Ethanol tolerance and membrane fatty acid adaptation in adh multiple and null mutants of Kluyveromyces lactis

Adaptation of the metolachlor-degrading fungus Trichoderma harzianum to the simultaneous presence of low-density polyethylene (LDPE) microplastics

Although it is known that microplastics (MPs) in soils cause a threat to this complex environment, the actual effects of MPs on soil microorganisms and their catabolic activities, particularly with the biodegradation of herbicides, remain unclear. Hence, the objective of this study was to investigate the effects of a simultaneous presence of metolachlor and low-density polyethylene (LDPE) microplastics on growth inhibition and adaptive responses of Trichoderma harzianum in soil microcosms. Using ergosterol content as an indicator of fungal biomass, it was observed that MPs alone had a marginal inhibitory effect on the growth of the fungus, whereas MET exhibited a dose-dependent inhibitory effect on T. harzianum. However, the presence of MPs did not influence the fungal transforming activity toward the herbicide. Conversely, analysis of lipid profiles in the presence of MPs and herbicides revealed a reduction in the overall fluidity of phospholipid fatty acids, primarily attributed to an increase in lysophospholipids. The activities of six extracellular enzymes in the soil, measured using methylumbelliferone-linked substrates, were significantly enhanced in the presence of MET. These findings contribute to a broader understanding of the alterations in fungal activity in soil resulting from the influence of MPs and MET.

Ethanol treatment for sterilization, concentration, and stabilization of a biodegradable plastic-degrading enzyme from Pseudozyma antarctica culture supernatant

Biodegradable plastics must be sufficiently stable to maintain functionality during use but need to be able to degrade rapidly after use. We previously reported that treatment with an enzyme named PaE, secreted by the basidiomycete yeast Pseudozyma antarctica can speed up this degradation. To facilitate the production of large quantities of PaE, here, we aimed to elucidate the optimal conditions of ethanol treatment for sterilization of the culture supernatant and for concentration and stabilization of PaE. The results showed that Pseudozyma antarctica completely lost its proliferating ability when incubated in ≥20% (v/v) ethanol. When the ethanol concentration was raised to 90% (v/v), PaE formed a precipitate; however, its activity was restored completely when the precipitate was dissolved in water. To reduce ethanol use, PaE was successfully concentrated and recovered by sequential ammonium sulfate precipitation and ethanol precipitation steps. Over 90% of the activity in the original culture supernatant was recovered and the specific activity was increased 3.4-fold. By preparing the enzyme solution at a final concentration of 20% (v/v) ethanol, about 60% of the initial activity was maintained at ambient temperature for over 6 months without growth of microbes. We conclude that ethanol treatment is effective for sterilization, concentration, and stabilization of PaE, and that concentrating PaE by sequential ammonium sulfate precipitation and ethanol precipitation substantially increases the PaE purity and decreases ethanol use.

Effects of limonene, n-decane and n-decanol on growth and membrane fatty acid composition of the microalga Botryococcus braunii

Botryococcus braunii is a promising microalga for the production of biofuels and other chemicals because of its high content of internal lipids and external hydrocarbons. However, due to the very thick cell wall of B. braunii, traditional chemical/physical downstream processing very often is not as effective as expected and requires high amounts of energy. In this cases, the application of two-phase aqueous-organic solvent systems could be an alternative to cultivate microalgae allowing for a simultaneous extraction of the valuable compounds without significant negative effects on cell growth. Two-phase systems have been applied before, however, there are no studies so far on the mechanisms used by microalgae to survive in contact with solvents present as a second-phase. In this study, the effects of the solvents limonene, n-decane and n-decanol on growth of the microalga B. braunii as well as the adaptive cell response in terms of their phospholipid fatty acid contents were analized. A concentration-dependent negative effect of all three solvents on cell growth was observed. Effects were accompanied by changes of the membrane fatty acid composition of the alga as manifested by a decrease of the unsaturation . In addition, an association was found between the solvent hydrophobicity (given as log octanol–water partition coefficient (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {P}_{O-W}$$\end{document}PO-W) values) and their toxic effects, whereby n-decanol and n-decane emerged as the most and least toxic solvent respectively. Among the tested solvents, the latter promises to be the most suitable for a two-phase extraction system.

