Engineering Yarrowia lipolytica for the selective and high-level production of isocitric acid through manipulation of mitochondrial dicarboxylate–tricarboxylate carriers

During cultivation under nitrogen starvation, Yarrowia lipolytica produces a mixture of citric acid and isocitric acid whose ratio is mainly determined by the carbon source used. We report that mitochondrial succinate–fumarate carrier YlSfc1 controls isocitric acid efflux from mitochondria. YlSfc1 purified and reconstituted into liposomes transports succinate, fumarate, oxaloacetate, isocitrate and α-ketoglutarate. YlSFC1 overexpression determined the inversion of isocitric acid/citric acid ratio towards isocitric acid, resulting in 33.4 ± 1.9 g/L and 43.3 ± 2.8 g/L of ICA production in test-tube cultivation with glucose and glycerol, respectively. These titers represent a 4.0 and 6.3-fold increase compared to the wild type. YlSFC1 gene expression was repressed in the wild type strain grown in glucose-based medium compared to olive oil medium explaining the reason for the preferred citric acid production during Y. lipolytica growth on carbohydrates. Coexpression of YlSFC1 and adenosine monophosphate deaminase YlAMPD genes together with inactivation of citrate mitochondrial carrier YlYHM2 gene enhanced isocitric acid accumulation up to 41.4 ± 4.1 g/L with an isocitric acid/citric acid ratio of 14.3 in a small-scale cultivation with glucose as a carbon source. During large-scale cultivation with glucose pulse-feeding, the engineered strain produced 136.7 ± 2.5 g/L of ICA with a process selectivity of 88.1%, the highest reported titer and selectivity to date. These results represent the first reported isocitric acid secretion by Y. lipolytica as a main organic acid during cultivation on carbohydrate. Moreover, we demonstrate for the first time that the replacement of one mitochondrial transport system for another can be an efficient tool for switching product accumulation.     

Citric acid production from glucose. II. Growth and excretion kinetics in a trickleflow fermentor

The growth and citric acid production kinetics of Saccharomycopsis lipolytica on glucose is investigated in a trickle-flow fermentor. Liquid hold-up and oxygen-transfer coefficient in the reactor column filled with cylindrical wood chips have been determined and found in agreement with chemical engineering correlations. Citric acid production starts at the end of the growth phase and proceeds at a constant specific rate of 0.025 hr^?1for about 80 hr. The fermentor can then be regenerated by addition of ammonia, which induces new growth and excretion phases. Comparing the metabolic behavior of free and immobilized cells, two main kinetic differences are observed. First, the growth phase is linear with the bound cells instead of exponential in the stirred fermentor. Second, in the trickle-bed fermentor acid productivity and oxygen acid yield are reduced by 30%. Oxygen diffusional limitations, mainly in the biomass film, and alterations in bound cell metabolism are shown to be responsible of the kinetic modifications. Simple modelizations of oxygen diffusion effects are also presented to support the interpretation of the experimental data.     

Production of citric acid from n-paraffins bySaccharomycopsis lipolytica: Kinetics and balance of the fermentation

Summary The excretion of citric and isocitric acids was studied in a stirred fermentor with control of various fermentation parameters. Growth being nitrogen-limited, excretion was found to start at the end of the growth phase, constant production rates being then obtained for the two acids for about 90 h. A linear relationship between these production rates and cell density is observed, thus allowing a definition of specific production rates. Variation of these rates with temperature, aeration, pH and medium iron content were studied. The main effects observed are those of pH, which shows a clear optimum at pH 5, and of iron content, the lower values of which promote citric acid excretion. During the excretion phase rate measurements for all reactants (n-paraffins-oxygen) and products (carbon dioxide-citric and isocitric acids) show that good carbon and oxygen balance are obtained. Comparison with a similar fermentation using glucose is also presented and discussed.Abbreviations v.v.m. volume of air per volume of medium per minute - st.p.m. strokes per minute This work is a part of a Doctorat de Spécialité thesis submitted by R. Marchal to the University of Nancy 24-7-1975     

