Understanding the hindrance factor of bacterial proliferation and γ-aminobutyric acid-producing capability of nondairy strains of Lactiplantibacillus plantarum in milk fermentation

γ-aminobutyric-acid (GABA) is a mental health-supporting substance that helps release anxiety and depression and improves memory. Lactiplantibacillus plantarum SKKL1, a GABA-producing bacterium, has been introduced to formulate a gut-brain axis product. However, growth and sugar consumption of L. plantarum SKKL1 in milk were ineffective. This obstacle was investigated by varying different types of milk, sugars, fermentation temperatures, and times. The results revealed that none of these parameters improved growth and bacterial metabolism in milk, except addition of soluble protein as found in yeast extract and malt extract. Although a protease deficiency of L. plantarum SKKL1 was discovered, it was not a primary barrier to cell propagation. Insight of this study showed clearly that soluble protein was an essential metabolic activator for growth, nutrient consumption, and protease synthesis, then stimulated lactic acid and GABA productions. While, milk casein and casein hydrolysate, a complex protein structure with low solubility, were not utilized by L. plantarum SKKL1. The novelty of this study is the first in-depth investigation to confirm a significant effect of soluble protein on enrich-GABA milk fermentation by L. plantarum SKKL1 as the sole starter without protease and monosodium glutamate addition.

Development of an animal-derived component-free medium for Spodoptera frugiperda (Sf9) cells using response surface methodology

OBJECTIVES

To develop an animal-derived component-free medium for Spodoptera frugiperda (Sf9) growth and green fluorescent protein (GFP) expression.

RESULTS

OSF9-ADCFM contained optimum concentrations of CDLC, YE and ST at 0.5% (v/v), 11.0 g/L, and 3.0 g/L, respectively. A mean viable cell concentration of 1.71 ± 0.14 × 10⁵ cells/mL was obtained from 5 passages (P1-P5). The use of both peptones after 10 kDa ultrafiltration had a significant effect on Sf9 cell growth. Grace's insect medium with 10% FBS gave higher un-infected cell number than SF-900II and OSF9-ADCFM for 4.29 and 5.38 times, respectively. The average cell number of un-infected cells and GFP-fluorescent cells of SF-900II were higher than OSF9-ADCFM 1.25 and 7 times, respectively.

CONCLUSION

In-house OSF9-ADCFM could support growth and GFP expression in Sf9 less than commercial SF-900II. However, it could lower the production cost at least 50% comparing to commercial SF-900II. The development of in- house OSF9-ADCFM would be continued to increase both cell numbers and protein expression in the next step.

Effects and mechanisms of animal-free hydrolysates on recombination protein yields in CHO cells

Chinese hamster ovary (CHO) cells are the commonly used cell lines for producing recombinant therapeutic proteins (RTPs) because they possess post-translational modifications similar to human cells. Culture media are necessary for cell growth, and their quality affects the yields and quality of RTPs. Due to safety concerns for the complex purification of RTPs, the development of serum-free media (SFM) is necessary for CHO cells. To meet the need for CHO cells with higher cell density and RTP productivity with consistent product quality in large-scale suspension cultures, the optimization of SFM through adding some enzymatic animal-free hydrolysates (AFHs) is preferred. The AFHs can improve cell culture performance and product yield of RTPs without affecting their quality. Here, the effect and mechanism of various AFHs in improving CHO cell culture performance and protein expression are reviewed. KEY POINTS: • AFHs that improve the recombinant protein yield of CHO cells are reviewed. • AFHs improve recombinant protein yield via influencing cell performance. • The AFHs do not affect the quality of recombinant protein in CHO cells. • AFHs can provide nutrients, block cell cycle, and reduce oxidative stress.