Characterization of the transcription factor encoding gene, KlADR1: metabolic role in Kluyveromyces lactis and expression in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, Adr1 is a zinc-finger transcription factor involved in the transcriptional activation of ADH2. Deletion of KlADR1, its putative ortholog in Kluyveromyces lactis, led to reduced growth in glycerol, oleate and yeast extract-peptone medium suggesting, as in S. cerevisiae, its requirement for glycerol, fatty acid and nitrogen utilization. Moreover, growth comparison on yeast extract and peptone plates showed in K. lactis a KlAdr1-dependent growth trait not present in S. cerevisiae, indicating different metabolic roles of the two factors in their environmental niches. KlADR1 is required for growth under respiratory and fermentative conditions like KlADH, alcohol dehydrogenase genes necessary for metabolic adaptation during the growth transition. Using in-gel native alcohol dehydrogenase assay, we showed that this factor affected the Adh pattern by altering the balance between these activities. Since the activity most affected by KlAdr1 is KlAdh3, a deletion analysis of the KlADH3 promoter allowed the isolation of a DNA fragment through which KlAdr1 modulated its expression. The expression of the KlADR1-GFP gene allowed the intracellular localization of the factor in K. lactis and S. cerevisiae, suggesting in the two yeasts a common mechanism of KlAdr1 translocation under fermentative and respiratory conditions. Finally, the chimeric Kl/ScADR1 gene encoding the zinc-finger domains of KlAdr1 fused to the transactivating domains of the S. cerevisiae factor activated in Scadr1Δ the transcription of ADH2 in a ScAdr1-dependent fashion.

Functional roles of the fatty acid desaturases encoded by KlOLE1, FAD2 and FAD3 in the yeast Kluyveromyces lactis

Functional properties of cell membranes depend on their composition, particularly on the relative amount of saturated, unsaturated and polyunsaturated fatty acids present in the phospholipids. The aim of this study was to investigate the effect of cell membrane composition on cell fitness, adaptation and stress response in Kluyveromyces lactis. To this purpose, we have deleted the genes FAD2 and FAD3 encoding Δ12 and ω3 desaturases in Kluyveromyces lactis, thus generating mutant strains with altered fatty acid composition of membranes. These strains were viable and able to grow in stressing conditions like hypoxia and low temperature. Deletion of the Δ9 desaturase-encoding gene KlOLE1 resulted in lethality, suggesting that this enzyme has an essential role in this yeast. Transcription of the desaturase genes KlOLE1, FAD2 and FAD3 and cellular localization of the corresponding enzymes, have been studied under hypoxia and cold stress. Our findings indicate that expression of these desaturase genes and membrane composition were modulated by hypoxia and temperature stress, although the changes induced by these and other assayed conditions did not dramatically affect the general cellular fitness.

Arsenite response in Coccomyxa sp. Carn explored by transcriptomic and non-targeted metabolomic approaches

Arsenic is a toxic metalloid known to generate an important oxidative stress in cells. In the present study, we focused our attention on an alga related to the genus Coccomyxa, exhibiting an extraordinary capacity to resist high concentrations of arsenite and arsenate. The integrated analysis of high-throughput transcriptomic data and non-targeted metabolomic approaches highlighted multiple levels of protection against arsenite. Indeed, Coccomyxa sp. Carn induced a set of transporters potentially preventing the accumulation of this metalloid in the cells and presented a distinct arsenic metabolism in comparison to another species more sensitive to that compound, i.e. Euglena gracilis, especially in regard to arsenic methylation. Interestingly, Coccomyxa sp. Carn was characterized by a remarkable accumulation of the strong antioxidant glutathione (GSH). Such observation could explain the apparent low oxidative stress in the intracellular compartment, as suggested by the transcriptomic analysis. In particular, the high amount of GSH in the cell could play an important role for the tolerance to arsenate, as suggested by its partial oxidation into oxidized glutathione in presence of this metalloid. Our results therefore reveal that this alga has acquired multiple and original defence mechanisms allowing the colonization of extreme ecosystems such as acid mine drainages.

Glucose 6-phosphate and alcohol dehydrogenase activities are components of dynamic macromolecular depots structures

BACKGROUND

Membrane-associated respiratory complexes, purinosome and many intracellular soluble activities have reported to be organized in dynamic multi-component macromolecular complexes using native PAGE, 2D SDS-PAGE, electron and systematic microscopy and genome-wide GFP fusion library.

METHODS

In-gel staining assays, SDS-PAGE and LC-MSMS techniques were performed on cellular extracts to analyze, isolate and identify the proteins associated with glucose 6-phosphate dehydrogenase (G6PDH) and fermentative alcohol dehydrogenase (ADH) I isoform in both Kluyveromyces lactis and Saccharomyces cerevisiae yeasts.