Excretion of citric and isocitric acids by the yeast Saccharomycopsis lipolytica

Summary We investigated the excretion of citric and isocitric acids in a strain of Saccharomycopsis lipolytica grown on either n-paraffins, glucose, or glycerol. These acids were excreted in the ratio of 67:33 on n-paraffins and roughly 92:8 on either glucose or glycerol. However, with all the carbon sources used, the relative amount of isocitric acid in the intracellular pool remained below 10%. The assimilation of citric and isocitric acids was prevented when glucose or glycerol were the carbon sources, but not when n-paraffins were used. Citric acid stopped isocitric acid assimilation. These phenomena of selective assimilation and/or uptake might explain the variations observed in the ratio of citric to isocitric acids excreted on different carbon sources.     

Production of 2-Ketogluconic Acid by Serratia marcescens

Production of 2-ketogluconic acid from glucose by fermentation with Serratia marcescens NRRL B-486 was studied in 20-liter stainless-steel fermentors. Conditions for 2-ketogluconic acid production included the following: glucose-salt medium, aeration rate of 0.75 volumes per volume per minute, agitation rate of 400 rev/min, temperature of 30 C, CaCO₃ to neutralize the acid formed, and a 5% (v/v) inoculum. Foaming was controlled with an antifoam agent added at intervals during the fermentation. When 120 g per liter of glucose were supplied, 95 to 100% yields of 2-ketogluconic acid were obtained in 16 hr. Larger amounts of glucose could be used in the fermentation provided that the carbohydrate was fed continuously. Continuous feeding of glucose to a total amount of 180 g per liter gave 95 to 100% yields of 2-ketogluconic acid in 24 hr; feeding glucose to a total amount of 240 g per liter gave 85 to 90% yields in 32 to 40 hr.     

Biomethanation: Anaerobic fermentation of CO2, H2 and CO to methane

Studies to examine the microbial fermentation of coal gasification products (CO₂, H₂ and CO) to methane have been done with a mixed culture of anaerobic bacteria selected from an anaerobic sewage digestor. The specific rate of methane production at 37°C reached 25 mmol/g cell hr. The stoichiometry for methane production was 4 mmol H₂/mol CO₂. Cell recycle was used to increase the cell concentration from 2.5 to 8.3 g/liter; the volumetric rate of methane production ran from 1.3 to 4 liter/liter hr. The biogasification was also examined at elevated pressure (450 psi) and temperature to facilitate interfacing with a coal gasifier. At 60°C, the specific rate of methane production reached 50 mmol/g cell hr. Carbon monoxide utilization by the mixed culture of anaerobes and by a Rhodopseudomonas species was examined. Both cultures are able to carry out the shift conversion of CO and water to CO₂ and hydrogen.     

Characteristics of the growth on rapeseed oil and synthesis of citric and isocitric acids by <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis> yeasts

The native strain Yarrowia lipolytica VKMY-2373 grown in a complete medium exhibited the maximum lipase activity at the concentration of rapesseed oil of at least 5.0 g/l. In the course of yeast growth, no considerable changes were observed in the glycerol concentration, the proportions of the major free fatty acids formed via oil hydrolysis, or the fatty acid composition of oil. Under nitrogen limitation of cell growth, the accumulation of citric acids reached 77.1 g/l with predominance of isocitric acid at pH 6.0, whereas at pH 4.5, almost equal amounts of citric and isocitric acids were produced. Cultivation of the mutant strain Y. lipolytica N 1 at pH 4.5 resulted in the predominant accumulation of citric acid (66.6 g/l) with an insignificant amount of isocitric acid. In the period of intense acid synthesis, high production of lipase was observed.     

