Improving RNA content of salt-tolerant Zygosaccharomyces rouxii by atmospheric and room temperature plasma (ARTP) mutagenesis and its application in soy sauce brewing

Application and research progress of ARTP mutagenesis in actinomycetes breeding

Atmospheric and room temperature plasma (ARTP) is an emerging artificial mutagenesis breeding technology. In comparison to traditional physical and chemical methods, ARTP technology can induce DNA damage more effectively and obtain mutation strains with stable heredity more easily after screening. It possesses advantages such as simplicity, safety, non-toxicity, and cost-effectiveness, showing high application value in microbial breeding. This article focuses on ARTP mutagenesis breeding of actinomycetes, specifically highlighting the application of ARTP mutagenesis technology in improving the performance of strains and enhancing the biosynthetic capabilities of actinomycetes. We analyzed the advantages and challenges of ARTP technology in actinomycetes breeding and summarized the common features, specific mutation sites and metabolic pathways of ARTP mutagenic strains, which could give guidance for genetic modification. It suggested that the future research work should focus on the establishment of high throughput rapid screening methods and integrate transcriptomics, proteomics, metabonomics and other omics to delve into the genetic regulations and synthetic mechanisms of the bioactive substances in ARTP mutated actinomycetes. This article aims to provide new perspectives for actinomycetes breeding through the establishment and application of ARTP mutagenesis technology, thereby promoting source innovation and the sustainable industrial development of actinomycetes.

Effect of Plasma-Activated Water on the Cellulase-Producing Strain Aspergillus niger A32

To investigate the effect and mechanism of plasma-activated water (PAW) on Aspergillus niger, PAW was prepared using a needle array-plate dielectric barrier discharge plasma system. The concentrations of long-lived reactive oxygen and nitrogen species (RONS), namely, H2O2, NO2-, and NO3-, in the PAW were 48.76 mg/L, 0.046 mg/L, and 172.36 mg/L, respectively. Chemically activated water (CAW) with the same concentration of long-lived RONS was also prepared for comparison. A. niger A32 was treated with PAW and CAW. After treatment, the treated strains were observed and analyzed with scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to screen probable mutants. The results indicated that the pH, conductivity, and ORP values of PAW were 2.42, 1935 μS/cm, and 517.07 mV, respectively. In contrast, the pH and ORP values of CAW were 6.15 and 301.73 mV, respectively, which differed significantly from those of PAW. In addition, the conductivity of CAW showed no change. SEM and TEM analyses revealed that A. niger A32 treated with CAW exhibited less damage compared with the control. In contrast, A. niger A32 treated with PAW showed significant shrinkage, deformation, and exudate attachment over time. Following PAW treatment, after four passages, a high cellulase-producing stable mutant strain A-WW5 was screened, exhibiting a filter paper enzyme activity of 29.66 U/mL, a cellulose endonuclease activity of 13.79 U/mL, and a β-glucosidase activity of 27.13 U/mL. These values were found to be 33%, 38%, and 2.1% higher than those of the original fungus sample, respectively. In total, 116 SNPs and 61 InDels were present in the genome of the mutant strain A-WW5. The above findings indicate that the impact of PAW on A. niger is not only attributed to long-lasting H2O2, NO2-, and NO3- particles but also to other short-lived active particles; PAW is expected to become a new microbial breeding mutagen.

Improvement of ribonucleic acid production in Cyberlindnera jadinii and optimization of fermentation medium

To enhance the ribonucleic acid (RNA) productivity for industrial applications, this study employed strain screening and medium optimization to improve the content of RNA in Cyberlindnera jadinii. A rapid screening method, combining atmospheric and room temperature plasma mutagenesis, 48-deep-well plates fermentation, and microplate reader detection, was developed. A mutant strain named WB15 with high RNA content was successfully obtained, exhibiting the RNA content of 156 ± 4.5 mg/g DCW, 1.4 times of the starting strain CCTCC AY 92020. Furthermore, Plackett-Burman design and response surface methodology were employed to identify three significant factors (yeast extract, soybean peptone, and KH2PO4) affecting the RNA content. By utilizing the optimal medium composed of 13.43 g/L yeast extract, 12.12 g/L soybean peptone and 2.78 g/L KH2PO4, the RNA content of WB15 further increased to 184 ± 4.9 mg/g DCW. Additionally, the mutant strain WB15 exhibited a greater cellular width compared to AY 92020, along with increased growth rate and single-cell RNA content by 22% and 48.9%, respectively. Perturbations in ribosome assembly, specifically a reduction in the ratio of ribosomal proteins to ribosomal RNA of the large subunit, might indirectly contribute to the higher RNA content in the WB15 strain. Overall, the combination of rapid screening with fermentation medium optimization proved to be an effective approach for improving the RNA content of C. jadinii, thus facilitating the industrial production of RNA.

