High-level production of heterologous proteins using untreated cane molasses and corn steep liquor in Escherichia coli medium

Machine learning modeling of the effects of media formulated with various yeast extracts on heterologous protein production in Escherichia coli

In microbial manufacturing, yeast extract is an important component of the growth media. The production of heterologous proteins often varies because of the yeast extract composition. To identify why this reduces protein production, the effects of yeast extract composition on the growth and green fluorescent protein (GFP) production of engineered Escherichia coli were investigated using a deep neural network (DNN)-mediated metabolomics approach. We observed 205 peaks from the various yeast extracts using gas chromatography-mass spectrometry. Principal component analyses of the peaks identified at least three different clusters. Using 20 different compositions of yeast extract in M9 media, the yields of cells and GFP in the yeast extract-containing media were higher than those in the control without yeast extract by approximately 3.0- to 5.0-fold and 1.5- to 2.0-fold, respectively. We compared machine learning models and found that DNN best fit the data. To estimate the importance of each variable, we performed DNN with a mean increase error calculation based on a permutation algorithm. This method identified the significant components of yeast extract. DNN learning with varying numbers of input variables provided the number of significant components. The influence of specific components on cell growth and GFP production was confirmed with a validation cultivation.

Efficient Allitol Bioproduction from D-Fructose Catalyzed by Recombinant E. coli Whole Cells, and the Condition Optimization, Product Purification

Allitol is a kind of rare sugar alcohol with potential application value. An engineered strain, which simultaneously expressed D-psicose-3-epimerase (DPE), ribitol dehydrogenase (RDH), and formate dehydrogenase (FDH) three enzymes, was constructed by cloning above three genes into one plasmid and transformed into the host E. coli strain, and used as the whole-cell catalysts for biotransformation of allitol from the low-cost substrate of D-fructose. The whole cell allitol biotransformation conditions were optimized. The medium, recombinant gene induction conditions, and the substrate feeding rate for cultivation of the catalytic cells were optimized. Then, the fed-batch culture was made and scaled up to 10 L fermentor. Finally, 63.44 g/L allitol was obtained from 100 g/L D-fructose after 3 h of biotransformation, and the allitol crystals of 99.9% purity were obtained by using cooling recrystallization. The allitol production method developed in this research has high product purity, and is highly efficient, easily scaled up, and suitable for large-scale production of highly purified allitol.

Development of a strategy for the production of docosahexaenoic acid by Schizochytrium sp. from cane molasses and algae-residue

The aim of this work was to reduce the algae-residue emission and make use of cane molasses as fermentation materials for docosahexaenoic acid (DHA) fermentaion by Schizochytrium sp., which further could cut the cost of DHA production. Algae-residue and cane molasses were respectively used as nitrogen and carbon sources to replace yeast extract and glucose. A significant DHA yield of 18.58 g/L was obtained using algae-residue, while cane molasses could not be used well as sole carbon source due to the presence of undesirable substance. A two-stage culture strategy with glucose followed by pretreated cane molasses as carbon source was developed, resulting in a final DHA yield of 15.22 g/L. This study therefore offers an economical and green strategy for DHA production by Schizochytrium sp.

Efficient production of 1,3-propanediol from crude glycerol by repeated fed-batch fermentation strategy of a lactate and 2,3-butanediol deficient mutant of Klebsiella pneumoniae

BACKGROUND

1,3-Propanediol (1,3-PDO) is important building blocks for the bio-based chemical industry, Klebsiella pneumoniae can be an attractive candidate for their production. However, 1,3-PDO production is high but productivity is generally low by K. pneumoniae. In this study, repeated fed-batch cultivation by a lactate and 2,3-butanediol (2,3-BDO) deficient mutant of K. pneumoniae were investigated for efficient 1,3-PDO production from industrial by-products such as crude glycerol.

RESULTS

First, optimal conditions for repeated fed-batch fermentation of a ΔldhA mutant defective for lactate formation due to deletion of the lactate dehydrogenase gene (ldhA) were determined. Maximal 1,3-PDO production level and productivity obtained by repeated fed-batch fermentation under optimized conditions were 81.1 g/L and 3.38 g/L/h, respectively, and these values were successfully maintained for five cycles of fermentation without any loss of fermentation capacity. This results were much higher than that of the normal fed-batch fermentation. The levels of 2,3-BDO, which is a major by-product, reaching up to ~ 50% of the level of 1,3-PDO, were reduced using a mutant strain [Δ(ldhA als)] containing an additional mutation in the biosynthetic pathway of 2,3-BDO (deletion of the acetolactate synthase gene). The levels of 2,3-BDO were reduced to about 20% of 1,3-PDO levels by repeated fed-batch fermentation of Δ(ldhA als), although maximal 1,3-PDO production and productivity also decreased owing to a defect in the growth of the 2,3-BDO-defective mutant strain.

