Increased furfural tolerance due to overexpression of NADH-dependent oxidoreductase FucO in Escherichia coli strains engineered for the production of ethanol and lactate

Deletion of yghZ in Escherichia coli promotes growth in presence of furfural with xylose as carbon source

Thermo-acidic pretreatment of lignocellulosic biomass is required to make it amenable to microbial metabolism and results in generation of furfural due to breakdown of pentose sugars. Furfural is toxic to microbial metabolism and results in reduced microbial productivity and increased production costs. This study asks if deletion of yghZ gene which encodes a NADPH-dependent aldehyde reductase enzyme results in improved furfural tolerance in Escherichia coli host. The ∆yghZ strain-SSK201-was tested for tolerance to furfural in presence of 5% xylose as a carbon source in AM1 minimal medium. At 96 h and in presence of 1.0 g/L furfural, the culture harboring strain SSK201 displayed 4.5-fold higher biomass, 2-fold lower furfural concentration and 15.75-fold higher specific growth rate (µ) as compared to the parent strain SSK42. The furfural tolerance advantage of SSK201 was retained when the carbon source was switched to glucose in AM1 medium and was lost in rich LB medium. The findings have potential to be scaled up to a hydrolysate culture medium, which contains furan inhibitors and lack nutritionally rich components, under bioreactor cultivation and observe growth advantage of the ∆yghZ host. It harbors potential to generate robust industrial strains which can convert lignocellulosic carbon into metabolites of interest in a cost-efficient manner.

Mechanism of furfural toxicity and metabolic strategies to engineer tolerance in microbial strains

Lignocellulosic biomass represents a carbon neutral cheap and versatile source of carbon which can be converted to biofuels. A pretreatment step is frequently used to make the lignocellulosic carbon bioavailable for microbial metabolism. Dilute acid pretreatment at high temperature and pressure is commonly utilized to efficiently solubilize the pentose fraction by hydrolyzing the hemicellulose fibers and the process results in formation of furans-furfural and 5-hydroxymethyl furfural-and other inhibitors which are detrimental to metabolism. The presence of inhibitors in the medium reduce productivity of microbial biocatalysts and result in increased production costs. Furfural is the key furan inhibitor which acts synergistically along with other inhibitors present in the hydrolysate. In this review, the mode of furfural toxicity on microbial metabolism and metabolic strategies to increase tolerance is discussed. Shared cellular targets between furfural and acetic acid are compared followed by discussing further strategies to engineer tolerance. Finally, the possibility to use furfural as a model inhibitor of dilute acid pretreated lignocellulosic hydrolysate is discussed. The furfural tolerant strains will harbor an efficient lignocellulosic carbon to pyruvate conversion mechanism in presence of stressors in the medium. The pyruvate can be channeled to any metabolite of interest by appropriate modulation of downstream pathway of interest. The aim of this review is to emphasize the use of hydrolysate as a carbon source for bioproduction of biofuels and other compounds of industrial importance.

Potential xylose transporters regulated by CreA improved lipid yield and furfural tolerance in oleaginous yeast Saitozyma podzolica zwy-2-3

Lignocellulose's hydrolysate, a significant renewable source, contains xylose and furfural, making it challenging for industrial production of oleaginous yeast. On xylose fermentation with furfural treatment, OE::DN7263 and OE::DN7661 increased lipid yield and furfural tolerance versus WT, while, which of OE::CreA were decreased owing to CreA regulating DN7263 and DN7661 negatively. OE::CreA generated reactive oxygen species (ROS) causing oxidative damage. OE::DN7263, OE::DN7661, and ΔCreA reduced furfural via NADH; while ΔCreA produced less ROS and OE::DN7263, and OE::DN7661 scavenged ROS quickly, minimizing oxidative damage. Overall, CreA knockout increased DN7263 and DN7661 expression to facilitate xylose assimilation, enhancing NADH generation and ROS clearance. Finally, with mixed sugar fermentation, ΔCreA and OE::DN7263's biomass and lipid yield rose without furfural addition, while that of ΔCreA remained higher than WT after furfural treatment. These findings revealed how oleaginous yeast zwy-2-3 resisted furfural stress and indicated ΔCreA and OE::DN7263 might develop into robust industrial chassis strains.

Bioupgrading of the aqueous phase of pyrolysis oil from lignocellulosic biomass: a platform for renewable chemicals and fuels from the whole fraction of biomass

Pyrolysis, a thermal decomposition without oxygen, is a promising technology for transportable liquids from whole fractions of lignocellulosic biomass. However, due to the hydrophilic products of pyrolysis, the liquid oils have undesirable physicochemical characteristics, thus requiring an additional upgrading process. Biological upgrading methods could address the drawbacks of pyrolysis by utilizing various hydrophilic compounds as carbon sources under mild conditions with low carbon footprints. Versatile chemicals, such as lipids, ethanol, and organic acids, could be produced through microbial assimilation of anhydrous sugars, organic acids, aldehydes, and phenolics in the hydrophilic fractions. The presence of various toxic compounds and the complex composition of the aqueous phase are the main challenges. In this review, the potential of bioconversion routes for upgrading the aqueous phase of pyrolysis oil is investigated with critical challenges and perspectives.

Microbial tolerance engineering for boosting lactic acid production from lignocellulose

Lignocellulosic biomass is an attractive non-food feedstock for lactic acid production via microbial conversion due to its abundance and low-price, which can alleviate the conflict with food supplies. However, a variety of inhibitors derived from the biomass pretreatment processes repress microbial growth, decrease feedstock conversion efficiency and increase lactic acid production costs. Microbial tolerance engineering strategies accelerate the conversion of carbohydrates by improving microbial tolerance to toxic inhibitors using pretreated lignocellulose hydrolysate as a feedstock. This review presents the recent significant progress in microbial tolerance engineering to develop robust microbial cell factories with inhibitor tolerance and their application for cellulosic lactic acid production. Moreover, microbial tolerance engineering crosslinking other efficient breeding tools and novel approaches are also deeply discussed, aiming to providing a practical guide for economically viable production of cellulosic lactic acid.