RESULTS

Analysis of LC-MSMS data showed that a large number of components, belonging to glycolysis, pentose phosphate, folding and stress response pathways, were associated with G6PDH and Adh1 putative complexes and that a number of these proteins were identical in either network in both yeasts. However, comparison of in-gel staining assays for hexokinase, phosphoglucoisomerase, acetaldehyde dehydrogenase, ADH and G6PDH showed that, despite their identification in these structures, functional localization of these activities varied according to growth conditions and to NAD(P)+/NAD(P)H redox ratio.

CONCLUSIONS

Reported data show that intracellular proteins are organized in large dynamic 'depots' and the NAD(P)+/NAD(P)H redox balance is one of the major factors regulating the assembly and the re-assortment of components inside the different metabolic structures.

GENERAL SIGNIFICANCE

The aim of this work is directed towards the comprehension of the mechanisms involved in the assembly, organization, functioning and dynamic re-assortment of cellular components according to physiological and/or pathological conditions.

ER stress induced by the OCH1 mutation triggers changes in lipid homeostasis in Kluyveromyces lactis

In Kluyveromyces lactis yeast, OCH1 encodes for the α-1,6-mannosyltrasferase that adds the initial α-1,6-mannose to the outer-chains of N-glycoproteins. Kloch1-1 mutant cells showed altered calcium homeostasis and endoplasmic reticulum (ER) stress. Since ER plays a major role in lipid biosynthesis and lipid droplet (LD) formation, herein the impact of Och1p depletion on lipid homeostasis was investigated. Transcriptional profiles of genes involved in biosynthesis of fatty acids, their amount and composition changed in mutant cells. An increased amount of ergosterol was determined in these cells. Enhanced transcription of genes involved in both synthesis and mobilization of LDs was also found in Kloch1-1 cells, accompanied by a reduced amount of LDs. We provide evidence that ER alterations, determined by protein misfolding as a result of reduced N-glycosylation, induced altered lipid homeostasis in Kloch1-1 cells. Chemical chaperone 4-phenyl butyrate (4-PBA) slightly alleviated the LD phenotype in cells depleted of Och1p. Remarkably, complete suppression of ER stress, via increased expression of plasma membrane calcium channel subunit Mid1, fully restored lipid homeostasis in mutant cells. To further reinforce this finding, low numbers of LDs were observed in wild type cells when ER stress was triggered by DTT treatment.

Enhanced production of triterpenoid in submerged cultures of Antrodia cinnamomea with the addition of citrus peel extract

In recent years, Antrodia cinnamomea has become a well-known medicinal mushroom in Taiwan. Triterpenoids are considered one of the most biologically active components found in A. cinnamomea. The aim of this research is to investigate the feasibility of enhancing triterpenoid production in shake flask cultures of A. cinnamomea by adding citrus peel extract. As a result of its containing essential oils, citrus peel extract is inhibitory to mycelial growth. In the experiments, the appropriate adding time is determined to be on day 7. Of the various citrus peel extracts tested, tangerine proves to be the most effective in enhancing polyphenol and triterpenoid production. With an addition of 2% (v/v), the content and production of total polyphenols rises from 5.95 mg/g DW of the control and 56.73 mg/L to 23.52 mg/g DW and 224.39 mg/L, respectively, on day 28. The production of triterpenoids also increases from 99.93 to 1,028.02 mg/L, for more than a tenfold increase. An optimal level of tangerine peel additive is determined to be around 4%. Furthermore, when compared with the mycelia of the control culture, the profiles of the HPLC analysis show that the mycelia cultured with the tangerine-peel addition contain more kinds of triterpenoids. This study demonstrates that the addition of citrus peel extract effectively enhances the production of bioactive metabolites in the submerged cultures of A. cinnamomea.

Adaptive alterations in the fatty acids composition under induced oxidative stress in heavy metal-tolerant filamentous fungus Paecilomyces marquandii cultured in ascorbic acid presence

The ability of the heavy metal-tolerant fungus Paecilomyces marquandii to modulate whole cells fatty acid composition and saturation in response to IC50 of Cd, Pb, Zn, Ni, and Cu was studied. Cadmium and nickel caused the most significant growth reduction. In the mycelia cultured with all tested metals, with the exception of nickel, a rise in the fatty acid unsaturation was noted. The fungus exposure to Pb, Cu, and Ni led to significantly higher lipid peroxidation. P. marquandii incubated in the presence of the tested metals responded with an increase in the level of linoleic acid and escalation of electrolyte leakage. The highest efflux of electrolytes was caused by lead. In these conditions, the fungus was able to bind up to 100 mg g(-1) of lead, whereas the content of the other metals in the mycelium was significantly lower and reached from 3.18 mg g(-1) (Cu) to 15.21 mg g(-1) (Zn). Additionally, it was shown that ascorbic acid at the concentration of 1 mM protected fungal growth and prevented the changes in the fatty acid composition and saturation but did not alleviate lipid peroxidation or affect the increased permeability of membranes after lead exposure. Pro-oxidant properties of ascorbic acid in the copper-stressed cells manifested strong growth inhibition and enhanced metal accumulation as a result of membrane damage. Toxic metals action caused cellular modulations, which might contributed to P. marquandii tolerance to the studied metals. Moreover, these changes can enhance metal removal from contaminated environment.

