Understanding the tolerance of the industrial yeast Saccharomyces cerevisiae against a major class of toxic aldehyde compounds

Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage

BACKGROUND

In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT).

RESULTS

Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway.

CONCLUSIONS

These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.

Patulin Biodegradation Mechanism Study in Pichia guilliermondii S15-8 Based on PgSDR-A5D9S1

Patulin contamination has become a bottleneck problem in the safe production of fruit products, although biodegradation technology shows potential application value in patulin control. In the present study, the patulin biodegradation mechanism in a probiotic yeast, Pichia guilliermondii S15-8, was investigated. Firstly, the short-chain dehydrogenase PgSDR encoded by gene A5D9S1 was identified as a patulin degradation enzyme, through RNA sequencing and verification by qRT-PCR. Subsequently, the exogenous expression system of the degradation protein PgSDR-A5D9S1 in E. coli was successfully constructed and demonstrated a more significant patulin tolerance and degradation ability. Furthermore, the structure of PgSDR-A5D9S1 and its active binding sites with patulin were predicted via molecular docking analysis. In addition, the heat-excited protein HSF1 was predicted as the transcription factor regulating the patulin degradation protein PgSDR-A5D9S1, which may provide clues for the further analysis of the molecular regulation mechanism of patulin degradation. This study provides a theoretical basis and technical support for the industrial application of biodegradable functional strains.

Four ways of implementing robustness quantification in strain characterisation

BACKGROUND

In industrial bioprocesses, microorganisms are generally selected based on performance, whereas robustness, i.e., the ability of a system to maintain a stable performance, has been overlooked due to the challenges in its quantification and implementation into routine experimental procedures. This work presents four ways of implementing robustness quantification during strain characterisation. One Saccharomyces cerevisiae laboratory strain (CEN.PK113-7D) and two industrial strains (Ethanol Red and PE2) grown in seven different lignocellulosic hydrolysates were assessed for growth-related functions (specific growth rate, product yields, etc.) and eight intracellular parameters (using fluorescent biosensors).

RESULTS

Using flasks and high-throughput experimental setups, robustness was quantified in relation to: (i) stability of growth functions in response to the seven hydrolysates; (ii) stability of growth functions across different strains to establish the impact of perturbations on yeast metabolism; (iii) stability of intracellular parameters over time; (iv) stability of intracellular parameters within a cell population to indirectly quantify population heterogeneity. Ethanol Red was the best-performing strain under all tested conditions, achieving the highest growth function robustness. PE2 displayed the highest population heterogeneity. Moreover, the intracellular environment varied in response to non-woody or woody lignocellulosic hydrolysates, manifesting increased oxidative stress and unfolded protein response, respectively.

CONCLUSIONS

Robustness quantification is a powerful tool for strain characterisation as it offers novel information on physiological and biochemical parameters. Owing to the flexibility of the robustness quantification method, its implementation was successfully validated at single-cell as well as high-throughput levels, showcasing its versatility and potential for several applications.

Discovery of new strains for furfural degradation using adaptive laboratory evolution in Saccharomyces cerevisiae

In industrial production, the excessive discharge of furfural can pose harm to soil microorganisms, aquatic animals and plants, as well as humans. Therefore, it is crucial to develop efficient and cost-effective methods for degrading furfural in the environment. Currently, the use of Saccharomyces cerevisiae for furfural degradation in water has shown effectiveness, but there is a need to explore improved efficiency and tolerance in S. cerevisiae for this purpose. In this study, we isolated and evolved highly efficient furfural degradation strains, namely YBA_08 and F60C. These strains exhibited remarkable capabilities, degrading 59% and 99% furfural in the YPD medium after 72 h of incubation, significantly higher than the 31% achieved by the model strain S288C. Through analysis of the efficient degradation mechanism in the evolutionary strain F60C, we discovered a 326% increase in the total amount of NADH and NADPH. This increase likely promotes faster furfural degradation through intracellular aldehyde reductases. Moreover, the decrease in NADPH content led to a 406% increase in glutathione content at the background level, which protects cells from damage caused by reactive oxygen species. Mutations and differential expression related to cell cycle and cell wall synthesis were observed, enabling cell survival in the presence of furfural and facilitating rapid furfural degradation and growth recovery. Based on these findings, it is speculated that strains YBA_08 and F60C have the potential to contribute to furfural degradation in water and the production of furfuryl alcohol, ethanol, and FDCA in biorefinery processes.

