Glycerol uptake and synthesis systems contribute to the osmotic tolerance of Kluyveromyces marxianus

Mechanism and improvement of yeast tolerance to biomass-derived inhibitors: A review

Lignocellulosic biomass is regarded as a potentially valuable second-generation biorefinery feedstock. Yeast has the ability to metabolize this substrate and convert it into fuel ethanol and an array of other chemical products. Nevertheless, during the pretreatment of lignocellulosic biomass, inhibitors (furanaldehydes, carboxylic acids, phenolic compounds, etc.) are generated, which impede the growth and metabolic activities of yeast cells. Consequently, developing yeast strains with enhanced tolerance to these inhibitors is a crucial technological objective, as it can significantly enhance the efficiency of lignocellulosic biorefineries. This review provides a concise overview of the process of inhibitor generation and the detrimental effects of these inhibitors on yeast. It also summarizes the current state of research on the mechanisms of yeast tolerance to these inhibitors, focusing specifically on recent advances in enhancing yeast tolerance to these inhibitors by rational and non-rational strategies. Finally, it discusses the current challenges and future research directions.

Enhanced multistress tolerance of Saccharomyces cerevisiae with the sugar transporter-like protein Stl1F427L mutation in the presence of glycerol

During microbial industrial production, microorganisms often face diverse stressors, including organic solvents, high salinity, and high sugar levels. Enhancing microorganism tolerance to such stresses is crucial for producing high-value-added products. Previous studies on the mechanisms of 2-phenylethanol (2-PE) tolerance in Saccharomyces cerevisiae revealed a potential connection between the sugar transporter-like protein (Stl1) mutation (F427L) and increased tolerance to high sugar and salt stress, suggesting a broader role in multistress tolerance. Herein, we showed that the Stl1F427L mutant strain (STL) exhibits significantly improved multistress tolerance in the presence of glycerol. Molecular dynamics simulations indicated that Stl1F427L may enhance glycerol molecular binding, resulting in a significant increase in the intracellular glycerol content of the mutant strain STL. Additionally, under multistress conditions, pyruvate and ergosterol levels and catalase (CAT) and superoxide dismutase (SOD) activities were significantly increased in the mutant strain STL compared with the control strain 5D. This resulted in a notable increase in cell membrane toughness and a decrease in intracellular reactive oxygen species levels. These findings highlight the mechanism by which Stl1F427L enhances S. cerevisiae tolerance to multistress. Importantly, they provide novel insights into and methodologies for improving the resilience of industrial microorganisms.

IMPORTANCE

Stl1F427L exhibits improved strain tolerance to multistress when adding glycerol, may enhance glycerol molecular binding, and can make a significant increase in intracellular glycerol content. It can reduce reactive oxygen species levels and increase ergosterol content. This paper provides novel insights and methods to get robust industrial microorganisms.

Physiological and transcriptome analyses of Kluyveromyces marxianus reveal adaptive traits in stress response

Kluyveromyces marxianus is a non-conventional yeast with outstanding physiological characteristics and a high potential for lignocellulosic ethanol production. However, achieving high ethanol productivity requires overcoming several biotechnological challenges due to the cellular inhibition caused by the inhibitors present in the medium. In this work, K. marxianus SLP1 was adapted to increase its tolerance to a mix of inhibitory compounds using the adaptive laboratory evolution strategy to study the adaptation and stress response mechanisms used by this non-Saccharomyces yeast. The fermentative and physiological parameters demonstrated that the adapted K. marxianus P8 had a better response against the synergistic effects of multiple inhibitors because it reduced the lag phase from 12 to 4 h, increasing the biomass by 40% and improving the volumetric ethanol productivity 16-fold than the parental K. marxianus SLP1. To reveal the effect of adaptation process in P8, transcriptome analysis was carried out; the result showed that the basal gene expression in P8 changed, suggesting the biological capability of K. marxianus to activate the adaptative prediction mechanism. Similarly, we carried out physiologic and transcriptome analyses to reveal the mechanisms involved in the stress response triggered by furfural, the most potent inhibitor in K. marxianus. Stress response studies demonstrated that P8 had a better physiologic response than SLP1, since key genes related to furfural transformation (ALD4 and ALD6) and stress response (STL1) were upregulated. Our study demonstrates the rapid adaptability of K. marxianus to stressful environments, making this yeast a promising candidate to produce lignocellulosic ethanol. KEY POINTS: • K. marxianus was adapted to increase its tolerance to a mix of inhibitory compounds • The basal gene expression of K. marxianus changed after the adaptation process • Adapted K. marxianus showed a better physiological response to stress by inhibitors • Transcriptome analyses revealed key genes involved in the stress response.

Improving glycerol utilization during high-temperature xylitol production with Kluyveromyces marxianus using a transient clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system

Glycerol is an ideal co-substrate for xylitol production with Kluyveromyces marxianus. This study demonstrated that K. marxianus catabolizes glycerol through the Gut1-Gut2 pathway instead of the previously speculated NADPH-dependent Gcy1-Dak1 pathway using the transient clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) system. Additionally, Utr1p was demonstrated to mediate NADPH generation through NADH phosphorylation. YZB392, which was constructed by integrating Utr1 into the Ypr1 site in the strain overexpressing NcXyl1 and CiGxf1 and harboring disrupted Xyl2, exhibited enhanced glycerol utilization for xylitol production (from 2.50- to 3.30- g/L after consuming 1 g/L glycerol). Fed-batch fermentation at 42 °C with YZB392 yielded 322.07 g/L xylitol, which is the highest known xylitol titer obtained via biological method. Feeding crude glycerol, xylose mother liquor, and corn steep liquor powder into a bioreactor resulted in the production of 235.69 g/L xylitol. This study developed a platform for xylitol production from industrial by-products.

