History, lineage and phenotypic differentiation of sake yeast

Physiological role of the EHL gene in sake yeast and its effects on quality of sake

The EHL1/2/3 genes were identified by whole-genome sequencing of Kyokai No. 7 (K7), which is a well-known representative Japanese sake yeast Saccharomyces cerevisiae. The genes are present in K7, but not in laboratory strain S288C. Although the genes were presumed to encode epoxide hydrolase based on homology analysis, their effect on cellular metabolism in sake yeast has not yet been clarified. We constructed ehl1/2/3 mutants harboring a stop codon in each gene using the haploid yeast strain H3 as the parental strain, which was derived from K701, and investigated the physiological role and effects of the EHL1/2/3 genes on sake quality. Metabolome analysis and vitamin requirement testing revealed that the EHL1/2/3 genes are partly responsible for the synthesis of pantothenate. For fermentation profiles, ethanol production by the ehl1/2/3 mutant was comparable with that of strain H3, but succinate production was decreased in the ehl1/2/3 mutant compared to strain H3 when cultured in yeast malt (YM) medium containing 10% glucose and during sake brewing. Ethyl hexanoate and isoamyl acetate levels in the ehl1/2/3 mutant strain were decreased compared to those of strain H3 during sake brewing. Thus, the EHL1/2/3 genes did not affect ethanol production but did affect the production of organic acids and aromatic components during sake brewing.

Japanese sake making using wild yeasts isolated from natural environments

Saccharomyces cerevisiae is one of the most important microorganisms for the food industry, including Japanese sake, beer, wine, bread, and other products. For sake making, Kyokai sake yeast strains are considered one of the best sake yeast strains because these strains possess fermentation properties that are suitable for the quality of sake required. In recent years, the momentum for the development of unique sake, which is distinct from conventional sake, has grown, and there is now a demand to develop unique sake yeasts that have different sake making properties than Kyokai sake yeast strains. In this minireview, we focus on "wild yeasts," which inhabit natural environments, and introduce basic research on the wild yeasts for sake making, such as their genetic and sake fermentation aspects. Finally, we also discuss the molecular breeding of wild yeast strains for sake fermentation and the possibility for sake making using wild yeasts.

Kuratsuki bacteria and sake making

Kuratsuki bacteria enter during the sake-making process and interact with sake yeast until their growth is attenuated by the ethanol produced by sake yeast. Due to the interaction between kuratsuki bacteria and sake yeast, the metabolism of sake yeast changes, affecting the composition of esters and organic acids and subsequently the flavor and taste of sake. We cultivated kuratsuki bacteria and sake yeast, and performed test making at sake breweries to clarify the interaction among microorganisms in the sake-making process. We aim to propose a sake-making process that controls the flavor and taste of sake by utilizing the functions of kuratsuki bacteria.

Effect of kuratsuki Kocuria on sake's taste varies depending on the sake yeast strain used in sake brewing

Although sake yeast mainly produces the taste of sake, sake brewery-inhabiting (kuratsuki) bacteria affect the taste of sake. Thus, kuratsuki bacteria may alter the metabolism of sake yeast through interactions between kuratsuki bacteria and sake yeast. This study aimed to confirm the effects of the combination of kuratsuki Kocuria TGY1127_2 and different sake yeast strains, AK25, K901, and K1801 on the taste of sake. Although the Brix and acidity during sake production using AK25 differed between sake with and without kuratsuki Kocuria, those using K901 and K1801 did not differ. Thus, sake yeast AK25 interacted with kuratsuki Kocuria and changed its characteristics of ethanol fermentation. In addition, the taste intensity changes, measured with a taste sensor TS-5000Z, showed that the effects of adding kuratsuki Kocuria varied among different sake yeasts. Thus, each sake yeast strain interacted with the kuratsuki bacterium and produced different metabolites, resulting in a change in the taste of sake. The findings of this study can lead to the brewing of sake using different types of kuratsuki bacteria which can affect the taste of sake.

