Metabolic engineering of Saccharomyces cerevisiae using the CRISPR/Cas9 system to minimize ethyl carbamate accumulation during Chinese rice wine fermentation

Progress in Gene Editing and Metabolic Regulation of Saccharomyces cerevisiae with CRISPR/Cas9 Tools

The CRISPR/Cas9 systems have been developed as tools for genetic engineering and metabolic engineering in various organisms. In this review, various aspects of CRISPR/Cas9 in Saccharomyces cerevisiae, from basic principles to practical applications, have been summarized. First, a comprehensive review has been conducted on the history of CRISPR/Cas9, successful cases of gene disruptions, and efficiencies of multiple DNA fragment insertions. Such advanced systems have accelerated the development of microbial engineering by reducing time and labor, and have enhanced the understanding of molecular genetics. Furthermore, the research progress of the CRISPR/Cas9-based systems in the production of high-value-added chemicals and the improvement of stress tolerance in S. cerevisiae have been summarized, which should have an important reference value for genetic and synthetic biology studies based on S. cerevisiae.

Research Progress on Flavor and Quality of Chinese Rice Wine in the Brewing Process

Chinese rice wine (CRW) is a traditional and unique alcoholic beverage in China, favored by many consumers for its rich aroma, unique taste, and complex ingredients. Its flavor is primarily composed of volatile and nonvolatile compounds. These flavor compounds are partly derived from grains and starters (Qu), while the other part is produced by microbial metabolism and chemical reactions during the brewing process. Additionally, ethyl carbamate (EC) in CRW, a hazardous chemical, necessitates controlling its concentration during brewing. In recent years, numerous new brewing techniques for CRW have emerged. Therefore, this paper aims to collect aroma descriptions and thresholds of flavor compounds in CRW, summarize the relationship between the brewing process of CRW and flavor formation, outline methods for reducing the concentration of EC in the brewing process of CRW, and summarize the four stages (pretreatment of grains, fermentation, sterilization, and aging process) of new techniques. Furthermore, we will compare the advantages and disadvantages of different approaches, with the expectation of providing a valuable reference for improving the quality of CRW.

The Screening and Isolation of Ethyl-Carbamate-Degrading Strains from Fermented Grains and Their Application in the Degradation of Ethyl Carbamate in Chinese Baijiu

Ethyl carbamate (EC), a 2A carcinogen produced during the fermentation of foods and beverages, primarily occurs in distilled spirits. Currently, most studies focus on strategies for EC mitigation. In the present research, we aimed to screen strains that can degrade EC directly. Here, we report two Candida ethanolica strains (J1 and J116), isolated from fermented grains, which can reduce EC concentrations directly. These two yeasts were grown using EC as the sole carbon source, and they grew well on different carbon sources. Notably, after immobilization with chitosan, the two strains degraded EC in Chinese Baijiu by 42.27% and 27.91% in 24 h (from 253.03 ± 9.89 to 146.07 ± 1.67 and 182.42 ± 5.05 μg/L, respectively), which was better than the performance of the non-immobilized strains. Furthermore, the volatile organic compound content, investigated using gas chromatography-mass spectrometry, did not affect the main flavor substances in Chinese Baijiu. Thus, the yeasts J1 and J116 may be potentially used for the treatment and commercialization of Chinese Baijiu.

Simulation and Control of the Formation of Ethyl Carbamate during the Fermentation and Distillation Processes of Chinese Baijiu

Baijiu is a popular alcoholic beverage with a long history in China. However, the widespread presence of the ethyl carbamate (EC) carcinogen has raised many food safety concerns. To date, the main precursors of EC and its formation process have not been determined, resulting in difficulty controlling EC in Baijiu. In this study, the main precursors of EC are identified as urea and cyanide during the process of brewing for different flavors of Baijiu, while the dominant stage in which EC formation occurs is during the process of distillation rather than fermentation. In addition, the effects of temperature, pH value, alcohol concentration and metal ions on the formation of EC are confirmed. In the following study, the main precursor of EC is identified as cyanide during the process of distillation, and a combination of optimizing the distillation device and adding copper wire is proposed. Furthermore, the effect of this novel strategy is examined in gaseous reactions between cyanide and ethanol, reducing the concentration of EC by 74.0%. Finally, the feasibility of this strategy is verified in simulated distillations of fermented grains, reducing the formation of EC by 33.7-50.2%. This strategy has great application potential in industrial production.

