A survey of yeast from the Yarrowia clade for lipid production in dilute acid pretreated lignocellulosic biomass hydrolysate

Yarrowia lipolytica is an oleaginous yeast species that has attracted attention as a model organism for synthesis of single cell oil. Among over 50 isolates of Y. lipolytica identified, only a few of the strains have been studied extensively. Furthermore, 12 other yeast species were recently assigned to the Yarrowia clade, and most are not well characterized in terms of cell growth and lipid accumulation, especially in industrially relevant conditions. In the present study, we investigated biomass and lipid production by 57 yeast isolates, representing all 13 species in the Yarrowia clade, on a non-detoxified dilute acid-pretreated switchgrass hydrolysate under highly aerobic conditions. The objective was to compare yeast physiology during growth in an abundant, low-cost biomass feedstock and to expand diversity of genetically tractable, oleaginous yeasts available for lipid research. Screening of 45 Y. lipolytica isolates demonstrated considerable variation within the species in terms of lipid accumulation (min = 0.1 g/L; max = 5.1 g/L; mean = 2.3 g/L); three strains (NRRL YB-420, YB-419, and YB-392) were especially promising for cellulosic biomass conversion with average improvements of 43, 57, and 64%, respectively, in final lipid titer as compared to control strain W29. Subsequently, evaluation of strains from 13 distinct species in the Yarrowia clade identified Candida phangngensis PT1-17 as the top lipid producer with a maximum titer of 9.8 g/L lipid, which was over twofold higher than the second-best species in the clade (Candida hollandica NRRL Y-48254). A small set of the most promising strains from the screenings was further characterized to evaluate inhibitor tolerance, lipid production kinetics, and fatty acid distribution. We expect that the results of this study will pave the way for new biotechnological applications involving previously overlooked and under-characterized strains within the Yarrowia clade.

Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae

In the important industrial yeast Saccharomyces cerevisiae, galactose metabolism requires energy production by respiration; therefore, this yeast cannot metabolize galactose under strict anaerobic conditions. While the respiratory dependence of galactose metabolism provides benefits in terms of cell growth and population stability, it is not advantageous for producing fuels and chemicals since a substantial fraction of consumed galactose is converted to carbon dioxide. In order to force S. cerevisiae to use galactose without respiration, a subunit (COX9) of a respiratory enzyme was deleted, but the resulting deletion mutant (Δcox9) was impaired in terms of galactose assimilation. Interestingly, after serial sub-cultures on galactose, the mutant evolved rapidly and was able to use galactose via fermentation only. The evolved strain (JQ-G1) produced ethanol from galactose with a 94% increase in yield and 6.9-fold improvement in specific productivity as compared to the wild-type strain. (13)C-metabolic flux analysis demonstrated a three-fold reduction in carbon flux through the TCA cycle of the evolved mutant with redirection of flux toward the fermentation pathway. Genome sequencing of the JQ-G1 strain revealed a loss of function mutation in a master negative regulator of the Leloir pathway (Gal80p). The mutation (Glu348*) in Gal80p was found to act synergistically with deletion of COX9 for efficient galactose fermentation, and thus the double deletion mutant Δcox9Δgal80 produced ethanol 2.4 times faster and with 35% higher yield than a single knockout mutant with deletion of GAL80 alone. When we introduced a functional COX9 cassette back into the JQ-G1 strain, the JQ-G1-COX9 strain showed a 33% reduction in specific galactose uptake rate and a 49% reduction in specific ethanol production rate as compared to JQ-G1. The wild-type strain was also subjected to serial sub-cultures on galactose but we failed to isolate a mutant capable of utilizing galactose without respiration. We concluded that the metabolic "death valley" (i.e. no galactose utilization by the Δcox9 mutant) is a necessary intermediate phenotype to facilitate galactose utilization without respiration in yeast. The results in this study demonstrate a promising approach for directing adaptive evolution toward fermentative metabolism and for generating evolved yeast strains with improved phenotypes under anaerobic conditions.

