Improved Stress Tolerance of Saccharomyces cerevisiae by CRISPR-Cas-Mediated Genome Evolution

Induction of point and structural mutations in engineered yeast Saccharomyces cerevisiae improve carotenoid production

β-Carotene is an attractive compound and that its biotechnological production can be achieved by using engineered Saccharomyces cerevisiae. In a previous study, we developed a technique for the efficient establishment of diverse mutants through the introduction of point and structural mutations into the yeast genome. In this study, we aimed to improve β-carotene production by applying this mutagenesis technique to S. cerevisiae strain that had been genetically engineered for β-carotene production. Point and structural mutations were introduced into β-carotene-producing engineered yeast. The resulting mutants showed higher β-carotene production capacity than the parental strain. The top-performing mutant, HP100_74, produced 37.6 mg/L of β-carotene, a value 1.9 times higher than that of the parental strain (20.1 mg/L). Gene expression analysis confirmed an increased expression of multiple genes in the glycolysis, mevalonate, and β-carotene synthesis pathways. In contrast, expression of ERG9, which functions in the ergosterol pathway competing with β-carotene production, was decreased in the mutant strain. The introduction of point and structural mutations represents a simple yet effective method for achieving mutagenesis in yeasts. This technique is expected to be widely applied in the future to produce chemicals via metabolic engineering of S. cerevisiae.

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.

Enhanced antimicrobial activity of lactic acid bacteria through genome shuffling and genetic variability among shuffled strains

In this investigation, lactic acid bacteria (LAB) isolated from milk were tested for their antibacterial properties and improved the antimicrobial activity of these isolates using genome shuffling. A total of sixty-one isolates were found in eleven samples, which were then tested using the agar diffusion method for their antibacterial activity against Staphylococcus aureus, Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa. Thirty-one strains exhibited antibacterial activity against at least one of the tested pathogens, with an inhibitory zone's diameter varying between 15.0 and 24.0 mm. Two isolates that showed the highest antimicrobial activity were identified as Lactobacillus plantarum CIP 103151 and Lactobacillus plantarum JCM 1149 according to 16S rRNA analysis. In the present study, applying genome shuffling approach significantly enhanced the antibacterial activity of L. plantarum. The initial populations were obtained via ultraviolet irradiation and were treated using the protoplast fusion method. The ideal condition for the production of protoplasts was 15 mg/ml of lysozyme and 10 μg/ml of mutanolysin. After two rounds of fusion, ten recombinants exhibited a significant increase in the inhibition zones versus S. aureus, S. typhimurium, P. aeruginosa, and E. coli, reaching up to 1.34, 1.31, 1.37, and 1.37-fold increase in inhibitory zone respectively. Random Amplified Polymorphic DNA results showed clear differences in DNA banding patterns among the wild strain of L. plantarum CIP 103151 and the three selected shuffled strains using primers 1283 & OPA09. On the other hand, no change was obtained using primers OPD03 neither among the wild strain and the three recombinant strains nor among the three shuffled strains.

Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae

Saccharomyces cerevisiae has a long-standing history of biotechnological applications even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches. In this review, we highlight the recent findings in the field with a focus on omics studies of S. cerevisiae to investigate its stress tolerance in different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries as well as metabolic engineering. Omics data analysis is key to the identification of exploitable native genes/proteins/pathways in S. cerevisiae with the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.

A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation

Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.

Recent advances in yeast genome evolution with stress tolerance for green biological manufacturing

Green biological manufacturing is a revolutionary industrial model utilizing yeast as a significant microbial cell factory to produce biofuels and other biochemicals. However, biotransformation efficiency is often limited owing to several stress factors resulting from environmental changes or metabolic imbalance, leading to the slow growth of cells, compromised yield, and enhanced energy consumption. These factors make biological manufacturing competitively less economical. In this regard, minimizing the stress impact on microbial cell factories and strong robust performance have been an interesting area of interest in the last few decades. In this review, we focused on revealing the stress factors and their associated mechanisms for yeast in biological manufacturing. To improve yeast tolerance, rational and irrational strategies were introduced, and the molecular basis of genome evolution in yeast was also summarized. Furthermore, strategies of genome-directed evolution such as homology directed repair and nonhomologous end-joining, and the synthetic chromosome recombination and modification by LoxP-mediated evolution and their association with stress tolerance was highlighted. We hope that genome evolution provides new insights for solving the limitations of the natural phenotypes of microorganisms in industrial fermentation for the production of valuable compounds.