CONCLUSION

This repeated fed-batch fermentation may be useful for reducing the cost of 1,3-PDO production and may be promising industrialization prospect for the 1,3-PDO production.

Co-production of microbial oil and exopolysaccharide by the oleaginous yeastSporidiobolus pararoseusgrown in fed-batch culture

The production cost of microbial oil was reduced by improving the exopolysaccharide (EPS) production to share the production cost using Sporidiobolus pararoseus JD-2. Batch fermentation demonstrated that S. pararoseus JD-2 has the potential to co-produce oil and EPS with 120 g L⁻¹ glucose, 20 g L⁻¹ corn steep liquor and 10 g L⁻¹ yeast extract as carbon and nitrogen sources. Using fed-batch fermentation for 72 h resulted in oil and EPS production of 41.6 ± 2.5 g L⁻¹ and 13.1 ± 0.6 g L⁻¹ with the productivity of 0.58 g L⁻¹ h⁻¹ and 0.182 g L⁻¹ h⁻¹, respectively. The fat soluble nutrients in the oil were studied, indicating that it was constituted of 79.19% unsaturated fatty acids and contained 505 mg per kg-oil of carotenoids. Moreover, the EPS contained only one type of polysaccharide; the main monosaccharide compositions were galactose, glucose and mannose in a proportion of 16 : 8 : 1. These results implied that EPS produced by S. pararoseus JD-2 was a new type of EPS.

The production cost of microbial oil was reduced by improving the exopolysaccharide (EPS) production to share the production cost using Sporidiobolus pararoseus JD-2.

Production of chlorothalonil hydrolytic dehalogenase from agro-industrial wastewater and its application in raw food cleaning

BACKGROUND

To reduce the fermentation cost for industrialization of chlorothalonil hydrolytic dehalogenase (Chd), agro-industrial wastewaters including molasses, corn steep liquor (CSL) and fermentation wastewater were used to substitute for expensive carbon and nitrogen sources and fresh water for lab preparation.

RESULTS

The results showed that molasses and CSL could replace 5% carbon source and 100% organic nitrogen source respectively to maintain the same fermentation level. Re-fermentation from raffinate of ultra-filtered fermentation wastewater could achieve 61.03% of initial Chd activity and reach 96.39% activity when cultured in a mixture of raffinate and 50% of original medium constituent. Typical raw foods were chosen to evaluate the chlorothalonil removal ability of Chd. After Chd treatment for 2 h at room temperature, 97.40 and 75.55% of 30 mg kg^-1 chlorothalonil on cherry tomato and strawberry respectively and 60.29% of 50 mg kg^-1 chlorothalonil on Chinese cabbage were removed. Furthermore, the residual activity of the enzyme remained at 78-82% after treatment, suggesting its potential for reuse.

CONCLUSION

This study proved the cost-feasibility of large-scale production of Chd from agro-industrial wastewater and demonstrated the potential of Chd in raw food cleaning. © 2016 Society of Chemical Industry.

Influence of nitrogen sources on the enzymatic activity and grown by Lentinula edodes in biomass Eucalyptus benthamii

Lignocellulose is the most abundant environmental component and a renewable organic resource in soil. There are some filamentous fungi which developed the ability to break down and use cellulose, hemicellulose and lignin as an energy source. The objective of this research was to analyze the effect of three nitrogen resources (ammonium sulfate, saltpetre, soybean) in the holocellulolitic activity of Lentinula edodes EF 50 using as substrate sawdust E. benthamii. An experimental design mixture was applied with repetition in the central point consisting of seven treatments (T) of equal concentrations of nitrogen in ammonium sulfate, potassium nitrate and soybean. The enzymatic activity of avicelase, carboxymetilcellulase, β-glucosidase, xylanases and manganese peroxidase was determined. The humidity, pH, water activity (aw) and qualitative analysis of mycelial growth in 8 times of cultivation were evaluated. The results showed negative effect on enzyme production in treatments with maximum concentration of ammonium sulfate and potassium nitrate. The treatments with cooked soybean flour expressed higher enzymatic activities in times of 3, 6 and 9 days of culture, except in the activity of manganese peroxidase. The highest production was observed in the treatment with ammonium sulfate, and soybean (83.86 UI.L-1) at 20 days of cultivation.