Enhanced hexose fermentation by Saccharomyces cerevisiae through integration of stoichiometric modeling and genetic screening

In order to determine beneficial gene deletions for ethanol production by the yeast Saccharomyces cerevisiae, we performed an in silico gene deletion experiment based on a genome-scale metabolic model. Genes coding for two oxidative phosphorylation reactions (cytochrome c oxidase and ubiquinol cytochrome c reductase) were identified by the model-based simulation as potential deletion targets for enhancing ethanol production and maintaining acceptable overall growth rate in oxygen-limited conditions. Since the two target enzymes are composed of multiple subunits, we conducted a genetic screening study to evaluate the in silico results and compare the effect of deleting various portions of the respiratory enzyme complexes. Over two-thirds of the knockout mutants identified by the in silico study did exhibit experimental behavior in qualitative agreement with model predictions, but the exceptions illustrate the limitation of using a purely stoichiometric model-based approach. Furthermore, there was a substantial quantitative variation in phenotype among the various respiration-deficient mutants that were screened in this study, and three genes encoding respiratory enzyme subunits were identified as the best knockout targets for improving hexose fermentation in microaerobic conditions. Specifically, deletion of either COX9 or QCR9 resulted in higher ethanol production rates than the parental strain by 37% and 27%, respectively, with slight growth disadvantages. Also, deletion of QCR6 led to improved ethanol production rate by 24% with no growth disadvantage. The beneficial effects of these gene deletions were consistently demonstrated in different strain backgrounds and with four common hexoses. The combination of stoichiometric modeling and genetic screening using a systematic knockout collection was useful for narrowing a large set of gene targets and identifying targets of interest.

Whole cell biosynthesis of a functional oligosaccharide, 2'-fucosyllactose, using engineered Escherichia coli

Background

2'-Fucosyllactose (2-FL) is a functional oligosaccharide present in human milk which protects against the infection of enteric pathogens. Because 2-FL can be synthesized through the enzymatic fucosylation of lactose with guanosine 5′-diphosphate (GDP)-l-fucose by α-1,2-fucosyltransferase (FucT2), an 2-FL producing Escherichia coli can be constructed through overexpressing genes coding for endogenous GDP- l-fucose biosynthetic enzymes and heterologous fucosyltransferase.

Results

The gene for FucT2 from Helicobacter pylori was introduced to the GDP- l-fucose producing recombinant E. coli BL21 star(DE3) strain. However, only small amount of 2-FL was produced in a batch fermentation because the E. coli BL21star(DE3) strain assimilated lactose instead of converting to 2-FL. As an alternative host, the E. coli JM109(DE3) strain which is incapable of assimilating lactose was chosen as a 2-FL producer. Whole cell biosynthesis of 2-FL from lactose was investigated in a series of batch fermentations using various concentrations of lactose. The results of batch fermentations showed that lactose was slowly assimilated by the engineered E. coli JM109(DE3) strain and 2-FL was synthesized without supplementation of another auxiliary sugar for cell growth. A maximum 2-FL concentration of 1.23 g/l was obtained from a batch fermentation with 14.5 g/l lactose. The experimentally obtained yield (g 2-FL/g lactose) corresponded to 20% of the theoretical maximum yield estimated by the elementary flux mode (EFM) analysis.

Conclusions

The experimental 2-FL yield in this study corresponded to about 20% of the theoretical maximum yield, which suggests further modifications via metabolic engineering of a host strain or optimization of fermentation processes might be carried out for improving 2-FL yield. Improvement of microbial production of 2-FL from lactose by engineered E. coli would increase the feasibility of utilizing 2-FL as a prebiotic in various foods.

The effects of zinc deficiency on pancreatic carboxypeptidase activity and protein digestion and absorption in the rat

1. Proteolytic enzyme activities were examined in the pancreas of zinc-deficient and control rats. 2. No change was detected in trypsin-plus-chymotrypsin activity. 3. Carboxypeptidase activity was appreciably lowered in zinc deficiency and returned rapidly to normal on zinc therapy. 4. In experiments in which U-(14)C-labelled Chlorella protein was fed no evidence was obtained which suggested that the reduction in carboxypeptidase activity had limited the rate of protein digestion or absorption. 5. The specific activity of pancreatic protein synthesized during these experiments was appreciably lower in zinc-deficient than in control rats. 6. A higher proportion of the total activity present, in each organ examined, was in the non-protein fraction in zinc-deficient rats.

A genetic and physiological study of impaired glucose homeostasis control in C57BL/6J mice

AIMS/HYPOTHESIS

C57BL/6J mice exhibit impaired glucose tolerance. The aims of this study were to map the genetic loci underlying this phenotype, to further characterise the physiological defects and to identify candidate genes.

METHODS

Glucose tolerance was measured in an intraperitoneal glucose tolerance test and genetic determinants mapped in an F2 intercross. Insulin sensitivity was measured by injecting insulin and following glucose disposal from the plasma. To measure beta cell function, insulin secretion and electrophysiological studies were carried out on isolated islets. Candidate genes were investigated by sequencing and quantitative RNA analysis.