Intracellular NADPH levels affect the oligomeric state of the glucose 6-phosphate dehydrogenase

In the yeast Kluyveromyces lactis, glucose 6-phosphate dehydrogenase (G6PDH) is detected as two differently migrating forms on native polyacrylamide gels. The pivotal metabolic role of G6PDH in K. lactis led us to investigate the mechanism controlling the two activities in respiratory and fermentative mutant strains. An extensive analysis of these mutants showed that the NAD(+)(H)/NADP(+)(H)-dependent cytosolic alcohol (ADH) and aldehyde (ALD) dehydrogenase balance affects the expression of the G6PDH activity pattern. Under fermentative/ethanol growth conditions, the concomitant activation of ADH and ALD activities led to cytosolic accumulation of NADPH, triggering an alteration in the oligomeric state of the G6PDH caused by displacement/release of the structural NADP(+) bound to each subunit of the enzyme. The new oligomeric G6PDH form with faster-migrating properties increases as a consequence of intracellular redox unbalance/NADPH accumulation, which inhibits G6PDH activity in vivo. The appearance of a new G6PDH-specific activity band, following incubation of Saccharomyces cerevisiae and human cellular extracts with NADP(+), also suggests that a regulatory mechanism of this activity through NADPH accumulation is highly conserved among eukaryotes.

Genetic structure of a novel biofuel-producing microorganism community

Biofuels are an important alternative, renewable source of energy in the face of the ongoing depletion of fossil fuels. Cheese whey is a dairy industry waste characterized by high lactose concentration, which represents a significant environmental problem. Bio-ethanol production by cheese whey could be an effective nonvegetable source for renewable energy production. Here, we report the isolation of a mixed microbial population, able to produce ethanol as main fermentation product from fermenting whey. The microbial consortium has been used to perform a batch fermentation of crude whey in both anoxic and hypoxic conditions. Maximum ethanol concentrations achieved in this study was obtained using the mixed culture in hypoxic conditions, grown at pH 4 and 30 °C, with ethanol production yield of 60 g/L. Our research has pointed out an alternative way to both dispose and valorize cheese whey, a dairy by-product that could cause water pollution and harm to the environment if not properly treated.

Knockout of fatty acid desaturase genes in Pichia pastoris GS115 and its effect on the fatty acid biosynthesis and physiological consequences

Unsaturated fatty acids (UFAs), including oleic acid (OA, C18:1n-9), linoleic acid (LA, C18:2n-6) and α-linolenic acid (ALA, C18:3n-3), are major components of membrane lipids in Pichia pastoris GS115. In order to clarify the biosynthesis pathway of UFAs on the molecular level and investigate their possible roles in growth and development of this strain, we here report modified strains with disrupted desaturase gene by homologous recombination. Gas chromatography analysis of fatty acid composition in the corresponding mutants confirmed that ∆(12)-desaturase encoded by Fad12 was responsible for the formation of LA, and ALA was synthesized by ∆(15)-desaturase encoded by Fad15. Simultaneous deletion of Fad9A and Fad9B was lethal and supplementation of OA could restore growth, indicating that possibly both Fad9A and Fad9B encoded ∆(9)-desaturase that converted SA into OA. Phenotypic analysis demonstrated that wild type and Fad15 mutant grew at almost the same rate, Fad12 mutant grew much slower than these two strains. Moreover, OA was positively correlated to cold tolerance and ethanol tolerance of GS115, whereas LA and ALA did not affect cold tolerance and ethanol tolerance of it. In addition, we showed that tolerance of GS115 to high concentration of methanol was independent of these three UFAs.

Application of comet assay for the assessment of DNA damage caused by chemical genotoxins in the dairy yeast Kluyveromyces lactis

Kluyveromyces lactis, also known as dairy yeast, has numerous applications in scientific research and practice. It has been approved as a GRAS (Generally Recognized As Safe) organism, a probiotic, a biotechnological producer of important enzymes at industrial scale and a bioremediator of waste water from the dairy industry. Despite these important practical applications the sensitivity of this organism to genotoxic substances has not yet been assessed. In order to evaluate the response of K. lactis cells to genotoxic agents we have applied several compounds with well-known cyto- and genotoxic activity. The method of comet assay (CA) widely used for the assessment of DNA damages is presented here with new special modifications appropriate for K. lactis cells. The comparison of the response of K. lactis to genotoxins with that of Saccharomyces cerevisiae showed that both yeasts, although considered close relatives, exhibit species-specific sensitivity toward the genotoxins examined.