Precision targeting of food biofilm-forming genes by microbial scissors: CRISPR-Cas as an effective modulator

The abrupt emergence of antimicrobial resistant (AMR) bacterial strains has been recognized as one of the biggest public health threats affecting the human race and food processing industries. One of the causes for the emergence of AMR is the ability of the microorganisms to form biofilm as a defense strategy that restricts the penetration of antimicrobial agents into bacterial cells. About 80% of human diseases are caused by biofilm-associated sessile microbes. Bacterial biofilm formation involves a cascade of genes that are regulated via the mechanism of quorum sensing (QS) and signaling pathways that control the production of the extracellular polymeric matrix (EPS), responsible for the three-dimensional architecture of the biofilm. Another defense strategy utilized commonly by various bacteria includes clustered regularly interspaced short palindromic repeats interference (CRISPRi) system that prevents the bacterial cell from viral invasion. Since multigenic signaling pathways and controlling systems are involved in each and every step of biofilm formation, the CRISPRi system can be adopted as an effective strategy to target the genomic system involved in biofilm formation. Overall, this technology enables site-specific integration of genes into the host enabling the development of paratransgenic control strategies to interfere with pathogenic bacterial strains. CRISPR-RNA-guided Cas9 endonuclease, being a promising genome editing tool, can be effectively programmed to re-sensitize the bacteria by targeting AMR-encoding plasmid genes involved in biofilm formation and virulence to revert bacterial resistance to antibiotics. CRISPRi-facilitated silencing of genes encoding regulatory proteins associated with biofilm production is considered by researchers as a dependable approach for editing gene networks in various biofilm-forming bacteria either by inactivating biofilm-forming genes or by integrating genes corresponding to antibiotic resistance or fluorescent markers into the host genome for better analysis of its functions both in vitro and in vivo or by editing genes to stop the secretion of toxins as harmful metabolites in food industries, thereby upgrading the human health status.

Identification of Microproteins in Saccharomyces cerevisiae under Different Stress Conditions

Small open reading frame-encoded peptides (SEPs) are microproteins with a length of 100 amino acids or less, which may play a critical role in maintaining cell homeostasis under stress. Therefore, we used mass spectrometry-based proteomics to explore microproteins potentially involved in cellular stress responses in Saccharomyces cerevisiae. A total of 225 microproteins with 1920 unique peptides were identified under six culture conditions: normal, oxidation, starvation, ultraviolet radiation, heat shock, and heat shock with starvation. Among these microproteins, we found 70 SEPs with 75 unique peptides. The annotated microproteins are involved in stress-related processes, such as cell redox reactions, cell wall modification, protein folding and degradation, and DNA damage repair. It suggests that SEPs may also play similar functions under stress conditions. For example, SEP IP_008057, translated from a short coding sequence of YJL159W, may play a role in heat shock. This study identified stress-responsive SEPs in S. cerevisiae and provided valuable information to determine the functions of these proteins, which enrich the genome and proteome of S. cerevisiae and show clues to improving the stress tolerance of S. cerevisiae.

CRISPR-Cas technology a new era in genomic engineering

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CRISPR-Cas systems offer a flexible and easy-to-use molecular platform to precisely modify and control organisms' genomes in a variety of fields, from agricultural biotechnology to therapeutics.

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With CRISPR technology, crop genomes can be precisely edited in a shorter and more efficient approach compared to traditional breeding or classic mutagenesis.

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CRISPR-Cas system can be used to manage the fermentation process by addressing phage resistance, antimicrobial activity, and genome editing.

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CRISPR-Cas technology has opened up a new era in gene therapy and other therapeutic fields and given hope to thousands of patients with genetic diseases.

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Anti-CRISPR molecules are powerful tools for regulating the CRISPR-Cas systems.