ScEnSor Kit for Saccharomyces cerevisiae Engineering and Biosensor-Driven Investigation of the Intracellular Environment

In this study, the three-step build-transform-assess toolbox for real-time monitoring of the yeast intracellular environment has been expanded and upgraded to the two-module ScEnSor (S. cerevisiae Engineering + Biosensor) Kit. The Biosensor Module includes eight fluorescent reporters for the intracellular environment; three of them (unfolded protein response, pyruvate metabolism, and ethanol consumption) were newly implemented to complement the original five. The Genome-Integration Module comprises a set of backbone plasmids for the assembly of 1-6 transcriptional units (each consisting of promoter, coding sequence, and terminator) for efficient marker-free single-locus genome integration (in HO and/or X2 loci). Altogether, the ScEnSor Kit enables rapid and easy construction of strains with new transcriptional units as well as high-throughput investigation of the yeast intracellular environment.

Copy number variants impact phenotype-genotype relationships for adaptation of industrial yeast Saccharomyces cerevisiae

The industrial yeast Saccharomyces cerevisiae possesses a plastic genome enabling its adaptation to varied environment conditions. A more robust ethanologenic industrial yeast strain NRRL Y-50049 was obtained through laboratory adaptation that is resistant to 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF), a major class of toxic chemicals associated with lignocellulose-to-biofuel conversion. A significant amount of knowledge has been achieved in characterizing its tolerant phenotypes and molecular mechanisms of the resistance. Recent findings on a limited number of nonsynonymous SNP (single nucleotide polymorphism) detected in NRRL Y-50049 compared with its progenitor NRRL Y-12632 raised doubt of SNP roles in the tolerance adaptation. The genotype-phenotype relationship for yeast adaptation to the toxic chemicals is yet unclear. Here, we examine copy number variant (CNV) of the adapted strain NRRL Y-50049 to address phenotype-genotype relationships. As a background information, CNV of model strain S288C of the reference genome was also examined versus the industrial-type strain NRRL Y-12632. More than 200 CNVs, mostly duplication events, were detected in NRRL Y-12632 compared with the laboratory model strain S288C. Such enriched genetic background supports its more diversified phenotype response for the industrial yeast than the laboratory strain S288C. Comparing the two industrial strains, we found extra nine CNVs in the mitochondrial genome and 28 CNVs in the nuclear genome of NRRL Y-50049 versus its progenitor NRRL Y-12632. Continued DNA recombination event and high rate of CNV observed in NRRL Y-50049 versus its progenitor suggests that CNV is more impactful than SNP in association with phenotype-genotype relationships of yeast adaptation to the toxic chemical stress. COX1 and COB loci were defined as DNA recombination hotspots in the mitochondrial genome for the industrial yeast based on the high frequency of CNVs observed in these loci. KEY POINTS: • COX1 and COB loci are identified as DNA recombination hotspots for the industrial yeast. • The industrial yeast type strain NRRL Y-12632 possesses more CNVs vs the reference genome S288C. • CNV is more important than SNP on phenotype-genotype relationships for yeast adaptation.

Improving Lipid Production of Yarrowia lipolytica by the Aldehyde Dehydrogenase-Mediated Furfural Detoxification

Yarrowia lipolytica, the non-conventional yeast capable of high lipogenesis, is a microbial chassis for producing lipid-based biofuels and chemicals from renewable resources such as lignocellulosic biomass. However, the low tolerance of Y. lipolytica against furfural, a major inhibitory furan aldehyde derived from the pretreatment processes of lignocellulosic biomass, has restricted the efficient conversion of lignocellulosic hydrolysates. In this study, the furfural tolerance of Y. lipolytica has been improved by supporting its endogenous detoxification mechanism. Specifically, the endogenous genes encoding the aldehyde dehydrogenase family proteins were overexpressed in Y. lipolytica to support the conversion of furfural to furoic acid. Among them, YALI0E15400p (FALDH2) has shown the highest conversion rate of furfural to furoic acid and resulted in two-fold increased cell growth and lipid production in the presence of 0.4 g/L of furfural. To our knowledge, this is the first report to identify the native furfural detoxification mechanism and increase furfural resistance through rational engineering in Y. lipolytica. Overall, these results will improve the potential of Y. lipolytica to produce lipids and other value-added chemicals from a carbon-neutral feedstock of lignocellulosic biomass.