Glycerol carbonate: a novel biosolvent with strong ionizing and dissociating powers

The activity of biocatalysts in nonaqueous solvents is related to the interaction of organic solvents with cells or enzymes. The behavior of proteins is strongly dependent on the protonation state of their ionizable groups, which ionization constants are greatly affected by the solvent. Due to the weak ionizing and dissociating powers of common organic solvents, the charge of the protein will change significantly when the protein is transferred from water to common organic solvents, resulting in protein denaturation. In this work, glycerol carbonate (GC) was synthesized, which ionizing and dissociating abilities were very close to those of water. Transesterification activities of Candida antarctica lipase B (CALB) in GC were comparable to those in water and remained constant during 4-week storage. Bacillus subtilis and Saccharomyecs cerevisiae were cultured in liquid media containing GC with test tubes. In the medium containing low GC concentration, Bacillus subtilis and Saccharomyecs cerevisiae grew well as in a medium containing no organic solvent, but, in the medium containing high GC concentration, the growth of Bacillus subtilis and Saccharomyecs cerevisiae was suppressed. The results suggested that GC is a potential biosolvent, which has great significance to biocatalysis in nonaqueous solvents.

A dual signalling pathway for the hypoxic expression of lipid genes, dependent on the glucose sensor Rag4, is revealed by the analysis of the KlMGA2 gene in Kluyveromyces lactis

In the respiratory yeast Kluyveromyces lactis, little is known about the factors regulating the metabolic response to oxygen shortage. After searching for homologues of characterized Saccharomyces cerevisiae regulators of the hypoxic response, we identified a gene that we named KlMGA2, which is homologous to MGA2. The deletion of KlMGA2 strongly reduced both the fermentative and respiratory growth rate and altered fatty acid composition and the unsaturation index of membranes. The reciprocal heterologous expression of MGA2 and KlMGA2 in the corresponding deletion mutant strains suggested that Mga2 and KlMga2 are functional homologues. KlMGA2 transcription was induced by hypoxia and the glucose sensor Rag4 mediated the hypoxic induction of KlMGA2. Transcription of lipid biosynthetic genes KlOLE1, KlERG1, KlFAS1 and KlATF1 was induced by hypoxia and was dependent on KlMga2, except for KlOLE1. Rag4 was required for hypoxic induction of transcription for both KlMga2-dependent (KlERG1) and KlMga2-independent (KlOLE1) structural genes.

Surface properties and intracellular speciation revealed an original adaptive mechanism to arsenic in the acid mine drainage bio-indicator Euglena mutabilis

Euglena mutabilis is a protist ubiquitously found in extreme environments such as acid mine drainages which are often rich in arsenic. The response of E. mutabilis to this metalloid was compared to that of Euglena gracilis, a protist not found in such environments. Membrane fatty acid composition, cell surface properties, arsenic accumulation kinetics, and intracellular arsenic speciation were determined. The results revealed a modification in fatty acid composition leading to an increased membrane fluidity in both Euglena species under sublethal arsenic concentrations exposure. This increased membrane fluidity correlated to an induced gliding motility observed in E. mutabilis in the presence of this metalloid but did not affect the flagellar dependent motility of E. gracilis. Moreover, when compared to E. gracilis, E. mutabilis showed highly hydrophobic cell surface properties and a higher tolerance to water-soluble arsenical compounds but not to hydrophobic ones. Finally, E. mutabilis showed a lower accumulation of total arsenic in the intracellular compartment and an absence of arsenic methylated species in contrast to E. gracilis. Taken together, our results revealed the existence of a specific arsenical response of E. mutabilis that may play a role in its hypertolerance to this toxic metalloid.