Targeted Mutations Produce Divergent Characteristics in Pedigreed Sake Yeast Strains

Modification of the genetic background and, in some cases, the introduction of targeted mutations can play a critical role in producing trait characteristics during the breeding of crops, livestock, and microorganisms. However, the question of how similar trait characteristics emerge when the same target mutation is introduced into different genetic backgrounds is unclear. In a previous study, we performed genome editing of AWA1, CAR1, MDE1, and FAS2 on the standard sake yeast strain Kyokai No. 7 to breed a sake yeast with multiple excellent brewing characteristics. By introducing the same targeted mutations into other pedigreed sake yeast strains, such as Kyokai strains No. 6, No. 9, and No. 10, we were able to create sake yeasts with the same excellent brewing characteristics. However, we found that other components of sake made by the genome-edited yeast strains did not change in the exact same way. For example, amino acid and isobutanol contents differed among the strain backgrounds. We also showed that changes in yeast cell morphology induced by the targeted mutations also differed depending on the strain backgrounds. The number of commonly changed morphological parameters was limited. Thus, divergent characteristics were produced by the targeted mutations in pedigreed sake yeast strains, suggesting a breeding strategy to generate a variety of sake yeasts with excellent brewing characteristics.

Development of sake yeast breeding and analysis of genes related to its various phenotypes

Sake is a traditional Japanese alcoholic beverage made from rice and water, fermented by the filamentous fungi Aspergillus oryzae and the yeast Saccharomyces cerevisiae. Yeast strains, also called sake yeasts, with high alcohol yield and the ability to produce desired flavor compounds in the sake, have been isolated from the environment for more than a century. Furthermore, numerous methods to breed sake yeasts without genetic modification have been developed. The objectives of breeding include increasing the efficiency of production, improving the aroma and taste, enhancing safety, imparting functional properties, and altering the appearance of sake. With the recent development of molecular biology, the suitable sake brewing characteristics in sake yeasts, and the causes of acquisition of additional phenotypes in bred yeasts have been elucidated genetically. This mini-review summarizes the history and lineage of sake yeasts, their genetic characteristics, the major breeding methods used, and molecular biological analysis of the acquired strains. The data in this review on the metabolic mechanisms of sake yeasts and their genetic profiles will enable the development of future strains with superior phenotypes.

A real-time monitoring system for automatic morphology analysis of yeast cultivation in a jar fermenter

The monitoring of microbial cultivation in real time and controlling their cultivation aid in increasing the production yield of useful material in a jar fermenter. Common sensors such as dissolved oxygen (DO) and pH can easily provide general-purpose indexes but do not reveal the physiological states of microbes because of the complexity of measuring them in culture conditions. It is well known from microscopic observations that the microbial morphology changes in response to the intracellular state or extracellular environment. Recently, studies have focused on rapid and quantitative image analysis techniques using machine learning or deep learning for gleaning insights into the morphological, physiological or gene expression information in microbes. During image analysis, it is necessary to retrieve high-definition images to analyze the microbial morphology in detail. In this study, we have developed a microfluidic device with a high-speed camera for the microscopic observation of yeast, and have constructed a system capable of generating their morphological information in real-time and at high definition. This system was connected to a jar fermenter, which enabled the automatic sampling for monitoring the cultivation. We successfully acquired high-definition images of over 10,000 yeast cells in about 2.2 s during ethanol fermentation automatically for over 168 h. We recorded 33,600 captures containing over 1,680,000 cell images. By analyzing these images, the morphological changes of yeast cells through ethanol fermentation could be captured, suggesting the expansion of the application of this system in controlling microbial fermentation using the morphological information generated. KEY POINTS: • Enables real-time visualization of microbes in a jar fermenter using microscopy. • Microfluidic device for acquiring high-definition images. • Generates a large amount of image data by using a high-speed camera.

Genome Editing to Generate Sake Yeast Strains with Eight Mutations That Confer Excellent Brewing Characteristics

Sake yeast is mostly diploid, so the introduction of recessive mutations to improve brewing characteristics requires considerable effort. To construct sake yeast with multiple excellent brewing characteristics, we used an evidence-based approach that exploits genome editing technology. Our breeding targeted the AWA1, CAR1, MDE1, and FAS2 genes. We introduced eight mutations into standard sake yeast to construct a non-foam-forming strain that makes sake without producing carcinogens or an unpleasant odor, while producing a sweet ginjo aroma. Small-scale fermentation tests showed that the desired sake could be brewed with our genome-edited strains. The existence of a few unexpected genetic perturbations introduced during breeding proved that genome editing technology is extremely effective for the serial breeding of sake yeast.

