Synergistic effect of thioredoxin and its reductase from Kluyveromyces marxianus on enhanced tolerance to multiple lignocellulose-derived inhibitors

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.

Kluyveromyces marxianus as a microbial cell factory for lignocellulosic biomass valorisation

The non-conventional yeast Kluyveromyces marxianus is widely used for several biotechnological applications, mainly due to its thermotolerance, high growth rate, and ability to metabolise a wide range of sugars. These cell traits are strategic for lignocellulosic biomass valorisation and strain diversity prompts the development of robust chassis, either with improved tolerance to lignocellulosic inhibitors or ethanol. This review summarises bioethanol and value-added chemicals production by K. marxianus from different lignocellulosic biomasses. Moreover, metabolic engineering and process optimization strategies developed to expand K. marxianus potential are also compiled, as well as studies reporting cell mechanisms to cope with lignocellulosic-derived inhibitors. The main lignocellulosic-based products are bioethanol, representing 71% of the reports, and xylitol, representing 17% of the reports. K. marxianus also proved to be a good chassis for lactic acid and volatile compounds production from lignocellulosic biomass, although the literature on this matter is still scarce. The increasing advances in genome editing tools and process optimization strategies will widen the K. marxianus-based portfolio products.

How adaptive laboratory evolution can boost yeast tolerance to lignocellulosic hydrolyses

The yeast Saccharomyces cerevisiae is an excellent candidate for establishing cell factories to convert lignocellulosic biomass into chemicals and fuels. To enable this technology, yeast robustness must be improved to withstand the fermentation inhibitors (e.g., weak organic acids, phenols, and furan aldehydes) resulting from biomass pretreatment and hydrolysis. Here, we discuss how evolution experiments performed in the lab, a method commonly known as adaptive laboratory evolution (ALE), may contribute to lifting yeast tolerance against the inhibitors of lignocellulosic hydrolysates (LCHs). The key is that, through the combination of whole-genome sequencing and reverse engineering, ALE provides a robust platform for discovering and testing adaptive alleles, allowing to explore the genetic underpinnings of yeast responses to LCHs. We review the insights gained from past evolution experiments with S. cerevisiae in LCH inhibitors and propose experimental designs to optimise the discovery of genetic variants adaptive to biomass toxicity. The knowledge gathered through ALE projects is envisaged as a roadmap to engineer superior yeast strains for biomass-based bioprocesses.

Influence of prefoldin subunit 4 on the tolerance of Kluyveromyces marxianus to lignocellulosic biomass-derived inhibitors

BACKGROUND

Kluyveromyces marxianus is a potentially excellent host for microbial cell factories using lignocellulosic biomass, due to its thermotolerance, high growth rate, and wide substrate spectrum. However, its tolerance to inhibitors derived from lignocellulosic biomass pretreatment needs to be improved. The prefoldin complex assists the folding of cytoskeleton which relates to the stress tolerance, moreover, several subunits of prefoldin have been verified to be involved in gene expression regulation. With the presence of inhibitors, the expression of a gene coding the subunit 4 of prefoldin (KmPFD4), a possible transcription factor, was significantly changed. Therefore, KmPFD4 was selected to evaluate its functions in inhibitors tolerance.

RESULTS

In this study, the disruption of the prefoldin subunit 4 gene (KmPFD4) led to increased concentration of intracellular reactive oxygen species (ROS) and disturbed the assembly of actin and tubulin in the presence of inhibitors, resulting in reduced inhibitor tolerance. Nuclear localization of KmPFD4 indicated that it could regulate gene expression. Transcriptomic analysis showed that upregulated gene expression related to ROS elimination, ATP production, and NAD+ synthesis, which is a response to the presence of inhibitors, disappeared in KmPFD4-disrupted cells. Thus, KmPFD4 impacts inhibitor tolerance by maintaining integration of the cytoskeleton and directly or indirectly affecting the expression of genes in response to inhibitors. Finally, overexpression of KmPFD4 enhanced ethanol fermentation with a 46.27% improvement in productivity in presence of the inhibitors.

CONCLUSION

This study demonstrated that KmPFD4 plays a positive role in the inhibitor tolerance and can be applied for the development of inhibitor-tolerant platform strains.

Kluyveromyces marxianus: Current State of Omics Studies, Strain Improvement Strategy and Potential Industrial Implementation

Bioethanol is considered an excellent alternative to fossil fuels, since it importantly contributes to the reduced consumption of crude oil, and to the alleviation of environmental pollution. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over others, e.g., it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars); tolerate high temperature, toxins, and a wide range of pH values; and produce volatile short-chain ester. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species. These attributes make K. marxianus promising as an industrial host for the biosynthesis of biofuels and other valuable chemicals.

