Carole Molina-Jouve

Transcriptomic Analyses during the Transition from Biomass Production to Lipid Accumulation in the Oleaginous Yeast Yarrowia lipolytica

We previously developed a fermentation protocol for lipid accumulation in the oleaginous yeast Y. lipolytica. This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this experiment, a biomass concentration of 54.6 gCDW/l, with 0.18 g/gCDW lipid was obtained in ca. 32 h, with low citric acid production. A transcriptomic profiling was performed on 11 samples throughout the fermentation. Through statistical analyses, 569 genes were highlighted as differentially expressed at one point during the time course of the experiment. These genes were classified into 9 clusters, according to their expression profiles. The combination of macroscopic and transcriptomic profiles highlighted 4 major steps in the culture: (i) a growth phase, (ii) a transition phase, (iii) an early lipid accumulation phase, characterized by an increase in nitrogen metabolism, together with strong repression of protein production and activity; (iv) a late lipid accumulation phase, characterized by the rerouting of carbon fluxes within cells. This study explores the potential of Y. lipolytica as an alternative oil producer, by identifying, at the transcriptomic level, the genes potentially involved in the metabolism of oleaginous species.

Minimization of Glycerol Production during the High-Performance Fed-Batch Ethanolic Fermentation Process in Saccharomyces cerevisiae, Using a Metabolic Model as a Prediction Tool

ABSTRACT On the basis of knowledge of the biological role of glycerol in the redox balance of Saccharomyces cerevisiae, a fermentation strategy was defined to reduce the surplus formation of NADH, responsible for glycerol synthesis. A metabolic model was used to predict the operating conditions that would reduce glycerol production during ethanol fermentation. Experimental validation of the simulation results was done by monitoring the inlet substrate feeding during fed-batch S. cerevisiae cultivation in order to maintain the respiratory quotient (RQ) (defined as the CO2 production to O2 consumption ratio) value between 4 and 5. Compared to previous fermentations without glucose monitoring, the final glycerol concentration was successfully decreased. Although RQ-controlled fermentation led to a lower maximum specific ethanol production rate, it was possible to reach a high level of ethanol production: 85 g · liter−1 with 1.7 g · liter−1 glycerol in 30 h. We showed here that by using a metabolic model as a tool in prediction, it was possible to reduce glycerol production in a very high-performance ethanolic fermentation process.

Carbon accumulation in Rhodotorula glutinis induced by nitrogen limitation

BackgroundOleaginous microorganisms, such as bacterium, yeast and algal species, can represent an alternative oil source for biodiesel production. The composition of their accumulated lipid is similar to the lipid of an oleaginous plant with a predominance of unsaturated fatty acid. Moreover this alternative to conventional biodiesel production does not create competition for land use between food and oleo-chemical industry supplies. Despite this promising potential, development of microbial production processes are at an early stage. Nutritional limited conditions, such as nitrogen limitation, with an excess of carbon substrate is commonly used to induce lipid accumulation metabolism. Nitrogen limitation implies modification of the carbon-to-nitrogen ratio in culture medium, which impacts on carbon flow distribution in the metabolic network.ResultsThe goal of the present study is to improve our knowledge of carbon flow distribution in oleaginous yeast metabolism by focusing carbon distribution between carbohydrate and lipid pools in order to optimize microbial lipid production. The dynamic effects of limiting nitrogen consumption flux according to carbon flow were studied to trigger lipid accumulation in the oleaginous yeast Rhodotorula glutinis. With a decrease of the specific nitrogen consumption rate from 0.052 Nmol.CmolX−1.h−1 to 0.003 Nmol.CmolX−1.h−1, a short and transitory intracellular carbohydrate accumulation occurred before the lipid accumulation phase. This phenomenon was studied in fed-batch culture under optimal operating conditions, with a mineral medium and using glucose as carbon source. Two different strategies of decreasing nitrogen flow on carbohydrate accumulation were investigated: an instantaneous decrease and a progressive decrease of nitrogen flow.ConclusionsLipid production performance in these fed-batch culture strategies with R. glutinis were higher than those reported in the previous literature; the catalytic specific lipid production rate was 0.07 Cmollip.CmolX*−1.h−1. Experimental results suggested that carbohydrate accumulation was an intrinsic phenomenon connected to the limitation of growth by nitrogen when the nitrogen-to-carbon ratio in the feed flow was lower than 0.045 Nmol.Cmol−1. Carbohydrate accumulation corresponded to a 440% increase of carbohydrate content. These results suggest that microbial lipid production can be optimized by culture strategy and that carbohydrate accumulation must be taken account for process design.