Oxygen supply to bacterial suspensions of high cell densities by hydrogen peroxide

The supply of heterotrophically growing suspensions of Alcaligenes eutrophus PHB^?4 with oxygen formed by the continuous addition of H₂O₂ in the presence of bovine liver catalase was found to be restricted to well-defined conditions. The catalase-H₂O₂ system proved to be suitable during the growth at low cell densities equivalent to 2 g dry weight/liter. When under these conditions the oxygen concentration was held constant at 1.8 mg O₂/liter, the cells grew for 6–8 hr at a rate almost identical to that observed with conventional aeration. However, aeration with H₂O₂ for longer durations (10–20 hr) and at higher cell densities (5?20 g dry weight/liter) led invariably to cell damage and retardation of growth. The impairment of growth observed during the oxygen supply by the catalase?H₂O₂ system was traced back to the formation of gradually increasing steady-state concentrations of H₂O₂ in the medium. Possible sites of cell damage by H₂O₂ such as membrane function, excretion and function of siderophores, and synthesis of cell polymers have been studied, and the cytotoxic mechanism of low concentrations of H₂O₂ was discussed.     

Genome-Based Metabolic Engineering of Mannheimia succiniciproducens for Succinic Acid Production

Succinic acid is a four-carbon dicarboxylic acid produced as one of the fermentation products of anaerobic metabolism. Based on the complete genome sequence of a capnophilic succinic acid-producing rumen bacterium, Mannheimia succiniciproducens, gene knockout studies were carried out to understand its anaerobic fermentative metabolism and consequently to develop a metabolically engineered strain capable of producing succinic acid without by-product formation. Among three different CO₂-fixing metabolic reactions catalyzed by phosphoenolpyruvate (PEP) carboxykinase, PEP carboxylase, and malic enzyme, PEP carboxykinase was the most important for the anaerobic growth of M. succiniciproducens and succinic acid production. Oxaloacetate formed by carboxylation of PEP was found to be converted to succinic acid by three sequential reactions catalyzed by malate dehydrogenase, fumarase, and fumarate reductase. Major metabolic pathways leading to by-product formation were successfully removed by disrupting the ldhA, pflB, pta, and ackA genes. This metabolically engineered LPK7 strain was able to produce 13.4 g/liter of succinic acid from 20 g/liter glucose with little or no formation of acetic, formic, and lactic acids, resulting in a succinic acid yield of 0.97 mol succinic acid per mol glucose. Fed-batch culture of M. succiniciproducens LPK7 with intermittent glucose feeding allowed the production of 52.4 g/liter of succinic acid, with a succinic acid yield of 1.16 mol succinic acid per mol glucose and a succinic acid productivity of 1.8 g/liter/h, which should be useful for industrial production of succinic acid.     

Production of Candida utilis protein from peat extracts

Sphagnum peat extracts or hydrolysates have been obtained and used as a culture medium for the production of Candida utilis biomass as single cell proteins. Acid hydrolysis of ground peat (4–60 mesh) in an autoclave operated under a set of conditions for acid strength (0.3-1.5 (v/v) H₂SO₄), holding time (1–4 hr), temperature (100–165°C), and weight ratio of dry peat to solution (3.3–16.7 g dry peat/100 g solution) yielded carbohydrate-rich extracts of different concentrations (1–34g/liter). The best yield (mg total carbohydrate/g dry peat) was obtained for a holding time of I hr and a temperature of 152°C. Low peat concentratio (4.1 g dry peat/100 g solution)resulted in high yield(280mg total carbohydrate/gdry peat) with a corresponding low carbohydrate content in hydrolysate (13 g/liter), while a lower yield with a higher carbohydrate content (34 g/liter)in hydrolysate were found when increasing peat concentration (16.7 g dry peat/100 g solution). Shake-fladk experiments using peat hydrolysates as the culture medium together with NH₄OH (～4.8 g/liter) and K₂HPO₄(5 g/liter) as nitrogen and phosphate supplement, respectively, gave a maximum biomass concentration of 7.5 g/liter after 60 hr at 30°C and 200rpm. Batch cultivation in a fermentor under controlled conditions for aeration (4.2 liter/min), agitation (500rpm), temperature (30°C), and pH (5.0) produced a maximum biomass of 10 g/liter after 20 hr with a specific growth rate of 0.13 hr^?1. For the continuous cultivation, a maximal biomass productivity of 1.24 g/gliter-he was obtained at a dilution rate of 0.125 hr ^?1. Monod's equation's equation has been used for the estimation of the coefficients μ_Max, K_s, and Y. It was found that the yield coefficient Y is not constant during the progress of batch cultivation.     

