Transcriptomic and proteomic effects of (-)-epigallocatechin 3-O-(3-O-methyl) gallate (EGCG3”Me) treatment on ethanol-stressed Saccharomyces cerevisiae cells

Transcriptomics and proteomics analyses reveal the molecular mechanisms of yeast cells regulated by Phe-Cys against ethanol-oxidation cross-stress

Antioxidant dipeptide Phe-Cys (FC) could dramatically improve yeast cells resistance to ethanol-oxidation cross-stress, but the regulatory mechanisms remain unclear. Therefore, transcriptomic and proteomic analyses were conducted to investigate the effects of FC treatment on yeast under ethanol-oxidation cross-stress. Following FC supplementation, 875 differential expressed genes (DEGs) and 1296 differential expressed proteins (DEPs) were identified. Integrated analysis revealed a substantial enrichment of DEGs and DEPs in the KEGG pathways of carbon metabolism, amino acid biosynthesis, cofactor biosynthesis, and glycolysis/gluconeogenesis. Furthermore, FC improved yeast cell membrane integrity by promoting fatty acids and steroids biosynthesis, and implemented a high-energy strategy by upregulating glycolysis and oxidative phosphorylation. Additionally, alterations in DEGs and DEPs levels associated with amino acids metabolism accelerated protein synthesis and enhanced cell viability. In conclusion, this study elucidated the response mechanisms of yeast to FC treatment under ethanol-oxidation cross-stress, providing a theoretical basis for the application of FC in high-gravity brewing.

Persimmon tannin promotes the growth of Saccharomyces cerevisiae under ethanol stress

BACKGROUND

Saccharomyces cerevisiae plays a pivotal role in various industrial processes, including bioethanol production and alcoholic beverage fermentation. However, during these fermentations, yeasts are subjected to various environmental stresses, such as ethanol stress, which hinder cell growth and ethanol production. Genetic manipulations and the addition of natural ingredients rich in antioxidants to the culture have been shown to overcome this. Here, we investigated the potential of persimmon tannins, known for their antioxidative properties, to enhance the ethanol stress tolerance of yeast.

RESULTS

Assessment of the effects of 6.25 mg mL-1 persimmon tannins after 48 h incubation revealed cell viability to be increased by 8.9- and 6.5-fold compared to the control treatment with and without 12.5% ethanol, respectively. Furthermore, persimmon tannins reduced ethanol-induced oxidative stress, including the production of cellular reactive oxygen species and acceleration of lipid peroxidation. However, persimmon tannins could hardly overcome ethanol-induced cell membrane damage.

CONCLUSION

The findings herein indicate the potential of persimmon tannin as a protective agent for increasing yeast tolerance to ethanol stress by restricting oxidative damage but not membrane damage. Overall, this study unveils the implications of persimmon tannins for industries relying on yeast. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Plant-derived antioxidant dipeptides provide lager yeast with osmotic stress tolerance for very high gravity fermentation

Osmotic stress in the yeast limits productivity in industrial beer production under very high gravity brewing. This study focused on assessing the protective impacts of eleven plant-derived antioxidant dipeptides (PADs) on the osmotic stress tolerance of lager yeast. The results showed that PADs provided yeast with stress tolerance under osmotic stress. PADs supplementation enhanced cell membrane integrity and reduced oxidative damage. PADs upregulated the expression of SOD2, PEX11 and CTT1 genes under osmotic stress. Moreover, the volatile compounds contents and antioxidant activities of beers were improved by PADs, suggesting favorable quality characteristics. Especially, Phe-Cys and Leu-His could increase the DPPH radical scavenging activity of beer by 41.92% and 18.78% respectively, compared with control. Therefore, PADs are industrially scalable enhancers to improve the ability of yeast to resist osmotic stress and beer quality during very high gravity brewing.

