologically characterized. One of the strains from the library, ScoSPL20, showed considerably higher yield of actinorhodin and final actinorhodin titer, compared to S. coelicolor wild type and S. coelicolor with actII orf4 expressed from a strong constitutive promoter. ScoSPL20 demonstrated exceptional productivity despite having a comparatively weak expression from the promoter. Interestingly, the ScoSPL20 promoter was activated at a much earlier stage of growth compared to the wild type, demonstrating the advantage of fine-tuning and temporal tuning of gene expression in metabolic engineering. Transcriptome studies were performed in exponential and actinorhodin-producing phase of growth to compare gene expression between ScoSPL20 and the wild type. To our knowledge, this is the first successful application of the SPL technology for secondary metabolite production in filamentous bacteria.

Molar-based targeted metabolic profiling of cyanobacterial strains with potential for biological production

Recently, cyanobacteria have become one of the most attractive hosts for biochemical production due to its high proliferative ability and ease of genetic manipulation. Several researches aimed at biological production using modified cyanobacteria have been reported previously. However, to improve the yield of bioproducts, a thorough understanding of the intercellular metabolism of cyanobacteria is necessary. Metabolic profiling techniques have proven to be powerful tools for monitoring cellular metabolism of various organisms and can be applied to elucidate the details of cyanobacterial metabolism. In this study, we constructed a metabolic profiling method for cyanobacteria using 13C-labeled cell extracts as internal standards. Using this method, absolute concentrations of 84 metabolites were successfully determined in three cyanobacterial strains which are commonly used as background strains for metabolic engineering. By comparing the differences in basic metabolic potentials of the three cyanobacterial strains, we found a well-correlated relationship between intracellular energy state and growth in cyanobacteria. By integrating our results with the previously reported biological production pathways in cyanobacteria, we found putative limiting step of carbon flux. The information obtained from this study will not only help gain insights in cyanobacterial physiology but also serve as a foundation for future metabolic engineering studies using cyanobacteria.

Saccharomyces cerevisiae vacuolar H+-ATPase regulation by disassembly and reassembly: one structure and multiple signals

Vacuolar H(+)-ATPases (V-ATPases) are highly conserved ATP-driven proton pumps responsible for acidification of intracellular compartments. V-ATPase proton transport energizes secondary transport systems and is essential for lysosomal/vacuolar and endosomal functions. These dynamic molecular motors are composed of multiple subunits regulated in part by reversible disassembly, which reversibly inactivates them. Reversible disassembly is intertwined with glycolysis, the RAS/cyclic AMP (cAMP)/protein kinase A (PKA) pathway, and phosphoinositides, but the mechanisms involved are elusive. The atomic- and pseudo-atomic-resolution structures of the V-ATPases are shedding light on the molecular dynamics that regulate V-ATPase assembly. Although all eukaryotic V-ATPases may be built with an inherent capacity to reversibly disassemble, not all do so. V-ATPase subunit isoforms and their interactions with membrane lipids and a V-ATPase-exclusive chaperone influence V-ATPase assembly. This minireview reports on the mechanisms governing reversible disassembly in the yeast Saccharomyces cerevisiae, keeping in perspective our present understanding of the V-ATPase architecture and its alignment with the cellular processes and signals involved.

¹³C-based metabolic flux analysis of recombinant Pichia pastoris

Overexpression of a foreign protein may negatively affect several cell growth parameters, as well as cause cellular stress. Central (or core) metabolism plays a crucial role since it supplies energy, reduction equivalents, and precursor molecules for the recombinant product, cell's maintenance, and growth needs. However, the number of quantitative physiology studies of the impact of recombinant protein production on the central metabolic pathways of yeast cell factories has been traditionally rather limited, thereby hampering the application of rational strain engineering strategies targeting central metabolism.The development and application of quantitative physiology and modelling tools and methodologies is allowing for a systems-level understanding of the effect of bioprocess parameters such as growth rate, temperature, oxygen availability, and substrate(s) choice on metabolism, and its subsequent interactions with recombinant protein synthesis, folding, and secretion.Here, we review the recent developments and applications of (13)C-based metabolic flux analysis ((13)C-MFA) of Pichia pastoris and the gained understanding of the metabolic behavior of this yeast in recombinant protein production bioprocesses. We also discuss the potential of multilevel studies integrating (13)C-MFA with other omics analyses, as well as future perspectives on the metabolic modelling approaches to study and design metabolic engineering strategies for improved protein production.

Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis

BACKGROUND

To engineer Saccharomyces cerevisiae for efficient xylose utilization, a fungal pathway consisting of xylose reductase, xylitol dehydrogenase, and xylulose kinase is often introduced to the host strain. Despite extensive in vitro studies on the xylose pathway, the intracellular metabolism rewiring in response to the heterologous xylose pathway remains largely unknown. In this study, we applied 13C metabolic flux analysis and stoichiometric modeling to systemically investigate the flux distributions in a series of xylose utilizing S. cerevisiae strains.

RESULTS

As revealed by 13C metabolic flux analysis, the oxidative pentose phosphate pathway was actively used for producing NADPH required by the fungal xylose pathway during xylose utilization of recombinant S. cerevisiae strains. The TCA cycle activity was found to be tightly correlated with the requirements of maintenance energy and biomass yield. Based on in silico simulations of metabolic fluxes, reducing the cell maintenance energy was found crucial to achieve the optimal xylose-based ethanol production. The stoichiometric modeling also suggested that both the cofactor-imbalanced and cofactor-balanced pathways could lead to optimal ethanol production, by flexibly adjusting the metabolic fluxes in futile cycle. However, compared to the cofactor-imbalanced pathway, the cofactor-balanced xylose pathway can lead to optimal ethanol production in a wider range of fermentation conditions.

CONCLUSIONS

By applying 13C-MFA and in silico flux balance analysis to a series of recombinant xylose-utilizing S. cerevisiae strains, this work brings new knowledge about xylose utilization in two aspects. First, the interplays between the fungal xylose pathway and the native host metabolism were uncovered. Specifically, we found that the high cell maintenance energy was one of the key factors involved in xylose utilization. Potential strategies to reduce the cell maintenance energy, such as adding exogenous nutrients and evolutionary adaptation, were suggested based on the in vivo and in silico flux analysis in this study. In addition, the impacts of cofactor balance issues on xylose utilization were systemically investigated. The futile pathways were identified as the key factor to adapt to different degrees of cofactor imbalances and suggested as the targets for further engineering to tackle cofactor-balance issues.

Improved polyhydroxybutyrate production by Saccharomyces cerevisiae through the use of the phosphoketolase pathway

The metabolic pathways of the central carbon metabolism in Saccharomyces cerevisiae are well studied and consequently S. cerevisiae has been widely evaluated as a cell factory for many industrial biological products. In this study, we investigated the effect of engineering the supply of precursor, acetyl-CoA, and cofactor, NADPH, on the biosynthesis of the bacterial biopolymer polyhydroxybutyrate (PHB), in S. cerevisiae. Supply of acetyl-CoA was engineered by over-expression of genes from the ethanol degradation pathway or by heterologous expression of the phophoketolase pathway from Aspergillus nidulans. Both strategies improved the production of PHB. Integration of gapN encoding NADP(+) -dependent glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans into the genome enabled an increased supply of NADPH resulting in a decrease in glycerol production and increased production of PHB. The strategy that resulted in the highest PHB production after 100 h was with a strain harboring the phosphoketolase pathway to supply acetyl-CoA without the need of increased NADPH production by gapN integration. The results from this study imply that during the exponential growth on glucose, the biosynthesis of PHB in S. cerevisiae is likely to be limited by the supply of NADPH whereas supply of acetyl-CoA as precursor plays a more important role in the improvement of PHB production during growth on ethanol.

Specific growth rate and substrate dependent polyhydroxybutyrate production in Saccharomyces cerevisiae

Production of the biopolymer polyhydroxybutyrate (PHB) in Saccharomyces cerevisiae starts at the end of exponential phase particularly when the specific growth rate is decreased due to the depletion of glucose in the medium. The specific growth rate and the type of carbon source (fermentable/non-fermentable) have been known to influence the cell physiology and hence affect the fermentability of S. cerevisiae. The production of PHB utilizes cytosolic acetyl-CoA as a precursor and the S. cerevisiae employed in this study is therefore a strain with the enhanced cytosolic acetyl-CoA supply. Growth and PHB production at different specific growth rates were evaluated on glucose, ethanol and a mixture of glucose and ethanol as carbon source. Ethanol as carbon source yielded a higher PHB production compared to glucose since it can be directly used for cytosolic acetyl-CoA production and hence serves as a precursor for PHB production. However, this carbon source results in lower biomass yield and hence it was found that to ensure both biomass formation and PHB production a mixture of glucose and ethanol was optimal, and this resulted in the highest volumetric productivity of PHB, 8.23 mg/L · h^-1, at a dilution rate of 0.1 h^-1.