Enhanced anti-oxidative activity and lignocellulosic ethanol production by biotin addition to medium in Pichia guilliermondii fermentation

Mining transcriptomic data to identify Saccharomyces cerevisiae signatures related to improved and repressed ethanol production under fermentation

Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Underlying the dynamics of gene expression in S. cerevisiae in response to fermentation could provide informative results, required for the establishment of any ethanol production improvement program. Thus, representing a new approach, this study was conducted to identify the discriminative genes between improved and repressed ethanol production as well as clarifying the molecular responses to this process through mining the transcriptomic data. The significant differential expression probe sets were extracted from available microarray datasets related to yeast fermentation performance. To identify the most effective probe sets contributing to discriminate ethanol content, 11 machine learning algorithms from RapidMiner were employed. Further analysis including pathway enrichment and regulatory analysis were performed on discriminative probe sets. Besides, the decision tree models were constructed, the performance of each model was evaluated and the roots were identified. Based on the results, 171 probe sets were identified by at least 5 attribute weighting algorithms (AWAs) and 17 roots were recognized with 100% performance Some of the top ranked presets were found to be involved in carbohydrate metabolism, oxidative phosphorylation, and ethanol fermentation. Principal component analysis (PCA) and heatmap clustering validated the top-ranked selective probe sets. In addition, the top-ranked genes were validated based on GSE78759 and GSE5185 dataset. From all discriminative probe sets, OLI1 and CYC3 were identified as the roots with the best performance, demonstrated by the most weighting algorithms and linked to top two significant enriched pathways including porphyrin biosynthesis and oxidative phosphorylation. ADH5 and PDA1 were also recognized as differential top-ranked genes that contribute to ethanol production. According to the regulatory clustering analysis, Tup1 has a significant effect on the top-ranked target genes CYC3 and ADH5 genes. This study provides a basic understanding of the S. cerevisiae cell molecular mechanism and responses to two different medium conditions (Mg²⁺ and Cu²⁺) during the fermentation process.

Adaptive laboratory evolution of Yarrowia lipolytica improves ferulic acid tolerance

Yarrowia lipolytica strain is a promising cell factory for the conversion of lignocellulose to biofuels and bioproducts. Despite the inherent robustness of this strain, further improvements to lignocellulose-derived inhibitors toxicity tolerance of Y. lipolytica are also required to achieve industrial application. Here, adaptive laboratory evolution was employed with increasing concentrations of ferulic acid. The adaptive laboratory evolution experiments led to evolve Y. lipolytica strain yl-XYL + *FA*4 with increased tolerance to ferulic acid as compared to the parental strain. Specifically, the evolved strain could tolerate 1.5 g/L ferulic acid, whereas 0.5 g/L ferulic acid could cause about 90% lethality of the parental strain. Transcriptome analysis of the evolved strain revealed several targets underlying toxicity tolerance enhancements. YALI0_E25201g, YALI0_F05984g, YALI0_B18854g, and YALI0_F16731g were among the highest upregulated genes, and the beneficial contributions of these genes were verified via reverse engineering. Recombinant strains with overexpressing each of these four genes obtained enhanced tolerance to ferulic acid as compared to the control strain. Fortunately, recombinant strains with overexpression of YALI0_E25201g, YALI0_B18854g, and YALI0_F16731g individually also obtained enhanced tolerance to vanillic acid. Overall, this work demonstrated a whole strain improvement cycle by "non-rational" metabolic engineering and presented new targets to modify Y. lipolytica for microbial lignocellulose valorization. KEY POINTS: • Adaptive evolution improved the ferulic acid tolerance of Yarrowia lipolytica • Transcriptome sequence was applied to analyze the ferulic acid tolerate strain • Three genes were demonstrated for both ferulic acid and vanillic acid tolerance.