Enhanced Production of Androst-1,4-Diene-3,17-Dione by Mycobacterium neoaurum JC-12 Using Three-Stage Fermentation Strategy

To improve the androst-1,4-diene-3,17-dione (ADD) production from phytosterol by Mycobacterium neoaurum JC-12, fructose was firstly found favorable as the initial carbon source to increase the biomass and eliminate the lag phase of M. neoaurum JC-12 in the phytosterol transformation process. Based on this phenomenon, two-stage fermentation by using fructose as the initial carbon source and feeding glucose to maintain strain metabolism was designed. By applying this strategy, the fermentation duration was decreased from 168 h to 120 h with the ADD productivity increased from 0.071 g/(L·h) to 0.108 g/(L·h). Further, three-stage fermentation by adding phytosterol to improve ADD production at the end of the two-stage fermentation was carried out and the final ADD production reached 18.6 g/L, which is the highest reported ADD production using phytosterol as substrate. Thus, this strategy provides a possible way in enhancing the ADD production in pharmaceutical industry.

Lipid Production of Heterotrophic Chlorella sp. from Hydrolysate Mixtures of Lipid-Extracted Microalgal Biomass Residues and Molasses

This study investigated the feasibility of lipid production of Chlorella sp. from waste materials. Lipid-extracted microalgal biomass residues (LMBRs) and molasses were hydrolyzed, and their hydrolysates were analyzed. Five different hydrolysate mixture ratios (w/w) of LMBRs/molasses (1/0, 1/1, 1/4, 1/9, and 0/1) were used to cultivate Chlorella sp. The results showed that carbohydrate and protein were the two main compounds in the LMBRs, and carbohydrate was the main compound in the molasses. The highest biomass concentration of 5.58 g/L, Y biomass/sugars of 0.59 g/g, lipid productivity of 335 mg/L/day, and Y lipids/sugars of 0.25 g/g were obtained at the hydrolysate mixture ratio of LMBRs/molasses of 1/4. High C/N ratio promoted the conversion of sugars into lipids. The lipids extracted from Chlorella sp. shared similar lipid profile of soybean oil and is therefore a potential viable biodiesel feedstock. These results showed that Chlorella sp. can utilize mixed sugars and amino acids from LMBRs and molasses to accumulate lipids efficiently, thus reducing the cost of microalgal biodiesel production and improving its economic viability.

Development of a substrate-coupled biocatalytic process driven by an NADPH-dependent sorbose reductase from Candida albicans for the asymmetric reduction of ethyl 4-chloro-3-oxobutanoate

A substrate-coupled biocatalytic process was developed based on the reactions catalyzed by an NADPH-dependent sorbose reductase (SOU1) from Candida albicans in which ethyl 4-chloro-3-oxobutanoate (COBE) was reduced to (S)-4-chloro-3-hydroxybutanoate [(S)-CHBE], while NADPH was regenerated by the same enzyme via oxidation of sugar alcohols. (S)-CHBE yields of 1,140, 1,150, and 780 mM were obtained from 1,220 mM COBE when sorbitol, mannitol, and xylitol were used as co-substrates, respectively. Optimization of COBE and sorbitol proportions resulted in a maximum yield of (S)-CHBE (2,340 mM) from 2,500 mM COBE, and the enantiomeric excess was 99.6 %. The substrate-coupled system driven by SOU1 maintained a stable pH and a robust intracellular NADPH circulation; thus, pH adjustment and addition of extra coenzymes were unnecessary.

Genetic background has a major impact on differences in sleep resulting from environmental influences in Drosophila

STUDY OBJECTIVES

To determine the effect of different genetic backgrounds on demographic and environmental interventions that affect sleep and evaluate variance of these measures; and to evaluate sleep and variance of sleep behaviors in 6 divergent laboratory strains of common origin.

DESIGN

Assessment of the effects of age, sex, mating status, food sources, and social experience using video analysis of sleep behavior in 2 different strains of Drosophila, white(1118ex) (w(1118ex)) and white Canton-S (w(CS10)). Sleep was also determined for 6 laboratory strains of Canton-S and 3 inbred lines. The variance of total sleep was determined for all groups and conditions.

