Multi-omics network model reveals key genes associated with p-coumaric acid stress response in an industrial yeast strain.

The production of ethanol from lignocellulosic sources presents increasingly difficult issues for the global biofuel scenario, leading to increased production costs of current second-generation (2G) ethanol when compared to first-generation (1G) plants. Among the setbacks encountered in industrial processes, the presence of chemical inhibitors from pre-treatment processes severely hinders the potential of yeasts in producing ethanol at peak efficiency. However, some industrial yeast strains have, either naturally or artificially, higher tolerance levels to these compounds. Such is the case of S. cerevisiae SA-1, a Brazilian fuel ethanol industrial strain that has shown high resistance to inhibitors produced by the pre-treatment of cellulosic complexes. Our study focuses on the characterization of the transcriptomic and physiological impact of an inhibitor of this type, p-coumaric acid (pCA), on this strain under chemostat cultivation via RNAseq and quantitative physiological data. It was found that strain SA-1 tend to increase ethanol yield and production rate while decreasing biomass yield when exposed to pCA, in contrast to pCA-susceptible strains, which tend to decrease their ethanol yield and fermentation efficiency when exposed to this substance. This suggests increased metabolic activity linked to mitochondrial and peroxisomal processes. The transcriptomic analysis also revealed a plethora of differentially expressed genes located in co-expressed clusters that are associated with changes in biological pathways linked to biosynthetic and energetical processes. Furthermore, it was also identified 20 genes that act as interaction hubs for these clusters, while also having association with altered pathways and changes in metabolic outputs, potentially leading to the discovery of novel targets for metabolic engineering toward a more robust industrial yeast strain.

Microbial lipid production: screening with yeasts grown on Brazilian molasses.

Rhodotorula glutinis CCT 2182, Rhodosporidium toruloides CCT 0783, Rhodotorula minuta CCT 1751 and Lipomyces starkeyi DSM 70296 were evaluated for the conversion of sugars from Brazilian molasses into single-cell oil (SCO) feedstock for biodiesel. Pulsed fed-batch fermentations were performed in 1.65 l working volume bioreactors. The maximum specific growth rate (µmax), lipid productivity (Pr) and cellular lipid content were, respectively, 0.23 h(-1), 0.41 g l(-1) h(-1), and 41% for Rsp. toruloides; 0.20 h(-1), 0.27 g l(-1) h(-1), and 36% for Rta. glutinis; 0.115 h(-1), 0.135 g l(-1) h(-1), and 27 % for Rta. minuta; and 0.11 h(-1), 0.13 g l(-1) h(-1), and 32% for L. starkeyi. Based on their microbial lipid productivity, content, and profile, Rsp. toruloides and Rta. glutinis are promising candidates for biodiesel production from Brazilian molasses. All the oils from the yeasts were similar to the composition of plant oils (rapeseed and soybean) and could be used as raw material for biofuels, as well as in food and nutraceutical products.

Sediments in coffee extracts: Composition and control by enzymatic hydrolysis.

The water-insolubility of some coffee extract components is one of the major limitations in the production of instant coffee. In this work, fractions from coffee extracts and sediments were prepared, and their chemical composition determined. Based on the carbohydrate analysis, galactomannan was found to be the main polysaccharide component of the insoluble fractions and probably responsible for sediment formation. The suitability of twelve commercial enzymes for the hydrolysis of the insoluble fractions was investigated. Pectinase 444L was the most effective enzyme in releasing sugars, mainly mannose and galactose, from these substrates. Biopectinase CCM, Rohapect B1L, Pectinase 444L and Galactomannanase ACH were found to be the most effective enzymes for reducing the sediment of coffee extracts. The highest sediment reduction was obtained using Rohapect B1L and Galactomannanase ACH, at enzyme concentrations of 0.3 and 0.1mg protein/g substrate, respectively.

Mass transfer in aqueous two-phases system packed column.