RESULTS

C57BL/6J mice showed normal insulin sensitivity and impaired insulin secretion. In beta cells, glucose did not stimulate a rise in intracellular calcium and its ability to close KATP channels was impaired. We identified three genetic loci responsible for the impaired glucose tolerance. Nicotinamide nucleotide transhydrogenase (Nnt) lies within one locus and is a nuclear-encoded mitochondrial proton pump. Expression of Nnt is more than sevenfold and fivefold lower respectively in C57BL/6J liver and islets. There is a missense mutation in exon 1 and a multi-exon deletion in the C57BL/6J gene. Glucokinase lies within the Gluchos2 locus and shows reduced enzyme activity in liver.

CONCLUSIONS/INTERPRETATION

The C57BL/6J mouse strain exhibits plasma glucose intolerance reminiscent of human type 2 diabetes. Our data suggest a defect in beta cell glucose metabolism that results in reduced electrical activity and insulin secretion. We have identified three loci that are responsible for the inherited impaired plasma glucose tolerance and identified a novel candidate gene for contribution to glucose intolerance through reduced beta cell activity.

The relationship between iron status and lead absorption in rats

The absorption of lead from loops of small intestinein situ was investigated in rats in which iron absorption was increased by stimuli varying in type, intensity, or duration. Lead absorption was increased by a short period of severe iron restriction before any change in hematological indices became apparent. A period of hypoxia, which markedly increased iron absorption, did not influence absorption of lead. An extended period of moderate iron restriction resulted in a marked reduction in liver iron stores and increased iron absorption throughout the 17-wk experiment. Under these conditions lead absorption was initially also increased, but after 12 wk, when iron intake had become adequate to meet essential requirements, lead absorption was similar to that in iron-supplemented rats. These results are discussed in the light of evidence for a receptor-mediated absorption process for iron.

Metal absorption and the intestinal mucus layer

The luminal mucus layer of the rat's small intestine was separated from the mucosa by filling the lumen with agar jelly. When the rats were fasted overnight and given 59Fe or 65Zn by stomach tube the mucus isolated by this technique contained more isotope and more sialic acid than fed controls, and more of the isotope was absorbed into the tissues. Saturation and time-course studies showed that the mucus layer has metal-binding activity distinct from that of the mucosa and it is postulated that the mucus layer may play a role in the process of metal absorption.

Effects of dietary phytic acid on lead and cadmium uptake and depletion in rats

Rats were given a semipurified diet supplemented with phytate (10 g/kg) or calcium (6 g/kg) and lead (200 mg/kg) or cadmium (5 mg/kg) for 4 weeks. Addition of phytate or calcium reduced the accumulation of lead in bone (P less than 0.001) and in blood and liver samples (P greater than 0.05). The greatest inhibition of tissue lead retention was evident when phytate and calcium were fed together. Cadmium accumulation was measured in the liver and kidney and was increased (P less than 0.05) by the addition of calcium. Phytate inhibited the increase in tissue cadmium promoted by calcium supplementation but did not otherwise influence tissue cadmium levels. In a further experiment, weanling rats were given diets supplemented with cadmium (5 mg/kg) or lead (200 mg/kg) for 4 weeks, and the accumulation of these elements in the body tissues was estimated in some animals. A phytate-supplemented (10 g/kg) or phytate-free semipurified diet (free of lead and cadmium) was then given to the remaining rats for 4 weeks. Phytate supplementation was found to have no significant effect on the rate of loss of lead or cadmium from tissues.

The production of zinc deficiency in the guinea pig

A diet which contained less than 1 microgram Zn per g was eaten readily by guinea pigs. No signs of zinc deficiency were produced unless the animals were deprived of access to zinc-supplemented solid food from birth and were maintained on grid floors to prevent coprophagy or ingestion of sawdust bedding material. At an early stage of deficiency, plasma zinc concentration, food intake and growth were reduced and large regular variations of food intake (food cycling) were observed. More severe deficiency produced decreases in the zinc content of other tissues and characteristic epidermal lesions. The requirement of guinea pigs for zinc for growth is probably about 2.5 micrograms per g feed which is much lower than for calves, rats and pigs.

The effects of short periods of fasting on the absorption of heavy metals

1. Rats were deprived of food for periods of from 0 to 40 h and then given 203Pb, 203Hg, 59Fe, 64Cu, 65Zn or 45Ca by stomach tube. The absorption and retention of these metals in tissues was measured 1 h and 2 d after dosing. 2. After 16-24 h of food deprivation between two and ten times more metal was retained than after 0-12 h. 3. The effects of length of fast on metal uptake by the intestinal mucosa were greatest in the duodenum. 4. Lactate production by duodenal mucosa was halved after 12 h of food deprivation but galactose absorption was little changed after a 40 h fast.