The response by microorganisms to steady state growth in controlled concentrations of oxygen and glucose. I. Candida utilis

Dissolved oxygen and glucose concentrations have been independently maintained at various concentrations for extended periods during growth of Candida utilis in continuous culture. Simultaneous observations of cytochrome concentration, growth rate, rates of uptake of oxygen and glucose and rates of production of CO₂, ethanol and acid have been made during steady states at various levels of oxygen and glucose. There is an inverse relationship between dissolved oxygen and cytochrome and between glucose cocentration and cytochrome. Studies of the transient state following a step change from high to low dissolved oxygen show that there is a lag of about 10 hr during which there is no change in the above parameters. This is followed by rapid oscillatory changes in cytochrome content and a change to a more fermentative metabolism.     

Identification of Flavone Compounds in Eighteen Gramineae Species

Conditions for tryptophan synthesis from pyruvic acid, indole and NH₄Cl by Enterobacter aerogenes AHU 1540 having a high tryptophanase activity, were investigated using a reaction mixture containing 1.7% of pyruvic acid. Under optimum conditions, 16.4g/liter of tryptophan was accumulated after 24 hr of incubation.

Agaricus campestris AHU 9382 produced pyruvic acid in amounts of 22 ~ 26.5 g/liter from 5% of glucose after 3-days shaking culture. When E. aerogenes was added to this fermentation broth together with indole and NH₄Cl, pyruvic acid produced was rapidly converted to tryptophan and yields of tryptophan as high as 15 g/liter were obtained after 12 hr of incubation. Furthermore, pyruvic acid fermentation by Saccharomyces exiguus AHU 3110 or Corynebacterium sp. 37-3A could also be used as a pyruvic acid source for subsequent tryptophan production.     

Production of high-quality edible protein from Candida yeast grown in continuous culture

Candida utilis NRRL Y-900 was grown in aerobic continuous culture with cane molasses as the source of the growth-limiting carbon. At 1% reducing sugar in the chemostal (10 liter working volume) feed medium, addition of Zn (25μM) to a minimal salts medium resulted in an increase in the biomass productivity of the chemostat from 1.7 to 2.6 g/liter/hr with a growth yield of 0.55 g dry biomass/g reducing sugar utilized at D_max. On the average, the yeast biomass was 50–55% protein. At S_R > 2% sugar, the biomass productivity was limited by the oxygen supply. With O₂-supplemented aeration (at S_R = 4.2%)the maximum biomass productivity Was 7.25 g/liter/hr. Aerobic ethanol production was not observed. A highquality undenatured protein fraction was isolate from the yeast homogenate by isoelectric precipitation at pH 4.5. Contaminating nucleic acid was removed as an insoluble complex by chelation with an organic cation (cetavlon). The final protein product contained about 3% RNA (DWB) and was suitable for use as a food additive.     

