Biosynthetic Pathway for Ethyl Butyrate Production in Saccharomyces cerevisiae

Machine learning-assisted aroma profile prediction in Jiang-flavor baijiu

The complex flavor of Jiang-flavor Baijiu (JFB) arises from the interaction of hundreds of compounds at both physicochemical and sensory levels, making accurate perception challenging. Modern machine learning techniques offer precise and scientific approaches for predicting sensory attributes. This study applied flavoromics and sensory profiling to 27 representative JFB samples from main regions in China, integrating five machine learning algorithms to establish a novel strategy for predicting global aroma characteristics. The results indicate that the neural network (NN) model outperformed others, effectively capturing the intricate interactions among flavor compounds. Model dissection identified 18 chemical parameters potentially influencing the overall aroma profile. The importance of these factors was further validated through spiking and omission tests, which notably enhanced the sensory experience of commercial liquor. This study demonstrates the potential of machine learning in JFB flavor research and offers valuable insights into the mechanisms underlying its flavor formation.

Breeding High-Yield Ethyl Caproate-Producing Saccharomyces cerevisiae in Sake: Flux Regulation from Glycolytic Fermentation to the FAS Pathway and Alcohol Acyltransferase Overexpression

Ethyl caproate is the characteristic aroma compound with an apple-like scent in Ginjoka sake. However, the medium-chain acyl-CoA flux of the fatty acid synthesis (FAS) pathway originating from glycolytic fermentation and the precursor-induced alcohol acyltransferase (AAT) activity by natural yeast limits the ethyl caproate content in sake. Here, we established combinatorial strategies involving genetic engineering and adaptive laboratory evolution (ALE) to increase the ethyl caproate production by Saccharomyces cerevisiae. In this study, we screened Saccharomyces cerevisiae YH-2, which exhibited high ethanol and ester yields , achieving a trade-off between FAS flux and energy metabolism. Subsequently, the cerulenin-resistant mutant strain YH-2-34, after 15 passages of adaptive domestication, produced 4.13 times more caproic acid than the wild type. This increase is attributed to the G1250S variation in the FAS2 sequences, which mediate acyl-CoA chain length in the FAS pathway, thereby producing more caproyl-CoA as the precursor. While AAT activity increased 2.40 times in the mutant YH-2-34, both EEB1 and EHT1 genes, which together encode AAT responsible for esterifying ethyl caproate, played critical roles. Although pEEB1s overexpression affected cell viability and ethyl caproate production, pEHT1s overexpression successfully increased the yield of ethyl caproate during post-fermentation. Finally, the yield of YH-2-34 with EHT1 overexpression achieved a significant increase from 1.21 to 7.40 mg/L in sake fermentation. By regulating the flux from glycolytic fermentation to the FAS pathway and overexpressing AAT, we constructed a high-yield ethyl-caproate-producing Saccharomyces cerevisiae strain. This may bring practical transformations to traditional brewing industries.

Efficient production of RNA in Saccharomyces cerevisiae through inducing high level transcription of functional ncRNA-SRG1

RNA (Ribonucleic Acid) is an essential component of organisms and is widely used in the food and pharmaceutical industries. Saccharomyces cerevisiae, recognized as a safe strain, is widely used for RNA production. In this study, the S. cerevisiae W303-1a was used as a starting strain and molecular modifications were made to the functional ncRNA-SRG1 to evaluate the effect on RNA production. At the same time, its transcriptionally associated helper genes (Spt2, Spt6 and Cha4) were overexpressed and the culture medium was supplemented with serine to induce SRG1 transcription, to increase SRG1 transcription levels and investigate its effect on intracellular RNA levels. The results showed that the intracellular RNA content of the recombinant strain W303-1a-SRG1 was 10.27 %, an increase of 11.15 % compared to the starting strain (W303-1a, with an intracellular RNA content of 9.24 %). On this basis, a gene co-overexpression strain-W303-1a-SRG1-Spt6 was constructed. Simultaneously, the addition of 2 % serine strategy was used to increase the transcription level of SRG1 and RNA content of the recombinant strain. The intracellular RNA of the recombinant strain reached 11.41 %, an increase of 23.38 % compared to the starting strain (W303-1a, without serine supplementation). In addition, the growth performance of the strain was assessed by measuring the SRG1 transcription level in the strain and plotting the growth curve. Therefore, we found that improving the transcription level of ncRNA can be used as a new idea to construct S. cerevisiae with high RNA content, which provides a strong help for subsequent research in related fields. This work provides a new strategy for increasing the nucleic acid content of S. cerevisiae.