Extracellular Polysaccharide Extraction from Streptococcus thermophilus in Fermented Milk

Lactic acid bacteria such as Streptococcus thermophilus are known to produce extracellular polysaccharide (EPS) in fermented foods that enhance the creaminess and mouthfeel of the product, such as yogurt. Strains producing larger amounts of EPS are highly sought-after, and therefore, robust and accurate quantification methodologies are important. This study found that two commonly used methodologies significantly underestimated the amount of EPS produced as measured using a milk matrix. To this end, a proteolytic step was implemented prior to EPS extraction (Method C). An initial proteolytic step using xanthan gum-spiked milk significantly increased recovery yield to 64%, compared to 27.8% for Method A and 34.3% for Method B. Method C showed no improvement when assessed using a chemically defined medium. Method C was further validated using three strains of S. thermophilus with varying EPS-production capabilities (ST^LOW, ST^MID, ST^HIGH). Overall, Method C demonstrated significant improvements in the EPS extraction yield for all three S. thermophilus strains in fermented milk. On average, Method C improved isolation yield by ∼3- to 6-fold compared with Method A and by ∼2- to 3-fold compared with method B. There were no significant differences between samples when they were grown in a chemically defined medium, highlighting the importance of a proteolytic step specifically for fermented milk samples. In commercial applications, accurate quantification of EPS-production is an important aspect when finding new strains. IMPORTANCE Extracellular polysaccharide (EPS) production by milk-fermenting microorganisms is a highly sought-after trait in improving the perceived thickness, creaminess, and mouthfeel of yogurt. Streptococcus thermophilus are commonly isolated and their EPS production is quantified in the search for higher-producing strains. In this study, we demonstrated that two commonly used methods for isolating EPS from milk samples significantly underestimated the true amount of EPS present. We demonstrated that the addition of a proteolytic step prior to EPS extraction isolated over 2-fold more EPS than identical samples processed using the traditional protocols. We further validated this method in fermented milk samples from three strains of S. thermophilus that included a low-, mid-, and high-EPS producing strain. Again, we showed significant improvements in EPS isolation using a proteolytic step. In the search for new S. thermophilus strains with enhanced EPS production, accurate quantification in an optimal medium is essential.

Yeast Extract Affecting the Transformation of Biogenic Tooeleite and Its Stability

Highly toxic As(III) is the main form of As in wastewater. The retention of As by tooeleite has gradually attracted attention in recent years due to its great potential for the direct removal of As(III). The existence of natural As-bearing minerals is closely related to microorganisms and organic matters. In this study, yeast extract was found to enhance the stability of biogenic tooeleite by Acidithiobacillus ferrooxidans (A. ferrooxidans). The effects of pH, Fe/As and yeast extract concentration were systematically studied, and the toxicity characteristic leaching procedure (TCLP) was conducted to evaluate the short-term stability of tooeleite. The mineral synthesized in the presence of yeast extract showed that the As leaching concentration decreased from 13.78 mg/L to 7.23 mg/L and the stability increased by more than 40%. In addition, various characteristics confirmed that the precursor was changed from amorphous schwertmannite to basic ferric sulfate in the presence of yeast extract, and then transformed to relatively purer tooeleite with less hollow structure and excellent dispersion, which is favorable for the stability of tooeleite. This result indicated that yeast extract resulted in the formation of different precursors and thus affected the transformation and stability of tooeleite.

Food-derived bioactive peptides-methods for purification and analysis

Bioactive peptides attract the attention of researchers thanks to their high potential to beneficially influence human health. Various activities are reported, and some of these peptides are commercialized as therapeutic agents. Food-related proteins represent an excellent source in this regard. However, the identification, purification, and characterization of bioactive peptides require а complex approach. The full range of analytical techniques is used in combination with the chemical and biological properties of the peptides. The emerging "omics" techniques and "in silico" methods have given a new direction to peptide analysis in recent years. Developing new methods, rapid and low-cost, for the identification, characterization and purification, is a challenging task because of the complexity of food samples. However, bioinformatics is a promising technique for their exploration. These new strategies can predict different types of peptides, their properties and represent a new horizon for releasing their potential. That is why, in this review, we summarize information about methods used for purification and analysis of food-derived bioactive peptides so far, as well as present our point of view about the role of bioinformatics in this process.

Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress

Bacteria encounter elevated copper (Cu) concentrations in multiple environments, varying from mining wastes to antimicrobial applications of copper. As the role of the environment in the bacterial response to Cu ion exposure remains elusive, we used a tagRNA-seq approach to elucidate the disparate responses of two morphotypes of Caulobacter crescentus NA1000 to moderate Cu stress in a complex rich (PYE) medium and a defined poor (M2G) medium. The transcriptome was more responsive in M2G, where we observed an extensive oxidative stress response and reconfiguration of the proteome, as well as the induction of metal resistance clusters. In PYE, little evidence was found for an oxidative stress response, but several transport systems were differentially expressed, and an increased need for histidine was apparent. These results show that the Cu stress response is strongly dependent on the cellular environment. In addition, induction of the extracytoplasmic function sigma factor SigF and its regulon was shared by the Cu stress responses in both media, and its central role was confirmed by the phenotypic screening of a sigF::Tn5 mutant. In both media, stalked cells were more responsive to Cu stress than swarmer cells, and a stronger basal expression of several cell protection systems was noted, indicating that the swarmer cell is inherently more Cu resistant. Our approach also allowed for detecting several new transcription start sites, putatively indicating small regulatory RNAs, and additional levels of Cu-responsive regulation.

Development of a rapid polarized total synchronous fluorescence spectroscopy (pTSFS) method for protein quantification in a model bioreactor broth

Protein quantification during bioprocess monitoring is essential for biopharmaceutical manufacturing and is complicated by the complex chemical composition of the bioreactor broth. Here we present the early-stage development and optimization of a polarized total synchronous fluorescence spectroscopy (pTSFS) method for protein quantification in a hydrolysate-protein model (mimics clarified bioreactor broth samples) using a standard benchtop laboratory fluorometer. We used UV transmitting polarizers to provide wider range pTSFS spectra for screening of the four different TSFS spectra generated by the measurement: parallel (||), perpendicular (⊥), unpolarized (T) intensity spectra and anisotropy maps. TSFS_|| (parallel polarized) measurements were the best for protein quantification compared to standard unpolarized measurements and the Bradford assay. This was because TSFS_|| spectra had a better analyte signal to noise ratio (SNR), due to the anisotropy of protein emission. This meant that protein signals were better resolved from the background emission of small molecule fluorophores in the cell culture media. SNR of >5000 was achieved for concentrations of bovine serum albumin/yeastolate 1.2/10 g L^-1 with TSFS_|| . Optimization using genetic algorithm and interval partial least squares based variable selection enabled reduction of spectral resolution and number of excitation wavelengths required without degrading performance. This enables fast (<3.5 min) online/at-line measurements, and the method had an LOD of 0.18 g L^-1 and high accuracy with a predictive error of <9%.

Screening of by-products from the food industry as growth promoting agents in serum-free media for skeletal muscle cell culture

The most significant cost driver for efficient bio-production of edible animal proteins is the cell culture media, where growth factors account for up to 96% of the total cost. The culture media must be serum-free, affordable, contain only food-grade ingredients, be efficient to promote cell growth and available in massive quantities. The commercially available serum substitutes are expensive and not necessarily food-grade. Identifying inexpensive food-safe alternatives to serum is crucial. By-products from food production are available in massive quantities, contain potential factors that can promote growth and are promising ingredients for serum replacement. The main goal of this study was to explore if food-grade by-product materials can be used as growth promoting agents in skeletal muscle cell culture to develop a tailor-made serum free media. Different by-products, including chicken carcass, cod backbone, eggshell membrane, egg white powder and pork plasma were enzymatically or chemically hydrolyzed. The hydrolysates in addition to lyophilized pork plasma and yeast extract were further characterized by size-exclusion chromatography, elemental combustion analysis and degree of hydrolysis. The materials were used as supplement to or replacement of commercial serum and further evaluated for their effect on metabolic activity, cell proliferation and cell cytotoxicity in muscle cells cultured in vitro. Our results indicate that none of the materials were cytotoxic to the skeletal muscle cells. Hydrolysates rich in peptides with approximately 2-15 amino acids in length were shown to improve cell growth and metabolic activity. Of all the materials tested pork plasma hydrolysates and yeast extract were the most promising. Pork plasma hydrolysates increased metabolic activity by 110% and cell proliferation with 48% when cultured in serum-free conditions for 3 days compared with control cells cultured with full serum conditions. Most interestingly, this response was dependent on both material and choice of enzyme used. We suggest that these materials have the potential to replace serum during cultivation and as such be included in a tailor-made serum-free media.