The CRISPR-Cas systems have offered a flexible, easy-to-use platform to precisely modify and control the genomes of organisms in various fields, ranging from agricultural biotechnology to therapeutics. This system is extensively used in the study of infectious, progressive, and life-threatening genetic diseases for the improvement of quality and quantity of major crops and in the development of sustainable methods for the generation of biofuels. As CRISPR-Cas technology continues to evolve, it is becoming more controllable and precise with the addition of molecular regulators, which will provide benefits for everyone and save many lives. Studies on the constant growth of CRISPR technology are important due to its rapid development. In this paper, we present the current applications and progress of CRISPR-Cas genome editing systems in several fields of research, we further highlight the applications of anti-CRISPR molecules to regulate CRISPR-Cas gene editing systems, and we discuss ethical considerations in CRISPR-Cas applications.

Bioengineering for the industrial production of 2,3-butanediol by the yeast, Saccharomyces cerevisiae

Owing to issues, such as the depletion of petroleum resources and price instability, the development of biorefinery related technologies that produce fuels, electric power, chemical substances, among others, from renewable resources is being actively promoted. 2,3-Butanediol (2,3-BDO) is a key compound that can be used to produce various chemical substances. In recent years, 2,3-BDO production using biological processes has attracted extensive attention for achieving a sustainable society through the production of useful compounds from renewable resources. With the development of genetic engineering, metabolic engineering, synthetic biology, and other research field, studies on 2,3-BDO production by the yeast, Saccharomyces cerevisiae, which is safe and can be fabricated using an established industrial-scale cultivation technology, have been actively conducted. In this review, we sought to describe 2,3-BDO and its derivatives; discuss 2,3-BDO production by microorganisms, in particular S. cerevisiae, whose research and development has made remarkable progress; describe a method for separating and recovering 2,3-BDO from a microbial culture medium; and propose future prospects for the industrial production of 2,3-BDO by microorganisms.

Directed genome evolution driven by structural rearrangement techniques

Directed genome evolution simulates the process of natural evolution at the genomic level in the laboratory to generate desired phenotypes. Here we review the applications of recent technological advances in genome writing and editing to directed genome evolution, with a focus on structural rearrangement techniques. We highlight how these techniques can be used to generate diverse genotypes, and to accelerate the evolution of phenotypic traits. We also discuss the perspectives of directed genome evolution.

Stress modulation as a means to improve yeasts for lignocellulose bioconversion

The second-generation (2G) fermentation environment for lignocellulose conversion presents unique challenges to the fermentative organism that do not necessarily exist in other industrial fermentations. While extreme osmotic, heat, and nutrient starvation stresses are observed in sugar- and starch-based fermentation environments, additional pre-treatment-derived inhibitor stress, potentially exacerbated by stresses such as pH and product tolerance, exist in the 2G environment. Furthermore, in a consolidated bioprocessing (CBP) context, the organism is also challenged to secrete enzymes that may themselves lead to unfolded protein response and other stresses. This review will discuss responses of the yeast Saccharomyces cerevisiae to 2G-specific stresses and stress modulation strategies that can be followed to improve yeasts for this application. We also explore published -omics data and discuss relevant rational engineering, reverse engineering, and adaptation strategies, with the view of identifying genes or alleles that will make positive contributions to the overall robustness of 2G industrial strains. KEYPOINTS: • Stress tolerance is a key driver to successful application of yeast strains in biorefineries. • A wealth of data regarding stress responses has been gained through omics studies. • Integration of this knowledge could inform engineering of fit for purpose strains.

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.

From baker's yeast to genetically modified budding yeasts: the scientific evolution of bioethanol industry from sugarcane

The peculiarities of Brazilian fuel ethanol fermentation allow the entry of native yeasts that may dominate over the starter strains of Saccharomyces cerevisiae and persist throughout the sugarcane harvest. The switch from the use of baker's yeast as starter to selected budding yeasts obtained by a selective pressure strategy was followed by a wealth of genomic information that enabled the understanding of the superiority of selected yeast strains. This review describes how the process of yeast selection evolved in the sugarcane-based bioethanol industry, the selection criteria and recent advances in genomics that could advance the fermentation process. The prospective use of genetically modified yeast strains, specially designed for increased robustness and product yield, with special emphasis on those obtained by the CRISPR (clustered regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) genome-editing approach, is discussed as a possible solution to confer higher performance and stability to the fermentation process for fuel ethanol production.

