Heterologous Expression and Rational Design of l-asparaginase from Rhizomucor miehei to Improve Thermostability

l-asparaginase (EC 3.5.1.1) hydrolyzes l-asparagine to produce l-aspartate and ammonia and is widely found in microorganisms, plants, and some rodent sera. l-asparaginase used for industrial production should have good thermostability. We heterologously expressed l-asparaginase from Rhizomucor miehei, selected nine loci for site-directed mutagenesis by rational design, and obtained two mutants with significantly improved thermostability. The optimal temperature of mutants S302I and S302M was 50 °C. After incubating the mutant and wild-type enzymes at 45 °C for 35 h, the residual activity of the wild-type enzyme (WT) was only about 10%. In contrast, the residual activity of S302I and S302M was more than 50%. After combination mutagenesis, Bacillus subtilis 168-pMA5-A344E/S302I was constructed using the food-safe host strain B. subtilis 168. Additionally, a 5′ untranslated region (UTR) modification strategy was adopted to enhance the expression level of R. miehei-derived l-asparaginase in B. subtilis. In a 5-L fermenter scale-up experiment, the enzyme activity of recombinant B. subtilis 168-pMA5-UTR-A344E/S302I reached 521.9 U·mL−1 by fed-batch fermentation.

Submerged Fermentation of Animal Fat By-Products by Oleaginous Filamentous Fungi for the Production of Unsaturated Single Cell Oil

Animal waste fats were explored as a fermentation substrate for the production of high-value unsaturated single cell oil (SCO) using oleaginous fungi, Mucor circinelloides and Mortierella alpina. Both strains showed good growth and lipid accumulation when using animal fat as a single carbon source. The biomass concentration of 16.7 ± 2.2 gDCW/L and lipid content of 54.1%wt (of dry cell weight) were obtained for Mucor circinelloides in shake flask experiments, surpassing the biomass yield achieved in batch and fed-batch fermentation. In contrast, Mortierella alpina gave the highest biomass concentration (8.3 ± 0.3 gDCW/L) and lipid content (55.8%wt) in fed-batch fermentation. Fat grown Mortierella alpina was able to produce arachidonic acid (ARA), and the highest ARA content of 23.8%wt (of total lipid weight) was in fed-batch fermentation. Gamma-linolenic acid (GLA) was produced by both fungal strains. At the end of fed-batch fermentation, the GLA yields obtained for Mucor circinelloides and Mortierella alpina were 4.51%wt and 2.77%wt (of total lipid weight), respectively. This study demonstrates the production of unsaturated SCO-rich fungal biomass from animal fat by fermentation.

Development of a plasmid stabilization system in Vibrio natriegens for the high production of 1,3-propanediol and 3-hydroxypropionate

Vibrio natriegens is a promising industrial chassis with a super-fast growth rate and high substrate uptake rates. V. natriegens was previously engineered to produce 1,3-propanediol (1,3-PDO) from glycerol by overexpressing the corresponding genes in a plasmid. However, antibiotic selection pressure for plasmid stability was not satisfactory and plasmid loss resulted in reduced productivity of the bioprocess. In this study, we developed an antibiotic-free plasmid stabilization system for V. natriegens. The system was achieved by shifting the glpD gene, one of the essential genes for glycerol degradation, from the chromosome to plasmid. With this system, engineered V. natriegens can stably maintain a large expression plasmid during the whole fed-batch fermentation and accumulated 69.5 g/L 1,3-PDO in 24 h, which was 23% higher than that based on antibiotic selection system. This system was also applied to engineering V. natriegens for the production of 3-hydroxypropionate (3-HP), enabling the engineered strain to accumulate 64.5 g/L 3-HP in 24 h, which was 30% higher than that based on antibiotic system. Overall, the developed strategy could be useful for engineering V. natriegens as a platform for the production of value-added chemicals from glycerol. Graphic Abstract

Improvement of 1,3-Propanediol Production From Crude Glycerol by Co-cultivation of Anaerobic and Facultative Microbes Under Non-strictly Anaerobic Conditions

