Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates

Strategic approaches for designing yeast strains as protein secretion and display platforms

Yeast has been established as a versatile platform for expressing functional molecules, owing to its well-characterized biology and extensive genetic modification tools. Compared to prokaryotic systems, yeast possesses advanced cellular mechanisms that ensure accurate protein folding and post-translational modifications. These capabilities are particularly advantageous for the expression of human-derived functional proteins. However, designing yeast strains as an expression platform for proteins requires the integration of molecular and cellular functions. By delving into the complexities of yeast-based expression systems, this review aims to empower researchers with the knowledge to fully exploit yeast as a functional platform to produce a diverse range of proteins. This review includes an exploration of the host strains, gene cassette structures, as well as considerations for maximizing the efficiency of the expression system. Through this in-depth analysis, the review anticipates stimulating further innovation in the field of yeast biotechnology and protein engineering.

Targeted microbial collaboration to enhance key flavor metabolites by inoculating Clostridium tyrobutyricum and Saccharomyces cerevisiae in the strong-flavor Baijiu simulated fermentation system

Ethyl hexanoate and ethyl butyrate are indispensable flavor metabolites in strong-flavor Baijiu (SFB), but batch production instability in fermenting grains can reduce the quality of distilled Baijiu. Biofortification of the fermentation process by designing a targeted microbial collaboration pattern is an effective method to stabilize the quality of Baijiu. In this study, we explored the metabolism under co-culture liquid fermentation with Clostridium tyrobutyricum DB041 and Saccharomyces cerevisiae YS219 and investigated the effects of inoculation with two functional microorganisms on physicochemical factors, flavor metabolites, and microbial communities in solid-state simulated fermentation of SFB for the first time. The headspace solid-phase microextraction-gas chromatography-mass spectrometry results showed that ethyl butyrate and ethyl hexanoate significantly increased in fermented grain. High-throughput sequencing analysis showed that Pediococcus, Lactobacillus, Weissella, Clostridium_sensu_stricto_12, and Saccharomyces emerged as the dominant microorganisms at the end of fermentation. Co-occurrence analysis showed that ethyl hexanoate and ethyl butyrate were significantly correlated (|r| > 0.5, P < 0.05) with a cluster of interactions dominated by lactic acid bacteria (Pediococcus, Lactobacillus, Weissella, and Lactococcus), which was driven by the functional C. tyrobutyricum and S. cerevisiae. Mantel test showed that moisture and reducing sugars were the main physicochemical factor affecting microbial collaboration (|r| > 0.7, P < 0.05). Taken together, the collaborative microbial pattern of inoculation with C. tyrobutyricum and S. cerevisiae showed positive results in enhancing typical flavor metabolites and the synergistic effects of microorganisms in SFB.

Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid-tolerant yeast, Issatchenkia orientalis. I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low-pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

A landing pad system for multicopy gene integration in Issatchenkia orientalis

The robust nature of the non-conventional yeast Issatchenkia orientalis allows it to grow under highly acidic conditions and therefore, has gained increasing interest in producing organic acids using a variety of carbon sources. Recently, the development of a genetic toolbox for I. orientalis, including an episomal plasmid, characterization of multiple promoters and terminators, and CRISPR-Cas9 tools, has eased the metabolic engineering efforts in I. orientalis. However, multiplex engineering is still hampered by the lack of efficient multicopy integration tools. To facilitate the construction of large, complex metabolic pathways by multiplex CRISPR-Cas9-mediated genome editing, we developed a bioinformatics pipeline to identify and prioritize genome-wide intergenic loci and characterized 47 gRNAs located in 21 intergenic regions. These loci are screened for guide RNA cutting efficiency, integration efficiency of a gene cassette, the resulting cellular fitness, and GFP expression level. We further developed a landing pad system using components from these well-characterized loci, which can aid in the integration of multiple genes using single guide RNA and multiple repair templates of the user's choice. We have demonstrated the use of the landing pad for simultaneous integrations of 2, 3, 4, or 5 genes to the target loci with efficiencies greater than 80%. As a proof of concept, we showed how the production of 5-aminolevulinic acid can be improved by integrating five copies of genes at multiple sites in one step. We have further demonstrated the efficiency of this tool by constructing a metabolic pathway for succinic acid production by integrating five gene expression cassettes using a single guide RNA along with five different repair templates, leading to the production of 9 g/L of succinic acid in batch fermentations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in a non-conventional yeast. This landing pad system will be a valuable tool for the metabolic engineering of I. orientalis.

Application of Clostridium butyricum, Rummeliibacillus suwonensis, and Issatchenkia orientalis for Nongxiangxing baijiu fermentation: Improves the microbial communities and flavor of upper fermented grain

Ethyl hexanoate and ethyl butyrate are essential to the flavor compounds in Nongxiangxing baijiu, but low levels of these two esters in upper fermented grains (FG) decreases the quality of upper distilled baijiu, representing the main challenge in Nongxiangxing baijiu production. This paper enhanced fermentation by inoculating functional Clostridium butyricum, Rummeliibacillus suwonensis, and Issatchenkia orientalis strains into upper FG. The results showed that the ethyl butyrate content in the upper FG increased significantly and the content of ethyl hexanoate did improve from the results of many determinations. High-throughput sequencing indicated that the dominant phyla in the FG were Firmicutes, Actinobacteriota, Proteobacteria, Ascomycota, and Basidiomycota. The canonical correspondence analysis (CCA) and person correlation network revealed the relationship between the microbial community, physicochemical environment, and flavor compounds. The temperature, oxygen, and acidity were closely related to the microbial community, while most flavor compounds were positively correlated with Caldicoprobacter, Caproiciproducens, Delftia, Hydrogenispora, Thermoactinomyces, Issatchenkia Bacillus, and Aspergillus. These results helped improve the quality of Nongxiangxing baijiu.

Enhanced protein degradation by black soldier fly larvae (Hermetia illucens L.) and its gut microbes

Black soldier fly larvae (BSFL) can convert a variety of organic wastes into biomass, and its gut microbiota are involved in this process. However, the role of gut microbes in the nutrient metabolism of BSFL is unclear. In this study, germ-free BSFL (GF) and gnotobiotic BSFL (GB) were evaluated in a high-protein artificial diet model. We used 16S rDNA sequencing, ITS1 sequencing, and network analysis to study gut microbiota in BSFL that degrade proteins. The protein reduction rate of the GB BSFL group was significantly higher (increased by 73.44%) than that of the GF BSFL group. The activity of gut proteinases, such as trypsin and peptidase, in the GB group was significantly higher than the GF group. The abundances of different gut microbes, including Pseudomonas spp., Orbus spp. and Campylobacter spp., were strongly correlated with amino acid metabolic pathways. Dysgonomonas spp. were strongly correlated with protein digestion and absorption. Issatchenkia spp. had a strong correlation with pepsin activity. Campylobacter spp., Pediococcus spp. and Lactobacillus spp. were strongly correlated with trypsin activity. Lactobacillus spp. and Bacillus spp. were strongly correlated with peptidase activity. Gut microbes such as Issatchenkia spp. may promote the gut proteolytic enzyme activity of BSFL and improve the degradation rate of proteins. BSFL protein digestion and absorption involves gut microbiota that have a variety of functions. In BSFL the core gut microbiota help complete protein degradation. These results demonstrate that core gut microbes in BSFL are important in protein degradation.

Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories

Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.