Cellulosic Ethanol Production Using a Dual Functional Novel Yeast

Reducing the cost of cellulosic ethanol production, especially for cellulose hydrolytic enzymes, is vital to growing a sustainable and efficient cellulosic ethanol industry and bio-based economy. Using an ethanologenic yeast able to produce hydrolytic enzymes, such as Clavispora NRRL Y-50464, is one solution. NRRL Y-50464 is fast-growing and robust, and tolerates inhibitory compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) associated with lignocellulose-to-fuel conversion. It produces three forms of β-glucosidase isozymes, BGL1, BGL2, and BGL3, and ferment cellobiose as the sole carbon source. These β-glucosidases exhibited desirable enzyme kinetic parameters and high levels of enzyme-specific activity toward cellobiose and many oligosaccharide substrates. They tolerate the product inhibition of glucose and ethanol, and are stable to temperature and pH conditions. These characteristics are desirable for more efficient cellulosic ethanol production by simultaneous saccharification and fermentation. NRRL Y-50464 provided the highest cellulosic ethanol titers and conversion rates at lower cellulase loadings, using either pure cellulose or agricultural residues, as so far reported in the literature. This review summarizes NRRL Y-50464 performance on cellulosic ethanol production from refined cellulose, rice straw, and corn stover processed in various ways, in the presence or absence of furfural and HMF. This dual functional yeast has potential to serve as a prototype for the development of next-generation biocatalysts. Perspectives on continued strain development and process engineering improvements for more efficient cellulosic ethanol production from lignocellulosic materials are also discussed.

Real-Time Monitoring of the Yeast Intracellular State During Bioprocesses With a Toolbox of Biosensors

Industrial fermentation processes strive for high robustness to ensure optimal and consistent performance. Medium components, fermentation products, and physical perturbations may cause stress and lower performance. Cellular stress elicits a range of responses, whose extracellular manifestations have been extensively studied; whereas intracellular aspects remain poorly known due to lack of tools for real-time monitoring. Genetically encoded biosensors have emerged as promising tools and have been used to improve microbial productivity and tolerance toward industrially relevant stresses. Here, fluorescent biosensors able to sense the yeast intracellular environment (pH, ATP levels, oxidative stress, glycolytic flux, and ribosome production) were implemented into a versatile and easy-to-use toolbox. Marker-free and efficient genome integration at a conserved site on chromosome X of Saccharomyces cerevisiae strains and a commercial Saccharomyces boulardii strain was developed. Moreover, multiple biosensors were used to simultaneously monitor different intracellular parameters in a single cell. Even when combined together, the biosensors did not significantly affect key physiological parameters, such as specific growth rate and product yields. Activation and response of each biosensor and their interconnection were assessed using an advanced micro-cultivation system. Finally, the toolbox was used to screen cell behavior in a synthetic lignocellulosic hydrolysate that mimicked harsh industrial substrates, revealing differences in the oxidative stress response between laboratory (CEN.PK113-7D) and industrial (Ethanol Red) S. cerevisiae strains. In summary, the toolbox will allow both the exploration of yeast diversity and physiological responses in natural and complex industrial conditions, as well as the possibility to monitor production processes.

Old yeasts, young beer-The industrial relevance of yeast chronological life span

Much like other living organisms, yeast cells have a limited life span, in terms of both the maximal length of time a cell can stay alive (chronological life span) and the maximal number of cell divisions it can undergo (replicative life span). Over the past years, intensive research revealed that the life span of yeast depends on both the genetic background of the cells and environmental factors. Specifically, the presence of stress factors, reactive oxygen species, and the availability of nutrients profoundly impact life span, and signaling cascades involved in the response to these factors, including the target of rapamycin (TOR) and cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) pathways, play a central role. Interestingly, yeast life span also has direct implications for its use in industrial processes. In beer brewing, for example, the inoculation of finished beer with live yeast cells, a process called "bottle conditioning" helps improve the product's shelf life by clearing undesirable carbonyl compounds such as furfural and 2-methylpropanal that cause staling. However, this effect depends on the reductive metabolism of living cells and is thus inherently limited by the cells' chronological life span. Here, we review the mechanisms underlying chronological life span in yeast. We also discuss how this insight connects to industrial observations and ultimately opens new routes towards superior industrial yeasts that can help improve a product's shelf life and thus contribute to a more sustainable industry.