Background: Natural microbial consortia could efficiently produce 1,3-propanediol, the most promising bulk biochemical derived from glycerol that can be used as a monomer in the synthesis of polytrimethylene terephthalate (PTT). While natural microbial communities are made up of a diverse range of microbes with frequently unknown functions, the construction of synthetic microbial consortia allows for creating more defined systems with lower complexity.Results: In this study, the synthetic microbial consortia were constructed by combing facultative microbes of Klebsiella pneumoniae DUT2 (KP) and/or Escherichia coli DUT3 (EC) cultures with the strict anaerobic microbe of Clostridium butyricum DUT1 (CB) cultures under micro-aerobic conditions. The function of EC and KP during the fermentation process was to deplete oxygen and provide an anaerobic environment for CB. Furthermore, KP competes with CB to consume crude glycerol and produce 1,3-PDO. The interaction of commensalism and competition resulted in synthetic microbial consortia that could efficiently convert crude glycerol to 1,3-PDO even under micro-aerobic conditions. In a batch fermentation, the synthetic CB:KP co-culture at an initial abundance ratio of 92.5:7.5 yielded a maximum 1,3-PDO concentration of 52.08 g/L, with a yield of 0.49 g/g and a productivity of 1.80 g/(L.h), which increased by 10%, 9%, and 12%, respectively, when compared to the CB mono-culture under strictly anaerobic conditions. Compared to the KP mono-culture, the final 1,3-PDO concentration, yield, and productivity by the synthetic CB:KP consortia increased by 16%, 19%, and 84%, respectively. The synthetic CB:KP:EC co-culture achieved the highest 1,3-PDO flux of 49.17% at an initial abundance ratio of 85:7.5:7.5, while 7.43%, 5.77%, 3.15% 4.24%, and 2.13% of flux was distributed to butyric acid, acetic acid, lactic acid, ethanol, and succinic acid pathways. In a fed-batch fermentation, synthetic CB:KP:EC co-culture demonstrated a maximum 1,3-PDO concentration of 77.68 g/L with a yield of 0.51 g/g which is 30% and 13% higher than the production by the CB mono-culture at 0.02 vvm N2 supply. The initial abundance of CB guaranteed to be at least 85% facilitates 1,3-PDO production from crude glycerol efficiently by the development of synthetic microbial consortia. Conclusion: Under micro-aerobic conditions, the synthetic microbial consortia demonstrated excellent performance on 1,3-propanediol production via the interaction of commensalism and competition. The experimental results demonstrated the potential benefit of using the synthetic microbial consortia to produce 1,3-propanediol from crude glycerol.

Engineering Saccharomyces Cerevisiae for the Production and Secretion of Affibody Molecules.

BackgroundAffibody molecules are synthetic peptides with a variety of therapeutic and diagnostic applications. To date, Affibody molecules have mainly been produced by the bacterial production host Escherichia coli. There is an interest in exploring alternative production hosts to address if improvements in terms of yield, ease of production and if purification advantages can be identified. In this study, we evaluated the feasibility of Saccharomyces cerevisiae as a production chassis for this group of proteins. Results We examined the production of three different Affibody molecules in S. cerevisiae and found that these Affibody molecules were partially degraded. An albumin-binding domain, which may be attached to the Affibody molecules to increase their half-life, showed to be a substrate for several S. cerevisiae proteases. We tested the removal of three vacuolar proteases, proteinase A, proteinase B and carboxypeptidase Y. Removal of one of these, proteinase A, resulted in intact secretion of one of the targeted Affibody molecules. Removal of either or both two additional proteases, carboxypeptidase Y and proteinase B, resulted in intact secretion of the two remaining Affibody molecules. The produced Affibody molecules were verified to bind human HER3 as potently as the corresponding molecules produced in E. coli in an in vitro surface-plasmon resonance binding assay. Finally, we performed a fed-batch fermentation with one of the engineered protease-deficient S. cerevisiae strains and achieved a protein titer of 530 mg Affibody molecule/L. ConclusionThis study shows that engineered S. cerevisiae has a great potential as a production host for recombinant Affibody molecules, reaching high yields and for proteins where endotoxin removal could be challenging, the use of S. cerevisiae obviates the need for endotoxin removal from protein produced in E. coli.

