Comparative Analysis of Oxidative Stress During Aging of Kluyveromyces marxianus in Synthetic and Whey Media

Characterization and optimization of 5´ untranslated region containing poly-adenine tracts in Kluyveromyces marxianus using machine-learning model

BACKGROUND

The 5´ untranslated region (5´ UTR) plays a key role in regulating translation efficiency and mRNA stability, making it a favored target in genetic engineering and synthetic biology. A common feature found in the 5´ UTR is the poly-adenine (poly(A)) tract. However, the effect of 5´ UTR poly(A) on protein production remains controversial. Machine-learning models are powerful tools for explaining the complex contributions of features, but models incorporating features of 5´ UTR poly(A) are currently lacking. Thus, our goal is to construct such a model, using natural 5´ UTRs from Kluyveromyces marxianus, a promising cell factory for producing heterologous proteins.

RESULTS

We constructed a mini-library consisting of 207 5´ UTRs harboring poly(A) and 34 5´ UTRs without poly(A) from K. marxianus. The effects of each 5´ UTR on the production of a GFP reporter were evaluated individually in vivo, and the resulting protein abundance spanned an approximately 450-fold range throughout. The data were used to train a multi-layer perceptron neural network (MLP-NN) model that incorporated the length and position of poly(A) as features. The model exhibited good performance in predicting protein abundance (average R2 = 0.7290). The model suggests that the length of poly(A) is negatively correlated with protein production, whereas poly(A) located between 10 and 30 nt upstream of the start codon (AUG) exhibits a weak positive effect on protein abundance. Using the model as guidance, the deletion or reduction of poly(A) upstream of 30 nt preceding AUG tended to improve the production of GFP and a feruloyl esterase. Deletions of poly(A) showed inconsistent effects on mRNA levels, suggesting that poly(A) represses protein production either with or without reducing mRNA levels.

CONCLUSION

The effects of poly(A) on protein production depend on its length and position. Integrating poly(A) features into machine-learning models improves simulation accuracy. Deleting or reducing poly(A) upstream of 30 nt preceding AUG tends to enhance protein production. This optimization strategy can be applied to enhance the yield of K. marxianus and other microbial cell factories.

Construction of Novel Yeast Strains from Candida tropicalis KBKTI 10.5.1 and Saccharomyces cerevisiae DBY1 to Improve the Performance of Ethanol Production Using Lignocellulosic Hydrolysate

Increased consumption of xylose-glucose and yeast tolerance to lignocellulosic hydrolysate are the keys to the success of second-generation bioethanol production. Candida tropicalis KBKTI 10.5.1 is a new isolated strain that has the ability to ferment xylose. In contrast to Saccharomyces cerevisiae DBY1 which only can produce ethanol from glucose fermentation. The research objective is the application of the genome shuffling method to increase the performance of ethanol production using lignocellulosic hydrolysate. Mutants were selected on xylose and glucose substrates separately and using random amplified polymorphic DNA (RAPD) analysis. The ethanol production using lignocellulosic hydrolysate by parents and mutants was evaluated using a batch fermentation system. Concentrations of ethanol, residual sugars, and by-products such as glycerol, lactate and acetate were measured using HPLC machine equipped with Hiplex H for carbohydrate column and a refraction index detector (RID). Ethanol produced by Fcs1 and Fcs4 mutants on acid hydrolysate increased by 26.58% and 24.17% from parent DBY1, by 14.94% and 21.84% from parent KBKTI 10.5.1. In contrast to the increase in ethanol production on alkaline hydrolysate, Fcs1 and Fcs4 mutants only experienced an increase in ethanol production by 1.35% from the parent KBKTI 10.5.1. Ethanol productivity by Fcs1 and Fcs4 mutants on acid hydrolysate reached 0.042 g/L/h and 0.044 g/L/h. The recombination of the genomes of different yeast species resulted in novel yeast strains that improved resistance performance and ethanol production on lignocellulosic hydrolysates.