Short-term dynamic behavior of Escherichia coli in response to successive glucose pulses on glucose-limited chemostat cultures.

The effect of repeated glucose perturbations on dynamic behavior of Escherichia coli DPD2085, yciG::LuxCDABE reporter strain, was studied and characterized on a short-time scale using glucose-limited chemostat cultures at dilution rates close to 0.18h(-1). The substrate disturbances were applied on independent steady-state cultures, firstly using a single glucose pulse under different aeration conditions and secondly using repeated glucose pulses under fully aerobic condition. The dynamic responses of E. coli to a single glucose pulse of different intensities (0.25 and 0.6gL(-1)) were significantly similar at macroscopic level, revealing the independency of the macroscopic microbial behavior to the perturbation intensity in the range of tested glucose concentrations. The dynamic responses of E. coli to repeated glucose pulses to simulate fluctuating environments between glucose-limited and glucose-excess conditions were quantified; similar behavior regarding respiration and by-product formations was observed, except for the first perturbation denoted by an overshoot of the specific oxygen uptake rate in the first minutes after the pulse. In addition, transcriptional induction of yciG promoter gene involved in general stress response, σ(S), was monitored through the bioluminescent E. coli strain. This study aims to provide and compare short-term quantitative kinetics data describing the dynamic behavior of E. coli facing repeated transient substrate conditions.

Real-time monitoring of metabolic shift and transcriptional induction of yciG::luxCDABE E. coli reporter strain to a glucose pulse of different concentrations

Ineffective mixing entailing heterogeneity issue within industrial bioreactors has been reported to affect microbial physiology and consequently bioprocess performances. Alteration of these performances results from microorganism ability to modulate their physiology at metabolic and/or transcriptional levels in order to survive in a given environment. Until now, dynamics of both metabolic and transcriptional microbial response to external stimuli have been investigated using mainly ex situ measurements with sampling and/or quenching constraints. This work showed an in situ bioluminescence approach for real-time monitoring of characteristic stress responses of Escherichia coli containing yciG::luxCDABE reporter to glucose pulses in well-controlled steady-state chemostat cultures. Reproducibility of in situ bioluminescence profiles was assessed. A dramatic transient increase in the bioluminescence intensity (sharp peak) was observed for a complete depletion of sugars and for a sudden decrease in the dilution rate. This response was connected to a sudden change of the metabolic activity. On the contrary a bell curve of bioluminescence intensity, dose-dependent, was related to an induction of transcriptional activity. Real-time monitoring of the bioluminescence signal with time-span less than a second gave access to the characteristic times of the metabolic shift and transcriptional induction of the stress response.

Dynamic metabolic modeling of lipid accumulation and citric acid production by Yarrowia lipolytica

Yarrowia lipolytica has the capacity to accumulate large amounts of lipids triggered by a depletion of nitrogen in excess of carbon source. However, under similar conditions this yeast also produces citric acid decreasing the lipid conversion yield. Three dynamic metabolic models are presented to describe lipid accumulation and citric acid production by Yarrowia lipolytica. First and second models were respectively based on the Hybrid Cybernetic Modeling (HCM) and the Macroscopic Bioreaction Modeling (MBM) approaches. The third model was a new approach based on the coupling between MBM and fuzzy sets. Simulation results of the three models fitted acceptably the experimental data sets for calibration and validation. However, MBM is time-dependent to consider metabolic shifts, and thus impractical for further applications. HCM and Fuzzy MBM adequately managed and described metabolic shifts presenting highlighting features for control and optimization. HCM and Fuzzy MBM were statistically compared reflecting similar results.