Microbial detoxification of lignocellulosic biomass hydrolysates: Biochemical and molecular aspects, challenges, exploits and future perspectives

Valorization of lignocellulosic biomass (LB) has the potential to secure sustainable energy production without impacting food insecurity, whist relieving over reliance on finite fossil fuels. Agro-derived lignocellulosic residues such as wheat straw, switchgrass, rice bran, and miscanthus have gained relevance as feedstocks for the production of biofuels and chemicals. However, the microorganisms employed in fermentative conversion of carbohydrates to fuels and chemicals are unable to efficiently utilize the sugars derived from LB due to co-production of lignocellulose-derived microbial inhibitory compounds (LDMICs) during LB pretreatment. LDMICs impact microbial growth by inhibition of specific enzymes, cause DNA and cell membrane damage, and elicit cellular redox imbalance. Over the past decade, success has been achieved with the removal of LDMICs prior to fermentation. However, LDMICs removal by chemical processes is often accompanied by sugar losses, which negatively impacts the overall production cost. Hence, in situ removal of LDMICs by fermentative organisms during the fermentation process has garnered considerable attention as the "go-to" approach for economical LDMICs detoxification and bio-chemicals production. In situ removal of LDMICs has been pursued by either engineering more robust biocatalysts or isolating novel microbial strains with the inherent capacity to mineralize or detoxify LDMICs to less toxic compounds. While some success has been made along this line, efficient detoxification and robust production of target bio-chemicals in lignocellulosic hydrolysates (LHs) under largely anaerobic fermentative conditions remains a lingering challenge. Consequently, LB remains an underutilized substrate for bio-chemicals production. In this review, the impact of microbial LH detoxification on overall target molecule production is discussed. Further, the biochemical pathways and mechanisms employed for in situ microbial detoxification of furanic LDMICs [e.g., furfural and 5-hydroxymethylfurfural (HMF)] and phenolic LDMICs (e.g., syringaldehyde, p-coumaric acid, 4-hydroxybenzaldehyde, vanillin, and ferulic acid) are discussed. More importantly, metabolic engineering strategies for the development of LDMIC-tolerant and bio-chemicals overproducing strains and processes are highlighted.

Unraveling the mechanism of furfural tolerance in engineered Pseudomonas putida by genomics

As a dehydration product of pentoses in hemicellulose sugar streams derived from lignocellulosic biomass, furfural is a prevalent inhibitor in the efficient microbial conversion process. To solve this obstacle, exploiting a biorefinery strain with remarkable furfural tolerance capability is essential. Pseudomonas putida KT2440 (P. putida) has served as a valuable bacterial chassis for biomass biorefinery. Here, a high-concentration furfural-tolerant P. putida strain was developed via adaptive laboratory evolution (ALE). The ALE resulted in a previously engineered P. putida strain with substantially increased furfural tolerance as compared to wild-type. Whole-genome sequencing of the adapted strains and reverse engineering validation of key targets revealed for the first time that several genes and their mutations, especially for PP_RS19785 and PP_RS18130 [encoding ATP-binding cassette (ABC) transporters] as well as PP_RS20740 (encoding a hypothetical protein), play pivotal roles in the furfural tolerance and conversion of this bacterium. Finally, strains overexpressing these three striking mutations grew well in highly toxic lignocellulosic hydrolysate, with cell biomass around 9-, 3.6-, and two-fold improvement over the control strain, respectively. To our knowledge, this study first unravels the furan aldehydes tolerance mechanism of industrial workhorse P. putida, which provides a new foundation for engineering strains to enhance furfural tolerance and further facilitate the valorization of lignocellulosic biomass.

Enhanced tolerance of Cupriavidus necator NCIMB 11599 to lignocellulosic derived inhibitors by inserting NAD salvage pathway genes

Polyhydroxybutyrate (PHB) is a bio-based, biodegradable and biocompatible plastic that has the potential to replace petroleum-based plastics. Lignocellulosic biomass is a promising feedstock for industrial fermentation to produce bioproducts such as polyhydroxybutyrate (PHB). However, the pretreatment processes of lignocellulosic biomass lead to the generation of toxic byproducts, such as furfural, 5-HMF, vanillin, and acetate, which affect microbial growth and productivity. In this study, to reduce furfural toxicity during PHB production from lignocellulosic hydrolysates, we genetically engineered Cupriavidus necator NCIMB 11599, by inserting the nicotine amide salvage pathway genes pncB and nadE to increase the NAD(P)H pool. We found that the expression of pncB was the most effective in improving tolerance to inhibitors, cell growth, PHB production and sugar consumption rate. In addition, the engineered strain harboring pncB showed higher PHB production using lignocellulosic hydrolysates than the wild-type strain. Therefore, the application of NAD salvage pathway genes improves the tolerance of Cupriavidus necator to lignocellulosic-derived inhibitors and should be used to optimize PHB production.

Furfural Produces Dose-Dependent Attenuating Effects on Ethanol-Induced Toxicity in the Liver

Background: Alcohol-associated liver disease (ALD) increases the health burden worldwide, but effective drugs to prevent ALD are lacking. Furfural is a small molecule that can limit alcohol production in microorganisms and may have the capacity to attenuate ethanol-induced toxicity.

Methods: Human HepG2 cells were incubated with ethanol and furfural, and cell viability, NAD⁺/NADH ratio, and mitochondrial function assays were performed. RNA sequencing (RNA-seq) data were used to annotate enriched pathways, and these findings were confirmed by reverse transcription-quantitative PCR (RT–qPCR) and Western blotting. C57BL/6J mice were fed a Lieber-DeCarli liquid diet. After 4 weeks, biochemical analysis of mouse serum and histological analysis of mouse livers were performed.

Results: Different concentrations of furfural exerted different effects on mitochondria: low-dose furfural reduced reactive oxygen species (ROS) production, maintained mitochondrial transmembrane potential, and inhibited apoptosis pathway activation, while high-dose furfural led to the opposite effects. In mice, furfural mitigated transaminase increases and attenuated the lipid metabolism disorder that had been induced by ethanol.

Conclusion: Low-dose furfural reduced ethanol-induced toxicity in the liver. Consuming food or beverages containing the appropriate level of furfural when drinking alcohol may be a convenient and useful way to prevent ALD.

Finding of novel polyhydroxybutyrate producer Loktanella sp. SM43 capable of balanced utilization of glucose and xylose from lignocellulosic biomass

Polyhydroxybutyrate (PHB) is a potential substitute for plastics derived from fossil fuels, owing to its biodegradable and biocompatible properties. Lignocellulosic biomass could be used to reduce PHB production costs; however, the co-utilization of sugars, such as glucose and xylose, without catabolite repression is a difficult problem to be solved. Here, we selected a novel Loktanella sp. SM43 from a marine environment and optimized the conditions for PHB production. Loktanella sp. SM43 showed high PHB production (66.5% content) from glucose. When glucose and xylose were used together, this strain showed high utilization of both substrates compared to other high PHB-producers such as Halomonas sp. and Cupriavidus necator, which showed glucose preference. Loktanella sp. SM43 showed high growth and PHB production with lignocellulosic hydrolysates. When pine tree hydrolysates were used, PHB production was the highest at 3.66 ± 0.01 g/L, followed by Miscanthus (3.46 ± 0.09 g/L) and barley straw hydrolysate (3.36 ± 0.36 g/L). Overall, these results reveal the potential of Loktanella sp. SM43 to produce PHB using various lignocellulosic hydrolysates as feedstock and the first systematic study for PHB production with Loktanella sp. The approach of screening novel strains is a strategy to overcome co-utilization of sugars without genetic engineering.