Combined adaptive evolution and transcriptomic profiles reveal aromatic aldehydes tolerance mechanisms in Yarrowia lipolytica

Yarrowia lipolytica is an efficient oleaginous yeast, whereas its activity is typically reduced by inhibitors present in lignocellulosic hydrolysate. Understanding the response mechanism of Y. lipolytica to hydrolysate inhibitors and developing inhibitor tolerant strains are vital to lignocellulose valorization by this promising species. In this study, through adaptive laboratory evolution on three representative aromatic aldehyde inhibitors, evolved strains were obtained. Fermentation phenotype suggested that aromatic aldehydes conversion was one main reason for high tolerance of adapted strains. Transcriptome profiling analysis and reverse metabolic engineering confirmed that overexpressing the aldehyde ketone reductase gene YALI0_B07117g and aldehyde dehydrogenase gene YALI0_B01298g effectively converted aromatic aldehyde to corresponding alcohols and acids. The potential degradation pathways for aromatic aldehyde inhibitors in Y. lipolytica XYL+ were then discussed. This study provided insights to the aromatic aldehyde degradation in Y. lipolytica and a reliable basis for the development of aromatic aldehyde tolerant strains.

Reasons for 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde resistance in Saccharomyces cerevisiae: current state of knowledge and perspectives for further improvements

Common toxic compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) are formed from dehydration of pentose and hexose, respectively, during decomposition of lignocellulosic biomass polymers. Furfural and HMF represent a major class of aldehyde toxic chemicals that inhibit microbial growth and interfere with subsequent fermentation for production of renewable fuels and chemicals. Understanding mechanisms of yeast tolerance aids development of tolerant strains as the most economic means to overcome the toxicity. This review updates current knowledge on yeast resistance to these toxic chemicals obtained from rapid advances in the past few years. Findings are largely exemplified by an adapted strain NRRL Y-50049 compared with its progenitor, the industrial yeast Saccharomyces cerevisiae type strain NRRL Y-12632. Newly characterized molecular phenotypes distinguished acquired resistant components of Y-50049 from innate stress response of its progenitor Y-12632. These findings also raised important questions on how to address more deeply ingrained changes in addition to local renovations for yeast adaptation. An early review on understandings of yeast tolerance to these inhibitory compounds is available and its contents omitted here to avoid redundancy. Controversial and confusing issues on identification of yeast resistance to furfural and HMF are further clarified aiming improved future research. Propositions and perspectives on research understanding molecular mechanisms of yeast resistance and future improvements are also presented. KEY POINTS: • Distinguished adapted resistance from innate stress response in yeast. • Defined pathway-based molecular phenotypes of yeast resistance. • Proposed genomic insight and perspectives on yeast resistance and adaptation.

Variable and dose-dependent response of Saccharomyces and non-Saccharomyces yeasts toward lignocellulosic hydrolysate inhibitors

Lignocellulosic hydrolysates will also contain compounds that inhibit microbial metabolism, such as organic acids, furaldehydes, and phenolic compounds. Understanding the response of yeasts toward such inhibitors is important to the development of different bioprocesses. In this work, the growth capacity of 7 industrial Saccharomyces cerevisiae and 7 non-Saccharomyces yeasts was compared in the presence of 3 different concentrations of furaldehydes (furfural and 5-hydroxymetil-furfural), organic acids (acetic and formic acids), and phenolic compounds (vanillin, syringaldehyde, ferulic, and coumaric acids). Then, Candida tropicalis JA2, Meyerozyma caribbica JA9, Wickerhamomyces anomalus 740, S. cerevisiae JP1, B1.1, and G06 were selected for fermentation in presence of acetic acid, HMF, and vanillin because they proved to be most tolerant to the tested compounds, while Spathaspora sp. JA1 because its xylose consumption rate. The results obtained showed a dose-dependent response of the yeasts toward the eight different inhibitors. Among the compared yeasts, S. cerevisiae strains presented higher tolerance than non-Saccharomyces, 3 of them with the highest tolerance among all. Regarding the non-Saccharomyces yeasts, C. tropicalis JA2 and W. anomalus 740 appeared as the most tolerant, whereas Spathaspora strains appeared very sensitive to the different compounds.

In-depth understanding of molecular mechanisms of aldehyde toxicity to engineer robust Saccharomyces cerevisiae