KlHsl1 is a component of glycerol response pathways in the milk yeast Kluyveromyces lactis

In Saccharomyces cerevisiae, HSL1 (NIK1) encodes a serine-threonine protein kinase involved in cell cycle control and morphogenesis. Deletion of its putative orthologue in Kluyveromyces lactis, KlHSL1, gives rise to sensitivity to the respiratory inhibitor antimycin A (AA). Resistance to AA on glucose (Rag+ phenotype) is associated with genes (RAG) required for glucose metabolism/glycolysis. To understand the relationship between RAG and KlHSL1, rag and Klhsl1Δ mutant strains were investigated. The analysis showed that all the mutants contained a phosphorylated form of Hog1 and displayed an inability to synthesize/accumulate glycerol as a compatible solute. In addition, rag mutants also showed alterations in both cell wall and membrane fatty acids. The pleiotropic defects of these strains indicate that a common pathway regulates glucose utilization and stress response mechanisms, suggesting impaired adaptation of the plasma membrane/cell wall during the respiratory-fermentative transition. KlHsl1 could be the link between these adaptive pathways and the morphogenetic checkpoint.

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

We have designed an experimental/computational framework for studying complex phenotypes in bacteria.

Our framework relies on whole-genome fitness profiling coupled with a module-level analysis to discover pathways that directly affect fitness.

As a proof-of-principle, we studied ethanol tolerance in Escherichia coli and we identified key pathways that contribute to this phenotype.

We then validated our findings through genetic manipulations, gene-expression profiling, metabolite-level measurements, and stable-isotope labeling.

Elucidating the genetic basis of complex phenotypes remains a fundamental challenge in biology. We have developed a systematic framework for comprehensive genetic analysis of microbial phenotypes. Our approach combines the power of fitness profiling (Girgis et al, 2007; Amini et al, 2009) with the sensitivity of module-level analysis (Goodarzi et al, 2009a) to identify key genetic modules that directly affect a phenotype under study. We applied our technology to ethanol tolerance, a complex phenotype with broad industrial relevance. Ethanol affects a variety of cellular components and pathways, including but not limited to membrane integrity (Dombek and Ingram, 1984), enzyme activities (Millar et al, 1982), and proton flux (D'Amore et al, 1990). Given the diversity of targets, the emergence of ethanol tolerance requires modifications to multiple pathway (D'Amore and Stewart, 1987).

To reveal the genetic basis of ethanol tolerance in Escherichia coli, we used two high-coverage mutant libraries (a transposon library and an overexpression library) to assess the fitness consequences of single-locus perturbations. Each cell in our transposon library contains a random transposon insertion in its genome (Girgis et al, 2007); whereas the cells in the overexpression library carry 1–3 kb genomic fragments cloned into a cloning vector (Amini et al, 2009). We grew these libraries under mild (4% v/v) and harsh (5.5% v/v) ethanol concentrations. On growth, the abundance of each transposon insertion or overexpression mutant changes as a function of its fitness, a process that can be monitored through parallel genetic footprinting and microarray hybridization (Figure 1A). This results in a global fitness profile, where the contribution of each genetic locus to ethanol tolerance can be quantified in parallel. However, in the context of ethanol tolerance and other complex phenotypes, single-locus perturbations typically result in modest changes in fitness. Although these small differences can be amplified through multiple rounds of selection, the number of generations is limited as spontaneous beneficial mutations emerge in the population and cause strong biases in the resulting fitness profiles. To boost our analytical power without introducing these biases in the data, we used a module-level computational method to discover the pathways and components that are strongly associated with the data as opposed to focusing on the genes individually (Goodarzi et al, 2009a). Genes function in the context of pathways and modules and module-level analyses increase statistical power through combining information from multiple genes functioning as part of a given pathway (Subramanian et al, 2005).

The module-level analysis of the fitness scores from both libraries revealed a diverse set of pathways that have a direct function in ethanol tolerance. Some of these pathways, including heat-shock stress response and osmoregulation, are known modifiers of ethanol tolerance; whereas others such as acid-stress response and fimbrial structures are novel pathways. Among our findings was the important function of three regulatory proteins: FNR, ArcA, and CafA. Knocking out FNR/ArcA that upregulates aerobic respiration proteins and TCA cycle components results in a marked increase in ethanol tolerance. Similarly, knocking out CafA, a post-transcriptional regulator of alcohol dehydrogenase, is beneficial for tolerance. Given these observations, we hypothesized that selection for ethanol tolerance can result in higher ethanol degradation.

As a large fraction of discovered pathways belonged to central metabolism, we used metabolomics to evaluate our findings. To directly assess the metabolic consequences of adaptation to ethanol, we evolved ethanol-tolerant strains in minimal media plus glucose for ∼30 and 160 generations. We then compared the steady-state level of metabolites in these strains to that of the wild type (Figure 1B). In agreement with our fitness profiling results, we observed a significant increase in TCA cycle metabolites in one of our ethanol-tolerant strains. Higher concentrations of TCA cycle components along with a high free coenzyme A (CoA) to acetyl-coenzyme A (acetyl-CoA) ratio hinted at the capacity of this strain to metabolize ethanol. To test this hypothesis, we performed stable-isotope labeling on our ethanol-tolerant strain versus wild type. After growth on labeled ethanol, we measured the fraction of metabolites that were labeled at each timepoint (Figure 1B). Our results confirmed that the ethanol-tolerant strain has the capacity to consume ethanol through its conversion into acetyl-CoA and further assimilation in the TCA cycle.