Improved furfural tolerance in Escherichia coli mediated by heterologous NADH-dependent benzyl alcohol dehydrogenases

While lignocellulose is a promising source of renewable sugars for microbial fermentations, the presence of inhibitory compounds in typical lignocellulosic feedstocks, such as furfural, has hindered their utilisation. In Escherichia coli, a major route of furfural toxicity is the depletion of NADPH pools due to its use as a substrate by the YqhD enzyme that reduces furfural to its less toxic alcohol form. Here, we examine the potential of exploiting benzyl alcohol dehydrogenases as an alternative means to provide this same catalytic function but using the more abundant reductant NADH, as a strategy to increase the capacity for furfural removal. We determine the biochemical properties of three of these enzymes, from Pseudomonas putida, Acinetobacter calcoaceticus, and Burkholderia ambifaria, which all demonstrate furfural reductase activity. Furthermore, we show that the P. putida and B. ambifaria enzymes are able to provide substantial increases in furfural tolerance in vivo, by allowing more rapid conversion to furfuryl alcohol and resumption of growth. The study demonstrates that methods to seek alternative cofactor dependent enzymes can improve the intrinsic robustness of microbial chassis to feedstock inhibitors.

Structural and Biochemical Analysis of the Furan Aldehyde Reductase YugJ from Bacillus subtilis

NAD(H)/NADP(H)-dependent aldehyde/alcohol oxidoreductase (AAOR) participates in a wide range of physiologically important cellular processes by reducing aldehydes or oxidizing alcohols. Among AAOR substrates, furan aldehyde is highly toxic to microorganisms. To counteract the toxic effect of furan aldehyde, some bacteria have evolved AAOR that converts furan aldehyde into a less toxic alcohol. Based on biochemical and structural analyses, we identified Bacillus subtilis YugJ as an atypical AAOR that reduces furan aldehyde. YugJ displayed high substrate specificity toward 5-hydroxymethylfurfural (HMF), a furan aldehyde, in an NADPH- and Ni²⁺-dependent manner. YugJ folds into a two-domain structure consisting of a Rossmann-like domain and an α-helical domain. YugJ interacts with NADP and Ni²⁺ using the interdomain cleft of YugJ. A comparative analysis of three YugJ structures indicated that NADP(H) binding plays a key role in modulating the interdomain dynamics of YugJ. Noticeably, a nitrate ion was found in proximity to the nicotinamide ring of NADP in the YugJ structure, and the HMF-reducing activity of YugJ was inhibited by nitrate, providing insights into the substrate-binding mode of YugJ. These findings contribute to the characterization of the YugJ-mediated furan aldehyde reduction mechanism and to the rational design of improved furan aldehyde reductases for the biofuel industry.

Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: The proteomics-guided metabolic engineering

Pretreatment of lignocellulosic biomass is crucial for the release of biofermentable sugars for biofuels production, which could greatly alleviate the burgeoning environment and energy crisis caused by the massive usage of traditional fossil fuels. Pyrolysis is a cost-saving pretreatment process that can readily decompose biomass into levoglucosan, a promising anhydrosugar; however, many undesired toxic compounds inhibitory to downstream microbial fermentation are also generated during the pyrolysis, immensely impeding the bioconversion of levoglucosan-containing pyrolysate. Here, we took the first insight into the proteomic responses of a levoglucosan-utilizing and ethanol-producing Escherichia coli to three representative biomass-derived inhibitors, identifying large amounts of differentially expressed proteins (DEPs) that could guide the downstream metabolic engineering for the development of inhibitor-resistant strains. Fifteen up- and eight down-regulated DEPs were further identified as the biomarker stress-responsive proteins candidate for cellular tolerance to multiple inhibitors. Among these biomarker proteins, YcfR exhibiting the highest expression fold-change level was chosen as the target of overexpression to validate proteomics results and develop robust strains with enhanced inhibitor tolerance and fermentation performance. Finally, based on four plasmid-borne genes encoding the levoglucosan kinase, pyruvate decarboxylase, alcohol dehydrogenase, and protein YcfR, a new recombinant strain E. coli LGE-ycfR was successfully created, showing much higher acetic acid-, furfural-, and phenol-tolerance levels compared to the control without overexpression of ycfR. The specific growth rate, final cell density, ethanol concentration, ethanol productivity, and levoglucosan consumption rate of the recombinant were also remarkably improved. From the proteomics-guided metabolic engineering and phenotypic observations, we for the first time corroborated that YcfR is a stress-induced protein responsive to multiple biomass-derived inhibitors, and also developed an inhibitors-resistant strain that could produce bioethanol from levoglucosan in the presence of inhibitors of relatively high concentration. The newly developed E. coli LGE-ycfR strain that could eliminate the commonly-used costly detoxicification processes, is of great potential for the in situ cost-effective bioethanol production from the biomass-derived pyrolytic substrates.

A comprehensive review on microbial production of 1,2-propanediol: micro-organisms, metabolic pathways, and metabolic engineering

1,2-Propanediol is an important building block as a component used in the manufacture of unsaturated polyester resin, antifreeze, biofuel, nonionic detergent, etc. Commercial production of 1,2-propanediol through microbial biosynthesis is limited by low efficiency, and chemical production of 1,2-propanediol requires petrochemically derived routes involving wasteful power consumption and high pollution emissions. With the development of various strategies based on metabolic engineering, a series of obstacles are expected to be overcome. This review provides an extensive overview of the progress in the microbial production of 1,2-propanediol, particularly the different micro-organisms used for 1,2-propanediol biosynthesis and microbial production pathways. In addition, outstanding challenges associated with microbial biosynthesis and feasible metabolic engineering strategies, as well as perspectives on the future microbial production of 1,2-propanediol, are discussed.

Overexpression of Oxidoreductase YghA Confers Tolerance of Furfural in Ethanologenic Escherichia coli Strain SSK42

Furfural is a common furan inhibitor formed due to dehydration of pentose sugars, like xylose, and acts as an inhibitor of microbial metabolism. Overexpression of NADH-specific FucO and deletion of NADPH-specific YqhD had been a successful strategy in the past in conferring tolerance against furfural in Escherichia coli, which highlights the importance of oxidoreductases in conferring tolerance against furfural. In a screen consisting of various oxidoreductases, dehydrogenases, and reductases, we identified the yghA gene as an overexpression target to confer tolerance against furfural. YghA preferably used NADH as a cofactor and had an apparent Km value of 0.03 mM against furfural. In the presence of 1 g liter-1 furfural and 10% xylose (wt/vol), yghA overexpression in an ethanologenic E. coli strain SSK42 resulted in an ethanol efficiency of ∼97%, with a 5.3-fold increase in ethanol titers compared to the control. YghA also exhibited activity against the less toxic inhibitor 5-hydroxymethyl furfural, which is formed due to dehydration of hexose sugars, and thus is a formidable target for overexpression in ethanologenic strain for fermentation of sugars in biomass hydrolysate. IMPORTANCE Lignocellulosic biomass represents an inexhaustible source of carbon for second-generation biofuels. Thermo-acidic pretreatment of biomass is performed to loosen the lignocellulosic fibers and make the carbon bioavailable for microbial metabolism. The pretreatment process also results in the formation of inhibitors that inhibit microbial metabolism and increase production costs. Furfural is a potent furan inhibitor that increases the toxicity of other inhibitors present in the hydrolysate. Thus, it is desirable to engineer furfural tolerance in E. coli for efficient fermentation of hydrolysate sugars.