Integrated microbiomic and metabolomic dynamics of Yi traditional fermented liquor

This study examines the microbial community composition, metabolite characteristics, and the relationship between the two during the fermentation process of Yi traditional fermented liquor. Yi traditional fermented foods have a profound historical and cultural background, with significant ethnic characteristics. As a case in point, Yi traditional fermented liquor is typically prepared using local plants or traditional Chinese herbs as fermentation substrates and undergoes a lengthy fermentation process, resulting in a fermented beverage that is reputed to have beneficial effects on human health. These foods are not only characterised by a distinctive flavor profile, but are also perceived to possess certain health benefits in the context of traditional ethnic medicine and wellness practices. The community composition of bacteria and fungi was analyzed using 16S rRNA and ITS1 sequencing technologies, which revealed that microbial diversity was higher in the early stages of fermentation but gradually decreased as fermentation progressed. A total of 130 major volatile flavor compounds and 26 key metabolites were identified at different stages of fermentation. These included acids, sugars, amino acids and flavonoids, which significantly influence the flavor and nutritional value of the fermented products. The study indicates a significant correlation between specific microbial populations (such as yeasts) and key metabolites (such as flavonoids and amino acids). These findings emphasise the significance of the interplay between microbial communities and metabolites in shaping the quality and efficacy of fermented products. They offer a scientific foundation for optimizing traditional fermented food production processes.

A probiotic Limosilactobacillus fermentum GR-3 mitigates colitis-associated tumorigenesis in mice via modulating gut microbiome

Bacterial therapy for colorectal cancer (CRC) represents a burgeoning frontier. The probiotic Limosilactobacillus fermentum GR-3, derived from traditional food "Jiangshui", exhibited superior antioxidant capacity by producing indole derivatives ICA and IPA. In an AOM/DSS-induced CRC mouse model, GR-3 treatment alleviated weight loss, colon shortening, rectal bleeding and intestinal barrier disruption by reducing oxidative stress and inflammation. GR-3 colonization in distant colon induced apoptosis and reduced tumor incidence by 51.2%, outperforming the control strain and vitamin C. The beneficial effect of GR-3 on CRC was associated with gut microbiome modulation, increasing SCFA producer Lachnospiraceae NK4A136 group and suppressing pro-inflammatory strain Bacteroides. Metagenomic and metabolic analyses revealed that GR-3 intervention upregulated antioxidant genes (xseA, ALDH) and butyrate synthesis gene (bcd), while increasing beneficial metabolites (SCFAs, ICA, IPA, VB12 and VD3) and reducing harmful secondary bile acids. Overall, GR-3 emerges as a promising candidate in CRC therapy, offering effective gut microbiome remediation.

CRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3

Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting that the knockdown of IAH1 may generate intracellular alterations in the balance of these metabolites, triggering a regulatory response. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.

Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals

In the twenty first century, biotechnology offers great opportunities and solutions to climate change mitigation, energy and food security and resource efficiency. The use of metabolic engineering to modify microorganisms for producing industrially significant chemicals is developing and becoming a trend. As a famous, generally recognized as a safe (GRAS) model microorganism, Saccharomyces cerevisiae is widely used due to its excellent operational convenience and high fermentation efficiency. This review summarizes recent advancements in the field of using metabolic engineering strategies to construct engineered S. cerevisiae over the past ten years. Five different types of compounds are classified by their metabolites, and the modified metabolic pathways and strategies are summarized and discussed independently. This review may provide guidance for future metabolic engineering efforts toward such compounds and analogues. Additionally, the limitations of S. cerevisiae as a cell factory and its future trends are comprehensively discussed.