Insights Into the Complexity of Yeast Extract Peptides and Their Utilization by Streptococcus thermophilus

Streptococcus thermophilus, an extensively used lactic starter, is generally produced in yeast extract-based media containing a complex mixture of peptides whose exact composition remains elusive. In this work, we aimed at investigating the peptide content of a commercial yeast extract (YE) and identifying dynamics of peptide utilization during the growth of the industrial S. thermophilus N4L strain, cultivated in 1 l bioreactors under pH-regulation. To reach that goal, we set up a complete analytical workflow based on mass spectrometry (peptidomics). About 4,600 different oligopeptides ranging from 6 to more than 30 amino acids in length were identified during the time-course of the experiment. Due to the low spectral abundance of individual peptides, we performed a clustering approach to decipher the rules of peptide utilization during fermentation. The physicochemical characteristics of consumed peptides perfectly matched the known affinities of the oligopeptide transport system of S. thermophilus. Moreover, by analyzing such a large number of peptides, we were able to establish that peptide net charge is the major factor for oligopeptide transport in S. thermophilus N4L.

Physiological responses of Chinese hamster ovary cells to a productivity-enhancing yeast extract

Hydrolysates play important roles in enhancing the productivity of recombinant proteins in mammalian cell cultures. Lacking of detailed understanding of the mechanisms, hydrolysate is commonly regarded as an unstable factor which should be used with cautions. A yeast extract (YE) was approved to improve the Fc-fusion protein productivity in a recombinant Chinese hamster ovary (CHO) cell line. To elucidate the responses of cells to hydrolysates, we further elaborate their physiological changes during the processes in the presence and absence of YE. Firstly, cell sizes and the cellular components including dry cell weight, cellular fatty acid, and total cellular protein were increased in the presence of YE. Then, by comparing the extracellular and intracellular concentrations of the main metabolites and their consumption rates, we excluded the possibility of nutrient depletion in the absence of YE and observed a distinct improvement on the net consumption rates of metabolites in the presence of YE. Furthermore, the increase on the contents of intracellular nucleotides illustrated an abundance of the nucleic acid precursors and energy charge for recombinant protein synthesis in the presence of YE. In conclusion, this study systematically elucidated YE enhanced cell mass and capacity, activated substrate and energy metabolism of cells in addition to a boost in product synthesis process. The findings provide valuable information for process optimization and cell engineering.

Metabolome analysis of Saccharomyces cerevisiae and optimization of culture medium for S-adenosyl-L-methionine production

S-Adenosyl-l-methionine (SAM) is a fine chemical used as a nutritional supplement and a prescription drug. It is industrially produced using Saccharomyces cerevisiae owing to its high SAM content. To investigate the optimization of culture medium components for higher SAM production, metabolome analysis was conducted to compare the intracellular metabolite concentrations between Kyokai no. 6 (high SAM-producing) and laboratory yeast S288C (control) under different SAM production conditions. Metabolome analysis and the result of principal component analysis showed that the rate-limiting step for SAM production was ATP supply and the levels of degradation products of adenosine nucleotides were higher in Kyokai 6 strain than in the S288C strain under the l-methionine supplemented condition. Analysis of ATP accumulation showed that the levels of intracellular ATP in the Kyokai 6 strain were also higher compared to those in the S288C strain. Furthermore, as expected from metabolome analysis, the SAM content of Kyokai 6 strain cultivated in the medium without yeast extract increased by 2.5-fold compared to that in the additional condition, by increasing intracellular ATP level with inhibited cell growth. These results suggest that high SAM production is attributed to the enhanced ATP supply with l-methionine condition and high efficiency of intracellular ATP consumption.