Aldehydes are ubiquitous electrophilic compounds that ferment microorganisms including Saccharomyces cerevisiae encounter during the fermentation processes to produce food, fuels, chemicals, and pharmaceuticals. Aldehydes pose severe toxicity to the growth and metabolism of the S. cerevisiae through a variety of toxic molecular mechanisms, predominantly via damaging macromolecules and hampering the production of targeted compounds. Compounds with aldehyde functional groups are far more toxic to S. cerevisiae than all other functional classes, and toxic potency depends on physicochemical characteristics of aldehydes. The yeast synthetic biology community established a design-build-test-learn framework to develop S. cerevisiae cell factories to valorize the sustainable and renewable biomass, including the lignin-derived substrates. However, thermochemically pretreated biomass-derived substrate streams contain diverse aldehydes (e.g., glycolaldehyde and furfural), and biological conversions routes of lignocellulosic compounds consist of toxic aldehyde intermediates (e.g., formaldehyde and methylglyoxal), and some of the high-value targeted products have aldehyde functional group (e.g., vanillin and benzaldehyde). Numerous studies comprehensively characterized both single and additive effects of aldehyde toxicity via systems biology investigations, and novel molecular approaches have been discovered to overcome the aldehyde toxicity. Based on those novel approaches, researchers successfully developed synthetic yeast cell factories to convert lignocellulosic substrates to valuable products, including aldehyde compounds. In this mini-review, we highlight the salient relationship of physicochemical characteristics and molecular toxicity of aldehydes, the molecular detoxification and macromolecules protection mechanisms of aldehydes, and the advances of engineering robust S. cerevisiae against complex mixtures of aldehyde inhibitors. KEY POINTS: • We reviewed structure-activity relationships of aldehyde toxicity on S. cerevisiae. • Two-tier protection mechanisms to alleviate aldehyde toxicity are presented. • We highlighted the strategies to overcome the synergistic toxicity of aldehydes.

A glimpse of potential transposable element impact on adaptation of the industrial yeast Saccharomyces cerevisiae

The adapted industrial yeast strain Saccharomyces cerevisiae NRRL Y-50049 is able to in situ detoxify major toxic aldehyde compounds derived from sugar conversion of lignocellulosic biomass while producing ethanol. Pathway-based studies on its mechanisms of tolerance have been reported previously, however, little is known about transposable element (TE) involvement in its adaptation to inhibitory compounds. This work presents a comparative dynamic transcription expression analysis in response to a toxic treatment between Y-50049 and its progenitor, an industrial type strain NRRL Y-12632, using a time-course study. At least 77 TEs from Y-50049 showed significantly increased expression compared with its progenitor, especially during the late lag phase. Sequence analysis revealed significant differences in TE sequences between the two strains. Y-50049 was also found to have a transposons of yeast 2 (Ty2) long terminal repeat-linked YAT1 gene showing significantly higher copy number changes than its progenitor. These results raise awareness of potential TE involvement in the adaptation of industrial yeast to the tolerance of toxic chemicals.

QTL analysis of natural Saccharomyces cerevisiae isolates reveals unique alleles involved in lignocellulosic inhibitor tolerance

Decoding the genetic basis of lignocellulosic inhibitor tolerance in Saccharomyces cerevisiae is crucial for rational engineering of bioethanol strains with enhanced robustness. The genetic diversity of natural strains present an invaluable resource for the exploration of complex traits of industrial importance from a pan-genomic perspective to complement the limited range of specialised, tolerant industrial strains. Natural S. cerevisiae isolates have lately garnered interest as a promising toolbox for engineering novel, genetically encoded tolerance phenotypes into commercial strains. To this end, we investigated the genetic basis for lignocellulosic inhibitor tolerance of natural S. cerevisiae isolates. A total of 12 quantitative trait loci underpinning tolerance were identified by next-generation sequencing linked bulk-segregant analysis of superior interbred pools. Our findings corroborate the current perspective of lignocellulosic inhibitor tolerance as a multigenic, complex trait. Apart from a core set of genetic variants required for inhibitor tolerance, an additional genetic background-specific response was observed. Functional analyses of the identified genetic loci revealed the uncharacterised ORF, YGL176C and the bud-site selection XRN1/BUD13 as potentially beneficial alleles contributing to tolerance to a complex lignocellulosic inhibitor mixture. We present evidence for the consideration of both regulatory and coding sequence variants for strain improvement.

Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations

Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.