Co-cultivation of sake yeast and Kocuria isolates from the sake brewing process

Kocuria isolates collected from the sake brewing process have inhabited the Narimasa Sake Brewery in Toyama, Japan. To investigate the effect of these actinobacterial isolates on the growth and metabolism of sake yeast, co-cultivation of sake yeast and Kocuria isolates was performed in a medium containing tryptone, glucose and yeast extract (TGY), and a solution containing koji (steamed rice covered with Aspergillus oryzae) and glucose. In the TGY medium, the ethanol concentration and the number of living cells of each microorganism were measured. In the koji solution, the concentrations of ethanol and organic acids (citric acid, lactic acid and succinic acid) were measured. The results showed that in TGY media, the growth of each Kocuria isolate in the co-culture of the two Kocuria isolates was similar to that in each monoculture. However, the growth of both Kocuria isolates was inhibited in the co-cultures of sake yeast and Kocuria isolates. On the other hand, the growth and ethanol productivity of sake yeast did not differ between its monoculture and co-cultures with Kocuria isolates. In the koji solution, Kocuria isolates TGY1120_3 and TGY1127_2 affected the concentrations of ethanol and lactic acid, respectively. Thus, Kocuria isolates affected the microbial metabolism, but the effects were not identical between the two isolates. This strongly suggests that bacteria inhabiting a sake brewery may influence the flavor and taste of sake products of the brewery.

Genomic information of Kocuria isolates from sake brewing process

Bacteria belonging to the genus Kocuria were identified as bacteria peculiar to a sake brewery in Toyama, Japan. Comparison of the 16S rRNA gene sequences revealed two groups of Kocuria isolates. Among known species, one group was similar to K. koreensis (Kk type), and the other, K. uropygioeca (Ku type). We determined complete genomic DNA sequences from two isolates, TGY1120_3 and TGY1127_2, which belong to types Kk and Ku, respectively. Comparison of these genomic information showed that these isolates differ at the species level with different genomic characters. Isolate TGY1120_3 comprised one chromosome and three plasmids, and the same transposon coding region was located on two loci on the chromosome and one locus on one plasmid, suggesting that the genetic element may be transferred between the chromosome and plasmid. Isolate TGY1127_2 comprised one chromosome and one plasmid. This plasmid encoded an identical transposase coding region, strongly suggesting that the genetic element may be transferred between these different isolates through plasmids. These four plasmids carried a highly similar region, indicating that they share a common ancestor. Thus, these two isolates may form a community and exchange their genetic information during sake brewing.

Never Change a Brewing Yeast? Why Not, There Are Plenty to Choose From

Fermented foods and particularly beer have accompanied the development of human civilization for thousands of years. Saccharomyces cerevisiae, the dominant yeast in the production of alcoholic beverages, probably co-evolved with human activity. Considering that alcoholic fermentations emerged worldwide, the number of strains used in beer production nowadays is surprisingly low. Thus, the genetic diversity is often limited. This is among others related to the switch from a household brewing style to a more artisan brewing regime during the sixteenth century and latterly the development of single yeast isolation techniques at the Carlsberg Research Laboratory in 1883, resulting in process optimizations in the brewing industry. However, due to fierce competition within the beer market and the increasing demand for novel beer styles, diversification is becoming increasingly important. Moreover, the emergence of craft brewing has influenced big breweries to rediscover yeast as a significant contributor to a beer's aroma profile and realize that there is still room for innovation in the fermentation process. Here, we aim at giving a brief overview on how currently used S. cerevisiae brewing yeasts emerged and comment on the rationale behind replacing them with novel strains. We will present potential sources of yeasts that have not only been used in beer brewing before, including natural sources and sources linked to human activity but also an overlooked source, such as yeast culture collections. We will briefly comment on common yeast isolation techniques and finally touch on additional challenges for the brewing industry in replacing their current brewer's yeasts.

Crossbreeding of Yeasts Domesticated for Fermentation: Infertility Challenges

Sexual reproduction is almost a universal feature of eukaryotic organisms, which allows the reproduction of new organisms by combining the genetic information from two individuals of different sexes. Based on the mechanism of sexual reproduction, crossbreeding provides an attractive opportunity to improve the traits of animals, plants, and fungi. The budding yeast Saccharomyces cerevisiae has been widely utilized in fermentative production since ancient times. Currently it is still used for many essential biotechnological processes including the production of beer, wine, and biofuels. It is surprising that many yeast strains used in the industry exhibit low rates of sporulation resulting in limited crossbreeding efficiency. Here, I provide an overview of the recent findings about infertility challenges of yeasts domesticated for fermentation along with the progress in crossbreeding technologies. The aim of this review is to create an opportunity for future crossbreeding of yeasts used for fermentation.