By using a variety of systems-level approaches, we have been able to genetically dissect ethanol tolerance in E. coli. We have shown that fitness profiling, in combination with module-level analysis tools, can serve as a powerful approach for revealing the genetic basis of complex phenotypes. The fact that laboratory evolution ended up using the very modules that we discovered, highlights the biological and adaptive relevance of the proposed framework.

Understanding the genetic basis of adaptation is a central problem in biology. However, revealing the underlying molecular mechanisms has been challenging as changes in fitness may result from perturbations to many pathways, any of which may contribute relatively little. We have developed a combined experimental/computational framework to address this problem and used it to understand the genetic basis of ethanol tolerance in Escherichia coli. We used fitness profiling to measure the consequences of single-locus perturbations in the context of ethanol exposure. A module-level computational analysis was then used to reveal the organization of the contributing loci into cellular processes and regulatory pathways (e.g. osmoregulation and cell-wall biogenesis) whose modifications significantly affect ethanol tolerance. Strikingly, we discovered that a dominant component of adaptation involves metabolic rewiring that boosts intracellular ethanol degradation and assimilation. Through phenotypic and metabolomic analysis of laboratory-evolved ethanol-tolerant strains, we investigated naturally accessible pathways of ethanol tolerance. Remarkably, these laboratory-evolved strains, by and large, follow the same adaptive paths as inferred from our coarse-grained search of the fitness landscape.

Ethanol-induced changes in expression profiles of cell growth, fatty acid and desaturase genes of Mucor rouxii

We investigated the response of Mucor rouxii to ethanolic stress conditions. A differential response was found that was dependent on growth phase and ethanol concentration. 5% (v/v) ethanol showed an inhibitory effect on the mycelial growth of all stages. However, the ethanol sensitivity was specifically observed in active growing phases (12 and 21 h-grown cultures), in which the biomass and ratio of unsaturated/saturated fatty acids (UFA/SFA) decreased greatly after ethanol exposure compared to non-ethanol adding culture. With respect to different ethanol concentrations, M. rouxii was tolerant to low ethanol concentrations (about 1-3%, v/v) such that there was not much change in biomass and UFA/SFA ratio, in contrast to the 5% ethanol-added culture. We also showed the molecular basis of this response mechanism, demonstrating that expression of Delta(9)-, Delta(12)- and Delta(6)-desaturase genes, responsible for fatty acid desaturation in M. rouxii, were coordinately down-regulated upon exposure to ethanol stress.

Electrochemical insights into the ethanol tolerance of Saccharomyces cerevisiae

It is expected that intracellular redox activity may closely related to catabolic states of living cells, based on which a mediated electrochemical method has been proposed to measure the ethanol tolerance of the yeast Saccharomyces cerevisiae AS 3800. The couple menadione/ferricyanide was employed as a carrier mediator system, sensing intracellular redox activity. Microelectrode voltammetric method was introduced to assay the ferrocyanide accumulations arising from menadione mediated reduction of ferricyanide by the yeast. The mediated electrochemical study show that the maximal ethanol tolerance limit of S. cerevisiae is about 25% (v/v) ethanol, which is consistent with the result obtained by the conventional fermentative ability measurement. Moreover, the electrochemical method for the first time confirmed that the specific activities of the glycolytic and alcohologenic enzymes within intact living cells remained high by the presence of sublethal ethanol, which was only predicted by in vitro enzymatic assay and cannot be measured by conventional method. The new method can be used as an easy and rapid method to determine the maximal ethanol tolerance of yeast cells.

Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum

Clostridium thermocellum, a cellulolytic, thermophilic anaerobe, has potential for commercial exploitation in converting fibrous biomass to ethanol. However, ethanol concentrations above 1% (w/v) are inhibitory to growth and fermentation, and this limits industrial application of the organism. Recent work with ethanol-adapted strains suggested that protein changes occurred during ethanol adaptation, particularly in the membrane proteome. A two-stage Bicine-doubled sodium dodecyl sulfate-polyacrylamide gel electrophoresis protocol was designed to separate membrane proteins and circumvent problems associated with membrane protein analysis using traditional gel-based proteomics approaches. Wild-type and ethanol-adapted C. thermocellum membranes displayed similar spot diversity and approximately 60% of proteins identified from purified membrane fractions were observed to be differentially expressed in the two strains. A majority (73%) of differentially expressed proteins were down-regulated in the ethanol-adapted strain. Based on putative identifications, a significant proportion of these down-regulated proteins were involved with carbohydrate transport and metabolism. Approximately one-third of the up-regulated proteins in the ethanol-adapted species were associated with chemotaxis and signal transduction. Overall, the results suggested that membrane-associated proteins in the ethanol-adapted strain are either being synthesized in lower quantities or not properly incorporated into the cell membrane.