Application of Atmospheric and Room-Temperature Plasma (ARTP) to Microbial Breeding

Atmospheric and room-temperature plasma (ARTP) is an efficient microbial mutagenesis method with broad application prospects. Compared to traditional methods, ARTP technology can more effectively induce DNA damage and generate stable mutant strains. It is characterized by its simplicity, cost-effectiveness, and avoidance of hazardous chemicals, presenting a vast potential for application. The ARTP technology is widely used in bacterial, fungal, and microalgal mutagenesis for increasing productivity and improving characteristics. In conclusion, ARTP technology holds significant promise in the field of microbial breeding. Through ARTP technology, we can create mutant strains with specific genetic traits and improved performance, thereby increasing yield, improving quality, and meeting market demands. The field of microbial breeding will witness further innovation and progress with continuous refinement and optimization of ARTP technology.

Synergistic Fermentation with Functional Microorganisms Improves Safety and Quality of Traditional Chinese Fermented Foods

Traditional fermented foods are favored by people around the world for their positive health and taste advantages. Many of the fermented foods, including Chinese traditional fermented foods, are produced through mixed-culture fermentation. Apart from reducing the formation of harmful compounds such as ethyl carbamate (EC) and biogenic amines (BAs) during food fermentation, it is also difficult to precisely control and regulate the fermentation process based on the control of environmental conditions alone, due to the complex microbiota and an unclarified fermentation mechanism. In this review, key microorganisms involved in Chinese fermented foods such as baijiu, soy sauce, and vinegar production are elaborated, and relations between microbial composition and the aroma or quality of food are discussed. This review focuses on the interpretation of functions and roles of beneficial (functional) microorganisms that participate in food fermentation and the discussion of the possibilities of the synergistic use of functional microorganisms to improve the safety and quality of Chinese fermented foods. Conducting work toward the isolation of beneficial microorganisms is a challenge for modern food fermentation technology. Thus, methods for the isolation and mutagenesis of functional microbial strains for synergistic food fermentation are summarized. Finally, the limitations and future prospects of the use of functional microorganisms in traditional Chinese fermented foods are reviewed. This review provides an overview of the applications of synergistic fermentation with functional microorganisms in the improvement of the safety or sensory qualities of fermented foods.

Adaptive Laboratory Evolution of Yeasts for Aroma Compound Production

Aroma compounds are important in the food and beverage industry, as they contribute to the quality of fermented products. Yeasts produce several aroma compounds during fermentation. In recent decades, production of many aroma compounds by yeasts obtained through adaptive laboratory evolution has become prevalent, due to consumer demand for yeast strains in the industry. This review presents general aspects of yeast, aroma production and adaptive laboratory evolution and focuses on the recent advances of yeast strains obtained by adaptive laboratory evolution to enhance the production of aroma compounds.

Development of multiplex HRM-based loop-mediated isothermal amplification method for specific and sensitive detection of Treponema pallidum

Syphilis is a sexually transmitted disease caused by the spirochaete bacterium Treponema pallidum. This study has developed a multiplex High-Resolution Melt-curve Loop-mediated isothermal amplification (multiplex HRM-LAMP) assay targeting the marker genes polA and tprL to detect T. pallidum. The multiplex HRM-LAMP assay conditions were optimized at 65 °C for 45 min. Real-time melt-curve analysis of multiplex HRM-LAMP shows two melt-curve peaks corresponding to polA and tprL with a Tm value of 80 ± 0.5 °C and 87 ± 0.5 °C, respectively. The detection limit of multiplex HRM-LAMP was found to be 6.4 × 10^-4 ng/μL (3.79 copies/μL) of T. pallidum. The specificity was evaluated using seven different bacterial species, and the developed method was 100% specific in detecting T. pallidum. A total of 64 blood samples of T. pallidum suspected cases were used to validate the assay method. The clinical validation showed that the assay was 96.43% sensitive and 100% specific in detecting syphilis. Thus, the developed method was more rapid and sensitive than other available methods and provides a multigene-based diagnostic approach to detect T. pallidum.

Combination of mutagenesis and adaptive evolution to engineer salt-tolerant and aroma-producing yeast for soy sauce fermentation

BACKGROUND

The moromi fermentation of high-salt liquid-state fermentation (HLF) soy sauce is usually performed in high-brine solution (17-20%, w/w), which decreases the metabolic activity of aroma-producing yeast. To enhance the soy sauce flavors, increasing the salt tolerance of aroma-producing yeasts is very important for HLF soy sauce fermentation.