The behavior of xylanase extraction in a packed column using polyethylene glycol (PEG) 4000 and dipotassium phosphate was studied. The possibility of using the packed column in continuous operations for enzyme extraction was studied since the previous work had only addressed the semi-continuous extraction of enzyme. The influence of several kinds of packings, Raschig rings, glass spheres and polystyrene rings were studied as well the superficial velocity ratio of the salt and the PEG phases. Packed column showed a good efficiency of overall mass transfer coefficient, around three times higher than sieve plate column, for xylanase extraction. The best selectivity was obtained with the polystyrene ring where 94% of xylanase was recovery to the polymeric whereas just 3% of contaminant was recovery to this phase. The residence time distribution was adjusted by the Model of Reactors in Series.

Xylanase mass transfer studies in aqueous two-phase systems using spray and sieve plate columns.

Aqueous two-phase systems (ATPSs) have long been used for biomolecule partitioning; these systems offer the possibility of using continuous or semicontinuous extraction processes. They require relatively simple equipment like spray or sieve plate columns that can be adapted for use in ATPSs. The aim of this work was to study the semicontinuous extraction of a model enzyme, xylanase, in spray and sieve plate columns, since, unlike centrifugal contactors, the cost of construction and maintenance of this equipment is low and it is easy to operate. For the spray column, the dispersed phase hold-up and overall mass transfer coefficients K(D) a were evaluated for different column heights and for different superficial velocities of the dispersed phase (light phase). Results indicated that an increase in superficial velocity in the range of 0-0.18 mm/s of the dispersed phase had a positive effect on K(D) a and on hold-up in all column heights studied, 75, 161 and 246 mm. For the same superficial velocity of the dispersed phase, the larger the hold-up was, the shorter the column. For the sieve plate column, the effects of the superficial velocity of the dispersed phase and the number of plates were also studied. Results showed that the K(D) a and hold-up increased with an increase in both parameters. The selectivity of separation of xylanase and BSA (model contaminant) was very high, since 60% of the enzyme was extracted in the light phase, whereas no significant amount of BSA was extracted. The possibility of using the sieve plate column in continuous operation for enzyme extraction was studied because previous work had only addressed the semicontinuous extraction of enzyme. The residence time distribution of the PEG phase using different superficial velocities of the salt phase was studied in continuous operation. The time required to reach the steady state was 40 min, and 70% of the xylanase was recovered. It was found that the Modified Power Spline software was well adjusted to the experimental results.

Effect of phosphate concentration on the production of dextransucrase by Leuconostoc mesenteroides NRRL B512F.

Leuconostoc mesenteroides NRRL B512F is the main strain used in industrial fermentations to produce dextransucrase and dextran. This process has been studied since the Second World War, when it was used as blood plasma expander. A study about the effect of phosphate concentration on cell propagation in a semicontinuous shake-flask culture is described in this work. Dextransucrase is obtained by fermentation of the Leuconostoc mesenteroides NRRL B512F in the presence of sucrose as substrate, a nitrogen source (corn liquor or yeast extract) and minerals. Phosphate is currently used in order to buffer the culture medium. Cell propagation can be done through a repeated batch culture, where dilution in a fresh medium is made with relatively short periods. The standard medium for dextransucrase production is prepared using 0.1 M of K(2)HPO(4). In this work the level of phosphate was increased to 0.3 M, and an increase on biomass and on the enzyme activity was found when phosphate enriched medium was used. Higher phosphate buffer concentration was also able to keep the pH values above 5.0 during the entire process, avoiding enzyme denaturation.

Activity of xylose reductase from Candida mogii grown in media containing different concentrations of rice straw hydrolysate.

Xylose reductase (XR) activity was evaluated in extracts of Candida mogii grown in media containing different concentrations of rice straw hydrolysate. Results of XR activity were compared to xylitol production and a similar behavior was observed for these parameters. Highest values of specific production and productivity were found for xylose reductase (35 U/g of cell and 0.97 U/[g of cell x h], respectively) and for xylitol (5.63 g/g of cell and 0.13 g/[g of cell x h]) in fermentation conducted in medium containing 49.2 g of xylose/L. The maximum value of XR:XD ratio (1.82) was also calculated under this initial xylose concentration with 60 h of fermentation.