Biotin plays an important role in Arabidopsis thaliana seedlings under carbonate stress

Globally, many saline-alkali soils are rich in NaHCO₃ and Na₂CO₃, which are characterized by a high pH Carbonate stress caused by this kind of soil severely damages plant cells and inhibits plant growth. Biotin and HCO₃^- participate in the first and rate-limiting reaction of the fatty acid biosynthesis pathway, but whether biotin contributes to plant responses to carbonate stress is unclear. In this study, we revealed that high carbonate and biotin concentrations inhibited Arabidopsis (Arabidopsis thaliana) seedling growth. However, specific concentrations of carbonate and biotin decreased the inhibitory effects of the other compound at the germination and seedling stages. Additionally, a carbonate treatment increased the endogenous biotin content and expression of AtBIO2, which encodes a biotin synthase. Moreover, phenotypic analyses indicated that the overexpression of AtBIO2 in Arabidopsis enhanced the tolerance to carbonate stress, whereas mutations to AtBIO2 had the opposite effect. Furthermore, the carbonate stress-induced accumulation of reactive oxygen species was lower in plants overexpressing AtBIO2 than in the wild-type and bio2 mutants. Accordingly, biotin, which is an essential vitamin for plants, can enhance the resistance to carbonate stress.

Enhancement of ε-poly-L-lysine production in Streptomyces griseofuscus by addition of exogenous astaxanthin

Addition of exogenous astaxanthin for improving ε-poly-L-lysine (ε-PL) production in Streptomyces griseofuscus was investigated in this study. By this unique strategy, the ε-PL production in shaker-flask fermentation was 2.48 g/L, which was 67.5% higher than the control at the addition dosage of 1.0 g/L, owing to the oxidation resistance of astaxanthin. In fed-batch fermentation, the ε-PL production reached 36.1 g/L, a 36.3% increase compared to the control. Intracellular response for oxidation in S. griseofuscus such as ROS generation and lipid peroxidation was reduced by astaxanthin addition. Illumina RNA deep sequencing (RNA-seq) technology further revealed that S. griseofuscus with astaxanthin addition showed down-regulated transcriptions of genes involved in oxidative stress. This research proved that the beneficial effect of astaxanthin addition was far better than glutathione (GSH) owing to the stronger antioxidant capacity, and provided a novel approach to regulate ε-PL synthesis.

Improving the acetylcholinesterase inhibitory effect of Illigera aromatica by fermentation with Clonostachys rogersoniana

Illigera aromatica was fermented by Clonostachys rogersoniana. The acetylcholinesterase (AChE) inhibitory effects of unfermented and fermented I. aromatica revealed that C. rogersoniana-fermented I. aromatica (CFIA) induced significantly more AChE inhibitory activity (IC₅₀: 35.4 ± 2.1 μg/mL). The biotransformation of actinodaphnine (1) into (4R,6aS)-4-hydroxyactinodaphnine (2) was found during the fermentation, which played an important role in the improvement of the AChE inhibitory activity of I. aromatica. Subsequently, the fermentation conditions-including the solid-liquid ratio, fermentation temperature, and fermentation time-were optimized. I. aromatica immersed in 100-200% water and fermented with C. rogersoniana at ambient temperature for 30 days was conducive to the biotransformation of actinodaphnine (1) and improved the AChE inhibitory activity of I. aromatica. The present study provides a novel approach for improving the pharmacological effect of I. aromatica and suggests that CFIA may be used as an alternative AChE inhibitor.

Enhancement of ethanol production in very high gravity fermentation by reducing fermentation-induced oxidative stress in Saccharomyces cerevisiae

During fermentation, yeast cells encounter a number of stresses, including hyperosmolarity, high ethanol concentration, and high temperature. Previous deletome analysis in the yeast Saccharomyces cerevisiae has revealed that SOD1 gene encoding cytosolic Cu/Zn-superoxide dismutase (SOD), a major antioxidant enzyme, was required for tolerances to not only oxidative stress but also other stresses present during fermentation such as osmotic, ethanol, and heat stresses. It is therefore possible that these fermentation-associated stresses may also induce endogenous oxidative stress. In this study, we show that osmotic, ethanol, and heat stresses promoted generation of intracellular reactive oxygen species (ROS) such as superoxide anion in the cytosol through a mitochondria-independent mechanism. Consistent with this finding, cytosolic Cu/Zn-SOD, but not mitochondrial Mn-SOD, was required for protection against oxidative stress induced by these fermentation-associated stresses. Furthermore, supplementation of ROS scavengers such as N-acetyl-L-cysteine (NAC) alleviated oxidative stress induced during very high gravity (VHG) fermentation and enhanced fermentation performance at both normal and high temperatures. In addition, NAC also plays an important role in maintaining the Cu/Zn-SOD activity during VHG fermentation. These findings suggest the potential role of ROS scavengers for application in industrial-scale VHG ethanol fermentation.