Bioactive dipeptides enhance the tolerance of lager yeast to ethanol-oxidation cross-stress by regulating the multilevel defense system

Although high gravity brewing technology has been widely used for beer industries due to its economic benefits, yeast cells are subjected to multiple environmental stresses throughout the fermentation process. Eleven bioactive dipeptides (LH, HH, AY, LY, IY, AH, PW, TY, HL, VY, FC) were selected to evaluate their effects on cell proliferation, cell membrane defense system, antioxidant defense system and intracellular protective agents of lager yeast against ethanol-oxidation cross-stress. Results showed that the multiple stresses tolerance and fermentation performance of lager yeast were enhanced by bioactive dipeptides. Cell membrane integrity was improved by bioactive dipeptides through altering the structure of macromolecular compounds of the cell membrane. Intracellular reactive oxygen species (ROS) accumulation was significantly decreased by bioactive dipeptides, especially for FC, decreasing by 33.1%, compared with the control. The decrease of ROS was closely related to the increase of mitochondrial membrane potential, intracellular antioxidant enzyme activities including superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD), and glycerol level. In addition, bioactive dipeptides could regulate the expression of key genes (GPD1, OLE1, SOD2, PEX11, CTT1, HSP12) to enhance the multilevel defense systems under ethanol-oxidation cross-stress. Therefore, bioactive dipeptides should be potentially efficient and feasible bioactive ingredients to improve the multiple stresses tolerance of lager yeast during high gravity fermentation.

Mechanisms of Antioxidant Dipeptides Enhancing Ethanol-Oxidation Cross-Stress Tolerance in Lager Yeast: Roles of the Cell Wall and Membrane

High concentrations of ethanol could cause intracellular oxidative stress in yeast, which can lead to ethanol-oxidation cross-stress. Antioxidant dipeptides are effective in maintaining cell viability and stress tolerance under ethanol-oxidation cross-stress. In this study, we sought to elucidate how antioxidant dipeptides affect the yeast cell wall and membrane defense systems to enhance stress tolerance. Results showed that antioxidant dipeptide supplementation reduced cell leakage of nucleic acids and proteins by changing cell wall components under ethanol-oxidation cross-stress. Antioxidant dipeptides positively modulated the cell wall integrity pathway and up-regulated the expression of key genes. Antioxidant dipeptides also improved the cell membrane integrity by increasing the proportion of unsaturated fatty acids and regulating the expression of key fatty acid synthesis genes. Moreover, the addition of antioxidant dipeptides significantly (p < 0.05) increased the content of ergosterol. Ala-His (AH) supplementation caused the highest content of ergosterol, with an increase of 23.68 ± 0.01% compared to the control, followed by Phe-Cys (FC) and Thr-Tyr (TY). These results revealed that the improvement of the cell wall and membrane functions of antioxidant dipeptides was responsible for enhancing the ethanol-oxidation cross-stress tolerance of yeast.

Antibacterial activity and mechanism of flavonoids from Chimonanthus salicifolius S. Y. Hu. and its transcriptome analysis against Staphylococcus aureus

Introduction

Chimonanthus salicifolius S. Y. Hu. (FCS) possess many biological activities, but the antibacterial activity and underlying mechanisms of flavonoids from Chimonanthus salicifolius S. Y. Hu. (FCS) is still unknown.

Method

Maximum diameter of inhibition zone (DIZ), maximum diameter of inhibition zone (DIZ), the lowest minimum inhibition concentration (MIC), and the lowest minimum bactericide concentration (MBC) were used to detect the antibacterial activity. Meanwhile, related enzyme activities, the transcriptome analysis and quantitative RT-PCR were used to investigate the antibacterial activity mechanisms.

Results

The results showed that FCS (with a purity of 84.2 ± 2.0%) has potential effects on tested strains with the maximum diameter of inhibition zone (DIZ) was 15.93 ± 2.63 mm, the lowest minimum inhibition concentration (MIC) was 1.56 mg/ml and the lowest minimum bactericide concentration (MBC) was 6.25 mg/ml. In addition, the bacterial growth curve test, release of extracellular alkaline phosphatase (AKP), loss of intracellular components, DNA damage and transmission electron microscope (TEM) suggested that FCS could destroy the cell wall and membrane, cause the loss of intracellular substance, cause DNA damage and even lead to cell death. Moreover, the antibacterial mechanism of FCS against Staphylococcus aureus (S. aureus, Gram-positive bacteria) was further confirmed by the transcriptome analysis and quantitative RT-PCR at the molecular level for the first time. A total of 671 differentially expressed genes (DEGs) were identified after treated with FCS (1/2 MIC), with 338 and 333 genes showing up-regulation and down-regulation, respectively. The highlighted changes were those related to the biosynthesis of bacteria wall and membrane, DNA replication and repair, and energy metabolism.

Discussion

Overall, our research provides theoretical guidance for the application of FCS, which is expected to be potentially used as a natural antimicrobial agent in food safety.