Partitioning of whey proteins, bovine serum albumin and porcine insulin in aqueous two-phase systems.

Partitioning of the proteins from cheese whey, bovine serum albumin and porcine insulin were analysed using aqueous two-phase systems (ATPS) prepared with PEG-phosphate, PEG-citrate and PEG-maltodextrin (MD). Proteins were quantified through one of the following methods: FPLC, Bradford and spectrophotometry at 280 nm. Results showed that whey proteins partitioned unevenly on the phases of the systems used, with alpha-lactoalbumin (alpha-La) concentrated in the upper phase and beta-lactoglobulin (beta-Lg) in the lower. Albumin in PEG-MD systems concentrated in the MD-rich lower phase. Porcine insulin showed great affinity with the PEG-rich phase, its partition coefficient was always over 10 and increases with PEG molecular mass.

Purification of soybean peroxidase (Glycine max) by metal affinity partitioning in aqueous two-phase systems.

Combining two concepts in downstream processing, this work investigates the partitioning of a crude soybean peroxidase (Glycine max) in an aqueous two-phase system by metal affinity. A liquid-liquid extraction process using metal ligands was developed in two steps with the aim of purifying the enzyme peroxidase. PEG 4000 was activated using thionyl chloride, covalently linked to iminodiacetic acid (IDA), and the specific metal ligand Cu2+ was attached to the PEG 4000-IDA. In the first step, the system was composed of 14% (w/w) PEG 4000-IDA-Cu2+ and 8% (w/w) Na2SO4, and the peroxidase partitioned mainly to the top phase (K = 24). In the second step, a system formed by 14% PEG 4000 and 10% phosphate was used to revert the value of the partition coefficient of peroxidase to the bottom salt-rich phase (K = 0.05), thereby achieving a recovery of 64% of the purified enzyme.

Extraction in aqueous two-phase systems of alkaline xylanase produced by Bacillus pumilus and its application in kraft pulp bleaching.

The aim of this work was to extract and to purify xylanase, produced by Bacillus pumilus from the crude fermentation broth, using aqueous two-phase systems (ATPS). The xylanase was extracted by partitioning in ATPS composed of phosphate and polyethylene glycol (PEG). The effect of tie-line length, PEG molecular mass and NaCl concentrations upon the purification factors and yields of xylanase were investigated by statistical design. The best system studied was that containing 22% PEG6000, 10% K2HPO4 and 12% NaCl with a purification factor of 33 and a 98% yield of enzyme activity. This system was also used for continuous extraction in a pulsed caps column. Subsequently, the xylanase from the crude fermentation broth was tested in hardwood kraft pulp bleaching.

Characterization of storage cell wall polysaccharides from Brazilian legume seeds and the formation of aqueous two-phase systems.

Cell wall storage polysaccharides from Brazilian legume seeds of Dimorphandra mollis, Schizolobium parahybum (galactomannans), Copaifera langsdorffii, Hymenaea courbaril (xyloglucans) and the galactan from cotyledons of the Mediterranean species Lupinus angustifolius were extracted and their apparent molecular masses were determined by high-performance size exclusion chromatography analysis. They were, to a large degree, polydisperse, showing molecular masses that varied from 100,000 to 2,000,000. Polyethylene glycol (PEG, 1500, 4000, 6000 and 8000), sodium citrate and dextran (73,000, 60,000-90,000, 505,000 and 2,000,000) were used for investigating phase formation with the seed polysaccharides. Galactomannans and xyloglucans demonstrated phase formation with sodium citrate concentrations lower than 30%, as well as dextrans and polyethylene glycol, and formed gels in the presence of high concentrations of sodium citrate (above 30%). Galactan did not promote phase formation with any of the reagents used. On the basis of the results obtained, the possibility of using legume seed polysaccharides for the partitioning and purification of polysaccharide enzymes in aqueous two-phase systems is suggested.

Conservative chemical modification of proteins to study the effects of a single protein property on partitioning in aqueous two-phase systems.