Integrative transcriptomic-proteomic analysis revealed the flavor formation mechanism and antioxidant activity in rice-acid inoculated with Lactobacillus paracasei and Kluyveromyces marxianus

In the study on fermented acid rice soup (rice-acid) inoculated with L. paracasei H4-11 and K. marxianus L1-1, the concentrations of main flavor components on the third day of fermentation were significantly higher than those on the first day. Transcriptome analysis and proteome analysis based on RNA sequencing and 4D label-free proteomic techniques were combined to provide new insights into the molecular mechanisms of flavor characteristics and antioxidant activity of the two strains during the development of rice-acid. The key up-regulated genes and proteins in L. paracasei and K. marxianus L1-1, which were involved in flavor formation and antioxidant activity in rice-acid development, were different. The KEGG pathways involving the up-regulated genes and proteins in L. paracasei included starch and sucrose metabolism, pyruvate metabolism, amino sugar, and nucleotide sugar metabolism, and glycolysis/guconeogenesis. The KEGG pathways involving the up-regulated genes and proteins in K. marxianus L1-1 mainly included glycolysis/gluconeogenesis, TCA cycle, pyruvate metabolism, and other pathways related to antioxidant capacity. We successfully identified key genes and proteins associated with the metabolism and accumulation of flavor components and antioxidant activity. These findings provide new insights into the molecular mechanisms of flavor formation in co-cultivation with L. paracasei and K. marxianus. SIGNIFICANCE: It is anticipated that this study would provide us an insight into the mechanisms of flavor components accumulation and antioxidant activity of acid rice soup in China's minority areas. Importantly, this research provides the foundation of biological and chemical analysis for the application of the co-culture of L. paracasei H4-11 and K. marxianus in non-dairy products.

Effect of Anoectochilus roxburghii flavonoids extract on H2O2 - Induced oxidative stress in LO2 cells and D-gal induced aging mice model

ETHNOPHARMACOLOGICAL RELEVANCE

Anoectochilus roxburghii (A. roxburghii) is a popular folk medicine in many Asian countries, which has been used traditionally for treatment of some diseases such as diabetes, tumors, hyperlipemia, and hepatitis. The ethanol extract from A. roxburghii was recently shown to exert better ability to scavenge free radicals in vitro and possess antioxidant on natural aging mice in vivo.

AIM OF THE STUDY

This study is to characterize the chemical composition, and investigate the protective effect of the A. roxburghii flavonoids extract (ARF) against hydrogen peroxide (H₂O₂)-induced oxidative stress in LO2 cells in vitro and D-galactose (D-gal)-induced aging mice model in vivo, and explore the underlying mechanisms.

MATERIALS AND METHODS

The chemical components of the flavonoids extract fromA. roxburghii were detected by ultraperformance lipid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UPLC-QTOF-MS/MS). H₂O₂ was used to establish an oxidative stress model in LO2 cells. Cytotoxic and protective effects of ARF on the LO2 cells were determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Moreover, the levels of superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), and malondialdehyde (MDA) in cell supernatants were measured by commercial reagent kits. Kun-Ming mice were induced to aging with D-gal (400 mg/kg, BW) by subcutaneous injection for 58 days. From the 28th day to the 58th day of D-gal treatment, ARF (122.5, 245 and 490 mg/kg, BW) and vitamin E (100 mg/kg, BW) were orally administrated to aging mice once a day for consecutive 30 days. After 25 days of the treatment with ARF, learning and memory were assessed using Morris Water Maze (MWM). At the end of the test period, the animals were euthanized by cervical dislocation, and the levels of SOD, GSH-PX, and MDA in serum, liver homogenates and brain homogenates were measured. The levels of monoamine oxidase (MAO) and acetylcholinesterase (AchE) were determined in brain homogenates. Skin and liver histopathological morphology were observed by H&E staining. Furthermore, antioxidant-related gene expression levels in the liver were carried out by quantitative real-time polymerase chain reaction (qRT-PCR).

RESULTS

Nine flavonoids were identified in the extracts of A. roxburghii. In vitro assay, a high concentration of ARF (>612.5 μg/ml) reduced the survival rate and had toxic effects on LO2 cells. In addition, ARF (245 μg/ml, 490 μg/ml) and Vitamin C (200 μg/ml) markedly inhibited generations of MDA and increased activities of SOD, GSH-PX in H₂O₂-induced LO2 cells supernatants. In vivo assay, ARF (122.5 mg/kg, 245 mg/kg and 490 mg/kg) and Vitamin E (100 mg/kg) not only ameliorated learning and memory ability but also improved skin and liver pathological alterations. Strikingly, ARF significantly decreased MDA and MAO levels, markedly enhanced antioxidant enzyme (SOD and GSH-PX) activities. Further, compared to the D-gal group, ARF could obviously up-regulate glutathione peroxidase-1 (GPx-1) and glutathione peroxidase-4 (GPx-4) mRNA levels.