Two Faces of Fermented Foods-The Benefits and Threats of Its Consumption

In underdeveloped and developing countries, due to poverty, fermentation is one of the most widely used preservation methods. It not only allows extending the shelf life of food, but also brings other benefits, including inhibiting the growth of pathogenic microorganisms, improving the organoleptic properties and product digestibility, and can be a valuable source of functional microorganisms. Today, there is a great interest in functional strains, which, in addition to typical probiotic strains, can participate in the treatment of numerous diseases, disorders of the digestive system, but also mental diseases, or stimulate our immune system. Hence, fermented foods and beverages are not only a part of the traditional diet, e.g., in Africa but also play a role in the nutrition of people around the world. The fermentation process for some products occurs spontaneously, without the use of well-defined starter cultures, under poorly controlled or uncontrolled conditions. Therefore, while this affordable technology has many advantages, it can also pose a potential health risk. The use of poor-quality ingredients, inadequate hygiene conditions in the manufacturing processes, the lack of standards for safety and hygiene controls lead to the failure food safety systems implementation, especially in low- and middle-income countries or for small-scale products (at household level, in villages and scale cottage industries). This can result in the presence of pathogenic microorganisms or their toxins in the food contributing to cases of illness or even outbreaks. Also, improper processing and storage, as by well as the conditions of sale affect the food safety. Foodborne diseases through the consumption of traditional fermented foods are not reported frequently, but this may be related, among other things, to a low percentage of people entering healthcare care or weaknesses in foodborne disease surveillance systems. In many parts of the world, especially in Africa and Asia, pathogens such as enterotoxigenic and enterohemorrhagic Escherichia coli, Shigella spp., Salmonella spp., enterotoxigenic Staphylococcus aureus, Listeria monocytogenes, and Bacillus cereus have been detected in fermented foods. Therefore, this review, in addition to the positive aspects, presents the potential risk associated with the consumption of this type of products.

Genetic Engineering Production of Ethyl Carbamate Hydrolase and Its Application in Degrading Ethyl Carbamate in Chinese Liquor

Ethyl carbamate (EC), classified as a Group 2A carcinogen, is most abundant in the fermented foods, such as Cachaca, Shaoxing wine, and Chinese liquor (baijiu). Although biodegradation can reduce its concentration, a high ethanol concentration and acidic environment often limit its degradation. In the present study, a novel ethyl carbamate hydrolase (ECH) with high specificity to EC was isolated from Acinetobacter calcoaceticus, and its enzymatic properties and EC degradability were investigated. ECH was immobilized to resist extreme environmental conditions, and the flavor substance changes were explored by gas chromatography-mass spectrometry (GC/MS). The specific enzymatic activity of ECH was 68.31 U/mg. Notably, ECH exhibited excellent thermal stability and tolerance to sodium chloride and high ethanol concentration (remaining at 40% activity in 60% (v/v) ethanol, 1 h). The treatment of immobilized ECH for 12 h decreased the EC concentration in liquor by 71.6 μg/L. Furthermore, the immobilized ECH exerted less effect on its activity and on the flavor substances, which could be easily filtrated during industrial production.

Occurrence of Ethyl Carbamate in Foods and Beverages: Review of the Formation Mechanisms, Advances in Analytical Methods, and Mitigation Strategies

ABSTRACT

Ethyl carbamate (EC) is a process contaminant that can be formed as a by-product during fermentation and processing of foods and beverages. Elevated EC concentrations are primarily associated with distilled spirits, but this compound has also been found at lower concentrations in foods and beverages, including breads, soy sauce, and wine. Evidence from animal studies suggests that EC is a probable human carcinogen. Consequently, several governmental institutions have established allowable limits for EC in the food supply. This review includes EC formation mechanisms, occurrence of EC in the food supply, and EC dietary exposure assessments. Current analytical methods used to detect EC will be covered, in addition to emerging technologies, such as nanosensors and surface-enhanced Raman spectroscopy. Various mitigation methods have been used to maintain EC concentrations below allowable limits, including distillation, enzymatic treatments, and genetic engineering of yeast. More research in this field is needed to refine mitigation strategies and develop methods to rapidly detect EC in the food supply.

HIGHLIGHTS

CRISPR/Cas9-mediated Inactivation of arginase in a yeast strain isolated from Nuruk and its impact on the whole genome

Despite the advantages of CRISPR/Cas9 technology in the food industry, controversy over its off-target effects exists. We engineered an industrial Saccharomyces cerevisiae strain isolated from a Korean rice wine starter, Nuruk, using CRISPR/Cas9 to decrease ethyl carbamate (EC) formation. We disrupted the CAR1 gene encoding arginase, which plays a key role in EC formation. Subsequently, we compared the whole genome of the engineered strain to that of the wild type by analyzing heterozygous and homozygous mutations through variant calling. Homozygous mutations in the genome of the engineered strains were identified as the target mutations in CAR1 induced by CRISPR/Cas9, and no other off-target effects were observed. Our findings have critical implications for the use of CRISRP/Cas9 technology in yeasts in the food industry.

Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

Traditional Fermented Beverages of Mexico: A Biocultural Unseen Foodscape

Mexico is one of the main regions of the world where the domestication of numerous edible plant species originated. Its cuisine is considered an Intangible Cultural Heritage of Humanity and ferments are important components but have been poorly studied. Traditional fermented foods are still diverse, but some are endangered, requiring actions to promote their preservation. Our study aimed to (1) systematize information on the diversity and cultural history of traditional Mexican fermented beverages (TMFB), (2) document their spatial distribution, and (3) identify the main research trends and topics needed for their conservation and recovery. We reviewed information and constructed a database with biocultural information about TMFB prepared and consumed in Mexico, and we analyzed the information through network approaches and mapped it. We identified 16 TMFB and 143 plant species involved in their production, species of Cactaceae, Asparagaceae, and Poaceae being the most common substrates. Microbiological research has been directed to the potential biotechnological applications of Lactobacillus, Bacillus, and Saccharomyces. We identified a major gap of research on uncommon beverages and poor attention on the cultural and technological aspects. TMFB are dynamic and heterogenous foodscapes that are valuable biocultural reservoirs. Policies should include their promotion for conservation. The main needs of research and policies are discussed.

An Overview of CRISPR-Based Technologies in Wine Yeasts to Improve Wine Flavor and Safety

Modern industrial winemaking is based on the use of specific starters of wine strains. Commercial wine strains present several advantages over natural isolates, and it is their use that guarantees the stability and reproducibility of industrial winemaking technologies. For the highly competitive wine market with new demands for improved wine quality and wine safety, it has become increasingly critical to develop new yeast strains. In the last decades, new possibilities arose for creating upgraded wine yeasts in the laboratory, resulting in the development of strains with better fermentation abilities, able to improve the sensory quality of wines and produce wines targeted to specific consumers, considering their health and nutrition requirements. However, only two genetically modified (GM) wine yeast strains are officially registered and approved for commercial use. Compared with traditional genetic engineering methods, CRISPR/Cas9 is described as efficient, versatile, cheap, easy-to-use, and able to target multiple sites. This genetic engineering technique has been applied to Saccharomyces cerevisiae since 2013. In this review, we aimed to overview the use of CRISPR/Cas9 editing technique in wine yeasts to combine develop phenotypes able to increase flavor compounds in wine without the development of off-flavors and aiding in the creation of “safer wines.”

CRISPR-Cas9: A Powerful Tool to Efficiently Engineer Saccharomyces cerevisiae

Saccharomyces cerevisiae has been for a long time a common model for fundamental biological studies and a popular biotechnological engineering platform to produce chemicals, fuels, and pharmaceuticals due to its peculiar characteristics. Both lines of research require an effective editing of the native genetic elements or the inclusion of heterologous pathways into the yeast genome. Although S. cerevisiae is a well-known host with several molecular biology tools available, a more precise tool is still needed. The clustered, regularly interspaced, short palindromic repeats-associated Cas9 (CRISPR-Cas9) system is a current, widespread genome editing tool. The implementation of a reprogrammable, precise, and specific method, such as CRISPR-Cas9, to edit the S. cerevisiae genome has revolutionized laboratory practices. Herein, we describe and discuss some applications of the CRISPR-Cas9 system in S. cerevisiae from simple gene knockouts to more complex processes such as artificial heterologous pathway integration, transcriptional regulation, or tolerance engineering.

Next Generation Winemakers: Genetic Engineering in Saccharomyces cerevisiae for Trendy Challenges

The most famous yeast of all, Saccharomyces cerevisiae, has been used by humankind for at least 8000 years, to produce bread, beer and wine, even without knowing about its existence. Only in the last century we have been fully aware of the amazing power of this yeast not only for ancient uses but also for biotechnology purposes. In the last decades, wine culture has become and more demanding all over the world. By applying as powerful a biotechnological tool as genetic engineering in S. cerevisiae, new horizons appear to develop fresh, improved, or modified wine characteristics, properties, flavors, fragrances or production processes, to fulfill an increasingly sophisticated market that moves around 31.4 billion € per year.