MEASUREMENTS AND RESULTS

The circadian periods and the effects of age upon sleep were the same between w(1118ex) and w(CS10) strains. However, the w(1118ex) and w(CS10) strains demonstrated genotype-dependent differences in the effects upon sleep of sex, mating status, social experience, and being on different foods. Variance of total sleep was found to differ in a genotype dependent manner for interventions between the w(1118ex) and w(CS10) strains. Six different laboratory Canton-S strains were found to have significantly different circadian periods (P < 0.001) and sleep phenotypes (P < 0.001). Three inbred lines showed reduced variance for sleep measurements.

CONCLUSIONS

One must control environmental conditions in a rigorously consistent manner to ensure that sleep data may be compared between experiments. Genetic background has a significant impact upon changes in sleep behavior and variance of behavior due to demographic factors and environmental interventions. This represents an opportunity to discover new genes that modify sleep/wake behavior.

Purification and characterization of a novel NADH-dependent carbonyl reductase from Pichia stipitis involved in biosynthesis of optically pure ethyl (S)-4-chloro-3-hydroxybutanoate

A novel NADH-dependent dehydrogenases/reductases (SDRs) superfamily reductase (PsCRII) was isolated from Pichia stipitis. It produced ethyl (S)-4-chloro-3-hydroxybutanoate [(S)-CHBE] in greater than 99% enantiomeric excess. This enzyme was purified to homogeneity by ammonium sulfate precipitation followed by Q-Sepharose chromatography. Compared to similar known reductases producing (S)-CHBE, PsCR II was more suitable for production since the purified PsCRII preferred the inexpensive cofactor NADH to NADPH as the electron donor. Furthermore, the Km of PsCRII for ethyl 4-chloro-3-oxobutanoate (COBE) was 3.3 mM, and the corresponding Vmax was 224 μmol/mg protein/min. The catalytic efficiency is the highest value ever reported for NADH-dependent reductases from yeasts that produce CHBE with high enantioselectivity. In addition, this enzyme exhibited broad substrate specificity for several β-keto esters using NADH as the coenzyme. The properties of PsCRII with those of other carbonyl reductases from yeasts were also compared in this study.

Biosynthesis of (S)-4-chloro-3-hydroxybutanoate ethyl using Escherichia coli co-expressing a novel NADH-dependent carbonyl reductase and a glucose dehydrogenase

A novel NADH-dependent carbonyl reductase (PsCR II) gene with an open reading frame of 855bp encoding 285 amino acids was cloned from Pichia stipitis. Analysis of the amino acid sequence of PsCR II revealed less than 55% identity to known reductases that produce (S)-4-chloro-3-hydroxybutanoates ethyl [(S)-CHBE]. When NADH was provided as an electron donor, Escherichia coli with pET-22b-PsCRII exhibited an activity of 15U/mg protein using 4-chloro-3-oxobutanoate ethyl (COBE) as a substrate. This activity was the highest ever reported for reductases, with the exception of PsCR I, which in our previous analysis required NADPH for catalysis. Biocatalysis of COBE to (S)-CHBE was investigated using E. coli with a polycistronic plasmid pET-BP II co-expressing PsCR II and a glucose dehydrogenase in a water/butyl acetate system for 24h. The transformants gave a molar yield of 91%, and an optical purity of the (S)-isomer of higher than 99% enantiomeric excess.

Construction and co-expression of a polycistronic plasmid encoding carbonyl reductase and glucose dehydrogenase for production of ethyl (S)-4-chloro-3-hydroxybutanoate

Biocatalysis of ethyl 4-chloro-3-oxobutanoate (COBE) to ethyl (S)-4-chloro-3-hydroxybutanoate [(S)-CHBE] was carried out using Escherichia coli co-expressing a carbonyl reductase gene from Pichia stipitis and a glucose dehydrogenase gene from Bacillus megaterium. An efficient polycistronic plasmid with a high-level of enzyme co-expression was constructed by changing the order of the genes, altering the Shine-Dalgarno (SD) regions, and aligned spacing (AS) between the SD sequence and the translation initiation codon. The optimal SD sequence was 5-TAAGGAGG-3, and the optimal AS distance was eight nucleotides. Asymmetric reduction of COBE to (S)-CHBE with more than 99% enantiomeric excess was demonstrated by transformants, using a water/ethyl caprylate system. The recombinant cells produced 1260 mM product in the organic phase, and the total turnover number, defined as moles (S)-CHBE formed per mole NADP(+), was 12,600, which was more than 10-fold higher than in aqueous systems.