Mutations in adaptively evolved Escherichia coli LGE2 facilitated the cost-effective upgrading of undetoxified bio-oil to bioethanol fuel

Levoglucosan is a promising sugar present in the lignocellulose pyrolysis bio-oil, which is a renewable and environment-friendly source for various value-added productions. Although many microbial catalysts have been engineered to produce biofuels and chemicals from levoglucosan, the demerits that these biocatalysts can only utilize pure levoglucosan while inhibited by the inhibitors co-existing with levoglucosan in the bio-oil have greatly limited the industrial-scale application of these biocatalysts in lignocellulose biorefinery. In this study, the previously engineered Escherichia coli LGE2 was evolved for enhanced inhibitor tolerance using long-term adaptive evolution under the stress of multiple inhibitors and finally, a stable mutant E. coli-H was obtained after ~ 374 generations' evolution. In the bio-oil media with an extremely acidic pH of 3.1, E. coli-H with high inhibitor tolerance exhibited remarkable levoglucosan consumption and ethanol production abilities comparable to the control, while the growth of the non-evolved strain was completely blocked even when the pH was adjusted to 7.0. Finally, 8.4 g/L ethanol was achieved by E. coli-H in the undetoxified bio-oil media with ~ 2.0% (w/v) levoglucosan, reaching 82% of the theoretical yield. Whole-genome re-sequencing to monitor the acquisition of mutations identified 4 new mutations within the globally regulatory genes rssB, yqhA, and basR, and the - 10 box of the putative promoter of yqhD-dgkA operon. Especially, yqhA was the first time to be revealed as a gene responsible for inhibitor tolerance. The mutations were all responsible for improved fitness, while basR mutation greatly contributed to the fitness improvement of E. coli-H. This study, for the first time, generated an inhibitor-tolerant levoglucosan-utilizing strain that could produce cost-effective bioethanol from the toxic bio-oil without detoxification process, and provided important experimental evidence and valuable genetic/proteinic information for the development of other robust microbial platforms involved in lignocellulose biorefining processes.

Principles and practice of designing microbial biocatalysts for fuel and chemical production

The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, non-food carbohydrates, such as lignocellulosic biomass, can be used to produce next generation biofuels, including cellulosic ethanol and other non-ethanol fuels like butanol. However, currently there is no native microorganism that can ferment all lignocellulosic sugars to fuel molecules. Thus, research is focused on engineering improved microbial biocatalysts for production of liquid fuels at high productivity, titer and yield. A clear understanding and application of the basic principles of microbial physiology and biochemistry are crucial to achieve this goal. In this review, we present and discuss the construction of microbial biocatalysts that integrate these principles with ethanol-producing Escherichia coli as an example of metabolic engineering. These principles also apply to fermentation of lignocellulosic sugars to other chemicals that are currently produced from petroleum.

Production of Ethylene Glycol from Glycerol Using an In Vitro Enzymatic Cascade

Glycerol is a readily available and inexpensive substance that is mostly generated during biofuel production processes. In order to ensure the viability of the biofuel industry, it is essential to develop complementing technologies for the resource utilization of glycerol. Ethylene glycol is a two-carbon organic chemical with multiple applications and a huge market. In this study, an artificial enzymatic cascade comprised alditol oxidase, catalase, glyoxylate/hydroxypyruvate reductase, pyruvate decarboxylase and lactaldehyde:propanediol oxidoreductase was developed for the production of ethylene glycol from glycerol. The reduced nicotinamide adenine dinucleotide (NADH) generated during the dehydrogenation of the glycerol oxidation product d-glycerate can be as the reductant to support the ethylene glycol production. Using this in vitro synthetic system with self-sufficient NADH recycling, 7.64 ± 0.15 mM ethylene glycol was produced from 10 mM glycerol in 10 h, with a high yield of 0.515 ± 0.1 g/g. The in vitro enzymatic cascade is not only a promising alternative for the generation of ethylene glycol but also a successful example of the value-added utilization of glycerol.

Deletion of pgi gene in E. coli increases tolerance to furfural and 5-hydroxymethyl furfural in media containing glucose-xylose mixture

BACKGROUND

Furfural and 5-hydroxymethyl furfural (5-HMF) are key furan inhibitors that are generated due to breakdown of lignocellulosic sugars at high temperature and acidic treatment conditions. Both furfural and 5-HMF act in a synergistic manner to inhibit microbial metabolism and resistance to both is a desirable characteristic for efficient conversion of lignocellulosic carbon to ethanol. Genetic manipulations targeted toward increasing cellular NADPH pools have successfully imparted tolerance against furfural and 5-HMF. In present study, deletion of pgi gene as a strategy to augment carbon flow through pentose phosphate pathway (PPP) was studied in ethanologenic Escherichia coli strain SSK101 to impart tolerance towards either furfural or 5-HMFor both inhibitors together.

RESULTS

A key gene of EMP pathway, pgi, was deleted in an ethanologenic E. coli strain SSK42 to yield strain SSK101. In presence of 1 g/L furfural in minimal AM1 media, the rate of biomass formation for strain SSK101 was up to 1.9-fold higher as compared to parent SSK42 strain, and it was able to clear furfural in half the time. Tolerance to inhibitor was associated with glucose as carbon source and not xylose, and the tolerance advantage of SSK101 was neutralized in LB media. Bioreactor studies were performed under binary stress of furfural and 5-HMF (1 g/L each) and different glucose concentrations in a glucose-xylose mixture with final sugar concentration of 5.5%, mimicking major components of dilute acid treated biomass hydrolysate. In the mixture having 6 g/L and 12 g/L glucose, SSK101 strain produced ~ 18 g/L and 20 g/L ethanol, respectively. Interestingly, the maximum ethanol productivity was better at lower glucose load with 0.46 g/(L.h) between 96 and 120 h, as compared to higher glucose load where it was 0.33 g/(L.h) between 144 and 168 h. Importantly, parent strain SSK42 did not exhibit significant metabolic activity under similar conditions of inhibitor load and sugar concentration.

CONCLUSIONS

E. coli strain SSK101 with pgi deletion had enhanced tolerance against both furfural and 5-HMF, which was associated with presence of glucose in media. Strain SSK101 also had improved fermentation characteristics under both hyperosmotic as well as binary stress of furfural and 5-HMF in media containing glucose-xylose mixture.