Effects of the Species and Growth Stage on the Antioxidant and Antifungal Capacities, Polyphenol Contents, and Volatile Profiles of Bamboo Leaves

Bamboo leaves contain high concentrations of various biologically active compounds, such as polyphenols and volatiles, making them attractive as raw resources for antioxidant additives in the food industry. Here, we investigated the total phenolic content (TPC) and total flavonoid content (TFC) of four bamboo leaf extracts from two species (Phyllostachys edulis and Chimonocalamus delicatus) at two growth stages (first and second years). Antioxidant capacity was determined based on the radical-scavenging capacity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS+). We also assessed the antifungal capacity based on mycelial growth inhibition of Colletotrichum musae (C. musae), Botrytis cinerea (B. cinereain), and Alternaria alternata (A. alternata). Pearson's correlation coefficients showed that the TPC was significantly (p < 0.01) negatively correlated with the half-maximal inhibitory concentrations against DPPH and ABTS+, whereas the TFC was positively correlated with C. musae and B. cinereain growth inhibition, which suggest that TPC and TFC might be the major contributors to the antioxidant and antifungal capacities of bamboo leaves, respectively. The volatile organic compounds (VOCs) of bamboo leaves were also analyzed using gas chromatography-ion mobility spectrometry. The VOCs included twenty-four aldehydes, eleven alcohols, four furans, seven esters, fifteen terpenes, three ketones, one pyrazine, and thirty unidentified compounds. Principal component analysis, partial least squares discriminant analysis, and hierarchical cluster analysis were performed to assess the differences in the volatile profiles of the four bamboo leaf samples, from which 23 discriminatory VOCs with variable importance in the projection values > 1 were screened, and part of them were impacted by species or growth stage. These findings provide a theoretical foundation for the use of bamboo leaves.

High-Yield Synthesis of Phosphatidylserine in a Well-Designed Mixed Micellar System

A sustainable enzymatic system is essential for efficient phosphatidylserine (PS) synthesis in industrial production. Conventional biphasic systems face challenges such as excessive organic solvent usage, enzyme-intensive processes, and increased costs. This study introduces a novel approach using chitin nanofibrils (ChNFs) as an immobilization material for phospholipase D (PLD) in a mixed micellar system stabilized by the food-grade emulsifier sodium deoxycholate (SDC). The immobilized enzyme, ChNF-chiA1, was quickly prepared in a one-step process, eliminating the need for purification. By optimizing the reaction conditions, including l-Ser concentration (1.0 M), SDC concentration (10 mM), reaction time (8 h), and enzyme dosage (1.0 U), a remarkable PS yield of 96.74% was achieved in the solvent-free mixed micellar system. The catalytic efficiency of ChNF-chiA1 surpassed that of the free PLD-chiA1 biphasic system by 6.0-fold. This innovative and green biocatalytic technology offers a reusable solution for the high-value enzymatic synthesis of phospholipids, providing a promising avenue for industrial applications.

Analysis of Volatile Components in Rosa roxburghii Tratt. and Rosa sterilis Using Headspace-Solid-Phase Microextraction-Gas Chromatography-Mass Spectrometry

Volatile organic compounds (VOCs) and flavor characteristics of Rosa roxburghii Tratt. (RR) and Rosa sterilis (RS) were analyzed using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). The flavor network was constructed by combining relative odor activity values (ROAVs), and the signature differential flavor components were screened using orthogonal partial least squares discriminant analysis (OPLS-DA) and random forest (RF). The results showed that 61 VOCs were detected in both RR and RS: 48 in RR, and 26 in RS. There were six key flavor components (ROAVs ≥ 1) in RR, namely nonanal, ethyl butanoate, ethyl hexanoate, (3Z)-3-hexen-1-yl acetate, ethyl caprylate, and styrene, among which ethyl butanoate had the highest contribution, whereas there were eight key flavor components (ROAVs ≥ 1) in RS, namely 2-nonanol, (E)-2-hexenal, nonanal, methyl salicylate, β-ocimene, caryophyllene, α-ionone, and styrene, among which nonanal contributed the most to RS. The flavor of RR is primarily fruity, sweet, green banana, and waxy, while the flavor of RS is primarily sweet and floral. In addition, OPLS-DA and RF suggested that (E)-2-hexenal, ethyl caprylate, β-ocimene, and ethyl butanoate could be the signature differential flavor components for distinguishing between RR and RS. In this study, the differences in VOCs between RR and RS were analyzed to provide a basis for further development and utilization.