Effects on Cell Membrane Integrity of Pichia anomala by the Accumulating Excessive Reactive Oxygen Species under Ethanol Stress

Ethanol stress to yeast is well recognized and exists widely during the brewing process of alcohol products. Pichia anomala is an important ester-producing yeast in the brewing process of Chinese Baijiu and other alcohol products. Therefore, it is of great significance for the alcohol products brewing industry to explore the effects of ethanol stress on the growth metabolism of P. anomala. In this study, the effects of ethanol stress on the growth, esters production ability, cell membrane integrity and reactive oxygen species (ROS) metabolism of P. anomala NCU003 were studied. Our results showed that ethanol stress could inhibit the growth, reduce the ability of non-ethyl ester compounds production and destroy the cell morphology of P. anomala NCU003. The results also showed that 9% ethanol stress produced excessive ROS and then increased the activities of antioxidant enzymes (superoxide dismutase, catalase, aseorbateperoxidase and glutathione reductase) compared to the control group. However, these increased antioxidant enzyme activities could not prevent the damage caused by ROS to P. anomala NCU003. Of note, correlation results indicated that high content of ROS could promote the accumulation of malondialdehyde content, resulting in destruction of the integrity of the cell membrane and leading to the leakage of intracellular nutrients (soluble sugar and protein) and electrolytes. These results indicated that the growth and the non-ethyl ester compounds production ability of P. anomala could be inhibited under ethanol stress by accumulating excessive ROS and the destruction of cell membrane integrity in P. anomala.

A research paper on the immunomodulatory and anti-inflammatory activities of olive tree (Olea europaea L.) leaf

Olive tree (Olea europaea L.) leaf is known to have a number of bioactive properties being antioxidant, antihypertensive, antiatherogenic, anti-inflammatory, antifungal, antiviral and antimicrobial. In this study, the immunomodulatory roles of Olive tree (Olea europaea L.) leaf against oxidative damage caused by carbon tetrachloride (CCl4) in Saccharomyces cerevisiae were investigated. In the study, four groups were formed; namely, (i) Control Group: Yeast only planted group; (ii) CCl4 Group: Group given CCl4 (15 mM); (iii) Olive Tree Leaf Group: The group given olive tree leaf (10%); and (iv) Olive Tree Leaf + CCl4 Group: Olive tree leaf (10%) + CCl4 (15 mM) given group. Cultures of Saccharomyces cerevisiae were grown at 30 °C for 1, 3, 5, and 24 hours. Malondialdehyde (MDA), glutathione levels (GSH), cell growth and catalase (CAT) activity measurements were determined by spectrophotometer. Total protein concentrations were determined by SDS-PAGE electrophoresis and the Bradford protein method. According to the results obtained; compared to the CCl4 group, cell growth (1, 3, 5 and 24 hours), total protein synthesis, and GSH and CAT activities (24 hours) increased in olive tree leaf groups, while MDA level (24 hours) decreased. Thanks to its strong bioactive properties, olive tree leaf has been found to increase cell growth and total protein synthesis by decreasing CCl4 induced oxidative stress in Saccharomyces cerevisiae culture. It has been concluded that if the olive tree leaf is used regularly, it will be beneficial in eliminating many health problems.

RNA-Seq Transcriptomic Analysis of Green Tea Polyphenols Modulation of Differently Expressed Genes in Enterococcus faecalis Under Bile Salt Stress

Enterococcus faecalis (E. faecalis) belongs to lactic acid bacteria which can be used as a probiotic additive and feed, bringing practical value to the health of humans and animals. The prebiotic function of tea polyphenols lays a foundation for green tea polyphenols (GTP) to repair the adverse changes of E. faecalis under stress conditions. In this study, RNA-sequence analysis was used to explore the protective effect of GTP on E. faecalis under bile salt stress. A total of 50 genes were found to respond to GTP under bile salts stress, containing 18 up-regulated and 32 down-regulated genes. The results showed that multiple genes associated with cell wall and membrane, transmembrane transport, nucleotide transport and metabolism were significantly differentially expressed (P < 0.05), while GTP intervention can partly alleviate the detrimental effects of bile salt on amino acid metabolism and transport. The present study provides the whole genome transcriptomics of E. faecalis under bile salt stress and GTP intervention which help us understand the growth and mechanism of continuous adaptation of E. faecalis under stress conditions.