Recent developments in pretreatment technologies on lignocellulosic biomass: Effect of key parameters, technological improvements, and challenges

Lignocellulosic biomass is an inexpensive renewable source that can be used to produce biofuels and bioproducts. The recalcitrance nature of biomass hampers polysaccharide accessibility for enzymes and microbes. Several pretreatment methods have been developed for the conversion of lignocellulosic biomass into value-added products. However, these pretreatment methods also produce a wide range of secondary compounds, which are inhibitory to enzymes and microorganisms. The selection of an effective and efficient pretreatment method discussed in the review and its process optimization can significantly reduce the production of inhibitory compounds and may lead to enhanced production of fermentable sugars and biochemicals. Moreover, evolutionary and genetic engineering approaches are being used for the improvement of microbial tolerance towards inhibitors. Advancements in pretreatment and detoxification technologies may help to increase the productivity of lignocellulose-based biorefinery. In this review, we discuss the recent advancements in lignocellulosic biomass pretreatment technologies and strategies for the removal of inhibitors.

Chromosomal mutations in Escherichia coli that improve tolerance to nonvolatile side-products from dilute acid treatment of sugarcane bagasse

Lignocellulosic biomass provides attractive nonfood carbohydrates for the production of ethanol, and dilute acid pretreatment is a biomass-independent process for access to these carbohydrates. However, this pretreatment also releases volatile and nonvolatile inhibitors of fermenting microorganisms. To identify unique gene products contributing to sensitivity/tolerance to nonvolatile inhibitors, ethanologenic Escherichia coli strain LY180 was adapted for growth in vacuum-treated sugarcane bagasse acid hydrolysate (VBHz) lacking furfural and other volatile inhibitors. A mutant, strain AQ15, obtained after approximately 500 generations of growth in VBHz, grew and fermented the sugars in a medium with 50% VBHz. Comparative genome sequence analysis of strains AQ15 and LY180 revealed 95 mutations in strain AQ15. Six of these mutations were also found in strain SL112, an independent inhibitor-tolerant derivative of strain LY180. Among these six mutations, null mutations in mdh and bacA were identified as contributing factors to VBHz tolerance in strain AQ15, based on the genetic and physiological analysis. The deletion of either gene in strain LY180 increased tolerance to VBHz from approximately 30-50% (vol/vol). Considering the location and physiological role of the two enzymes in the cell, it is likely that the two enzymes contribute to the VBHz sensitivity of ethanologenic E. coli by different mechanisms.

Bioprospecting of Native Efflux Pumps To Enhance Furfural Tolerance in Ethanologenic Escherichia coli

Efficient microbial conversion of lignocellulose into valuable products is often hindered by the presence of furfural, a dehydration product of pentoses in hemicellulose sugar syrups derived from woody biomass. For a cost-effective lignocellulose microbial conversion, robust biocatalysts are needed that can tolerate toxic inhibitors while maintaining optimal metabolic activities. A comprehensive plasmid-based library encoding native multidrug resistance (MDR) efflux pumps, porins, and select exporters from Escherichia coli was screened for furfural tolerance in an ethanologenic E. coli strain. Small multidrug resistance (SMR) pumps, such as SugE and MdtJI, as well as a lactate/glycolate:H⁺ symporter, LldP, conferred furfural tolerance in liquid culture tests. Expression of the SMR pump potentially increased furfural efflux and cellular viability upon furfural assault, suggesting novel activities for SMR pumps as furfural efflux proteins. Furthermore, induced expression of mdtJI enhanced ethanol fermentative production of LY180 in the presence of furfural or 5-hydroxymethylfurfural, further demonstrating the applications of SMR pumps. This work describes an effective approach to identify useful efflux systems with desired activities for nonnative toxic chemicals and provides a platform to further enhance furfural efflux by protein engineering and mutagenesis.IMPORTANCE Lignocellulosic biomass, especially agricultural residues, represents an important potential feedstock for microbial production of renewable fuels and chemicals. During the deconstruction of hemicellulose by thermochemical processes, side products that inhibit cell growth and production, such as furan aldehydes, are generated, limiting cost-effective lignocellulose conversion. Here, we developed a new approach to increase cellular tolerance by expressing multidrug resistance (MDR) pumps with putative efflux activities for furan aldehydes. The developed plasmid library and screening methods may facilitate new discoveries of MDR pumps for diverse toxic chemicals important for microbial conversion.

Simultaneous biosynthesis of (R)-acetoin and ethylene glycol from D-xylose through in vitro metabolic engineering

(R)-acetoin is a four-carbon platform compound used as the precursor for synthesizing novel optically active materials. Ethylene glycol (EG) is a large-volume two-carbon commodity chemical used as the anti-freezing agent and building-block molecule for various polymers. Currently established microbial fermentation processes for converting monosaccharides to either (R)-acetoin or EG are plagued by the formation of undesirable by-products. We show here that a cell-free bioreaction scheme can generate enantiomerically pure acetoin and EG as co-products from biomass-derived D-xylose. The seven-step, ATP-free system included in situ cofactor regeneration and recruited enzymes from Escherichia coli W3110, Bacillus subtilis shaijiu 32 and Caulobacter crescentus CB 2. Optimized in vitro biocatalytic conditions generated 3.2 mM (R)-acetoin with stereoisomeric purity of 99.5% from 10 mM D-xylose at 30 °C and pH 7.5 after 24 h, with an initial (R)-acetoin productivity of 1.0 mM/h. Concomitantly, EG was produced at 5.5 mM, with an initial productivity of 1.7 mM/h. This in vitro biocatalytic platform illustrates the potential for production of multiple value-added biomolecules from biomass-based sugars with no ATP requirement.

Improved production of isobutanol in pervaporation-coupled bioreactor using sugarcane bagasse hydrolysate in engineered Enterobacter aerogenes

A process of isobutanol production from sugarcane bagasse hydrolysates in Enterobacter aerogenes was developed here with a pervaporation-integrated procedure. Isobutanol pathway was overexpressed in a mutant strain with eliminated byproduct-forming enzymes (LdhA, BudA, and PflB). A glucose-and-xylose-coconsuming ptsG mutant was constructed for effective utilization of lignocellulosic biomass. Toxic effects of isobutanol were alleviated by in situ recovery via a pervaporation procedure. Compared to single-batch fermentation, cell growth and isobutanol titer were improved by 60% and 100%, respectively, in the pervaporation-integrated fermentation process. A lab-made cross-linked polydimethylsiloxane membrane was cast on polyvinylidene fluoride and used in the pervaporation process. The membrane-penetrating condensate contained 55-226 g m^-2 h^-1 isobutanol with 6-25 g L^-1 ethanol after separation. This study offers improved fermentative production of isobutanol from lignocellulosic biomass with a pervaporation procedure.

Industrial production, application, microbial biosynthesis and degradation of furanic compound, hydroxymethylfurfural (HMF)

Biorefinery is increasingly embraced as an environmentally friendly approach that has the potential to shift current petroleum-based chemical and material manufacture to renewable sources. Furanic compounds, particularly hydroxymethylfurfurals (HMFs) are platform chemicals, from which a variety of value-added chemicals can be derived. Their biomanufacture and biodegradation therefore will have a large impact. Here, we first review the potential industrial production of 4-HMF and 5-HMF, then we summarize the known microbial biosynthesis and biodegradation pathways of furanic compounds with emphasis on the enzymes in each pathway. We especially focus on the structure, function and catalytic mechanism of MfnB (4-(hydroxymethyl)-2-furancarboxyaldehyde-phosphate synthase) and hmfH (HMF oxidase), which catalyze the formation of phosphorylated 4-HMF and the oxidation of 5-HMF to furandicarboxylic acid (2,5-FDCA), respectively. Understanding the structure-function relationship of these enzymes will provide important insights in enzyme engineering, which eventually will find industry applications in mass-production of biobased polymers and other bulk chemicals in future.