Modulation of the Glycerol Phosphate availability led to concomitant reduction in the citric acid excretion and increase in lipid content and yield in Yarrowia lipolytica

In order to improve TriAcylGycerol (TAG) lipids accumulation in the yeast Yarrowia lipolytica on glucose, double over-expression of the major acyl-CoA:diacylglycerol acyltransferase encoding gene (ylDGA2) and of the glycerol-phosphate dehydrogenase encoding gene (ylGPD1) was carried out. The genes were over-expressed in a strain impaired for the mobilization of the accumulated lipids, through the deletion of the genes encoding acyl-coenzyme A oxidases (POX1-6 genes) and the deletion of the very efficient lipase attached to the lipid bodies, encoded by ylTGL4. This metabolic engineering strategy had the objective of pulling the C-flow into the TAG synthesis by increasing the availability of glycerol-3-phosphate and its binding to fatty acids for the TAG synthesis. This strain showed a strong improvement in production performances on glucose in terms of lipid content (increase from 18 to 55%), lipid yield (increase from 0,035 to 0.14gg -1) and by-product formation (decrease in citric acid yield from 0.68 to 0.4gg -1). For developing bioprocess for the production of triacylglycerol from renewable carbon sources as glucose it is of first importance to control the C/N ratio in order to avoid citric acid excretion during lipid accumulation. Our engineered strain showed a delay in the onset of citric acid excretion as suggested by the 15% modulation of the critical C/N ratio.

Assessment of Candida shehatae viability by flow cytometry and fluorescent probes.

Quantification of different physiological states of Candida shehatae cells was performed by flow cytometry associated with two fluorescent probes. Propidium iodide and carboxyfluorescein diacetate acetoxymethyl ester fluorescent dyes were chosen based on data from the literature. A staining procedure, developed from the previous works was applied to the yeast. Then, the protocol was improved to fit with fermentation constraints such as no physiological interference between the staining procedure and the cells, shortest preparation time and small amounts of dyes. From this optimisation, propidium iodide was included in the sample at 8 mg/L whereas carboxyfluorescein was first diluted in Pluronic® agent and used at 3mg/L, samples were incubated for 10 min at 40°C. Repeatability and accuracy were evaluated to validate this flow cytometry procedure for viability determination.

Impacts of environmental conditions on product formation and morphology of Yarrowia lipolytica

The yeast Yarrowia lipolytica is an industrially important microorganism with distinctive physiological and metabolic characteristics. A variety of external factors (e.g., pH, temperature, and nutrient availability) influences the behavior of the yeast and may act as stress conditions which the cells must withstand and adapt. In this mini review, the impacts of environmental factors on the morphology and metabolite production by Y. lipolytica are summarized. In this regard, detailed insights into the effectors involved in the dimorphic transition of Y. lipolytica, the cultivation conditions employed, as well as the methods applied for the morphological characterization are highlighted. Concerning the metabolism products, a special focus is addressed on lipid and citric acid metabolites which have attracted significant attention in recent years. The dependence of lipid and citric acid productivity on key process parameters, such as media composition and physico-chemical variables, is thoroughly discussed. This review attempts to provide a recent update on the topic and will serve as a meaningful resource for researchers working in the field.

Improving carbon and energy distribution by coupling growth and medium chain length polyhydroxyalkanoate production from fatty acids by Pseudomonas putida KT2440

The production of medium chain length polyhydroxyalkanoates by Pseudomonas putida KT2440 from fatty acids leads to the loss of a large proportion of carbon. We studied the possibility of a shift of potentially available energy and carbon towards monitored residual growth during the production phase. A Fed-Batch culture achieving 125.6 g/L of total biomass containing 54.4% (g/g) of medium chain length polyhydroxyalkanoates was carried out leading to an overall experimental carbon yield of 0.7 Cmole/Cmole. The analysis of modeling fluxes deduced from experimental data indicated how carbon and reduced cofactors (NADH and FADH2) were managed to conclude that part of the carbon and reduced cofactors made available by polymer production were used in anabolic pathways. The strategy which consisted in coupled growth and medium chain length polyhydroxyalkanoate production enhanced the global yields compared to growth followed by a production phase. The understanding of carbon and energy fluxes distribution allowed deducing optimized culture strategy to perform the highest reported in the literature.