Pathway-based signature transcriptional profiles as tolerance phenotypes for the adapted industrial yeast Saccharomyces cerevisiae resistant to furfural and HMF

The industrial yeast Saccharomyces cerevisiae has a plastic genome with a great flexibility in adaptation to varied conditions of nutrition, temperature, chemistry, osmolarity, and pH in diversified applications. A tolerant strain against 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) was successfully obtained previously by adaptation through environmental engineering toward development of the next-generation biocatalyst. Using a time-course comparative transcriptome analysis in response to a synergistic challenge of furfural-HMF, here we report tolerance phenotypes of pathway-based transcriptional profiles as components of the adapted defensive system for the tolerant strain NRRL Y-50049. The newly identified tolerance phenotypes were involved in biosynthesis superpathway of sulfur amino acids, defensive reduction-oxidation reaction process, cell wall response, and endogenous and exogenous cellular detoxification. Key transcription factors closely related to these pathway-based components, such as Yap1, Met4, Met31/32, Msn2/4, and Pdr1/3, were also presented. Many important genes in Y-50049 acquired an enhanced transcription background and showed continued increased expressions during the entire lag phase against furfural-HMF. Such signature expressions distinguished tolerance phenotypes of Y-50049 from the innate stress response of its progenitor NRRL Y-12632, an industrial type strain. The acquired yeast tolerance is believed to be evolved in various mechanisms at the genomic level. Identification of legitimate tolerance phenotypes provides a basis for continued investigations on pathway interactions and dissection of mechanisms of yeast tolerance and adaptation at the genomic level.

Protein expression analysis revealed a fine-tuned mechanism of in situ detoxification pathway for the tolerant industrial yeast Saccharomyces cerevisiae

Inhibitory compounds liberated from lignocellulose pretreatment are representative toxic chemicals that repress microbial growth and metabolism. A tolerant strain of the industrial yeast Saccharomyces cerevisiae is able to detoxify a major class of toxic compounds while producing ethanol. Knowledge on the yeast tolerance was mostly obtained by gene expression analysis and limited protein expression evidence is yet available underlying the yeast adaptation. Here we report a comparative protein expression profiling study on Y-50049, a tolerant strain compared with its parental industrial type strain Y-12632. We found a distinctive protein expression of glucose-6-phosphate dehydrogenase (Zwf1) in Y-50049 but not in Y-12632, in the relatively conserved glycolysis and pentose phosphate pathway (PPP) in response to a combinational challenge of 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF). A group of proteins with aldehyde reduction activity was uniquely induced expressed in Y-50049 but not in Y-12632. Such evidence allowed fine-tuning a mechanism of the renovated in situ detoxification by Y-50049. As the key protein, Zwf1 drove the glucose metabolism in favor of the oxidative branch of the PPP facilitating in situ detoxification of the toxic chemicals by Y-50049. The activated expression of Zwf1 generated the essential cofactor nicotinamide adenine dinucleotide phosphate (NADPH) enabling reduction of furfural and HMF through a group of aldehyde reduction enzymes. In return, the activate aldehyde reductions released desirable feedbacks of NADP⁺ stimulating continued oxidative activity of Zwf1. Thus, a well-maintained cofactor regeneration cycle was established to restore the cofactor imbalance caused by furfural-HMF. Challenges and perspectives on adaptation of significantly differential expressions of ribosomal proteins and other unique proteins are also discussed.

Functions of aldehyde reductases from Saccharomyces cerevisiae in detoxification of aldehyde inhibitors and their biotechnological applications

Bioconversion of lignocellulosic biomass to high-value bioproducts by fermentative microorganisms has drawn extensive attentions worldwide. Lignocellulosic biomass cannot be efficiently utilized by microorganisms, such as Saccharomyces cerevisiae, but has to be pretreated prior to fermentation. Aldehyde compounds, as the by-products generated in the pretreatment process of lignocellulosic biomass, are considered as the most important toxic inhibitors to S. cerevisiae cells for their growth and fermentation. Aldehyde group in the aldehyde inhibitors, including furan aldehydes, aliphatic aldehydes, and phenolic aldehydes, is identified as the toxic factor. It has been demonstrated that S. cerevisiae has the ability to in situ detoxify aldehydes to their corresponding less or non-toxic alcohols. This reductive reaction is catalyzed by the NAD(P)H-dependent aldehyde reductases. In recent years, detoxification of aldehyde inhibitors by S. cerevisiae has been extensively studied and a huge progress has been made. This mini-review summarizes the classifications and structural features of the characterized aldehyde reductases from S. cerevisiae, their catalytic abilities to exogenous and endogenous aldehydes and effects of metal ions, chemical protective additives, and salts on enzyme activities, subcellular localization of the aldehyde reductases and their possible roles in protection of the subcellular organelles, and transcriptional regulation of the aldehyde reductase genes by the key stress-response transcription factors. Cofactor preference of the aldehyde reductases and their molecular mechanisms and efficient supply pathways of cofactors, as well as biotechnological applications of the aldehyde reductases in the detoxification of aldehyde inhibitors derived from pretreatment of lignocellulosic biomass, are also included or supplemented in this mini-review.