Ergosterol production at elevated temperatures by Upc2-overexpressing Kluyveromyces marxianus using Jerusalem artichoke tubers as feedstock

Ergosterol is an important precursor in the pharmaceutical industry for the production of numerous drugs. In this study, Kluyveromyces marxianus that showed more potential for ergosterol production than some other yeasts was reported. The effects of transcription factors UPC2, MOT3, and ROX1 of K. marxianus on ergosterol synthesis were explored, and a Upc2-overexpressing strain produced 1.78 times more ergosterol (167.33 mg/L) than the wild-type strain (60.04 mg/L). A total of 239.98 mg/L ergosterol was produced when glucose was replaced with fructose to limit ethanol production. Enhanced aeration increased ergosterol titer from 63.09 mg/L to 128.46 mg/L at 42 °C. The ergosterol titer reached 304.37 mg/L in a shake flask at 37 °C, or 1124.38 and 948.32 mg/L at 37 °C and 42 °C, respectively, in a 5 L bioreactor, using Jerusalem artichoke tubers as the sole carbon source. This study establishes a platform for ergosterol biosynthesis using inexpensive materials.

RNA polymerase II-driven CRISPR-Cas9 system for efficient non-growth-biased metabolic engineering of Kluyveromyces marxianus

The thermotolerant yeast Kluyveromyces marxianus has gained significant attention in recent years as a promising microbial candidate for industrial biomanufacturing. Despite several contributions to the expanding molecular toolbox for gene expression and metabolic engineering of K. marxianus, there remains a need for a more efficient and versatile genome editing platform. To address this, we developed a CRISPR-based editing system that enables high efficiency marker-less gene disruptions and integrations using only 40 bp homology arms in NHEJ functional and non-functional K. marxianus strains. The use of a strong RNA polymerase II promoter allows efficient expression of gRNAs flanked by the self-cleaving RNA structures, tRNA and HDV ribozyme, from a single plasmid co-expressing a codon optimized Cas9. Implementing this system resulted in nearly 100% efficiency of gene disruptions in both NHEJ-functional and NHEJ-deficient K. marxianus strains, with donor integration efficiencies reaching 50% and 100% in the two strains, respectively. The high gRNA targeting performance also proved instrumental for selection of engineered strains with lower growth rate but improved polyketide biosynthesis by avoiding an extended outgrowth period, a common method used to enrich for edited cells but that fails to recover advantageous mutants with even slightly impaired fitness. Finally, we provide the first demonstration of simultaneous, markerless integrations at multiple loci in K. marxianus using a 2.6 kb and a 7.6 kb donor, achieving a dual integration efficiency of 25.5% in a NHEJ-deficient strain. These results highlight both the ease of use and general robustness of this system for rapid and flexible metabolic engineering in this non-conventional yeast.

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RNAP II-driven tRNA-gRNA-HDV ribozyme cassette built for K. marxianus genome editing.

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Gene integrations up to 7.6 kb were achieved with only 40 bp homology sequences.

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Recovery of growth-biased modifications achievable as extended outgrowth not required.

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Application (ZWF1 and GPD1 knockouts) increased polyketide specific titers.

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Expressing two unique gRNAs from one cassette enabled integrations at separate loci.

Insights into the glycerol transport of Yarrowia lipolytica

Cellular membranes separate cells from the environment and hence, from molecules essential for their survival. To overcome this hurdle, cells developed specialized transport proteins for the transfer of metabolites across these membranes. Crucial metabolites that need to cross the membrane of each living organism, are the carbon sources. While many organisms prefer glucose as a carbon source, the yeast Yarrowia lipolytica seems to favor glycerol over glucose. The fast growth of Y. lipolytica on glycerol and its flexible metabolism renders this yeast a fascinating organism to study the glycerol metabolism. Based on sequence similarities to the known fungal glycerol transporter ScStl1p and glycerol channel ScFps1p, ten proteins of Y. lipolytica were found that are potentially involved in glycerol uptake. To evaluate, which of these proteins is able to transport glycerol in vivo, a complementation assay with a glycerol transport‐deficient strain of Saccharomyces cerevisiae was performed. Six of the ten putative transporters enabled the growth of S. cerevisiae stl1Δ on glycerol and thus, were confirmed as glycerol transporting proteins. Disruption of the transporters in Y. lipolytica abolished its growth on 25 g/L glycerol, but the individual expression of five of the identified glycerol transporters restored growth. Surprisingly, the transporter‐disrupted Y. lipolytica strain retained its ability to grow on high glycerol concentrations. This study provides insight into the glycerol uptake of Y. lipolytica at low glycerol concentrations through the characterization of six glycerol transporters and indicates the existence of further mechanisms active at high glycerol concentrations.

Six proteins of Yarrowia lipolytica were identified as glycerol transporters.

Two channel proteins and four active transporters facilitated glycerol uptake.

Identified transporters are involved in glycerol uptake <25 g/L glycerol.

Indication of further glycerol transporters in Y. lipolytica was obtained.