Relatively conservative modifications of three proteins were carried out to alter their surface properties. The protein properties modified were hydrophobicity and charge. This was done by acylation of amino groups with anhydrides. For the hydrophobic modification experiments, two proteins (beta-lactoglobulin and bovine serum albumin [BSA]) and four anhydrides (hexanoic, butyric, succinic, acetic) were used. For the modification of surface charge the protein thaumatin was selected and various proportions of the free amino groups were blocked with acetic anhydride to give a series of proteins with differing isoelectric points. Detailed characterization and purification of selected modified proteins was carried out including molecular weight measurements and conformational analysis. The criteria used for selecting the modified proteins for subsequent investigation of their partitioning in aqueous two-phase systems (ATPS) is described. With a judicious choice of starting material it was found that limited chemical modifications to proteins could effectively alter surface hydrophobicity or charge almost independently, with little effect on other molecular properties. It appears, however, that the method for chemical modification and the reaction conditions must also be carefully controlled. (c) 1996 John Wiley & Sons, Inc.

Use of chemically modified proteins to study the effect of a single protein property on partitioning in aqueous two-phase systems: Effect of surface hydrophobicity.

Two different series of hydrophobically modified proteins were partitioned in a number of aqueous two-phase systems (ATPS) to investigate the effect of hydrophobicity as a single property on partitioning. The modified proteins were derived from beta-lactoglobulin and bovine serum albumin (BSA). Measurement of the surface hydrophobicity of the proteins is important; hydrophobic interaction chromatography (HIC) was used for this purpose. The resolution of the systems (R) in terms of protein surface hydrophobicity and the intrinsic hydrophobicity (log P(0)) of the systems was established. The effect of the addition of NaCl to PEG/phosphate and PEG/dextran systems was analyzed in terms of the hydrophobicity difference between the phases and their ability to promote hydrophobic interactions between the protein surface and the PEG molecules. The values for R and log P(0) differed somewhat depending on which group of modified proteins was used for partitioning. The addition of NaCl to PEG/phosphate systems promoted an increase in the values of R, showing an important effect on the resolution of the systems for protein surface hydrophobicity (twice as high when compared with systems without NaCl). For PEG/dextran systems, the addition of 9% NaCl (w/w) promoted an improvement in the resolution toward surface hydrophobicity with an increase of 60% on the value of R. (c) 1996 John Wiley & Sons, Inc.

Use of chemically modified proteins to study the effect of a single protein property on partitioning in aqueous two-phase systems: Effect of surface charge.

A series of charge-modified thaumatins with different values of surface charge were partitioned in aqueous two-phase systems (ATPS) to study the effect of surface charge as a single property on partitioning. Electrophoretic mobility of the proteins in titration curves was used as a measure of surface charge. Four modified proteins derived from thaumatin with the following values of isoelectric point: 8.70, 8.15, 5.60, and 4.50 were used for partitioning. The resolution of the systems in terms of protein surface charge was calculated. Partitioning of modified thaumatins in PEG 4000/dextran systems with phosphate buffer, Tris buffer, NaCl, KCl, and sulfate salts was carried out. Among the sulfate salts tested, the addition of 50 mM Li(2)SO(4) to the system buffered with phosphate gave the highest value of resolution for differences in surface protein charge (RSPC). It shows a decrease in the value of K (partition coefficient) with an increase in the protein's charge. The addition of 100 mM KCl to the system promoted the opposite effect on the RSPC value. Charge-modified proteins were partitioned in PEG/salt systems to investigate the ability of these systems for resolving differences in surface charge. The PEG/citrate system seemed to have almost no ability for resolving proteins on the basis of surface charge differences; PEG/phosphate systems had some capability for resolving differently charged proteins. The more negative proteins tended to have higher values of K than the more positively charged fractions. The use of charge-modified proteins allowed the investigation of the effect of protein surface charge on partitioning in aqueous two-phase systems independently from other protein parameters as they were prepared from a common parent protein thaumatin. This technique provides an interesting novel tool to investigate the effect of protein surface charge on partitioning in ATPS taking protein charge as an independent parameter. (c) 1996 John Wiley & Sons, Inc.