Advances in bio-based production of dicarboxylic acids longer than C4

Growing concerns of environmental pollution and fossil resource shortage are major driving forces for bio-based production of chemicals traditionally from petrochemical industry. Dicarboxylic acids (DCAs) are important platform chemicals with large market and wide applications, and here the recent advances in bio-based production of straight-chain DCAs longer than C4 from biological approaches, especially by synthetic biology, are reviewed. A couple of pathways were recently designed and demonstrated for producing DCAs, even those ranging from C5 to C15, by employing respective starting units, extending units, and appropriate enzymes. Furthermore, in order to achieve higher production of DCAs, enormous efforts were made in engineering microbial hosts that harbored the biosynthetic pathways and in improving properties of biocatalytic elements to enhance metabolic fluxes toward target DCAs. Here we summarize and discuss the current advantages and limitations of related pathways, and also provide perspectives on synthetic pathway design and optimization for hyper-production of DCAs.

Rich biotin content in lignocellulose biomass plays the key role in determining cellulosic glutamic acid accumulation by Corynebacterium glutamicum

BACKGROUND

Lignocellulose is one of the most promising alternative feedstocks for glutamic acid production as commodity building block chemical, but the efforts by the dominant industrial fermentation strain Corynebacterium glutamicum failed for accumulating glutamic acid using lignocellulose feedstock.

RESULTS

We identified the existence of surprisingly high biotin concentration in corn stover hydrolysate as the determining factor for the failure of glutamic acid accumulation by Corynebacterium glutamicum. Under excessive biotin content, induction by penicillin resulted in 41.7 ± 0.1 g/L of glutamic acid with the yield of 0.50 g glutamic acid/g glucose. Our further investigation revealed that corn stover contained 353 ± 16 μg of biotin per kg dry solids, approximately one order of magnitude greater than the biotin in corn grain. Most of the biotin remained stable during the biorefining chain and the rich biotin content in corn stover hydrolysate almost completely blocked the glutamic acid accumulation. This rich biotin existence was found to be a common phenomenon in the wide range of lignocellulose biomass and this may be the key reason why the previous studies failed in cellulosic glutamic acid fermentation from lignocellulose biomass. The extended recording of the complete members of all eight vitamin B compounds in lignocellulose biomass further reveals that the major vitamin B members were also under the high concentration levels even after harsh pretreatment.

CONCLUSIONS

The high content of biotin in wide range of lignocellulose biomass feedstocks and the corresponding hydrolysates was discovered and it was found to be the key factor in determining the cellulosic glutamic acid accumulation. The highly reserved biotin and the high content of their other vitamin B compounds in biorefining process might act as the potential nutrients to biorefining fermentations. This study creates a new insight that lignocellulose biorefining not only generates inhibitors, but also keeps nutrients for cellulosic fermentations.

Endogenous lycopene improves ethanol production under acetic acid stress in Saccharomyces cerevisiae

BACKGROUND

Acetic acid, generated from the pretreatment of lignocellulosic biomass, is a significant obstacle for lignocellulosic ethanol production. Reactive oxidative species (ROS)-mediated cell damage is one of important issues caused by acetic acid. It has been reported that decreasing ROS level can improve the acetic acid tolerance of Saccharomyces cerevisiae.

RESULTS

Lycopene is known as an antioxidant. In the study, we investigated effects of endogenous lycopene on cell growth and ethanol production of S. cerevisiae in acetic acid media. By accumulating endogenous lycopene during the aerobic fermentation of the seed stage, the intracellular ROS level of strain decreased to 1.4% of that of the control strain during ethanol fermentation. In the ethanol fermentation system containing 100 g/L glucose and 5.5 g/L acetic acid, the lag phase of strain was 24 h shorter than that of control strain. Glucose consumption rate and ethanol titer of yPS002 got to 2.08 g/L/h and 44.25 g/L, respectively, which were 2.6- and 1.3-fold of the control strain. Transcriptional changes of INO1 gene and CTT1 gene confirmed that endogenous lycopene can decrease oxidative stress and improve intracellular environment.