Furfural-tolerant Zymomonas mobilis derived from error-prone PCR-based whole genome shuffling and their tolerant mechanism

Furfural-tolerant strain is essential for the fermentative production of biofuels or chemicals from lignocellulosic biomass. In this study, Zymomonas mobilis CP4 was for the first time subjected to error-prone PCR-based whole genome shuffling, and the resulting mutants F211 and F27 that could tolerate 3 g/L furfural were obtained. The mutant F211 under various furfural stress conditions could rapidly grow when the furfural concentration reduced to 1 g/L. Meanwhile, the two mutants also showed higher tolerance to high concentration of glucose than the control strain CP4. Genome resequencing revealed that the F211 and F27 had 12 and 13 single-nucleotide polymorphisms. The activity assay demonstrated that the activity of NADH-dependent furfural reductase in mutant F211 and CP4 was all increased under furfural stress, and the activity peaked earlier in mutant than in control. Also, furfural level in the culture of F211 was also more rapidly decreased. These indicate that the increase in furfural tolerance of the mutants may be resulted from the enhanced NADH-dependent furfural reductase activity during early log phase, which could lead to an accelerated furfural detoxification process in mutants. In all, we obtained Z. mobilis mutants with enhanced furfural and high concentration of glucose tolerance, and provided valuable clues for the mechanism of furfural tolerance and strain development.

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

Microbial production of fuels and chemicals from lignocellulosic biomass provides promising biorenewable alternatives to the conventional petroleum-based products. However, heterogeneous sugar composition of lignocellulosic biomass hinders efficient microbial conversion due to carbon catabolite repression. The most abundant sugar monomers in lignocellulosic biomass materials are glucose and xylose. Although industrial Escherichia coli strains efficiently use glucose, their ability to use xylose is often repressed in the presence of glucose. Here we independently evolved three E. coli strains from the same ancestor to achieve high efficiency for xylose fermentation. Each evolved strain has a point mutation in a transcriptional activator for xylose catabolic operons, either CRP or XylR, and these mutations are demonstrated to enhance xylose fermentation by allelic replacements. Identified XylR variants (R121C and P363S) have a higher affinity to their DNA binding sites, leading to a xylose catabolic activation independent of catabolite repression control. Upon introducing these amino acid substitutions into the E. coli D-lactate producer TG114, 94% of a glucose-xylose mixture (50 g⋅L-1 each) was used in mineral salt media that led to a 50% increase in product titer after 96 h of fermentation. The two amino acid substitutions in XylR enhance xylose utilization and release glucose-induced repression in different E. coli hosts, including wild type, suggesting its potential wide application in industrial E. coli biocatalysts.

Enhancement of furan aldehydes conversion in Zymomonas mobilis by elevating dehydrogenase activity and cofactor regeneration

BACKGROUND

Furfural and 5-hydroxymethylfurfural (HMF) are the two major furan aldehyde inhibitors generated from lignocellulose dilute acid pretreatment which significantly inhibit subsequent microbial cell growth and ethanol fermentation. Zymomonas mobilis is an important strain for cellulosic ethanol fermentation but can be severely inhibited by furfural and (or) HMF. Previous study showed that Z. mobilis contains its native oxidoreductases to catalyze the conversion of furfural and HMF, but the corresponding genes have not been identified.

RESULTS

This study identified a NADPH-dependent alcohol dehydrogenase gene ZMO1771 from Z. mobilis ZM4, which is responsible for the efficient reduction of furfural and HMF. Over-expression of ZMO1771 in Z. mobilis significantly increased the conversion rate to both furfural and HMF and resulted in an accelerated cell growth and improved ethanol productivity in corn stover hydrolysate. Further, the ethanol fermentation performance was enhanced again by co-expression of the transhydrogenase gene udhA with ZMO1771 by elevating the NADPH availability.

CONCLUSIONS

A genetically modified Z. mobilis by co-expressing alcohol dehydrogenase gene ZMO1771 with transhydrogenase gene udhA showed enhanced conversion rate of furfural and HMF and accelerated ethanol fermentability from lignocellulosic hydrolysate. The results presented in this study provide an important method on constructing robust strains for efficient ethanol fermentation from lignocellulose feedstock.

Mutations in adenine-binding pockets enhance catalytic properties of NAD(P)H-dependent enzymes

NAD(P)H-dependent enzymes are ubiquitous in metabolism and cellular processes and are also of great interest for pharmaceutical and industrial applications. Here, we present a structure-guided enzyme engineering strategy for improving catalytic properties of NAD(P)H-dependent enzymes toward native or native-like reactions using mutations to the enzyme's adenine-binding pocket, distal to the site of catalysis. Screening single-site saturation mutagenesis libraries identified mutations that increased catalytic efficiency up to 10-fold in 7 out of 10 enzymes. The enzymes improved in this study represent three different cofactor-binding folds (Rossmann, DHQS-like, and FAD/NAD binding) and utilize both NADH and NADPH. Structural and biochemical analyses show that the improved activities are accompanied by minimal changes in other properties (cooperativity, thermostability, pH optimum, uncoupling), and initial tests on two enzymes (ScADH6 and EcFucO) show improved functionality in Escherichia coli.

Furfural tolerance and detoxification mechanism in Candida tropicalis

BACKGROUND

Current biomass pretreatment by hydrothermal treatment (including acid hydrolysis, steam explosion, and high-temperature steaming) and ionic liquids generally generate inhibitors to the following fermentation process. Furfural is one of the typical inhibitors generated in hydrothermal treatment of biomass. Furfural could inhibit cell growth rate and decrease biofuel productivity of microbes. Candida tropicalis is a promising microbe for the production of biofuels and value-added chemicals using hemicellulose hydrolysate as carbon source. In this study, C. tropicalis showed a comparable ability of furfural tolerance during fermentation. We investigated the mechanism of C. tropicalis's robust tolerance to furfural and relevant metabolic responses to obtain more information for metabolic engineering of microbes for efficient lignocellulose fermentation.