Alcohol acyltransferases for the biosynthesis of esters

Esters are widely used in food, energy, spices, chemical industry, etc., becoming an indispensable part of life. However, their production heavily relies on the fossil energy industry, which presents significant challenges associated with energy shortages and environmental pollution. Consequently, there is an urgent need to identify alternative green methods for ester production. One promising solution is biosynthesis, which offers sustainable and environmentally friendly processes. In ester biosynthesis, alcohol acyltransferases (AATs) catalyze the condensation of acyl-CoAs and alcohols to form esters, enabling the biosynthesis of nearly 100 different kinds of esters, such as ethyl acetate, hexyl acetate, ethyl crotonate, isoamyl acetate, and butyl butyrate. However, low catalytic efficiency and low selectivity of AATs represent the major bottlenecks for the biosynthesis of certain specific esters, which should be addressed with protein molecular engineering approaches before practical biotechnological applications. This review provides an overview of AAT enzymes, including their sequences, structures, active sites, catalytic mechanisms, and metabolic engineering applications. Furthermore, considering the critical role of AATs in determining the final ester products, the current research progresses of AAT modification using protein molecular engineering are also discussed. This review summarized the major challenges and prospects of AAT enzymes in ester biosynthesis.

Oenological characteristics of two indigenous Starmerella bacillaris strains isolated from Chinese wine regions

To broaden knowledge about the oenological characteristics of Starmerella bacillaris, the influence of two Chinese indigenous S. bacillaris strains on the conventional enological parameters and volatile compounds of Cabernet Sauvignon wines were investigated under different inoculation protocols (single inoculation and simultaneous/sequential inoculation with the commercial Saccharomyces cerevisiae EC1118). The results showed that the two S. bacillaris strains could complete alcohol fermentation alone under high sugar concentrations while increasing the content of glycerol and decreasing the content of acetic acid. Compared with wines fermented by EC1118 single inoculation, S. bacillaris single inoculation and S. bacillaris/EC1118 sequential inoculation increased the contents of isobutanol, ethyl isobutanoate, terpenes, and ketones and decreased the contents of isopentanol, phenylethyl alcohol, fatty acids, acetate esters, and total ethyl esters. Furthermore, for S. bacillaris/EC1118 simultaneous inoculation, the concentrations of ethyl esters were increased, contributing to a higher score of "floral" and "fruity" notes in agreement with sensory analysis. KEY POINTS: • S. bacillaris single and simultaneous/sequential inoculation. • Conventional enological parameters and volatile compounds were investigated. • S. bacillaris/EC1118 simultaneous fermentation increased ethyl esters.

Enhanced Production of Ethyl Lactate in Saccharomyces cerevisiae by Genetic Modification

Ethyl lactate is an important flavor substance in baijiu, and it is also one of the common raw materials in the production of flavors and spices. In this study, we first established the ethyl lactate biosynthesis pathway in Saccharomyces cerevisiae α(L) by introducing propionyl coenzyme A transferase (Pct) and alcohol acyltransferase (AAT), and the results showed that strain α(L)-CP-Ae produced the most ethyl lactate 239.53 ± 5.45 mg/L. Subsequently, the copy number of the Pct_cp gene and AeAT9 gene was increased, and the modified strain α(L)-tCP-tAe produced 346.39 ± 3.99 mg/L ethyl lactate. Finally, the porin gene (por₂) and the mitochondrial pyruvate carrier gene (MPC2) were knocked to impede mitochondrial transport of pyruvate, and the final modified strain α(L)-tCP-tAeΔpor₂ produced ethyl lactate 420.48 ± 6.03 mg/L.