Influence of growth phase on the phospholipidic fatty acid composition of two marine bacterial strains in pure and mixed cultures

This in vitro study was conducted in order to determine the effects of hydrocarbons and growth phase on the phospholipid ester-linked fatty acid composition of two marine sedimentary hydrocarbon-degrading bacteria. These two strains, namely Corynebacterium sp. and Sphingomonas sp. 2MPII, were cultivated on either a simple soluble substrate (ammonium acetate) or a hydrocarbon (respectively n-eicosane and phenanthrene). The incubations were stopped at different times corresponding to point of lag (2 days), exponential (7 days) and stationary phases (21 and 56 days). The effects of growth phase and hydrophobic substrates were successfully demonstrated by a simple index, given as the sum of saturated fatty acids divided by the sum of unsaturated fatty acids ( summation operatorSFA/ summation operatorMUFA), ranging from 1.4 to 3, 0.3 to 0.6, and 0.5 to 1.0 for Corynebacterium sp., Sphingomonas sp. 2MPII, and mixed cultures, respectively. This result was validated by a principal component analysis. In pure cultures, the phospholipid fatty acid (PLFA) composition was strongly influenced by both the carbon source and the growth phase. Nevertheless, the two strains showed different "behaviors". For 2MPII, the main PLFA composition changes were observed at 2 days while they were progressive as a function of time for Corynebacterium sp. These differences could explain the evolution of PLFAs of mixed cultures.

Lipid analysis of the plasma membrane and mitochondria of brewer's yeast

The plasma membrane and mitochondria of bottom fermenting brewer's yeast obtained as a by-product of industrial beer production were isolated and the lipid fraction was analyzed. The phospholipid content accounted for 78 mg/g protein in the plasma membrane and 59 mg/g protein in the mitochondria. Major phospholipids in both preparations were phosphatidylinositol, phosphatidylcholine and phosphatidylethanolamine but their proportions differed significantly. In the plasma membrane phosphatidylinositol, and in the mitochondria phosphatidylcholine were present in the highest concentration (37 and 30%, respectively). The main classes of neutral lipids (triacylglycerols, ergosterol, squalene and steryl esters) were twice more abundant in the plasma membrane than in the mitochondria (61 and 33 mg/g protein, respectively). A characteristic of the neutral lipid composition of both organelles was the low content of ergosterol (12 and 7 mg/g protein, respectively) and a high content of squalene (25 and 22 mg/g protein). The main feature of the fatty acid composition of both organelles was the preponderance of saturated fatty acids (78 and 79%, respectively), among which palmitic acid was the principal one. The most expressed characteristics of lipid fractions of the analyzed plasma membranes and mitochondria, high concentration of squalene and preponderance of saturated fatty acids are the consequences of anaerobic growth conditions. The lack of oxygen had possibly the strongest effect on the lipid composition of the plasma membranes and mitochondria of bottom fermenting brewer's yeast.

Expression profiling of the response of Saccharomyces cerevisiae to 5-fluorocytosine using a DNA microarray

5-Fluorocytosine is a commonly used antifungal agent. It acts by inhibiting the synthesis of fungal DNA and protein. In order to understand the global response of Saccharomyces cerevisiae to changes in DNA and protein synthesis caused by 5-fluorocytosine, genome-wide transcript profiling following 5-fluorocytosine exposure was obtained. A total of 96 genes were identified as responsive to 25 microg/ml fluorocytosine treatment for 90 min, which caused approximately 17% specific growth inhibition. The transcript levels of 57 genes were increased more than 2-fold, while it was found that the transcript levels of the other 39 genes decreased to a similar extent. Genes involved in DNA repair, synthesis and replication represented the highest proportion of induced genes identified, which may account for the easily acquired resistance to 5-fluorocytosine. Two enzyme encoding genes CTS1 and EGT2, which function in the separation of daughter cells from their mother cells, were down-regulated by a factor of 3.7 and 10.2, respectively, indicating that 5-fluorocytosine may also inhibit the separation of fungal cells.