Analysis of Cyclocarya paliurus flavonoids modulation on the physiology and gene expression in Enterococcus faecalis under bile salt stress

Enterococcus faecalis (E. faecalis) is one of the probiotic groups in the intestinal tract which has varieties of functional effects in the host, such as a protective barrier, nutritional efficacy and antibacterial effects. Stress conditions such as low pH, bile salts, and hypertonicity are inevitable negative factors for the normal survival of E. faecalis in the gastrointestinal tract. Under the stress and inhibition of bile salt, E. faecalis needs specific adaptation and coping style if it wants to successfully colonize the intestine stably. The appropriate concentration of flavonoids can assist probiotics to serve a beneficial role and help them resist the stress of external irresistible environmental factors. In the present research, RNA-sequence (RNA-seq) technology was employed to investigate the influence of Cyclocarya paliurus flavonoids (CPF) on Enterococcus faecalis 131-2 (E. faecalis 131-2) exposed to bile salt stress. Analysis results revealed that under bile salt stress, many genes related to cellular process, catalytic activity, and transport activity were significantly differentially expressed (P < 0.05), and some not expected variations of which could be partly alleviated by supplementation of CPF, indicating its capacity to improve the bile salt tolerances of E. faecalis 131-2. Additionally, CPF alleviated the obvious inhibitory effects of bile salt stress on the exponential growth of E. faecalis 131-2. An overall view of the physiological and transcriptomic changes of E. faecalis 131-2 under bile salt stresses with or without CPF will further deepen our understanding of the mechanism by which CPF assists E. faecalis 131-2 to perform beneficial functions in the gastrointestinal environment.

Transcriptome analysis of Cyclocarya paliurus flavonoids regulation of differently expressed genes in Enterococcus faecalis under low pH stress

Enterococcus faecalis (E. faecalis) is an indigenous intestinal bacterium and has potential to be applied as probiotic supplement. Low pH is one of the main stresses that E. faecalis has to deal with to colonize in the gastrointestinal tract. Previous study indicated low concentration of flavonoids may enhance the tolerance of probiotic to environmental stress. In the present research, transcriptome analysis was employed to investigate the influence of Cyclocarya paliurus flavonoids (CPF) on E. faecalis exposed to low pH environment. The results revealed that under the stress of low pH, genes related to cell wall and membrane, transmembrane transport, metabolism process, energy production, and conversion stress proteins were significantly differentially expressed. And certain undesired changes of which (such as genes for MFS transporter were downregulated) could be partially mitigated by CPF intervention, indicating their capacity to improve the low pH tolerance of E. faecalis. Results from this study deepened our understanding of the beneficial role of CPF on the probiotic in the gastrointestinal environment.

A transcriptome analysis of the antibacterial mechanism of flavonoids from Sedum aizoon L. against Shewanella putrefaciens

Flavonoids from Sedum aizoon L. (FSAL) possess prominent antibacterial activity against Shewanella putrefaciens isolated from sea food. In the current study, the involved molecular mechanisms were investigated using transcriptome analyses combined with bioinformatics analysis in vitro for the first time. Results showed that treatment of FSAL (1.0 MIC) damaged the permeability and integrity of cell membrane and induced 721 differentially expressed genes (DEGs) in tested bacteria at transcriptional levels, including 107 DEGs were up-regulated and 614 DEGs were down-regulated. In addition, the RNA-Seq analysis revealed that the majority of DEGs mainly involved in pathways of lipopolysaccharide biosynthesis, glycerophospholipid metabolism, biosynthesis of amino acids, purine metabolism, ABC transporters and response to stimulus. In summary, the integrated results indicated that the intervention of FSAL induced destruction of cell wall and membrane, disorder of the metabolic process and redox balance, and damage of nucleic acids in S. putrefaciens, at last resulted in the death of cells. This study provided new insights into the anti- S. putrefaciens molecular mechanism underlying the treatment of FSAL, which may be served as the basis guide for identifying potential antimicrobial targets and application of FSAL in food safety.