The influence of high dietary calcium and phosphate on lead uptake and release

The effects of calcium and phosphate supplements on the retention of dietary lead and the loss of lead from the body were studied in young rats. There were three experiments in which rats were given a diet containing 200 or 400 micrograms of lead/g for 3 or 6 weeks. The diet contained adequate calcium and phosphate. Calcium and phosphate supplements were given alone or together. Lead uptake after a period of lead feeding was measured by analysis of the whole gut-free carcass. Lead loss was measured by a similar analysis after the rats had received diets containing lead and then diets free of lead. The uptake of lead from the diet was reduced by about half when either dietary calcium or phosphate or both was doubled. The rate of release of body lead was decreased by calcium supplementation.

The effects of dietary calcium and phosphorus on the retention and excretion of lead in rats

1. Rats were given diets containing different amounts of calcium, phosphorus and lead. 2. Pb retention was greatly increased when the diets contained less Ca or P than the minimum estimated requirement of the rat. 3. The release of Pb already incorporated into the skeleton was inhibited by diets low in Ca but was not affected by diets low in P. 4. The retention of Pb given intraperitoneally was not affected by dietary Ca or P. 5. It can be concluded that dietary Ca and P influence the absorption of Pb by the gut and dietary Ca influences the metabolism of Pb in the bone. 6. There were changes in the distribution of Pb among the tissues due to changes of dietary Ca. 7. At low body concentrations, Pb probably affected skeletal growth.

An apparatus for the regulation of the food supply to rats

1. An apparatus is described for supplying small amounts of food to rats uniformly and continuously.

2. The apparatus consists of a Perspex disc carrying a groove containing food, which is rotated once each day by an electric motor. Access of rats to the food is restricted by suitably placed baffles.

Effects of zinc deficiency on food intake and feeding patterns of rats

1. The effects of alterations of the protein and zinc concentrations of a semi-synthetic diet on the food intake and dietary preferences of Zn-deficient and normal rats have beencompared.

2. The voluntary food intake of Zn-deficient rats fell to 70% 96 of that of the controls. The day-to-day variation of intake increased markedly and was associated with a cyclical pattern of food consumption. When the food intake of deficient rats was slightly restricted the troughs of the cycles disappeared.

3. Concurrent with the fall in food intake, Zn-deficient rats ceased to gain weight, but a similar change was found with pair-fed controls.

4. Force-feeding Zn-deficient rats with 140 % of their voluntary intake rapidly induced signs of ill-health.

5. Reduction of the protein content of the diet from 20 to 5 % resulted in an increased food intake and the disappearance of the cyclical pattern of intake. Growth, however, was not renewed.

6. Zn-deficient rats responded to a Zn-supplemented diet within 1–2 h by an increased food intake.

7. Zn-deficient rats were able to discriminate between diets containing 6 and I ppm Zn when both diets were offered simultaneously.

8. The responses of Zn-deficient rats to Zn-containing diets did not occur if the diets did not contain protein.

Zinc deficiency and the zinc requirements of calves and lambs

1. The effects of changes in zinc intake on weight gain, plasma Zn concentration and the development of clinical lesions of Zn deficiency have been studies in Zn depletion and repletion studies with calves and lambs.

2. A basal diet, the principal components of which are urea, dried egg white, starch, glucose, cellulose and arachis oil has been developed for trace element deficiency studies with ruminants.

3. Weight gain ceased abruptly in both calves and lambs when either the unsupplemented basal diet was given or when Zn supplements provided only 0.05 mg Zn/kg live weight per day. Mean plasma Zn concentrations in these animals fell from pre-experiment values of between 0.8 and 1.2 μg Zn/ml to below 0.4 μg Zn/ml after 1 week on these treatments.

4. Supplements providing 0.2 mg Zn/kg live weight per day were sufficient to maintain a good rate of growth but insufficient to prevent a fall in plasma Zn.

5. Growth arrest occurring within 2 weeks and a rapid fall in plasma Zn occurring within 1 week after Zn supplements were withheld from calves and lambs that had previously received 0.7 mg Zn/kg live weight per day for 6 and 14 weeks respectively indicated that these species have only a limited capacity to store Zn in a form that can be utilized during periods of inadequate Zn intake.

6. Tentative estimates are presented of the Zn requirements of calves maintained on this type of basal diet and the influence of ration composition of Zn availability is discussed.

7. The possible value and the limitations of plasma Zn determination as an aid to the field diagnosis of Zn deficiency are considered.