RESULTS

Candida tropicalis showed comparable intrinsic tolerance to furfural and a fast rate of furfural detoxification. C. tropicalis's half maximal inhibitory concentration for furfural with xylose as the sole carbon source was 3.69 g/L, which was higher than that of most wild-type microbes reported in the literature to our knowledge. Even though furfural prolonged the lag phase of C. tropicalis, the final biomass in the groups treated with 1 g/L furfural was slightly greater than that in the control groups. By real-time PCR analysis, we found that the expression of ADH1 in C. tropicalis (ctADH1) was induced by furfural and repressed by ethanol after furfural depletion. The expression of ctADH1 could be regulated by both furfural and ethanol. After the disruption of gene ctADH1, we found that C. tropicalis's furfural tolerance was weakened. To further confirm the function of ctADH1 and enhance Escherichia coli's furfural tolerance, ctADH1 was overexpressed in E. coli BL21 (DE3). The rate of furfural degradation in E. coli BL21 (DE3) with pET-ADH1 (high-copy plasmid) and pCS-ADH1 (medium-copy plasmid) was increased by 1.59-fold and 1.28-fold, respectively.

CONCLUSIONS

Candida tropicalis was a robust strain with intrinsic tolerance to inhibitor furfural. The mechanism of furfural detoxification and metabolic responses were identified by multiple analyses. Alcohol dehydrogenase 1 was confirmed to be responsible for furfural detoxification. C. tropicalis showed a complex regulation system during furfural detoxification to minimize adverse effects caused by furfural. Furthermore, the mechanism we uncovered in this work was successfully applied to enhance E. coli's furfural tolerance by heterologous expression of ctADH1. The study provides deeper insights into strain modification for biofuel production by efficient lignocellulose fermentation.

Combinatorial application of two aldehyde oxidoreductases on isobutanol production in the presence of furfural

Furfural is a toxic by-product formulated from pretreatment processes of lignocellulosic biomass. In order to utilize the lignocellulosic biomass on isobutanol production, inhibitory effect of the furfural on isobutanol production was investigated and combinatorial application of two oxidoreductases, FucO and YqhD, was suggested as an alternative strategy. Furfural decreased cell growth and isobutanol production when only YqhD or FucO was employed as an isobutyraldehyde oxidoreductase. However, combinatorial overexpression of FucO and YqhD could overcome the inhibitory effect of furfural giving higher isobutanol production by 110 % compared with overexpression of YqhD. The combinatorial oxidoreductases increased furfural detoxification rate 2.1-fold and also accelerated glucose consumption 1.4-fold. When it compares to another known system increasing furfural tolerance, membrane-bound transhydrogenase (pntAB), the combinatorial aldehyde oxidoreductases were better on cell growth and production. Thus, to control oxidoreductases is important to produce isobutanol using furfural-containing biomass and the combinatorial overexpression of FucO and YqhD can be an alternative strategy.

Isolation and Characterization of Bacteria That Use Furans as the Sole Carbon Source

Five bacterial strains were isolated from wastewater treatment facilities which were able to use furfural as the sole carbon source. Based on 16S rRNA phylogenetic analysis, these strains were identified as Cupriavidus pinatubonensis (designated ALS1280), Pigmentiphaga sp. (ALS1172), Pseudomonas sp. BWDY (ALS1279), Pseudomonas mendocina (ALS1131), and Pseudomonas putida (ALS1267). In all cases, growth under oxygenated conditions on furfural was accompanied by the transient accumulation of 2-furoic acid (furoate) with no furfuryl alcohol observed. ALS1267 and ALS1279 were also able to metabolize 5-(hydroxymethyl)furfural. The five isolates and their phylogenetic near neighbors were compared for furfural dehydrogenase activity and tolerance to furfural and furoate in defined and complex media. P. putida ALS1267 was the most tolerant to furans and tolerated 17 mM furfural or 195 mM furoate before its growth rate was reduced by 50 % in a defined medium. This strain also had the greatest specific growth rate on furfural (0.6/h at 27-30 °C) and showed the highest specific activity of furfural dehydrogenase (170 mIU/mg) of any furfural-utilizing strain that has been characterized to date.

Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis

An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using ¹³C-labeled sugars and [¹⁵N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.

Adaptation and transcriptome analysis of Aureobasidium pullulans in corncob hydrolysate for increased inhibitor tolerance to malic acid production

Malic acid is a dicarboxylic acid widely used in the food industry, and is also a potential C4 platform chemical. Corncob is a low-cost renewable feedstock from agricultural industry. However, side-reaction products (furfural, 5-hydroxymethylfurfural (HMF), formic acid, and acetic acid) that severely hinder fermentation are formed during corncob pretreatment. The process for producing malic acid from a hydrolysate of corncob was investigated with a polymalic acid (PMA)-producing Aureobasidium pullulans strain. Under the optimal hydrolysate sugar concentration 110 g/L, A. pullulans was further adapted in an aerobic fibrous bed bioreactor (AFBB) by gradually increasing the sugar concentration of hydrolysate. After nine batches of fermentation, the production and productivity of malic acid reached 38.6 g/L and 0.4 g/L h, respectively, which was higher than that in the first batch (27.6 g/L and 0.29 g/L h, respectively). The adapted strain could grow under the stress of 0.5 g/L furfural, 3 g/L HMF, 2g/L acetic acid, and 0.5 g/L formic acid, whereas the wild type did not. Transcriptome analysis revealed that the differentially expressed genes were related to carbohydrate transport and metabolism, lipid transport and metabolism, signal transduction mechanism, redox metabolism, and energy production and conversion under 0.5 g/L furfural and 3 g/L HMF stress conditions. In total, 42 genes in the adapted strain were upregulated by 15-fold or more, and qRT-PCR also confirmed that the expression levels of key genes (i.e. SIR, GSS, CYS, and GSR) involved in sulfur assimilation pathway were upregulated by over 10-fold in adapted strain for cellular protection against oxidative stress.

Engineering Sugar Utilization and Microbial Tolerance toward Lignocellulose Conversion

Production of fuels and chemicals through a fermentation-based manufacturing process that uses renewable feedstock such as lignocellulosic biomass is a desirable alternative to petrochemicals. Although it is still in its infancy, synthetic biology offers great potential to overcome the challenges associated with lignocellulose conversion. In this review, we will summarize the identification and optimization of synthetic biological parts used to enhance the utilization of lignocellulose-derived sugars and to increase the biocatalyst tolerance for lignocellulose-derived fermentation inhibitors. We will also discuss the ongoing efforts and future applications of synthetic integrated biological systems used to improve lignocellulose conversion.

By-products resulting from lignocellulose pretreatment and their inhibitory effect on fermentations for (bio)chemicals and fuels

Lignocellulose might become an important feedstock for the future development of the biobased economy. Although up to 75 % of the lignocellulose dry weight consists of sugar, it is present in a polymerized state and cannot be used directly in most fermentation processes for the production of chemicals and fuels. Several methods have been developed to depolymerize the sugars present in lignocellulose, making the sugars available for fermentation. In this review, we describe five different pretreatment methods and their effect on the sugar and non-sugar fraction of lignocellulose. For several pretreatment methods and different types of lignocellulosic biomass, an overview is given of by-products formed. Most unwanted by-products present after pretreatment are dehydrated sugar monomers (furans), degraded lignin polymers (phenols) and small organic acids. Qualitative and quantitative effects of these by-products on fermentation processes have been studied. We conclude this review by giving an overview of techniques and methods to decrease inhibitory effects of unwanted by-products.