RESULTS

In the present study, atmospheric and room-temperature plasma (ARTP) was first used to mutate the aroma-producing yeast Wickerhamomyces anomalus, and the salt tolerant strains were obtained by selection of synthetic medium with a sodium chloride concentration of 18% (w/w). Furthermore, adaptive laboratory evolution (ALE) was used to improve the salt tolerance of the mutant strains. The results obtained indicated that the combination use of ARTP and ALE markedly increased the NaCl tolerance of the yeast by increasing the cellular accumulation of K+ and removal of cytosolic Na+ , in addition to promoting the production of glycerin and strengthening the integrity of the cell membrane and cell wall. In soy sauce fermentation, the engineered strains improved the physicochemical parameters of HLF soy sauce compared to those produced by the wild-type strain, and the engineered strains also increased the alcohol, acid and aldehyde production, and enriched the types of esters in the soy sauce.

CONCLUSION

The results of the present study indicated that the combination of ARTP mutagenesis and ALE significantly improved the salt tolerance of the aroma-producing yeast, and also enhanced the production of volatiles of HLF soy sauce. © 2021 Society of Chemical Industry.

The revenge of Zygosaccharomyces yeasts in food biotechnology and applied microbiology

Non-conventional yeasts refer to a huge and still poorly explored group of species alternative to the well-known model organism Saccharomyces cerevisiae. Among them, Zygosaccharomyces rouxii and the sister species Zygosaccharomyces bailii are infamous for spoiling food and beverages even in presence of several food preservatives. On the other hand, their capability to cope with a wide range of process conditions makes these yeasts very attractive factories (the so-called "ZygoFactories") for bio-converting substrates poorly permissive for the growth of other species. In balsamic vinegar Z. rouxii is the main yeast responsible for converting highly concentrated sugars into ethanol, with a preference for fructose over glucose (a trait called fructophily). Z. rouxii has also attracted much attention for the ability to release important flavor compounds, such as fusel alcohols and the derivatives of 4-hydroxyfuranone, which markedly contribute to fragrant and smoky aroma in soy sauce. While Z. rouxii was successfully proposed in brewing for producing low ethanol beer, Z. bailii is promising for lactic acid and bioethanol production. Recently, several research efforts exploited omics tools to pinpoint the genetic bases of distinctive traits in "ZygoFactories", like fructophily, tolerance to high concentrations of sugars, lactic acid and salt. Here, I provided an overview of Zygosaccharomyces industrially relevant phenotypes and summarized the most recent findings in disclosing their genetic bases. I suggest that the increasing number of genomes available for Z. rouxii and other Zygosaccharomyces relatives, combined with recently developed genetic engineering toolkits, will boost the applications of these yeasts in biotechnology and applied microbiology.

An innovative protein expression system using RNA polymerase I for large-scale screening of high-nucleic-acid content Saccharomyces cerevisiae strains

Saccharomyces cerevisiae is the preferred source of RNA derivatives, which are widely used as supplements for foods and pharmaceuticals. As the most abundant RNAs, the ribosomal RNAs (rRNAs) transcribed by RNA polymerase I (Pol I) have no 5' caps, thus cannot be translated to proteins. To screen high-nucleic-acid content yeasts more efficiently, a cap-independent protein expression system mediated by Pol I has been designed and established to monitor the regulatory changes of rRNA synthesis by observing the variation in the reporter genes expression. The elements including Pol I-recognized rDNA promoter, the internal ribosome entry site from cricket paralytic virus which can recruit ribosomes internally, reporter genes (URA3 and yEGFP3), oligo-dT and an rDNA terminator were ligated to a yeast episomal plasmid. This system based on the URA3 gene worked well by observing the growth phenotype and did not require the disruption of cap-dependent initiation factors. The fluorescence intensity of strains expressing the yEGFP3 gene increased and drifted after mutagenesis. Combined with flow cytometry, cells with higher GFP level were sorted out. A strain showed 58% improvement in RNA content and exhibited no sequence alteration in the whole expression cassette introduced. This study provides a novel strategy for breeding high-nucleic-acid content yeasts.

Tartary buckwheat protein hydrolysates enhance the salt tolerance of the soy sauce fermentation yeast Zygosaccharomyces rouxii

Supplementation of protein hydrolysate is an important strategy to improve the salt tolerance of soy sauce aroma-producing yeast. In the present study, Tartary buckwheat protein hydrolysates (BPHs) were prepared and separated by ultrafiltration into LM-1 (<1 kDa) and HM-2 (1-300 kDa) fractions. The supplementation of HM-2 fraction could significantly improve cell growth and fermentation of soy sauce aroma-producing yeast Zygosaccharomyces rouxii As2.180 under high salt (12%, w/w) conditions. However, the LM-1 fraction inhibited strain growth and fermentation. The addition of HM-2 promoted yeast cell accumulation of K⁺, removal of cytosolic Na⁺ and accumulation of glycerol. Furthermore, the HM-2 fraction improved the cell membrane integrity and mitochondrial membrane and decreased intracellular ROS accumulation of the strain. The above results indicated that the supplementation of BPHs with a molecular weight of 1-300 kDa is a potentially effective and feasible strategy for improving the salt tolerance of soy sauce aroma-producing yeast Z. rouxii.