CONCLUSIONS

These findings suggested that ARF protects LO2 cells against H₂O₂-induced oxidative stress and exerts the potent anti-aging effects in D-gal aging mice model, which may be related to the inhibition of oxidative stress. Flavonoid compounds may contribute to the anti-oxidative capability and modulating aging.

Yeast Life Span and its Impact on Food Fermentations

Yeasts are very important microorganisms for food production. The high fermentative capacity, mainly of the species of the genus Saccharomyces, is a key factor for their biotechnological use, particularly to produce alcoholic beverages. As viability and vitality are essential to ensure their correct performance in industry, this review addresses the main aspects related to the cellular aging of these fungi as their senescence impacts their proper functioning. Laboratory strains of S. cerevisiae have proven a very successful model for elucidating the molecular mechanisms that control life span. Those mechanisms are shared by all eukaryotic cells. S. cerevisiae has two models of aging, replicative and chronological. Replicative life span is measured by the number of daughter cells a mother can produce. This kind of aging is relevant when the yeast biomass is reused, as in the case of beer fermentations. Chronological life span is measured by the time cells are viable in the stationary phase, and this is relevant for batch fermentations when cells are most of the time in a non-dividing state, such as wine fermentations. The molecular causes and pathways regulating both types of aging are explained in this review.

Mechanistic Insights Into Probiotic Properties of Lactic Acid Bacteria Associated With Ethnic Fermented Dairy Products

Gut microbes and their metabolites maintain the health and homeostasis of the host by communicating with the host via various biochemical and physical factors. Changing lifestyle, chronic intake of foods rich in refined carbohydrates and fats have caused intestinal dysbiosis and other lifestyle-based diseases. Thus, supplementation with probiotics has gained popularity as biotherapies for improving gut health and treating disorders. Research shows that probiotic organisms enhance gastrointestinal health, immunomodulation, generation of essential micronutrients, and prevention of cancer. Ethnically fermented milk and dairy products are hotspots for novel probiotic organisms and bioactive compounds. These ethnic fermented foods have been traditionally prepared by indigenous populations, and have preserved unique microflora for ages. To apply these unique microflora for amelioration of human health, it is important that probiotic properties of the bacterial species are well studied. Majority of the published research and reviews focus on the probiotic organisms and their properties, fermented food products, isolation techniques, and animal studies with their health pathologies. As a consequence, there is a dearth of information about the underlying molecular mechanism behind probiotics associated with ethnically prepared dairy foods. This review is targeted at stimulating research on understanding these mechanisms of bacterial species and beneficial attributes of ethnically fermented dairy products.

Physiological growth and galactose utilization by dairy yeast Kluyveromyces marxianus in mixed sugars and whey during fermentation

The dairy yeast Kluyveromyces marxianus represents a promising industrial strain useful for the production of bioethanol from cheese whey. Physiology of the five K. marxianus strains on galactose was examined during batch cultivation under controlled aerobic conditions on minimal media and one of the strains designated K. marxianus strain 6C17 which presented the highest specific galactose consumption rate. A maximum specific growth rate of 0.34 and 0.37 h^-1, respectively, was achieved using batch cultivation in a minimal medium and a complex medium amended with galactose (50 g/L) at 37 °C. The sugar was metabolized for the production of ethanol as the chief metabolite with a maximum ethanol yield of 0.39 g/g of galactose. Different growth behaviors were observed when galactose was used with other sugar such as glucose, lactose and fructose. The growth rates on hydrolyzed cheese whey were also measured, and a maximum specific growth rate of 0.39 and 0.32 h^-1 was observed with glucose and galactose, respectively, with the maximum flux diverted toward ethanol production. This approach of studying the physiology of thermotolerant K. marxianus on hydrolyzed whey during fermentation would be helpful in achieving higher yields of ethanol.