Detoxification of furfural in Corynebacterium glutamicum under aerobic and anaerobic conditions

The toxic fermentation inhibitors in lignocellulosic hydrolysates raise serious problems for the microbial production of fuels and chemicals. Furfural is considered to be one of the most toxic compounds among these inhibitors. Here, we describe the detoxification of furfural in Corynebacterium glutamicum ATCC13032 under both aerobic and anaerobic conditions. Under aerobic culture conditions, furfuryl alcohol and 2-furoic acid were produced as detoxification products of furfural. The ratio of the products varied depending on the initial furfural concentration. Neither furfuryl alcohol nor 2-furoic acid showed any toxic effect on cell growth, and both compounds were determined to be the end products of furfural degradation. Interestingly, unlike under aerobic conditions, most of the furfural was converted to furfuryl alcohol under anaerobic conditions, without affecting the glucose consumption rate. Both the NADH/NAD(+) and NADPH/NADP(+) ratio decreased in the accordance with furfural concentration under both aerobic and anaerobic conditions. These results indicate the presence of a single or multiple endogenous enzymes with broad and high affinity for furfural and co-factors in C. glutamicum ATCC13032.

Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification

Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts.

Polyamine transporters and polyamines increase furfural tolerance during xylose fermentation with ethanologenic Escherichia coli strain LY180

Expression of genes encoding polyamine transporters from plasmids and polyamine supplements increased furfural tolerance (growth and ethanol production) in ethanologenic Escherichia coli LY180 (in AM1 mineral salts medium containing xylose). This represents a new approach to increase furfural tolerance and may be useful for other organisms. Microarray comparisons of two furfural-resistant mutants (EMFR9 and EMFR35) provided initial evidence for the importance of polyamine transporters. Each mutant contained a single polyamine transporter gene that was upregulated over 100-fold (microarrays) compared to that in the parent LY180, as well as a mutation that silenced the expression of yqhD. Based on these genetic changes, furfural tolerance was substantially reconstructed in the parent, LY180. Deletion of potE in EMFR9 lowered furfural tolerance to that of the parent. Deletion of potE and puuP in LY180 also decreased furfural tolerance, indicating functional importance of the native genes. Of the 8 polyamine transporters (18 genes) cloned and tested, half were beneficial for furfural tolerance (PotE, PuuP, PlaP, and PotABCD). Supplementing AM1 mineral salts medium with individual polyamines (agmatine, putrescine, and cadaverine) also increased furfural tolerance but to a smaller extent. In pH-controlled fermentations, polyamine transporter plasmids were shown to promote the metabolism of furfural and substantially reduce the time required to complete xylose fermentation. This increase in furfural tolerance is proposed to result from polyamine binding to negatively charged cellular constituents such as nucleic acids and phospholipids, providing protection from damage by furfural.

Furfural and hydroxymethylfurfural tolerance in Escherichia coli ΔacrR regulatory mutants

The presence of the highly toxic furfural and hydroxymethylfurfural (HMF) in the hydrolysate of lignocellulosic biomass prompted the investigation of the Escherichia coli ΔacrR regulatory mutant for higher tolerance to these compounds, to facilitate the production of biofuels and biochemicals, and further biocatalytic conversions. In comparison with the parental strain, the regulatory mutant with the upregulated efflux pump AcrAB-TolC produced moderately better growth and higher tolerance to concentrations of furfural and HMF between 1 and 2 g L(-1) .

Glycerol supplementation of the growth medium enhances in situ detoxification of furfural by Clostridium beijerinckii during butanol fermentation

Lignocellulose-derived microbial inhibitors such as furfural and 5-hydroxymethyl furfural adversely affect fermentation of lignocellulosic biomass hydrolysates to fuels and chemicals due to their toxicity on fermenting microbes. To harness the potential of lignocellulose as a cheap source of fermentable sugars, in situ detoxification of furfural and other lignocellulose-derived microbial inhibitors is essential. To enhance in situ detoxification and tolerance of furfural by Clostridium beijerinckii NCIMB 8052 during acetone-butanol-ethanol (ABE) fermentation, the effect of glycerol on NADH/NADPH generation and ABE production by furfural (4, 5, and 6 g/L)-challenged cultures was investigated in this study. In all instances, beneficial outcomes were observed. For example, the fermentation medium supplemented with glycerol and subjected to 5 g/L furfural elicited up to 1.8- and 3-fold increases, respectively, in NADH and NADPH levels in C. beijerinckii 8052 relative to the control culture. These critical changes are the likely underpinnings for the glycerol-mediated 2.3-fold increase in the rate of detoxification of 5 g/L furfural, substrate consumption, and ABE production compared to the unsupplemented medium. Collectively, these results demonstrate that increased intracellular NADH/NADPH in C. beijerinckii 8052 due to glycerol utilization engenders favorable effects on many aspects of cellular metabolism, including enhanced furfural reduction and increased ABE production.

Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors

Lignocellulosic hydrolysate (LCH) inhibitors are a large class of bioactive molecules that arise from pretreatment, hydrolysis, and fermentation of plant biomass. These diverse compounds reduce lignocellulosic biofuel yields by inhibiting cellular processes and diverting energy into cellular responses. LCH inhibitors present one of the most significant challenges to efficient biofuel production by microbes. Development of new strains that lessen the effects of LCH inhibitors is an economically favorable strategy relative to expensive detoxification methods that also can reduce sugar content in deconstructed biomass. Systems biology analyses and metabolic modeling combined with directed evolution and synthetic biology are successful strategies for biocatalyst development, and methods that leverage state-of-the-art tools are needed to overcome inhibitors more completely. This perspective considers the energetic costs of LCH inhibitors and technologies that can be used to overcome their drain on conversion efficiency. We suggest academic and commercial research groups could benefit by sharing data on LCH inhibitors and implementing "translational biofuel research."

Genome-wide mapping of furfural tolerance genes in Escherichia coli

Advances in genomics have improved the ability to map complex genotype-to-phenotype relationships, like those required for engineering chemical tolerance. Here, we have applied the multiSCale Analysis of Library Enrichments (SCALEs; Lynch et al. (2007) Nat. Method.) approach to map, in parallel, the effect of increased dosage for >10(5) different fragments of the Escherichia coli genome onto furfural tolerance (furfural is a key toxin of lignocellulosic hydrolysate). Only 268 of >4,000 E. coli genes (∼ 6%) were enriched after growth selections in the presence of furfural. Several of the enriched genes were cloned and tested individually for their effect on furfural tolerance. Overexpression of thyA, lpcA, or groESL individually increased growth in the presence of furfural. Overexpression of lpcA, but not groESL or thyA, resulted in increased furfural reduction rate, a previously identified mechanism underlying furfural tolerance. We additionally show that plasmid-based expression of functional LpcA or GroESL is required to confer furfural tolerance. This study identifies new furfural tolerant genes, which can be applied in future strain design efforts focused on the production of fuels and chemicals from lignocellulosic hydrolysate.