Citric Acid Production from Hydrolysate of Pretreated Straw Cellulose by Yarrowia lipolytica SWJ-1b Using Batch and Fed-Batch Cultivation

In this study, crude cellulase produced by Trichoderma reesei Rut-30 was used to hydrolyze pretreated straw. After the compositions of the hydrolysate of pretreated straw were optimized, the study showed that natural components of pretreated straw without addition of any other components such as (NH₄)₂SO₄, KH₂PO₄, or Mg²⁺ were suitable for citric acid production by Yarrowia lipolytica SWJ-1b, and the optimal ventilatory capacity was 10.0 L/min/L medium. Batch and fed-batch production of citric acid from the hydrolysate of pretreated straw by Yarrowia lipolytica SWJ-1b has been investigated. In the batch cultivation, 25.4 g/L and 26.7 g/L citric acid were yields from glucose and hydrolysate of straw cellulose, respectively, while the cultivation time was 120 hr. In the three-cycle fed-batch cultivation, citric acid (CA) production was increased to 42.4 g/L and the cultivation time was extended to 240 hr. However, iso-citric acid (ICA) yield in fed-batch cultivation (4.0 g/L) was similar to that during the batch cultivation (3.9 g/L), and only 1.6 g/L of reducing sugar was left in the medium at the end of fed-batch cultivation, suggesting that most of the added carbon was used in the cultivation.     

Comparison of citric acid production from glycerol and glucose by different strains of <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis>

A wild type strain A-101 of Y. lipolytica and its three acetate-negative mutants (Wratislavia 1.31, Wratislavia AWG7, and Wratislavia K1) were compared for the production of citric acid from glucose and glycerol (pure and crude) in batch cultures. The substrates were used either as single carbon sources or as mixtures of glucose and pure or crude glycerol. The kinetic parameters, i.e., the volumetric citric acid production rate and yield obtained in the study show that the Wratislavia 1.31 and Wratislavia AWG7 strains produced the highest amount of citric acid from glycerol, with a yield from 0.40 to 0.53 g g⁻¹. This substrate was found to be a better carbon source for the biosynthesis of citric acid than glucose. The results obtained with the same strains have shown low content of isocitric acid and polyols, such as erythritol and mannitol. Y. lipolytica A-101 strain produced the highest amount of isocitric acid, from 13.8 to 21% isocitric acid in the sum of citric acids. However, the highest concentrations of erythritol were found in cultures with Y. lipolytica Wratislavia K1, from 18.1 to 30 g l⁻¹, for glucose and pure glycerol, respectively.     

Use of continuous-culture techniques for determining the growth kinetics of a celluloytic Thermoactinomyces sp.

In order to better understand the kinetics of cellulose degradation by Thermoactinomyces sp., continuous-culture experiments were performed utilizing the various intermediates of cellulose degradation as the feed substrates. Steady-state data from the glucose runs suggest that this organism has a growth yield of 0.42 g cell/g glucose, and a specific maintenance of 0.24 g glucose/g cell/hr. The Monod equation did not seen to model the growth well, since a plot of 1/D vs. 1/S gave a maximum specific growth rate that was even lower than one of the steady-state dilution rates. A dynamic washout experiment suggested a maximum specific specific growth rate of 0.36 hr^?1 and indicated that glucose is only slightly growth inhibitory as the inhibition constant, K_i, is 19 g glucose/liter. An equation for substrate concentration for washout conditions was derived. This equation predicted the transient glucose concentration relatively well. A fill-and-draw technique was investigated for determination of the growth parameters. It was not successful because of difficulties in contamination and accurately monitoring the dissolved oxygen in the small highly agitated vessel. However, the technique could be useful in studying the growth characteristics of sludge in a waste treatment system where contamination is not a worry. One could cover the medium surface and use a nonsterilizable dissolved oxygen probe of high sensitivity membrane to overcome these difficulties.     