CONCLUSIONS

Biosynthesis of endogenous lycopene is first associated with enhancing tolerance to acetic acid in S. cerevisiae. We demonstrate that endogenous lycopene can decrease intracellular ROS level caused by acetic acid, thus increasing cell growth and ethanol production. This work innovatively   puts forward a new strategy for second generation bioethanol production during lignocellulosic fermentation.

Enhancement of ε-poly-L-lysine synthesis in Streptomyces by exogenous glutathione

Our previous work indicated that the vigor of Streptomyces decreased at the later stage of ε-poly-L-lysine (ε-PL) fermentation. In this study, we observed that the level of reactive oxygen species (ROS) in vivo increased sharply after 24 h, and the addition of an antioxidant glutathione (GSH) before this increase in ROS stimulated ε-PL synthesis in shake-flask fermentation. The enhancement of ε-PL production by GSH was further verified in batch and fed-batch fermentations. On a 5-l fermenter scale, the highest increasement was 68.8% in batch fermentation and the highest ε-PL level was 46.5 g l^- 1 in fed-batch fermentation. The RT-qPCR analysis showed that the transcriptional level of the catalase gene was down-regulated, and the decrease in cell activity was alleviated by the addition of GSH. The results revealed that exogenous antioxidant might maintain the cell vigor by reducing the excess ROS which provided a novel approach to regulate ε-PL synthesis.

Enhancing Saccharomyces cerevisiae reactive oxygen species and ethanol stress tolerance for high-level production of protopanoxadiol

Protopanaxadiol (PPD) is an active compound in Panax ginseng. Recently, an optimized PPD synthesis pathway contained a ROS releasing step (a P450-type PPD synthase, PPDS) was introduced into Saccharomyces cerevisiae. Here reported a synergistic effect of PPDS-CPR (CPR, cytochrome P450 reductase) uncoupling and ethanol stress on ROS releasing, which reduced cells viability. To build a robust strain, a cell wall integrity associated gene SSD1 was high-expressed to improve ethanol tolerance, and ROS level decreased for 24.7%. Then, regulating the expression of an oxidative stress regulation gene YBP1 decreased 75.2% of ROS releasing, and improved cells viability from 71.3±1.3% to 88.3±1.4% at 84h. Increased cells viability enables yeast to produce more PPD through feeding additional ethanol. In 5L fermenter, PPD production of W3a-ssPy reached to 4.25±0.18g/L (19.48±0.28mg/L/OD600), which is the highest yield reported so far. This work makes the industrial production of PPD possible by microbial fermentation.

Biocatalytic Reduction of HMF to 2,5-Bis(hydroxymethyl)furan by HMF-Tolerant Whole Cells

Catalytic upgrading of 5-hydroxymethylfurfural (HMF), an important biobased platform chemical for high-value products, is currently of great interest. In this work, a new highly HMFtolerant yeast strain-Meyerozyma guilliermondii SC1103 was isolated, and biocatalytic reduction of HMF to 2,5-bis(hydroxymethyl)furan (BHMF) using its resting cells was reported. Cosubstrates exerted a significant effect on the catalytic activity and selectivity of microbial cells as well as their HMF-tolerant levels whereas the nitrogen source and mineral salts had no effects. In addition, M. guilliermondii SC1103 cells exhibited good catalytic performances within the range of pH 4.0-10.0. The yeast was highly tolerant to both HMF (up to 110 mm) and BHMF (up to 200 mm). In addition, 100 mm HMF could be selectively reduced to BHMF within 12 h by its resting cells in the presence of 100 mm glucose (as cosubstrate), with a yield of 86 % and selectivity of >99 %. The production of 191 mm of BHMF was realized within 24.5 h by using a fed-batch strategy, with a productivity of approximately 24 g L^-1 per day. In addition, this new biocatalytic approach was applied for the reduction of furfural and 5-methylfurfural, affording the corresponding furfuryl alcohols with yields of 83 and 89 %, respectively.