Metabolic Response of the Yeast Candida utilis During Enrichment in Selenium

Selenium (Se) was found to inhibit the growth of the yeast Candida utilis ATCC 9950. Cells cultured in 30 mg selenite/L supplemented medium could bind 1368 µg Se/g of dry weight in their structures. Increased accumulation of trehalose and glycogen was observed, which indicated cell response to stress conditions. The activity of antioxidative enzymes (glutathione peroxidase, glutathione reductase, thioredoxin reductase, and glutathione S-transferase) was significantly higher than that of the control without Se addition. Most Se was bound to water-insoluble protein fraction; in addition, the yeast produced 20–30 nm Se nanoparticles (SeNPs). Part of Se was metabolized to selenomethionine (10%) and selenocysteine (20%). The HPLC-ESI-Orbitrap MS analysis showed the presence of five Se compounds combined with glutathione in the yeast. The obtained results form the basis for further research on the mechanisms of Se metabolism in yeast cells.

The significance of proline on lignocellulose-derived inhibitors tolerance in Clostridium acetobutylicum ATCC 824

When lignocellulosic biomass was used for acetone-butanol-ethanol (ABE) fermentation, several lignocellulose-derived inhibitors, which are toxic to Clostridium acetobutylicum, were generated during acid hydrolysis process and seriously hindered the industrialization of lignocellulosic butanol. In this study, an engineered strain 824(proABC) with significantly improved tolerance to multiple lignocellulose-derived inhibitors (formic acid and phenolic compounds) was constructed by strengthening the proline biosynthesis. The engineered strain exhibited more effective synthesis ability of proline and scavenging ability of reactive oxygen species (ROS). Consequently, the butanol produced by 824(proABC) was 1-, 2.4- or 3.4-fold higher than that of the wild type strain when using the undetoxified hydrolysate of soybean straw, rice straw or corn straw as the substrate, respectively. Therefore, enhancing the proline biosynthesis can be used as an effective strategy to improve the tolerance of C. acetobutylicum to multiple lignocellulose-derived inhibitors, and 824(proABC) has great potential to produce butanol from undetoxified lignocellulosic hydrolysates.

Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways

BACKGROUND

Kluyveromyces marxianus, the known fastest-growing eukaryote on the earth, has remarkable thermotolerance and capacity to utilize various agricultural residues to produce low-cost bioethanol, and hence is industrially important to resolve the imminent energy shortage crisis. Currently, the poor ethanol tolerance hinders its operable application in the industry, and it is necessary to improve K. marxianus' ethanol resistance and unravel the underlying systematical mechanisms. However, this has been seldom reported to date.

RESULTS

We carried out a wild-type haploid K. marxianus FIM1 in adaptive evolution in 6% (v/v) ethanol. After 100-day evolution, the KM-100d population was obtained; its ethanol tolerance increased up to 10% (v/v). Interestingly, DNA analysis and RNA-seq analysis showed that KM-100d yeasts' ethanol tolerance improvement was not due to ploidy change or meaningful mutations, but founded on transcriptional reprogramming in a genome-wide range. Even growth in an ethanol-free medium, many genes in KM-100d maintained their up-regulation. Especially, pathways of ethanol consumption, membrane lipid biosynthesis, anti-osmotic pressure, anti-oxidative stress, and protein folding were generally up-regulated in KM-100d to resist ethanol. Notably, enhancement of the secretory pathway may be the new strategy KM-100d developed to anti-osmotic pressure, instead of the traditional glycerol production way in S. cerevisiae. Inferred from the transcriptome data, besides ethanol tolerance, KM-100d may also develop the ability to resist osmotic, oxidative, and thermic stresses, and this was further confirmed by the cell viability test. Furthermore, under such environmental stresses, KM-100d greatly improved ethanol production than the original strain. In addition, we found that K. marxianus may adopt distinct routes to resist different ethanol concentrations. Trehalose biosynthesis was required for low ethanol, while sterol biosynthesis and the whole secretory pathway were activated for high ethanol.

CONCLUSIONS

This study reveals that ethanol-driven laboratory evolution could improve K. marxianus' ethanol tolerance via significant up-regulation of multiple pathways including anti-osmotic, anti-oxidative, and anti-thermic processes, and indeed consequently raised ethanol yield in industrial high-temperature and high-ethanol circumstance. Our findings give genetic clues for further rational optimization of K. marxianus' ethanol production, and also partly confirm the positively correlated relationship between yeast's ethanol tolerance and production.