Transcriptome analysis of Penicillium italicum in response to the flavonoids from Sedum aizoon L

Natural products extracted from plants are an alternative method for controlling postharvest citrus blue mold, caused by Penicillium italicum (P. italicum). In this study, RNA sequence analysis was used to investigate the underlying anti-fungal mechanism of flavonoids from Sedum aizoon L. (FSAL) on P. italicum. Significant differences in 3592 genes were observed, including 2507 up-regulated and 1085 down-regulated genes between the FSAL-treated and the control groups. Furthermore, the GO and KEGG analysis results indicated that FSAL inhibited genes related to the integral components of membrane, oxidation-reduction process, mitochondrion, ribosome, and amino acid metabolism. In the presence of FSAL, the cellular constituents, including DNA and RNA were leaked from hyphae of P. italicum. Reactive oxygen species (ROS) production in P. italicum was also determined with a significant concentration-effect under the treatment of FSAL. Thus, we speculate that the inhibitory activity of FSAL on P. italicum is mainly achieved by damaging the structure of the cell membrane and cell wall, disrupting the process of mitochondrial respiratory metabolism, protein biosynthesis, and amino acid metabolism, leading to cell death. The present study provided a global perspective on the molecular mechanism of FSAL on P. italicum through transcriptome analysis, which may help develop a novel plant-derived anti-fungal agent for the blue mold of citrus.

Optimization Techniques to Deeply Mine the Transcriptomic Profile of the Sub-Genomes in Hybrid Fish Lineage

It has been shown that reciprocal cross allodiploid lineage with sub-genomes derived from the cross of Megalobrama amblycephala (BSB) × Culter alburnus (TC) generates the variations in phenotypes and genotypes, but it is still a challenge to deeply mine biological information in the transcriptomic profile of this lineage owing to its genomic complexity and lack of efficient data mining methods. In this paper, we establish an optimization model by non-negative matrix factorization approach for deeply mining the transcriptomic profile of the sub-genomes in hybrid fish lineage. A new so-called spectral conjugate gradient algorithm is developed to solve a sequence of large-scale subproblems such that the original complicated model can be efficiently solved. It is shown that the proposed method can provide a satisfactory result of taxonomy for the hybrid fish lineage such that their genetic characteristics are revealed, even for the samples with larger detection errors. Particularly, highly expressed shared genes are found for each class of the fish. The hybrid progeny of TC and BSB displays significant hybrid characteristics. The third generation of TC-BSB hybrid progeny (BTF3 and TBF3) shows larger trait separation.

Hepatic transcriptome and proteome analyses provide new insights into the regulator mechanism of dietary avicularin in diabetic mice

Many dietary flavonoids existing as glycosides in fruits and vegetables are considered bioactive food components with various potential health benefits. Type 2 diabetes mellitus (T2DM) is a complex and polygenic disease with increasing global prevalence and economic burden. In this study, the hypoglycemic effect of avicularin (quercetin-3-O-α-arabinofuranoside), a flavonoid glycoside commonly found in natural plants and fruits, was determined in a high fat diet/streptozotocin induced type 2 diabetes mouse model. Our results demonstrated that dietary avicularin treatment reduced levels of fasting blood glucose, serum TG and LDL-C, liver AST and ALT, and increased hepatic glycogen in T2DM mice. Furthermore, we used RNA-Seq and iTRAQ to compare the gene and protein expression in the livers of the normal control mice (NC), diabetic control mice (DC) and avicularin treated mice (DA100). The differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were analyzed based on gene annotations and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Integrated analysis of the RNA-Seq and iTRAQ data indicated that the fifteen DEGs/DEPs showed the same trend in mRNA and protein expression levels in comparisons of both NC vs DC and DC vs DA100. KEGG analysis revealed that four DEGs/DEPs (PKM, PEPCK, PYG, and PLA2) in the glycolysis, gluconeogenesis, and arachidonic acid pathway, and six DEPs (Ndufb4, Ndufa6, Cox5a, Cox5b, Cox6c, and ATPSβ) in the oxidative phosphorylation signaling pathway, play important roles in avicularin's hypoglycemic effect. We also found six other DEGs/DEPs related to T2DM (CA1, Serpinb6a, AK, Pcolce, Cand2, and Atp2a3), and five related to cancer (Phgdh, Tes, Papss1, Psat1, and Fam49b). We did further verify by qRT-PCR and explored the possible binding modes of avicularin with targeted proteins with molecular docking simulations. Taken together, our results demonstrated the protective effects of avicularin against diabetes and provided a global view about the system-level hypoglycemic mechanisms of avicularin by the comprehensive analysis of transcriptomic and proteomic data in T2DM mice.