Bacterial Cellulose Synthesis by Gluconacetobacter xylinus: Enhancement via Fed-batch Fermentation Strategies in Glycerol Media

Bacterial cellulose (BC) is an abundant polysaccharide, which is secreted by several genera of bacteria. It has remarkable characteristics, which include high purity, high tensile strength, high biocompatibility and non-toxic. The main feature that differentiates BC and plant cellulose (PC) is the absence of contaminants such as lignin, hemicellulose and pectin. However, the main drawbacks in producing BC are low yield and expensive carbon source. Due to that, this study was carried out to enhance BC volumetric productivity in fed-batch operation mode using glycerol as a carbon source. BC was produced in fill-and-draw and pulse-feed fed-batch cultures of Gluconacetobacter xylinus DSM 46604 in a 3-L bench-top bioreactor. The fed-batch fermentation trials were conducted in agitated and aerobic conditions at 30 ºC. For fill-and-draw fed-batch culture, a total of 24.2 g/L of BC accumulated in the bioreactor after 9 days, which corresponded to a yield and productivity of 0.2 g/g and 2.69 g/L/day, respectively. Pulse-feed fed-batch fermentation resulted in a yield and volumetric productivity of 0.38 g/g and 2.71 g/L/day, respectively. The pulse-feed fed-batch culture proved to be a better fermentation system for utilizing glycerol, which is a low-cost and abundant carbon source. HIGHLIGHTS Komagataeibacter species, which were formerly known as Acetobacter or Gluconacetobacter is one of the Gram-negative BC producers that secretes a large quantity of BC microfibrils extracellularly One of the main challenges in bacterial cellulose (BC) production is low productivity and high processing cost As fed-batch fermentation is one of the operation modes in bioprocess that can control the microbial growth rate, this operation mode is conducted to enhance the yield of BC, substrate consumption and also volumetric productivity Fill-and-draw and pulse feed fed-batch culture were conducted to enhance yield and volumetric productivity. The pulse-feed fed-batch culture resulted to be a favorable operation mode for utilizing glycerol, which is a low-cost and abundant carbon source GRAPHICAL ABSTRACT

Chemical, Microbiological and Volatile Composition of Kefir-like Beverages Produced from Red Table Grape Juice in Repeated 24-h Fed-batch Subcultures

The aim of this work was to study the production of kefir-like beverage by fed-batch fermentation of red table grape juice at initial pHs of 3.99 (fermentation A) and 5.99 (fermentation B) with kefir grains during four repeated 24-h fed-batch subcultures. However, all kefir-like beverages (KLB) were characterized by low alcoholic grade (≤ 3.6%, v/v) and lactic and acetic acid concentrations. The beverages obtained from fermentation B had lower concentrations of sugars and higher microbial counts than the KLB obtained in fermentation A. In addition, the KLB from fermentation B were the most aromatic and had the highest contents in alcohols, esters, aldehydes and organic acids compared to the non-fermented juice and KLB from fermentation A. These results indicate the possibility of obtaining red table grapes KLB with their own distinctive aromatic characteristics and a high content in probiotic viable cells, contributing to the valorization of this fruit.

Enhancement of β-Alanine Biosynthesis in Escherichia coli Based on Multivariate Modular Metabolic Engineering

β-alanine is widely used as an intermediate in industrial production. However, the low production of microbial cell factories limits its further application. Here, to improve the biosynthesis production of β-alanine in Escherichia coli, multivariate modular metabolic engineering was recruited to manipulate the β-alanine biosynthesis pathway through keeping the balance of metabolic flux among the whole metabolic network. The β-alanine biosynthesis pathway was separated into three modules: the β-alanine biosynthesis module, TCA module, and glycolysis module. Global regulation was performed throughout the entire β-alanine biosynthesis pathway rationally and systematically by optimizing metabolic flux, overcoming metabolic bottlenecks and weakening branch pathways. As a result, metabolic flux was channeled in the direction of β-alanine biosynthesis without huge metabolic burden, and 37.9 g/L β-alanine was generated by engineered Escherichia coli strain B0016-07 in fed-batch fermentation. This study was meaningful to the synthetic biology of β-alanine industrial production.