Improvement of 2,3-butanediol tolerance in Saccharomyces cerevisiae by using a novel mutagenesis strategy

Although the yeast Saccharomyces cerevisiae has been used to produce various bio-based chemicals, including solvents and organic acids, most of these products inhibit yeast growth at high concentrations. In general, it is difficult to rationally improve stress tolerance in yeast by modifying specific genes, because many of the genes involved in stress response remain unidentified. Previous studies have reported that various forms of stress tolerance in yeast were improved by introducing random mutations, such as DNA point mutations and DNA structural mutations. In this study, we developed a novel mutagenesis strategy that allows for the simultaneous performance of these two types of mutagenesis to construct a yeast variant with high 2,3-butanediol (2,3-BDO) tolerance. The mutations were simultaneously introduced into S. cerevisiae YPH499, accompanied by a stepwise increase in the concentration of 2,3-BDO. The resulting mutant YPH499/pol3δ/BD_392 showed 4.9-fold higher cell concentrations than the parental strain after 96 h cultivation in medium containing 175 g/L 2,3-BDO. Afterwards, we carried out transcriptome analysis to characterize the 2,3-BDO-tolerant strain. Gene ontology enrichment analysis with RNA sequence data revealed an increase in expression levels of genes related to amino acid metabolic processes. Therefore, we hypothesize that the yeast acquired high 2,3-BDO tolerance by amino acid function. Our research provides a novel mutagenesis strategy that achieves efficient modification of the genome for improving tolerance to various types of stressors.

Yeast Cellular Stress: Impacts on Bioethanol Production

Bioethanol is the largest biotechnology product and the most dominant biofuel globally. Saccharomyces cerevisiae is the most favored microorganism employed for its industrial production. However, obtaining maximum yields from an ethanol fermentation remains a technical challenge, since cellular stresses detrimentally impact on the efficiency of yeast cell growth and metabolism. Ethanol fermentation stresses potentially include osmotic, chaotropic, oxidative, and heat stress, as well as shifts in pH. Well-developed stress responses and tolerance mechanisms make S. cerevisiae industrious, with bioprocessing techniques also being deployed at industrial scale for the optimization of fermentation parameters and the effective management of inhibition issues. Overlap exists between yeast responses to different forms of stress. This review outlines yeast fermentation stresses and known mechanisms conferring stress tolerance, with their further elucidation and improvement possessing the potential to improve fermentation efficiency.

Innovative Tools and Strategies for Optimizing Yeast Cell Factories

Metabolic engineering (ME) aims to develop efficient microbial cell factories that can produce a wide variety of valuable compounds, ideally at the highest yield and from various feedstocks. We summarize recent developments in ME methods for tailoring different yeast cell factories (YCFs). In particular, we highlight the most timely and cutting-edge molecular tools and strategies for biosynthetic pathway optimization (including genome-editing tools), combinatorial transcriptional and post-transcriptional engineering (cis/trans regulators), dynamic control of metabolic fluxes (e.g., rewiring of primary metabolism), and spatial reconfiguration of metabolic pathways. Finally, we discuss challenges and perspectives for adaptive laboratory evolution (ALE) of yeast to advance ME of microbial cell factories.

Development and Application of CRISPR/Cas in Microbial Biotechnology

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has been rapidly developed as versatile genomic engineering tools with high efficiency, accuracy and flexibility, and has revolutionized traditional methods for applications in microbial biotechnology. Here, key points of building reliable CRISPR/Cas system for genome engineering are discussed, including the Cas protein, the guide RNA and the donor DNA. Following an overview of various CRISPR/Cas tools for genome engineering, including gene activation, gene interference, orthogonal CRISPR systems and precise single base editing, we highlighted the application of CRISPR/Cas toolbox for multiplexed engineering and high throughput screening. We then summarize recent applications of CRISPR/Cas systems in metabolic engineering toward production of chemicals and natural compounds, and end with perspectives of future advancements.