THE UPTAKE OF GLUCOSE BY CHLAMYDOMONAS SP.12

The glucose uptake of a species of Chlamydomonas was studied at various concentrations of d -glucose plus glucose-1-¹⁴C (0.003–10.0 mg/liter) and at various light levels (0–220 ft-c). The alga grows at 4 C either in the light or in the dark with added glucose, cellobiose, maltose, or fructose. Uptake of glucose could be described by the Michaelis-Menten equation, and both the maximum velocity of uptake and the half-saturation constant increased when the cells were exposed to glucose in the dark. However, the high value of the half-saturation constant (5 mg glucose/liter) compared with the low levels of glucose in nature (5–10 μg/liter) makes it unlikely that a transport system is effective under natural conditions. Even if a total of 10.0 mg/liter of glucose plus other organic compounds were available as substrate, the rate of photosynthesis would still be more than 10 times higher (at 220 ft-c) than the rate of organic substrate uptake. Light had no effect on the total uptake of glucose but did reduce the percentage of ¹⁴CO₂ evolved from 61% of the total ¹⁴CO taken up in the dark to 0% at 220 ft-c. This decrease could be due to either preferential use of the ¹⁴CO₂ in photosynthesis or of the photosynthate in respiration.     

Fermentation pattern of sucrose to ethanol conversions by Zymomonas mobilis

General patterns of sucrose fermentation by two strains of Zymomonas mobilis, designated Z7 and Z10, were established using sucrose concentrations from 50 to 200 g/liter. Strain Z7 showed a higher invertase activity than Z10. Strain Z10 showed a reduced specific growth rate at high sucrose concentration while Z7 was unaffected. High sucrose hydrolyzing activity in strain Z7 lead to glucose accumulation in the medium at high sucrose concentrations. Ethanol production and fermentation time depend on the rate of catabolism of the products of sucrose hydrolysis, glucose and fructose. The metabolic quotients for sucrose utilization, q_s, and ethanol production, q_p (g/g·hr), are unsuitable for describing sucrose utilization by Zymomonas mobilis, as the logarithmic phase of growth precedes the phase of highest substrate utilization (g/liter·hr) and ethanol production (g/liter·hr) in batch culture.     

Selectivity in citric acid production by Yarrowia lipolytica

This experimental study reports about production selectivity in the fermentation of glucose to citric acid by Yarrowia lipolytica as a function of substrate concentration. Batch runs featuring biomass growth and one or two citric acid production phases were carried out in a 15-l stirred tank fermentor. The presented results demonstrate that working at high initial substrate concentration in the production phase is beneficial both in terms of a higher production rate of citric acid, the desired metabolite (reaching 0.077 h(-1)) and of a higher utilization degree of the employed carbon source (yield up to 0.384 g(c.a.)/g(glucose)). The production rate of isocitric acid, the major undesired metabolite, was found to be practically constant over the tested initial substrate concentration range.     

Growth and respiratory activity of mold fungus (Trichoderma lignorum)

The growth ofTrichoderma lignorum was studied in relation to the carbon balance of the culture system and the respiratory activity at different growth phases. Conidia, after inoculation into the medium, swelled and germinated rapidly. The growth rate of the hyphae at the exponential phase was 0.46 hr⁻¹ (2.2 hr for mass doubling) at 25 C. The yield efficiency of hyphal biomass-C at the cost of glucose-C was 67%, while those of the waste products-C excreted and of CO₂-C evolved were, 6.5% and 26.5%, respectively. The yield efficiency of conidia-C to the decrease of hyphae-C was 34%. The germination, growth rate and carbon balance were not affected by different concentrations of glucose from 10 to 2×10³ mg glucose-C/l. Carbon dioxide was needed as the growth factor for the initiation of the germination of conidia, but there was no increase in yield efficiency as a result of CO₂ fixation. The respiratory rate of the fungus changed drastically as the growth proceeded. The rate of endogenous respiration of conidia was less than 0.2 mg CO₂-C/g conidia-C/hr which increased immediately after inoculation into the medium. The highest respiratory rate of hyphae (100–110 mg CO₂-C/g hyphae-C/hr) was obtained throughout the exponential phase. Thereafter, decreasing rapidly, the respiratory rate of submerged hyphae of 1-week-old showed only 1.8 mg CO₂-C/g biomass-C/hr, whereas the rate of aerial hyphae forming conidia increased again, but did not exceed 10 mg CO₂-C/g biomass-C/hr.