Profiling of Fungal Diversity and Fermentative Yeasts in Traditional Chinese Xiaoqu

To increase the safety and quality of baijiu and rice wine in China, controlling the use of traditional Xiaoqu by studying the beneficial yeasts present has recently been considered. The fungal diversity of six Chinese Xiaoqu including five traditional and one commercial samples was investigated to screen fermentative yeasts with low yields of higher alcohols. A high throughput sequencing approach detected fifteen fungal species with relative abundance higher than 1%, and displayed dissimilarities of fungal diversity among Xiaoqu samples. The 15 fungal species were composed of 11 filamentous fungi with Rhizopus arrhizus as the most common specie and four yeast species, containing Hyphopichia burtonii, Saccharomyces cerevisiae, Saccharomycopsis fibuligera, and Saccharomycopsis malanga. Classic culture-dependent approaches, including 5.8S-ITS-RFLP analysis and D1/D2 sequencing of the 26S rRNA gene, identified nine yeast species in the five traditional Chinese Xiaoqu. In addition to the four yeast species also detected by high throughput sequencing approach, the other five yeast species isolated were Clavispora lusitaniae, Cryptococcus neoformans, Komagataella pastoris, Trichosporon asahii, and Wickerhamomyces anomalus. Further micro-fermentations of rice wine were performed using 19 single yeast isolates, and after the fermentation of rice wine, higher alcohols and ethanol were analyzed by gas chromatography. Two yeast strains, Saccharomyces cerevisiae FBKL2.8022 and Wickerhamomyces anomalus FBKL2.8023, were found to have low yields of higher alcohols and could produce 11.70%vol and 7.10%vol ethanol separately. This study for the first time, to the best of our knowledge, explored the fungal resources in traditional Xiaoqu from different regions of Guizhou, China. The screened S. cerevisiae and W. anomalus strains could be used to establish specific starters to promote the standardization of the production of baijiu and rice wine.

Cloning of the SPO11 gene that complements a meiotic recombination defect in sake yeast

Cross hybridization breeding of sake yeasts is hampered by difficulty in acquisition of haploid cells through sporulation. We previously demonstrated that typical sake yeast strains were defective in meiotic chromosome recombination, which caused poor sporulation and loss of spore viability. In this study, we screened a single copy plasmid genomic DNA library of the laboratory Saccharomyces cerevisiae GRF88 for genes that might complement the meiotic recombination defect of UTCAH-3, a strain derived from the sake yeast Kyokai no. 7 (K7). We identified the SPO11 gene of the laboratory strain (ScSPO11), encoding a meiosis-specific endonuclease that catalyzes DNA double-strand breaks required for meiotic recombination, as a gene that restored meiotic recombination and spore viability of UTCAH-3. K7SPO11 could not restore sporulation efficiency and spore viability of UTCAH-3 and a laboratory strain BY4743 spo11Δ/spo11Δ, indicating that K7SPO11 is not functional. Sequence analysis of the SPO11 genes of various Kyokai sake yeasts (K1, and K3-K10) revealed that the K7 group of sake yeasts (K6, K7, K9, and K10) had a mutual missense mutation (C73T) in addition to other three common mutations present in all Kyokai yeasts tested. ScSPO11^C73T created through in vitro mutagenesis could not restore spore viability of BY4743 spo11Δ/spo11Δ. On the other hand, K8SPO11, which have the three common mutations except for C73T could restore spore viability of BY4743 spo11Δ/spo11Δ. These results suggest that C73T might be a causative mutation of recombination defect in K7SPO11. Moreover, we found that the introduction of ScRIM15 restored sporulation efficiency but not spore viability.

Characteristic analysis of the fermentation and sporulation properties of the traditional sake yeast strain Hiroshima no.6

General sake yeasts (e.g., Kyokai no.7, K7) show high fermentation ability and low sporulation frequency. Former is related to stress-response defect due to the loss-of-function of MSN4 and RIM15. Later is mainly caused by low IME1 expression, leading to difficulty in breeding and genetic analysis. Sake yeast Hiroshima no.6 (H6), which had been applied for sake fermentation, has sporulation ability. However, its detailed properties have not been unveiled. Here we present that the fermentation ability of H6 is suitable for sake brewing, and the precursor of dimethyl trisulfide in sake from H6 is low. MSN4 but not RIM15 of H6 has the same mutation as K7. Our phylogenetic analysis indicated that H6 is closely related to the K7 group. Unlike K7, H6 showed normal sporulation frequency in a partially RIM15-dependent manner, and IME1 in H6 was expressed. H6 possesses excellent properties as a partner strain for breeding by crossing.